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<title>26 July, 2023</title>
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<title>Covid-19 Sentry</title><meta content="width=device-width, initial-scale=1.0" name="viewport"/><link href="styles/simple.css" rel="stylesheet"/><link href="../styles/simple.css" rel="stylesheet"/><link href="https://unpkg.com/aos@2.3.1/dist/aos.css" rel="stylesheet"/><script src="https://unpkg.com/aos@2.3.1/dist/aos.js"></script></head>
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<h1 data-aos="fade-down" id="covid-19-sentry">Covid-19 Sentry</h1>
<h1 data-aos="fade-right" data-aos-anchor-placement="top-bottom" id="contents">Contents</h1>
<ul>
<li><a href="#from-preprints">From Preprints</a></li>
<li><a href="#from-clinical-trials">From Clinical Trials</a></li>
<li><a href="#from-pubmed">From PubMed</a></li>
<li><a href="#from-patent-search">From Patent Search</a></li>
</ul>
<h1 data-aos="fade-right" id="from-preprints">From Preprints</h1>
<ul>
<li><strong>Mammalian cells-based platforms for the generation of SARS-CoV-2 virus-like particles</strong> -
<div>
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19. Though many COVID-19 vaccines have been developed, most of them are delivered via intramuscular injection and thus confer relatively weak mucosal immunity against the natural infection. Virus-Like Particles (VLPs) are self-assembled nanostructures composed of key viral structural proteins, that mimic the wild-type virus structure but are non-infectious and non-replicating due to the lack of viral genetic material. In this study, we efficiently generated SARS-CoV-2 VLPs by co-expressing the four SARS-CoV-2 structural proteins, specifically the membrane (M), small envelope (E), spike (S) and nucleocapsid (N) proteins. We show that these proteins are essential and sufficient for the efficient formation and release of SARS-CoV-2 VLPs. Moreover, we used lentiviral vectors to generate human cell lines that stably produce VLPs. Because VLPs can bind to the virus natural receptors, hence leading to entry into cells and viral antigen presentation, this platform could be used to develop novel vaccine candidates that are delivered intranasally.
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2023.07.24.550415v1" target="_blank">Mammalian cells-based platforms for the generation of SARS-CoV-2 virus-like particles</a>
</div></li>
<li><strong>Predictive Systems Biology Modeling: Unraveling Host Metabolic Disruptions and Potential Drug Targets in SARS-CoV-2 and Its Variants</strong> -
<div>
Background: Host response is critical to the onset, progression, and outcome of viral infections. Since viruses hijack the host cellular metabolism for their replications, we hypothesized that restoring host cell metabolism can efficiently reduce viral production. Here, we present a viral-host Metabolic Modeling (vhMM) method to systematically evaluate the disturbances in host metabolism in viral infection and computationally identify targets for modulation by integrating genome-wide precision metabolic modeling and cheminformatics. Results: In SARS-CoV-2 infections, we identified consistent changes in host metabolism and gene and endogenous metabolite targets between the original SARS-COV-2 and different variants (Alpha, Delta, and Omicron). Among six compounds predicted for repurposing, methotrexate, cinnamaldehyde, and deferiprone were tested in vitro and effective in inhibiting viral production with IC50 less than 4uM. Further, an analysis of real-world patient data showed that cinnamon usage significantly reduced the SARS-CoV-2 infection rate with an odds ratio of 0.65 [95%CI: 0.55~0.75]. Conclusions: These results demonstrated that vhMM is an efficient method for predicting targets and drugs for viral infections.
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2023.07.24.550423v1" target="_blank">Predictive Systems Biology Modeling: Unraveling Host Metabolic Disruptions and Potential Drug Targets in SARS-CoV-2 and Its Variants</a>
</div></li>
<li><strong>Real-time Dissection and Forecast of Infection Dynamics during a Pandemic</strong> -
<div>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
Pandemic preparedness requires institutions, including public health authorities and governments, to detect, survey and control outbreaks. To maintain an accurate, quantitative and up-to-date picture of an epidemic crisis is key. For SARS-CoV-2, this was mostly achieved by ascertaining incidence numbers and the effective reproductive number (R_eff), which counts how many people an infected person is likely to infect on average. These numbers give strong hints on past infection dynamics in a population but fail to clearly characterize current and future dynamics as well as potential effects of pharmaceutical and non-pharmaceutical interventions. We show that, by using and combining infection surveillance and population-scale contact statistics, we can obtain a better understanding of the drivers of epidemic waves and the effectiveness of interventions. This approach can provide a real-time picture, thus saving not only many lives by quickly allowing adaptation of the health policies but also alleviating economic and other burdens if an intervention proves ineffective. We factorize R_eff into contacts and relative transmissibility: Both signals can be used, individually and combined, to identify driving forces of an epidemic, monitoring and assessing interventions, as well as projecting an epidemic9s future trajectory. Using data for SARS-CoV-2 and Influenza from 2019 onward in Germany, we provide evidence for the usefulness of our approach. In particular, we find that the effects from physical distancing and lockdowns as well as vaccination campaigns are dominant.
</p>
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2023.03.02.23286502v3" target="_blank">Real-time Dissection and Forecast of Infection Dynamics during a Pandemic</a>
</div></li>
<li><strong>Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey</strong> -
<div>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
The Office for National Statistics COVID-19 Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non-SGTF over time. Evolution was characterised by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens, particularly in the current phase of the pandemic with routine RT-PCR testing now ended in the community.
</p>
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.01.05.21268323v2" target="_blank">Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey</a>
</div></li>
<li><strong>A low-cost molecular test for SARS-CoV-2 detection suitable for variant discrimination and community testing using saliva</strong> -
<div>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
The gold standard for COVID-19 diagnostic testing relies on RNA extraction from naso/oropharyngeal swab followed by amplification through RT-PCR with fluorogenic probes. While the test is extremely sensitive and specific, its high cost and the potential discomfort associated with specimen collection make it suboptimal for public health screening purposes. In this study, we developed an equally reliable, but cheaper and less invasive alternative test based on a one-step RT-PCR with the DNA-intercalating dye SYBR Green, which enables the detection of SARS-CoV-2 directly from saliva samples or RNA isolated from nasopharyngeal swabs. Importantly, we found that this type of testing can be fine-tuned to discriminate SARS-CoV-2 variants of concern. The saliva RT-PCR SYBR Green test was successfully used in a mass-screening initiative targeting nearly 4500 asymptomatic children under the age of 12. Testing was performed at a reasonable cost of less than € 0.8 per child, and in some cases, the saliva test outperformed nasopharyngeal rapid antigen tests in identifying infected children. Whole genome sequencing revealed that the antigen testing failure could not be attributed to a specific lineage of SARS-CoV-2. To further reduce testing costs, we produced all the necessary enzymes and established a new RT-PCR protocol based on the EvaGreen dye. Overall, this work strongly supports the view that RT-PCR saliva tests based on DNA-intercalating dyes represent a powerful strategy for community screening of SARS-CoV-2. The tests can be easily applied to other infectious agents and, therefore, constitute a powerful resource for an effective response to future pandemics.
</p>
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2023.07.20.23292863v1" target="_blank">A low-cost molecular test for SARS-CoV-2 detection suitable for variant discrimination and community testing using saliva</a>
</div></li>
<li><strong>Prevalence, determinants, and trends in the experience and perpetration of intimate partner violence among a cohort of gay, bisexual, and other men who have sex with men in Montréal, Toronto, and Vancouver, Canada (2017-2022)</strong> -
<div>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
Purpose: Longitudinal data on the experience and perpetration of intimate partner violence (IPV) among gay, bisexual, and other men who have sex with men (GBM) is limited. We estimated the prevalence of past six-month (P6M) physical and/or sexual IPV (hereafter IPV) experience and perpetration, identified their determinants, and assessed temporal trends, including the impact of the COVID-19 pandemic. Methods: We used data from the Engage Cohort Study (2017-2022) of GBM recruited using respondent-driven sampling in Montréal, Toronto, and Vancouver. Adjusted prevalence ratios (aPR) for determinants and self-reported P6M IPV were estimated using generalized estimating equations, accounting for attrition (inverse probability of censoring weights) and relevant covariates. Longitudinal trends of IPV were also assessed. Results: Between 2017-2022, 1,455 partnered GBM (median age 32 years, 82% gay, and 71% white) had at least one follow-up visit. Baseline proportions were 31% for lifetime IPV experience and 17% for lifetime perpetration. During follow-up, P6M IPV experience was more common (6%, 95%CI: 5-7%) than perpetration (4%, 95%CI: 3-5%). Factors associated with P6M IPV experience include prior IPV experience (aPR=2.79, 95%CI: 1.83-4.27), less education (aPR=2.08, 95%CI: 1.14-3.79), and substance use (injection aPR=5.68, 95%CI: 2.92-11.54, non-injection aPR=1.70, 95%CI: 1.05-2.76). Similar factors were associated with IPV perpetration. IPV was stable over time; periods of COVID-19 restrictions were not associated with IPV changes in this cohort. Conclusion: Prevalence of IPV was high among GBM. Determinants related to marginalization are associated with an increased risk of IPV. Interventions should address these determinants to reduce IPV and improve health.
</p>
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2023.07.24.23293112v1" target="_blank">Prevalence, determinants, and trends in the experience and perpetration of intimate partner violence among a cohort of gay, bisexual, and other men who have sex with men in Montréal, Toronto, and Vancouver, Canada (2017-2022)</a>
</div></li>
<li><strong>Quantification of Covid-19 Vaccine Coercion in India: A Survey Study</strong> -
<div>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
Introduction: Informed consent is the cornerstone of medical ethics, enshrined in the constitution of most countries, as well as in international documents. However, mandates for Covid-19 vaccination as well as coercion was prevalent in many places in the world, including in India. Against this background, we did a cross sectional study to assess and quantify the extent of Covid-19 vaccine coercion in India. Methods: A cross sectional study was conducted after obtaining ethical clearance from IIT Bombay. This survey was conducted using a pretested questionnaire anonymously amongst the college students and adults in Mumbai from October 2022 to December 2022. The questionnaire contained details of why the vaccine was taken, and if the participant was a student. Descriptive analysis was conducted and frequencies, percentages along with 95% confidence intervals were used to summarize the findings. Results: A total of 483 participants responded, which included both students and non students, of which 470 participants reported having taken the vaccine. A total of 106 (21.95%, 95% C.I. 18.48% to 25.85%) reported to have pressured into taking the vaccine. The level of coercion was similar among college students 78 (21.61%, 95% C.I. 17.67% to 26.14%) and non student adults 28 (22.95%, 95% C.I. 15.82% to 31.43%). Conclusion: A significant proportion was coerced into taking the vaccines, violating the requirement for informed consent. These results are of paramount importance for future policies as well as for posterity.
</p>
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2023.07.24.23293089v1" target="_blank">Quantification of Covid-19 Vaccine Coercion in India: A Survey Study</a>
</div></li>
<li><strong>The Impact of Nontransparent Health Communication During the COVID-19 Pandemic on Vaccine- Hesitant Peoples Perception of Vaccines</strong> -
<div>
Although transparency is crucial for building public trust, public health communication during the COVID-19 pandemic was often nontransparent. In a cross-sectional online study with COVID-19 vaccine-hesitant German residents (N = 763), we explored the impact of COVID-19 public health communication on the attitudes of vaccine-hesitant individuals towards vaccines as well as their perceptions of incomprehensible and incomplete information. We also investigated whether specific formats of public health messaging were perceived as more trustworthy. Of the 763 participants, 90 (11.8%) said they had become more open-minded towards vaccines in general, 408 (53.5%) reported no change, and 265 (34.7%) said they had become more skeptical as a result of public health communication on COVID-19 vaccines. These subgroups differed in how incomprehensible they found public health communication and whether they thought information had been missing. Participants ranking of trustworthy public health messaging did not provide clear-cut results: the fully transparent message, which reported the benefit and harms in terms of absolute risk, and the nontransparent message, which reported only the benefit in terms of relative risk were both considered equally trustworthy (p = .848). Increased skepticism about vaccines during the COVID-19 pandemic may have partly been fueled by subpar public health communication. Given the importance of public trust for coping with future health crises, public health communicators should ensure that their messaging is clear and transparent.
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://osf.io/znwyx/" target="_blank">The Impact of Nontransparent Health Communication During the COVID-19 Pandemic on Vaccine- Hesitant Peoples Perception of Vaccines</a>
</div></li>
<li><strong>Comprehensive analysis of next-generation sequencing data in COVID-19 and its secondary complications</strong> -
<div>
The ongoing pandemic of coronavirus disease 2019 (COVID-19) has made a serious public health threat globally. To discover key molecular changes in COVID-19 and its secondary complications, we analyzed next-generation sequencing (NGS) data of COVID-19. NGS data (GSE163151) was screened and downloaded from the Gene Expression Omnibus database (GEO). Differentially expressed genes (DEGs) were identified in the present study, using DESeq2 package in R programming software. Gene ontology (GO) and pathway enrichment analysis were performed, and the protein-protein interaction (PPI) network, module analysis, miRNA-hub gene regulatory network and TF-hub gene regulatory network were established. Subsequently, receiver operating characteristic curve (ROC) analysis was used to validate the diagonostics valuesof the hub genes. Firstly, 954 DEGs (477 up regulated and 477 down regulated) were identified from the four NGS dataset. GO enrichment analysis revealed enrichment of DEGs in genes related to the immune system process and multicellular organismal process, and REACTOME pathway enrichment analysis showed enrichment of DEGs in the immune system and formation of the cornified envelope. Hub genes were identified from the PPI network, module analysis, miRNA-hub gene regulatory network and TF-hub gene regulatory network. Furthermore, the ROC analysis indicate that COVID-19 and its secondary complications with following hub genes, namely, RPL10, FYN, FLNA, EEF1A1, UBA52, BMI1, ACTN2, CRMP1, TRIM42 and PTCH1, had good diagnostics values. This study identified several genes associated with COVID-19 and its secondary complications, which improves our knowledge of the disease mechanism.
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.02.03.478930v2" target="_blank">Comprehensive analysis of next-generation sequencing data in COVID-19 and its secondary complications</a>
</div></li>
<li><strong>Reduced Olfactory Bulb Volume Accompanies Olfactory Dysfunction After Mild SARS-CoV-2 Infection</strong> -
<div>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
Background: Despite its high prevalence, the determinants of smelling impairment in COVID-19 remain not fully understood. In this work, we aimed to examine the association between olfactory bulb volume and the clinical trajectory of COVID-19-related smelling impairment in a large-scale magnetic resonance imaging (MRI) analysis. Methodology/Principal: Data of non-vaccinated COVID-19 convalescents recruited within the framework of the Hamburg City Health Study COVID Program between March and December 2020 were analyzed. On average 8 months after recruitment, participants underwent MRI and neuropsychological testing as well as a structured questionnaire for olfactory function. Between March and April 2022 olfactory function was assessed at an additional timepoint including quantitative olfactometric testing with Sniffin Sticks. Results: This study included 233 individuals recovered from mainly mild to moderate SARS-CoV-2 infections. Longitudinal assessment demonstrated a declining prevalence of olfactory dysfunction from 67.1% at acute infection, 21.0% at baseline examination and 17.5% at follow-up. Participants with post-acute olfactory dysfunction had a significantly lower olfactory bulb volume at scan-time than normally smelling individuals. Olfactory bulb volume predicted olfactometric scores at follow-up. Performance in neuropsychological testing was not significantly associated with the olfactory bulb volume. Conclusions: Our work demonstrates an association of long-term smelling dysfunction and olfactory bulb integrity in a sample of individuals recovered from mainly mild to moderate COVID-19. Collectively, our results highlight olfactory bulb volume as a surrogate marker that may inform diagnosis and guide rehabilitation strategies in COVID-19.
</p>
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.07.24.22277973v3" target="_blank">Reduced Olfactory Bulb Volume Accompanies Olfactory Dysfunction After Mild SARS-CoV-2 Infection</a>
</div></li>
<li><strong>The use and acceptability of preprints in health and social care settings: a scoping review</strong> -
<div>
Background: Preprints are open and accessible scientific manuscript or report that is shared publicly, through a preprint server, before being submitted to a journal. The value and importance of preprints has grown since its contribution during the public health emergency of the COVID-19 pandemic. Funders and publishers are establishing their position on the use of preprints, in grant applications and publishing models. However, the evidence supporting the use and acceptability of preprints varies across funders, publishers, and researchers. The scoping review explored the current evidence on the use and acceptability of preprints in health and social care settings by publishers, funders, and the research community throughout the research lifecycle. Methods: A scoping review was undertaken with no study or language limits. The search strategy was limited to the last five years (2017-2022) to capture changes influenced by COVID-19 (e.g., accelerated use and role of preprints in research). The review included international literature, including grey literature, and two databases were searched: Scopus and Web of Science (24 August 2022). Results: 379 titles and abstracts and 193 full text articles were assessed for eligibility. Ninety-eight articles met eligibility criteria and were included for full extraction. For barriers and challenges, 26 statements were grouped under four main themes (e.g., volume/growth of publications, quality assurance/trustworthiness, risks associated to credibility, and validation). For benefits and value, 34 statements were grouped under six themes (e.g., openness/transparency, increased visibility/credibility, open review process, open research, democratic process/systems, increased productivity/opportunities). Conclusions: Preprints provide opportunities for rapid dissemination but there is a need for clear policies and guidance from journals, publishers, and funders. Cautionary measures are needed to maintain the quality and value of preprints, paying particular attention to how findings are translated to the public. More research is needed to address some of the uncertainties addressed in this review.
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://osf.io/preprints/socarxiv/nug4p/" target="_blank">The use and acceptability of preprints in health and social care settings: a scoping review</a>
</div></li>
<li><strong>Revealing and evaluation of antivirals targeting multiple druggable sites of RdRp complex in SARS-CoV-2</strong> -
<div>
SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex consisting of nsp12, nsp7, and nsp8 as the key enzyme for viral genome replication and is a proven antiviral drug target. In this study, molecular interactions of nsp7 and nsp8 with nsp12 and the active site of nsp12 were coterminously targeted using in-silico screening of small molecule libraries to identify potential antivirals. Surface plasmon resonance (SPR) based assay using purified nsp7 and nsp8 proteins was developed, and the binding of identified molecules to targets was validated. The antiviral efficacy of identified small molecules was evaluated using cell-based assays, and potent antiviral effect with EC50 values of 0.56 uM, 0.73 uM, and 2.8 uM was demonstrated by fangchinoline, cepharanthine, and sennoside B, respectively. Further in vivo, investigation using hACE2 mice is being conducted. This is the first study that targets multiple sites in the RdRp complex of SARS-CoV-2 using a structure-based molecular repurposing approach and suggests potential therapeutic options for emerging variants of SARS-CoV-2.
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2023.07.24.550324v1" target="_blank">Revealing and evaluation of antivirals targeting multiple druggable sites of RdRp complex in SARS-CoV-2</a>
</div></li>
<li><strong>Endothelial SARS-CoV-2 infection is not the underlying cause of COVID19-associated vascular pathology in mice</strong> -
<div>
Endothelial damage and vascular pathology have been recognized as major features of COVID-19 since the beginning of the pandemic. Two main theories regarding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) damages endothelial cells and causes vascular pathology have been proposed: direct viral infection of endothelial cells or indirect damage mediated by circulating inflammatory molecules and immune mechanisms. However, these proposed mechanisms remain largely untested in vivo. Here, we utilized a set of new mouse genetic tools1 developed in our lab to test both the necessity and sufficiency of endothelial human angiotensin-converting enzyme 2 (hACE2) in COVID19 pathogenesis. Our results demonstrate that endothelial ACE2 and direct infection of vascular endothelial cells does not contribute significantly to the diverse vascular pathology associated with COVID-19.
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2023.07.24.550352v1" target="_blank">Endothelial SARS-CoV-2 infection is not the underlying cause of COVID19-associated vascular pathology in mice</a>
</div></li>
<li><strong>Biophysical principles predict fitness of SARS-CoV-2 variants</strong> -
<div>
SARS-CoV-2 is under constant selective pressure from antibodies while requiring efficient binding to host cells for successful infection. Here we focus specifically on the receptor binding domain (RBD) of the SARS-CoV-2 spike protein, a key determinant of viral entry into host cells. Through a comprehensive approach, comprising large-scale sequence analysis of SARS-CoV-2 variants and the formulation of a fitness function based on protein folding and binding thermodynamics, we unravel the relationship between the epidemiological fitness contribution of the RBD and its biophysical properties. We developed a biophysical model mapping the phenotype space, characterized by binding constants to cell receptors and antibodies, onto the fitness landscape for variants ranging from the ancestral Wuhan Hu-1 to the Omicron BA.1 . Using equilibrium statistical mechanics, we show how fitness can be expressed as a function of binding constants to cell receptors and antibodies and validate our findings through experimentally measured binding affinities and population data on frequencies of variants. This forms the basis for a comprehensive epistatic map, relating the genotype space to fitness. Our study thus delivers a tool for predicting the fitness of variants harboring previously unseen mutations, and sheds light on the impact of specific mutations on viral fitness. These insights offer not only greater understanding of viral evolution but also potentially aid in guiding public health decisions in the battle against COVID-19 and future pandemics.
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2023.07.23.549087v1" target="_blank">Biophysical principles predict fitness of SARS-CoV-2 variants</a>
</div></li>
<li><strong>AmpliDiff: An Optimized Amplicon Sequencing Approach to Estimating Lineage Abundances in Viral Metagenomes</strong> -
<div>
Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains or species to infer the relative abundances of sequences present in a sample. This observation plays an important role in the analysis of diverse microbial communities, where targeted sequencing of 16S and 18S rRNA, both well-known hypervariable genomic regions, have led to insights in microbial diversity and the discovery of novel organisms. However, the variable nature of discriminatory regions can also act as a double-edged sword, as the sought after variability can make it difficult to design primers for their amplification through PCR. Moreover, the most variable regions are not necessarily the most informative regions for the purpose of differentiation; one should focus on regions which maximize the number of lineages that can be distinguished. Here we present AmpliDiff, a computational tool that simultaneously finds such highly discriminatory genomic regions, as well as primers allowing for the amplification of these regions. We show that regions and primers found by AmpliDiff can be used to accurately estimate relative abundances of SARS-CoV-2 lineages, for example in wastewater sequencing data. We obtain mean absolute prediction errors that are comparable with using whole genome information to estimate relative abundances. Furthermore, our results show that AmpliDiff is robust against incomplete input data, and that primers designed by AmpliDiff continue to bind to genomes originating from months after the primers were selected. With AmpliDiff we provide an effective and efficient alternative to whole genome sequencing for estimating lineage abundances in viral metagenomes.
</div>
<div class="article-link article-html-link">
🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2023.07.22.550164v1" target="_blank">AmpliDiff: An Optimized Amplicon Sequencing Approach to Estimating Lineage Abundances in Viral Metagenomes</a>
</div></li>
</ul>
<h1 data-aos="fade-right" id="from-clinical-trials">From Clinical Trials</h1>
<ul>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Smell in COVID-19 and Efficacy of Nasal Theophylline (SCENT 3)</strong> - <b>Condition</b>:   COVID-19<br/><b>Interventions</b>:   Drug: theophylline;   Drug: Placebo<br/><b>Sponsor</b>:   Washington University School of Medicine<br/><b>Recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Lymph Node Aspiration to Decipher the Immune Response of Beta-variant Recombinant Protein Booster Vaccine (VidPrevtyn Beta, Sanofi) Compared to a Bivalent mRNA Vaccine (Comirnaty Original/Omicron BA.4-5, BioNTech-Pfizer) in Adults Previously Vaccinated With at Least 3 Doses of COVID-19 mRNA Vaccine.</strong> - <b>Condition</b>:   COVID-19<br/><b>Intervention</b>:   Procedure: Lymph node aspiration / Blood sampling<br/><b>Sponsor</b>:   Assistance Publique - Hôpitaux de Paris<br/><b>Recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>COVID-19 Trial of the Candidate Vaccine MVA-SARS-2-S in Adults</strong> - <b>Condition</b>:   Covid19<br/><b>Interventions</b>:   Biological: MVA-SARS-2-S;   Other: Placebo<br/><b>Sponsors</b>:   Universitätsklinikum Hamburg-Eppendorf;   German Center for Infection Research;   Philipps University Marburg Medical Center;   Ludwig-Maximilians - University of Munich;   University Hospital Tuebingen;   CTC-NORTH<br/><b>Withdrawn</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Treatment of Long COVID (TLC) Feasibility Trial</strong> - <b>Condition</b>:   COVID-19<br/><b>Interventions</b>:   Drug: Low-dose Naltrexone (LDN);   Drug: Cetirizine;   Drug: Famotidine;   Drug: LDN Placebo;   Drug: Cetirizine Placebo;   Drug: Famotidine Placebo<br/><b>Sponsors</b>:   Emory University;   CURE Drug Repurposing Collaboratory (CDRC)<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Immunoadsorption vs. Sham Treatment in Post COVID-19 Patients With Chronic Fatigue Syndrome</strong> - <b>Conditions</b>:   Fatigue;   Post-Acute COVID-19 Syndrome<br/><b>Intervention</b>:   Procedure: Immunoadsorption vs. sham immunoadsorption<br/><b>Sponsor</b>:   Hannover Medical School<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Non-ventilated Prone Positioning in the COVID-19 Population</strong> - <b>Conditions</b>:   COVID-19;   Proning;   Oxygenation;   Length of Stay<br/><b>Interventions</b>:   Other: Proning group;   Other: Control group<br/><b>Sponsor</b>:   Baylor St. Lukes Medical Center<br/><b>Completed</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Safety, Efficacy, and Dosing of VIX001 in Patients With Neurological Symptoms of Post Acute COVID-19 Syndrome (PACS).</strong> - <b>Conditions</b>:   Post-Acute COVID-19 Syndrome;   Cognitive Impairment;   Neurological Complication<br/><b>Intervention</b>:   Drug: VIX001<br/><b>Sponsor</b>:   Neobiosis, LLC<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Study on the Safety and Immune Response of a Booster Dose of Investigational COVID-19 mRNA Vaccines in Healthy Adults</strong> - <b>Condition</b>:   SARS-CoV-2<br/><b>Interventions</b>:   Biological: CV0701 Bivalent High dose;   Biological: CV0701 Bivalent Medium dose;   Biological: CV0701 Bivalent Low dose;   Biological: CV0601 Monovalent High dose;   Biological: Control vaccine<br/><b>Sponsors</b>:   GlaxoSmithKline;   CureVac<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>PROTECT-APT 1: Early Treatment and Post-Exposure Prophylaxis of COVID-19</strong> - <b>Condition</b>:   SARS-CoV-2<br/><b>Interventions</b>:   Drug: Upamostat;   Drug: Placebo (PO)<br/><b>Sponsors</b>:   Henry M. Jackson Foundation for the Advancement of Military Medicine;   Joint Program Executive Office Chemical, Biological, Radiological, and Nuclear Defense Enabling Biotechnologies;   FHI Clinical, Inc.;   RedHill Biopharma Limited<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Clinical Evaluation of the Safety and Efficacy of Randomized Placebo Versus the 8-aminoquinoline Tafenoquine for Early Symptom Resolution in Patients With Mild to Moderate COVID 19 Disease and Low Risk of Disease Progression</strong> - <b>Conditions</b>:   COVID 19 Disease;   Mild to Moderate COVID 19 Disease;   SARS-CoV-2;   Infectious Disease;   Severe Acute Respiratory Syndrome Coronavirus 2<br/><b>Interventions</b>:   Drug: Tafenoquine Oral Tablet;   Drug: Placebo<br/><b>Sponsor</b>:   60P Australia Pty Ltd<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Study to Evaluate the Efficacy, Safety, Tolerability and PK of SNS812 in Mild to Moderate COVID-19 Patients</strong> - <b>Condition</b>:   Disease Caused by Severe Acute Respiratory Syndrome Coronavirus 2 (Disorder)<br/><b>Interventions</b>:   Drug: MBS-COV;   Drug: Placebo<br/><b>Sponsor</b>:   Oneness Biotech Co., Ltd.<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Impact of Covid 19 on Sinus Augmentation Surgery</strong> - <b>Condition</b>:   Bone Loss<br/><b>Interventions</b>:   Procedure: Sinus lift in patients with COVID-19 history;   Procedure: Sinus lift with no COVID-19 history<br/><b>Sponsor</b>:   Cairo University<br/><b>Completed</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>MR-spectroscopy in Post-covid Condition Prior to and Following a Yoga Breathing Intervention</strong> - <b>Conditions</b>:   Post COVID-19 Condition;   Somatic Symptom Disorder<br/><b>Interventions</b>:   Behavioral: yoga;   Behavioral: social contact<br/><b>Sponsor</b>:   Medical University Innsbruck<br/><b>Recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Clinical Evaluation of SARS-COV-2 (COVID-19), Influenza and RSV 8-Well MT-PCR Panel for In Vitro Diagnostics</strong> - <b>Condition</b>:   Respiratory Viral Infection<br/><b>Interventions</b>:   Diagnostic Test: SARS-COV-2, Influenza and RSV 8-Well MT-PCR Panel;   Diagnostic Test: BioFire Respiratory Panel 2.1<br/><b>Sponsor</b>:   AusDiagnostics Pty Ltd.<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Expressive Interviewing Agents to Support Health-Related Behavior Change</strong> - <b>Condition</b>:   Mental Stress<br/><b>Intervention</b>:   Other: Expressive Interviewing<br/><b>Sponsors</b>:   University of Michigan;   University of Texas at Austin<br/><b>Completed</b></p></li>
</ul>
<h1 data-aos="fade-right" id="from-pubmed">From PubMed</h1>
<ul>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Chemoinformatics approach to design and develop vanillin analogs as COX-1 inhibitor</strong> - CONCLUSION: In comparison to other vanillin derivative compounds, 4-formyl-2-methoxyphenyl benzoate has the lowest binding energy value; hence, this analog can continue to be synthesized and its potential as an antithrombotic agent might be confirmed by in vivo studies.</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Korean Red Ginseng Relieves Inflammation and Modulates Immune Response Induced by Pseudo-Type SARS-CoV-2</strong> - Few studies have reported the therapeutic effects of Korean red ginseng (KRG) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the positive effects of KRG on other viruses have been reported and the effects of KRG on pulmonary inflammatory diseases have also been studied. Therefore, this study investigated the therapeutic effects of KRG-water extract (KRG-WE) in a pseudo-type SARS-CoV-2 (PSV)-induced lung injury model. Constructing the pseudovirus, human…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Vector-delivered artificial miRNA effectively inhibits Porcine epidemic diarrhea virus replication</strong> - CONCLUSIONS: In summary, these results suggest that an RNAi based on amiRNA targeting the conserved region of the virus is an effective method to improve PEDV nucleic acid inhibitors and provide a novel treatment strategy for PEDV infection.</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Deciphering the role of fucoidan from brown macroalgae in inhibiting SARS-CoV-2 by targeting its main protease and receptor binding domain: Invitro and insilico approach</strong> - The current study investigated the role of fucoidan from Padina tetrastromatica and Turbinaria conoides against 3-chymotrypsin like protease (3CL^(pro)) and receptor binding domain (RBD) spike protein of SARS-CoV-2 using an invitro and computational approach. The 3CL^(pro) and RBD genes were successfully cloned in pET28a vector, expressed in BL-21DE3 E. coli rosetta cells and purified by ion exchange affinity and size exclusion chromatography. Fucoidan extracted from both biomass using green…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Inactivated SARS-CoV-2 booster vaccine enhanced immune responses in patients with chronic liver diseases</strong> - Chronic liver disease (CLD) entails elevated risk of COVID-19 severity and mortality. The effectiveness of the booster dose of inactivated SARS-CoV-2 vaccine in stimulating antibody response in CLD patients is unclear. Therefore, we conducted a cross-sectional study involving 237 adult CLD patients and 170 healthy controls (HC) to analyze neutralizing antibodies (NAbs) against SARS-CoV-2 prototype and BA.4/5 variant, anti-receptor binding domain (RBD) IgG, and total anti-SARS-CoV-2 antibodies….</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>The kynurenine pathway of tryptophan metabolism: a neglected therapeutic target of COVID-19 pathophysiology and immunotherapy</strong> - SARS-CoV-2 (COVID-19) exerts profound changes in the kynurenine (Kyn) pathway (KP) of tryptophan (Trp) metabolism that may underpin its pathophysiology. The KP is the main source of the vital cellular effector NAD+ and intermediate metabolites that modulate immune and neuronal functions. Trp metabolism is the top pathway influenced by COVID-19. Sixteen studies established virus-induced activation of the KP mediated mainly by induction of indoleamine 2,3-dioxygenase (IDO1) in most affected…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Regulation of autophagy by SARS-CoV-2: The multifunctional contributions of ORF3a</strong> - Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) regulates autophagic flux by blocking the fusion of autophagosomes with lysosomes, causing the accumulation of membranous vesicles for replication. Multiple SARS-CoV-2 proteins regulate autophagy with significant roles attributed to ORF3a. Mechanistically, open reading frame 3a (ORF3a) forms a complex with UV radiation resistance associated, regulating the functions of the PIK3C3-1 and PIK3C3-2 lipid kinase complexes, thereby…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Fangchinoline inhibits the PEDV replication in intestinal epithelial cells via autophagic flux suppression</strong> - Animal and human health are severely threatened by coronaviruses. The enteropathogenic coronavirus, porcine epidemic diarrhea virus (PEDV), is highly contagious, leading to porcine epidemic diarrhea (PED), which causes large economic losses in the worlds swine industry. Piglets are not protected from emerging PEDV variants; therefore, new antiviral measures for PED control are urgently required. Herein, the anti-PEDV effects and potential mechanisms of fangchinoline (Fan) were investigated. Fan…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Silver N-heterocyclic carbene complexes are potent uncompetitive inhibitors of the papain-like protease with antiviral activity against SARS-CoV-2</strong> - The ongoing SARS-CoV-2 pandemic has caused a high demand for novel innovative antiviral drug candidates. Despite promising results, metal complexes have been relatively unexplored as antiviral agents in general and in particular against SARS-CoV-2. Here we report on silver NHC complexes with chloride or iodide counter ligands that are potent inhibitors of the SARS-CoV-2 papain-like protease (PL^(pro)) but inactive against 3C-like protease (3CL^(pro)) as another SARS-CoV-2 protease. Mechanistic…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Nanoparticle approaches for the renin-angiotensin system</strong> - The renin-angiotensin system (RAS) is a hormonal cascade that contributes to several disorders: systemic hypertension, heart failure, kidney disease, and neurodegenerative disease. Activation of the RAS can promote inflammation and fibrosis. Drugs that target the RAS can be classified into 3 categories, AT1 angiotensin receptor blockers (ARBs), angiotensin-converting enzyme (ACE) inhibitors, and renin inhibitors. The therapeutic efficacy of current RAS-inhibiting drugs is limited by poor…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Natural fucoidans inhibit coronaviruses by targeting viral spike protein and host cell furin</strong> - Fucoidans are a class of long chain sulfated polysaccharides and have multiple biological functions. Herein, four natural fucoidans extracted from Fucus vesiculosus, F. serratus, Laminaria japonica and Undaria pinnatifida, were tested for their HCoV-OC43 inhibition and found to demonstrate EC(50) values ranging from 0.15 to 0.61 µg/mL. That from U. pinnatifida exhibited the most potent anti-HCoV-OC43 activity with an EC(50) value of 0.15 ± 0.02 µg/mL, a potency largely independent of its sulfate…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>One master and two servants: One Zr(Ⅳ) with two ligands of TCPP and NH<sub>2</sub>-BDC form the MOF as the electrochemiluminescence emitter for the biosensing application</strong> - Here we put forward an innovative “one master and two servants” strategy for enhancing the ECL performance. A novel ECL luminophore named Zr-TCPP/NH(2)-BDC (TCPP@UiO-66-NH(2)) was synthesized by self-assembly of meso-tetra(4-carboxyphenyl)porphine (TCPP) and 4-aminobenzoic acid (NH(2)-BDC) with Zr clusters. TCPP@UiO-66-NH(2) has a porous structure and a highly ordered structure, which allows the molecular motion of TCPP to be effectively confined, thereby inhibiting nonradiative energy transfer….</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Understanding structure activity relationships of Good HEPES lipids for lipid nanoparticle mRNA vaccine applications</strong> - Lipid nanoparticles (LNPs) have shown great promise as delivery vehicles to transport messenger ribonucleic acid (mRNA) into cells and act as vaccines for infectious diseases including COVID-19 and influenza. The ionizable lipid incorporated within the LNP is known to be one of the main driving factors for potency and tolerability. Herein, we describe a novel family of ionizable lipids synthesized with a piperazine core derived from the HEPES Good buffer. These ionizable lipids have unique…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Identification and validation of fusidic acid and flufenamic acid as inhibitors of SARS-CoV-2 replication using DrugSolver CavitomiX</strong> - In this work, we present DrugSolver CavitomiX, a novel computational pipeline for drug repurposing and identifying ligands and inhibitors of target enzymes. The pipeline is based on cavity point clouds representing physico-chemical properties of the cavity induced solely by the protein. To test the pipelines ability to identify inhibitors, we chose enzymes essential for SARS-CoV-2 replication as a test system. The active-site cavities of the viral enzymes main protease (M^(pro)) and papain-like…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Antibody Fc-binding profiles and ACE2 affinity to SARS-CoV-2 RBD variants</strong> - Emerging SARS-CoV-2 variants, notably Omicron, continue to remain a formidable challenge to worldwide public health. The SARS-CoV-2 receptor-binding domain (RBD) is a hotspot for mutations, reflecting its critical role at the ACE2 interface during viral entry. Here, we comprehensively investigated the impact of RBD mutations, including 5 variants of concern (VOC) or interest-including Omicron (BA.2)-and 33 common point mutations, both on IgG recognition and ACE2-binding inhibition, as well as…</p></li>
</ul>
<h1 data-aos="fade-right" id="from-patent-search">From Patent Search</h1>
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<h1 data-aos="fade-down" id="daily-dose">Daily-Dose</h1>
<h1 data-aos="fade-right" data-aos-anchor-placement="top-bottom" id="contents">Contents</h1>
<ul>
<li><a href="#from-new-yorker">From New Yorker</a></li>
<li><a href="#from-vox">From Vox</a></li>
<li><a href="#from-the-hindu-sports">From The Hindu: Sports</a></li>
<li><a href="#from-the-hindu-national-news">From The Hindu: National News</a></li>
<li><a href="#from-bbc-europe">From BBC: Europe</a></li>
<li><a href="#from-ars-technica">From Ars Technica</a></li>
<li><a href="#from-jokes-subreddit">From Jokes Subreddit</a></li>
</ul>
<h1 data-aos="fade-right" id="from-new-yorker">From New Yorker</h1>
<ul>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>In Israel, a Glimpse of a Trumpian Future</strong> - Netanyahu is willing to undermine the rule of law in order to insure his own political survival. Sound familiar? - <a href="https://www.newyorker.com/news/daily-comment/in-israel-a-glimpse-of-a-trumpian-future">link</a></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Minor Reboot Wont Save Ron DeSantiss Toxic Campaign</strong> - Floridas governor will need to do much more than shake hands with voters at greasy spoons if he wants to beat Donald Trump. - <a href="https://www.newyorker.com/news/our-columnists/the-troubles-of-ron-desantis">link</a></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Will Bidens Meetings with A.I. Companies Make Any Difference?</strong> - Voluntary commitments from the likes of OpenAI, Microsoft, and Google could be a small step toward meaningful A.I. regulations—or a way for Big Tech to write its own rules. - <a href="https://www.newyorker.com/news/daily-comment/will-bidens-meetings-with-ai-companies-make-any-difference">link</a></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Should Hotel Chains Be Held Liable for Human Trafficking?</strong> - For decades, franchised hotels have been a common scene of sex-trafficking crimes in the U.S. A new legal strategy is targeting the corporations that collect royalties from them. - <a href="https://www.newyorker.com/news/a-reporter-at-large/should-hotel-chains-be-held-liable-for-human-trafficking">link</a></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>How Prosecutors Might Charge Trump for January 6th</strong> - The Justice Department is reportedly using a civil-rights law that “puts front and center the injury to the American people,” rather than to the government. - <a href="https://www.newyorker.com/culture/q-and-a/how-prosecutors-might-charge-trump-for-january-6th">link</a></p></li>
</ul>
<h1 data-aos="fade-right" id="from-vox">From Vox</h1>
<ul>
<li><strong>Bidens $250 billion lure to clean up the dirty legacy of fossil fuels</strong> -
<figure>
<img alt="A man stands in front of the ruins of a demolished coal power plant" src="https://cdn.vox-cdn.com/thumbor/tyMMfm781usk6BYoXO_XiH0k24A=/304x0:5168x3648/1310x983/cdn.vox-cdn.com/uploads/chorus_image/image/72484963/GettyImages_1245582733.0.jpg"/>
<figcaption>
Twenty-eight-year-old New Jersey coal-fired power plant Logan Generating Station was demolished last year in pursuit of cleaner electricity. | Hannah Beier/Bloomberg via Getty Images
</figcaption>
</figure>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
Theres hidden climate potential in overlooked fossil fuel infrastructure.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="KqAJ4n">
The International Energy Agency expects the world to invest about <a href="https://www.iea.org/reports/world-energy-investment-2023/overview-and-key-findings">a billion dollars</a> a day into solar in 2023, marking the first time the renewable has surpassed global investment in oil production. Its astonishing growth for an industry that was in its infancy just a decade ago. And Jigar Shah, the director of the Loan Programs Office at the US Department of Energy, thinks his office should get partial credit for kick-starting the solar revolution.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="QSCDMD">
The technology for solar has been well established for years, but the business case for installing it on a mass scale hasnt developed as quickly. Around 20 years ago, there wasnt a single large utility solar project in the US, and it was risky business to be the first. But thats what the <a href="https://www.energy.gov/lpo/loan-programs-office">Loan Programs Office</a> was created to accomplish in 2005, before being given an expanded mandate in 2009. It filled a gap where the private sector wouldnt, by providing loans for innovative clean technologies that were not yet implemented on a mass scale.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="V4W4Nc">
“When you think about all the dominoes that fell to get to a billion dollars a day, we started that process,” Shah said in an interview last month with Vox. “Were the ones who hit the first domino.”
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="srUDRN">
Shah pointed out that the first five large-scale — 100-megawatt or more — solar plants in the US were all funded by the Loan Programs Office early in the Obama administration. A similar story was true for the rise of electric cars: The DOE office gave a <a href="https://www.energy.gov/lpo/tesla">$465 million loan</a> to <a href="https://www.vox.com/tesla">Tesla</a> in 2010 to produce the successful Model S.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="QFyhbD">
The Loan Programs Office has been dormant for over a decade. The <a href="https://www.vox.com/2022/8/8/23296951/inflation-reduction-act-biden-democrats-climate-change">Inflation Reduction Act</a> along with the bipartisan infrastructure law rescued the office from obscurity but gave it a new challenge to tackle. Now, the Loan Programs Office has an expanded mandate from <a href="https://www.vox.com/congress">Congress</a> to distribute up to $250 billion in loans to “retool, repower, repurpose, or replace energy infrastructure” for the <a href="https://www.energy.gov/lpo/energy-infrastructure-reinvestment">Energy Infrastructure Reinvestment</a> program (EIR).
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="tec4j3">
Its a brand-new domino to topple: how to tap the potential of existing fossil fuel infrastructure so it can be put to use in a clean energy transition.
</p>
<h3 id="CvEFLh">
Giving pipelines and gas stations new life
</h3>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="fxbpls">
The goals of the EIR are different than most of the Inflation Reduction Acts spending. Congress passed the Inflation Reduction Act a year ago to usher in a new era of clean technology and manufacturing aimed at slashing US climate pollution. Billions of dollars of the climate law focuses on what it will build through tax credits, grants, and direct investments, technologies like <a href="https://www.vox.com/energy-and-environment/2022/10/8/23387530/home-electrification-heat-pumps-gas-furnace-contractors">heat pumps</a>, <a href="https://www.vox.com/recode/2022/12/22/23521519/tesla-electric-vehicles-milestones-ira-biden">electric cars</a>, <a href="https://www.vox.com/policy-and-politics/2022/7/28/23281757/whats-in-climate-bill-inflation-reduction-act">solar fields, offshore wind, power lines</a>, and <a href="https://www.vox.com/23771809/nuclear-power-smr-small-modular-reactor-energy-climate-nuscale">modern nuclear power</a>.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="9hjX9N">
What happens on the other side of the equation — the fossil fuel infrastructure left behind — is less clear. With <a href="https://coal.sierraclub.org/campaign">370 coal-fired power plant retirements</a> announced in the past decade and more to come, this transition is already underway.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="LMluLO">
The DOEs EIR has far-reaching potential to transform what we think of as traditional energy infrastructure, including utilities, power lines, and pipelines, as well as things like gas stations and hospitals. Executed in its full vision, the loans could help to lower climate pollution in the near term, but even more importantly, prove theres a market for retooling the infrastructure we already have.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="JB6nqe">
“This is a way that we can upgrade our existing system in a meaningful way, at a much lower cost than would otherwise be possible and move quickly,” RMIs senior principal of Carbon-Free Electricity <a href="https://rmi.org/people/uday-varadarajan/">Uday Varadarajan</a> said.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="TIQS5b">
So how would it work? The Loan Programs Office reviews applications for proposals, which are typically in the hundreds of millions of dollars. Unlike other types of loans approved by the office, the technology here does not have to be innovative. All the projects must do is show they are slashing, avoiding, or sequestering carbon dioxide or other kinds of pollution.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="9eT01N">
This leaves the potential for a vast number of projects. One of the most direct ways architects of the EIR envisioned the program working would be to fund clean electricity generation that would take the place of retiring coal power plants. That could involve physically converting toxic coal mines into a large array of <a href="https://www.vox.com/solar-energy">solar panels</a> with battery storage, or adding transmission lines that boost interconnection and reliability of the grid.
</p>
<figure class="e-image">
<img alt="Jigar Shah speaking." src="https://cdn.vox-cdn.com/thumbor/_XjcGYb3NAiirEu8RFnChFWMOIM=/800x0/filters:no_upscale()/cdn.vox-cdn.com/uploads/chorus_asset/file/24807176/GettyImages_1247941383.jpg"/> <cite>Aaron M. Sprecher/Bloomberg via Getty Images</cite>
<figcaption>
Jigar Shah, director of the Loan Programs Office at the Department of Energy, speaks during 2023 CERAWeek in Houston, Texas, in March.
</figcaption>
</figure>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="l1jjmK">
Other potential projects that could receive EIR funding <strong>may</strong> include converting old gas pipelines into ones fit to carry <a href="https://www.vox.com/recode/22973204/hydrogen-energy-power-toyota-mirai-climate-change">hydrogen</a>, a potentially clean fuel whose main waste product is water. Or the funding might be used to retrofit pipelines to be able to transport carbon so it can be stored deep underground and not escape into the atmosphere. Carbon capture and storage received a major boost from the EPA in its <a href="https://www.vox.com/climate/2023/5/11/23695884/biden-epa-climate-power-plant-regulation">draft power plant rules,</a> as an option for gas plants to lower their emissions, but this technology is a nonstarter without the infrastructure.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="fCIk1z">
There are still other, more creative approaches left on the table. RMIs Varadarajan suggested that even <a href="https://www.vox.com/recode/23023671/ev-charging-network-gas-station-fast-charger">abandoned gas stations</a> could be put to new use through the EIR. Old gas stations are notoriously hard to reclaim and put to better use, but with more financing and an interested developer, they could be converted to EV charging stations and part of a distributed virtual power plant network.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="euRwHL">
<a href="https://www.hklaw.com/en/insights/publications/2023/02/doe-loan-programs-office-2023-updates-overview-and-key-insights">Taite McDonald,</a> a partner at the law firm Holland and Knight who helps clients navigate DOE loan program applications, said she sees the most potential for large industrial complexes, like hospitals and college campuses, that have already made public commitments to reaching net zero.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="Wbf1yd">
This list of potential projects shows quite a range in ambition and also raises some critical questions. Will the EIR loans mostly be put to financing large institutions on their journey to net zero or, more ambitiously, to creating an entirely new market for abandoned gas stations and coal mines? The answer will depend on the kinds of applications that start to come in.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="E8TyhN">
“People are going to start to look at this when the other options start to be expended,” McDonald said. “And because its such a new program, we just havent really seen a lot of folks start to do that. What the program essentially becomes will remain to be seen.”
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="aYN061">
Jigar Shah explained his job involves a lot of “cajoling folks,” and explaining to industries how the DOE could help with low-cost financing for goals they have already committed to publicly.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="9rKhGl">
“I see this as an economic development program,” Shah explained. “Its our primary goal to help ensure that we can see investments and opportunity in the clean <a href="https://www.vox.com/economy">economy</a> line up with communities that are currently producing energy. Whether thats a coal plant thats scheduled to retire but could become the site of an advanced nuclear power plant, or an interconnection point for a large battery and wind farm to access the grid, theres a lot of useful infrastructure, local talent, and know-how in the workforce that could be put to good use.”
</p>
<h3 id="alX2PM">
Balancing ambition, exhaustiveness, and speed will make all the difference
</h3>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="vXoy0X">
The Loan Programs Office can be truly transformative if the full $250 billion is loaned out for slashing carbon footprints. But the history of the office is also a reminder of all the potential pitfalls for this kind of government funding.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="Mn67O1">
Solyndra was a solar panel manufacturer that received a loan under a different program to fund innovative technologies in 2009, but went bankrupt a few years later. It made for a field day for the Tea Party takeover of the House in 2010, which launched investigations calling the program an example of the governments wasteful spending and its capacity to pick winners and losers. The House ultimately passed the “<a href="https://www.politico.com/story/2012/09/house-passes-no-more-solyndras-081223">No More Solyndras Act</a>” in 2012 to block any more loan approvals (the bill didnt pass the Senate).
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="l9k4P7">
The Loan Programs Office itself has had some successes, however. The Obama administration approved <a href="https://www.energy.gov/lpo/history">40 projects</a> at a total of $36 billion that included companies such as Tesla and Nissan, which were looking to expand EV manufacturing, and <a href="https://www.washingtonpost.com/national/health-science/beacon-power-declares-bankruptcy-second-loan-guarantee-recipient-to-falter/2011/10/31/gIQACNAaaM_story.html">Beacon Power</a>, a company that would help store power to ensure grid reliability.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="JoBRmW">
But the political fallout from the Solyndra bankruptcy did permanent damage. For about a decade, the Loan Programs Office went dormant until its first signs of life late in the <a href="https://www.vox.com/trump-administration">Trump administration</a>.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="CwO5Wg">
Both the Inflation Reduction Act and bipartisan infrastructure law have given the office its expanded mandate, and one of the most powerful positions in financing a clean energy revolution. Shah, a former clean energy entrepreneur, was tapped to lead the rapidly expanding team.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="0Rn8Wx">
However, Shah and his office of 250 cant afford more scandal — or being too timid, either. The clock is ticking down on the timeline Congress gave the EIR program, which has just until 2026 to approve up to $250 billion in loans, a deadline that will be tough to make.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="kRNdDI">
Getting the word out and convincing applicants is another challenge. Shah acknowledged that DOE loans might not be “a natural thing for a lot of these applicants to use.”
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="onRvyJ">
While there isnt a huge market today for retrofitting and repurposing existing fossil fuel sites, the hope is the EIR starts to make it much more commonsense. Shah argues thats exactly the role the government should play, helping sectors make a leap to becoming no-brainer investments. “If we dont start that process, theres no one else,” he said.
</p></li>
<li><strong>Oppenheimer is the surprise fashion movie of the summer</strong> -
<figure>
<img alt="Cillian Murphy as J. Robert Oppenheimer in a brimmed hat and well-cut suit" src="https://cdn.vox-cdn.com/thumbor/9ZAKsLtLbf4W9xkfs027XkX3nNg=/145x0:1478x1000/1310x983/cdn.vox-cdn.com/uploads/chorus_image/image/72484829/oppenheimer_still2_62e2a85a448bb_1.0.jpg"/>
<figcaption>
Cillian Murphy as J. Robert Oppenheimer. | Universal
</figcaption>
</figure>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
Is Oppenheimercore on the way?
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="muF3lD">
Theres a moment in <em>Oppenheimer </em>that seems almost like something out of a superhero movie or an <em>Indiana Jones </em>flick. Standing in his office at Los Alamos, J. Robert Oppenheimer (Cillian Murphy) puts on a hat and picks up a pipe, each item lingered on by director Christopher Nolans camera. Nolan films these actions from behind like Oppenheimer is assuming his armor as he emerges to lead the Manhattan Project, the WWII effort that will result in the development of the atomic bomb. His shoulders are broad. His silhouette is totemic. “A rock star is born,” costume designer Ellen Mirojnick explains. “Theres an elegance, an empowerment, and a strength about who that man has become as he walks out of his office in the totality of this outfit.”
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="yCx7th">
<em>Oppenheimer </em>the movie<em> </em>is clear that Oppenheimer, the man, is not actually a superhero or a rock star, even if he might at times think of himself as such. Nolans film recognizes that its protagonist is both deeply conflicted and the orchestrator of atrocity. At the same time, it also acknowledges that Death, the Destroyer of Worlds, was deeply stylish.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="GrYoEV">
Greta Gerwigs <em>Barbie </em>has been dominating the movie fashion conversation this summer with its hot pink ensembles, but for menswear enthusiasts <em>Oppenheimer </em>might actually be the sartorial event of the season. Vogue<em> </em>coined <a href="https://www.vogue.com/article/oppenheimercore">Oppenheimercore</a> to note how the boxy tailoring of the physicist has been reflected on runways, while <a href="https://www.vox.com/twitter">Twitter</a> observers speculated that the film might unleash a new level of <a href="https://twitter.com/IanFayArt/status/1676121670036201472">“hat guys.”</a>
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="OI6ycF">
For fashion writers Tom Fitzgerald and Lorenzo Marquez, also known as <a href="https://tomandlorenzo.com/">Tom and Lorenzo</a>, a Nolan production always means great suits. “Christopher Nolan is a director after our own hearts, because he makes sure his leading men all know the value of a good suit, from <em>Batman Begins</em> to <em>Inception</em> to <em>Tenet</em>,” Fitzgerald writes in an email. “When we think of those films, we cant help but picture how great the men looked in them.”
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="GuIfjn">
The fact that Oppenheimer looks so good is not irrelevant to the plot. Nolan depicts him as a ladies man — which he was — and as someone who can convene a cult of personality around him. People are drawn to him not just because of his brilliance but because of his general suaveness. Which is all to say, the striking image of Oppenheimer on screen is very much not incidental, according to Mirojnick. “Its seductive in a way,” she says. “Because what you feel in the silhouette is that you feel the person. His silhouette embraced the body where it needed to be embraced.”
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="8ic0ad">
Oppenheimers personal connection to the world of great tailoring is a matter of record. His father, Julius, worked in the world of menswear. According to <em>American Prometheus: The Triumph and Tragedy of J. Robert Oppenheimer</em>, the biography on which <em>Oppenheimer </em>is based, Julius has a reputation as “one of the most knowledgeable fabrics men in” New York. <em>American Prometheus </em>authors Kai Bird and Martin J. Sherwin wrote that Julius “dressed to fit the part, always adorned in a white high-collared shirt, a conservative tie, and a dark business suit.”
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="1QaLBv">
In her initial research, Mirojnick was struck that over time Oppenheimer maintained a steady style, despite looking at images that spanned from the 20s through the 60s. He shifted his dress a little during his time at Los Alamos, she says, to adapt to the environment of the New Mexico desert — he loses the waistcoat, for instance — but that “silhouette” remains the same. (Mirojnick loves designing for a male “silhouette,” a fact she learned designing the costumes for <em>Wall Street </em>in 1987.)
</p>
<div class="c-float-right">
<aside id="OeVqmu">
<q>Maybe a burst of Oppenheimer-inspired looks are on the horizon — at least when it comes to tailoring</q>
</aside>
</div>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="yrYfk6">
Oppenheimers jacket might look a little large on his frame to the modern viewer, which gets skinnier as time passes; his tie might look a little short; his waistband might look a little high; and his hat might look a little big. (The style of the hat has been called “pork pie” but Mirojnick believes its a variation on that with a larger brim.) Its all a bit “voluminous,” a word that Mirojnick uses, but thats what makes it actually look “fashionable,” she adds.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="k71H3P">
While some men might scoff at a bigger shoulder for fear of looking like Talking Heads-era David Byrne, a little length in that area actually looks good. “When you extend the shoulders like that you get a much more flattering proportion for the male figure because youre able to build a kind of V-shaped silhouette for the suit,” says Derek Guy of the blog <a href="https://dieworkwear.com/">Die, Workwear!</a> (Guy is probably best known as the <a href="https://twitter.com/dieworkwear?ref_src=twsrc%5Egoogle%7Ctwcamp%5Eserp%7Ctwgr%5Eauthor">Twitter menswear dude</a>.)
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="MIAhjp">
Mirojnick notes that she and Nolan werent too concerned with making the costumes of <em>Oppenheimer </em>look perfectly period accurate. “We were not one to keep it so strict, that it would take somebody out of the story,” she says. “I had to make it [so] a young audience would be as seduced as an older audience would be.” One key historical inaccuracy: Oppenheimer is one of the only characters to wear a hat. Normally during these eras, everyone would be donning headwear, but Nolan wanted Oppenheimer to stand out among his peers.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="cP4BN4">
Its hard to tell how much the influence of <em>Oppenheimer</em>s costuming will trickle down into everyday life; after all, the suit in <a href="https://www.vox.com/the-goods/2019/9/30/20869237/suits-control-menswear-decline">general has been in decline</a>. (Even Murphy didnt wear one to <a href="https://www.gettyimages.com/detail/news-photo/cillian-murphy-attends-a-photocall-for-oppenheimer-in-news-photo/1537043931?adppopup=true">every <em>Oppenheimer </em>event</a>.) High fashion might take notice, however. Vogues <a href="https://www.vogue.com/article/oppenheimercore">Laia Garcia-Furtado argued</a>: “My guess is the sartorial influence of this movie will be reflected in seasons to come.” Tom and Lorenzo believe that if the cyclical nature of trends accounts for anything, a 40s revival is on the way.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="rFXHp0">
“With menswear, we went from a very <em>Mad Men</em>-inspired mid-60s silhouette for mens suits for the better part of a decade, then lockdown happened and after that we entered a period of funkiness and minor experimentation as the pants flared and a rainbow of color and print options became trendy again,” Fitzgerald explains. “If you go by the theory that fashion repeats itself, then were in roughly 1979 or so, which is right about the time that menswear went through a 40s-inspired trend period.”
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="AuqHvC">
So maybe a burst of Oppenheimer-inspired looks are on the horizon — at least when it comes to tailoring. It may even filter into womens looks given how menswear has been a dominant trend <a href="https://www.gq.com/story/taylor-swift-jennifer-lawrence-menswear-style">for female celebrities this summer</a>. (Tom and Lorenzo think the hat has taken too much of a beating from its “Mlady” associations to really weather a comeback.)
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="nD5Xzb">
For Mirojnick, theres a thematic way in which the film reflects modern society. The horrors of today, after all, are very visible in the horrors of the past. “The world that they inhabit and the time periods that they inhabit are not dissimilar to the time periods we live in today,” she says. “So naturally fashion would imitate fashion or costumes would become fashion.” Its also, as she said before, very seductive. In the context of the movie, that seduction is tinged with the evil Oppenheimer knows he has wrought. In the context of good clothes, that seduction is just, well, hot.
</p></li>
<li><strong>Birds have co-opted our anti-bird weapons in a genius counterattack</strong> -
<figure>
<img alt="" src="https://cdn.vox-cdn.com/thumbor/GGGo71YcUoAHBShiNraaG5Eavhc=/386x0:5159x3580/1310x983/cdn.vox-cdn.com/uploads/chorus_image/image/72484801/Auke_Florian_Hiemstra___foto_Alexander_Schippers__1_.0.jpg"/>
<figcaption>
Biologist Auke-Florian Hiemstra with a massive magpie nest made using anti-bird pins. | Alexander Schippers/Naturalis
</figcaption>
</figure>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
Humans install spikes so birds will go away. Birds steal them and do this instead.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="G8sFSs">
Humans are so cute. They think they can outsmart birds. They place nasty metal spikes on rooftops and ledges to prevent birds from nesting there.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="a9cFWS">
Its a classic human trick known in urban design as “evil architecture”: designing a place in a way thats meant to deter others. Think of the city benches you see segmented by bars to stop homeless people sleeping there.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="KKYh05">
But birds are genius rebels. Not only are they undeterred by evil architecture, they actually use it to their advantage, according to <a href="https://www.hetnatuurhistorisch.nl/fileadmin/user_upload/documents-nmr/Publicaties/Deinsea/Deinsea_21/Deinsea_21_17_25_2023_Hiemstra_et_al.pdf">a new Dutch study</a> published in the journal <em>Deinsea</em>.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="b5DdXU">
Crows and magpies, it turns out, are learning to rip strips of anti-bird spikes off of buildings and use them to build their nests. Its an incredible addition to the growing body of evidence about the intelligence of birds, so wrongly maligned as stupid that “bird-brained” is still commonly used as an insult.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="plxUkm">
Just take a look at this crow nest from Rotterdam in the Netherlands, built with anti-bird spikes. The crows have cleverly pointed every spike inward so that, instead of harming the birds, the spikes will form a perfect lattice for a nest.
</p>
<figure class="e-image">
<img alt="A crows nest made from anti-bird spikes." src="https://cdn.vox-cdn.com/thumbor/Si-Rm8Z34S0J0MGW8xHYawE0rUM=/800x0/filters:no_upscale()/cdn.vox-cdn.com/uploads/chorus_asset/file/24806605/Crow_nest__Rotterdam__NL__photo_Kees_Moeliker.JPG"/> <cite>Kees Moeliker</cite>
<figcaption>
A crows nest from Rotterdam in the Netherlands.
</figcaption>
</figure>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="wWrGnB">
Magpies also use anti-bird spikes for their nests. In 2021, a hospital patient in Antwerp, Belgium, looked out the window and noticed a huge magpies nest in a tree in the courtyard. Biologist Auke-Florian Hiemstra of Leiden-based Naturalis Biodiversity Center, one of the studys authors, went to collect the nest and found that it was made out of 50 meters of anti-bird strips, containing no fewer than 1,500 metal spikes.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="SChTTC">
Hiemstra describes the magpie nest as “an impregnable fortress.”
</p>
<figure class="e-image">
<img alt=" " src="https://cdn.vox-cdn.com/thumbor/_TvANFEx9LVfrd7YZA5ZsraX0S0=/800x0/filters:no_upscale()/cdn.vox-cdn.com/uploads/chorus_asset/file/24806523/Magpie_nest_Antwerp__BE___Photo_Auke_Florian_Hiemstra.jpg"/> <cite>Auke-Florian Hiemstra</cite>
<figcaption>
A huge magpie nest made out of 1,500 metal spikes.
</figcaption>
</figure>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="Gj9m3g">
Magpies are known to build roofs over their nests to prevent other birds from stealing their eggs and young. Usually, they scrounge around in nature for thorny plants or spiky branches to form the roof. But city birds dont need to search for the perfect branch — they can just use the anti-bird spikes that humans have so kindly put at their disposal.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="QKsXsx">
“The magpies appear to be using the pins exactly the same way we do: to keep other birds away from their nest,” Hiemstra said.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="7TNrLk">
Another urban magpie nest, this one from Scotland, really shows off the roof-building tactic:
</p>
<figure class="e-image">
<img alt="A nest from Scotland shows how urban magpies are using anti-bird spikes to construct a roof meant to protect their young and eggs from predators." src="https://cdn.vox-cdn.com/thumbor/E0vRoDgW29I276bXsZmbCgP4g4o=/800x0/filters:no_upscale()/cdn.vox-cdn.com/uploads/chorus_asset/file/24799233/Magpie_nest_with_roof__photo_Max_Crawford.jpg"/> <cite>Max Crawford</cite>
<figcaption>
A nest from Scotland shows how urban magpies are using anti-bird spikes to construct a roof meant to protect their young and eggs from predators.
</figcaption>
</figure>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="uiQWof">
Birds had already been spotted using upward-pointing anti-bird spikes as foundations for nests. In 2016, the so-called <a href="https://www.broadsheet.com.au/melbourne/city-file/article/face-adversity-saga-parkdale-pigeon">Parkdale Pigeon</a> became Twitter-famous for refusing to give up when humans removed her first nest and installed spikes on her chosen nesting site, the top of an LCD monitor on a subway platform in Melbourne. The avian architect rebelled and built an even better home there, using the spikes as a foundation to hold her nest more securely in place.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="ojH5Ku">
But Hiemstras study is the first to show that birds, adapting to city life, are learning to seek out and use our anti-bird spikes as their nesting material. Pretty badass, right?
</p>
<h3 id="Abc7Ue">
The genius of birds — and other animals we underestimate
</h3>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="ncLGTV">
Studies like Hiemstras are important because they can challenge our conventional views of which animals possess intelligence and to what degree.
</p>
<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom" id="z3DGDW">
When we attribute a higher degree of intelligence to an animal, were more likely to include it in <a href="https://www.vox.com/future-perfect/2019/4/4/18285986/robot-animal-nature-expanding-moral-circle-peter-singer">our moral circle</a>, the imaginary boundary we draw around those we consider worthy of ethical consideration. (Mind you, some would argue that animal intelligence shouldnt be measured by a human yardstick and that <a href="https://www.vox.com/the-highlight/22373580/animals-intelligent-smart-orcas-chickens">intelligence shouldnt be the standard for inclusion in the moral circle</a> anyway — maybe being sentient or even simply being alive is enough.)
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Its a well-established fact that many bird species are highly intelligent. Members of the corvid family, which includes crows and magpies, are especially renowned for their smarts. Crows can solve complex puzzles, while magpies can pass the <a href="https://www.vox.com/2014/10/15/6960123/consciousness-tests-levels-define-mirror-animals-psychology">“mirror test”</a> — the classic test that scientists use to determine if a species is self-aware.
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<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2517622/">Studies</a> show that some birds have evolved cognitive skills similar to our own: They have amazing memories, remembering for months the thousands of different hiding places where theyve stashed seeds, and they use their own experiences to predict the behavior of other birds, suggesting theyve got some theory of mind.
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And, as author Jennifer Ackerman details in <em>The Genius of Birds</em>, birds are brilliant at using tools. Black palm cockatoos use twigs as drumsticks, tapping out a beat on a tree trunk to get a females attention. Jays use sticks as spears to attack other birds. New Caledonian crows turn spiny leaves into hooks for fishing grasshoppers, crickets, slugs, and spiders out of crevices. (As far as we know, that ability to make hook tools is shared with only one other animal on the planet: humans. Not even chimps or orangutans can do it.)
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Birds have also been known to use human tools to their advantage. When carrion crows want to crack a walnut, for example, they position the nut on a busy road, wait for a passing car to crush the shell, then swoop down to collect the nut and eat it. This behavior has been <a href="https://www.youtube.com/watch?v=BGPGknpq3e0">recorded</a> several times in Japanese crows.
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But whats unique about Hiemstras study is that it shows birds using human tools, specifically designed to thwart birds plans, in order to thwart our plans instead. We humans try to keep birds away with spikes, and the birds — ingenious rebels that they are — retort: Thanks, humans!
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</ul>
<h1 data-aos="fade-right" id="from-the-hindu-sports">From The Hindu: Sports</h1>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Fast Rain and Moonshot please</strong> -</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Lionel Messi shines again in first Inter Miami start, scores twice in 4-0 win over Atlanta</strong> - Messi exited in the 78th minute to a standing ovation, with many in the crowd wearing his No. 10 jersey</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Morning Digest | Indian economy to grow at 6.1% in 2023, IMF projects; Opposition for no-trust vote against Narendra Modi government, and more</strong> - Here is a select list of stories to start the day</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>They got carried away a bit: Ponting on Englands Bazball approach</strong> - Australia retained the Ashes with an unassailable 2-1 series lead on Sunday after the Manchester Test was drawn following a washed-out fifth day</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Siraj has taken such a giant step: Rohit Sharma</strong> - Asked if Siraj is ready to spearhead the pace attack, Rohit said he is not looking for only one bowler to play the lead role</p></li>
</ul>
<h1 data-aos="fade-right" id="from-the-hindu-national-news">From The Hindu: National News</h1>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Kollam port yet to meet ICP requirements</strong> - It will be declared as designated immigration check-post after infrastructure and manpower requirements are fulfilled: Union Minister</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>BRS, Cong., Majlis are the same: Kishan Reddy</strong> -</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>House under We Are for Alleppey initiative</strong> -</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Explained | Why is the Opposition insisting on a debate about Manipur under Rule 267?</strong> - What is Rule 267? How is it different from Rule 176? Why is the Opposition against the Centres plan to discuss Manipur in the Rajya Sabha under Rule 176?</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Trains to Goa cancelled, diverted, rescheduled after landslide near Castle Rock in Karnataka</strong> - Incessant rains caused landslide between Castle Rock-Caranzol stations in Braganza Ghat section of Hubballi division on July 25 night</p></li>
</ul>
<h1 data-aos="fade-right" id="from-bbc-europe">From BBC: Europe</h1>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Deadly Mediterranean wildfires kill more than 40</strong> - Wildfires have claimed most lives in Algeria, but blazes are also widespread in Greece and Italy.</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Greece fires in maps and satellite images show extent of damage</strong> - Maps, satellite images and before and after pictures show the extent of wildfires across Greece.</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Brussels bombers found guilty after long murder trial</strong> - Six of the 10 suspects are convicted of terrorist murder for the twin bombings that killed 32 people.</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Ameland rescue: Ship with 3,000 cars in deadly fire off Dutch coast</strong> - Environmental groups warn the fire could harm an area of the North Sea that is a World Heritage site.</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Paris 2024 chief wants Olympics and Paralympics to be new model of spectacular and sustainable</strong> - Paris 2024 chief Tony Estanguet says he wants next years event to be a new model for staging the Olympics.</p></li>
</ul>
<h1 data-aos="fade-right" id="from-ars-technica">From Ars Technica</h1>
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<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Dinosaurs and the evolution of breathing through bones</strong> - Dinosaurs hyper-efficient breathing system also evolved in two other lineages. - <a href="https://arstechnica.com/?p=1955859">link</a></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Pandemic deaths in Ohio and Florida show partisan divide after vaccine rollout</strong> - The death gap between Democrats and Republicans was larger in counties with lower vaccination rates. - <a href="https://arstechnica.com/?p=1956547">link</a></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>How developers will test their apps before Vision Pro launches</strong> - Apple opened up access to three ways to test apps on real hardware. - <a href="https://arstechnica.com/?p=1956470">link</a></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>FCC chair: Speed standard of 25Mbps down, 3Mbps up isnt good enough anymore</strong> - Chair proposes 100Mbps national standard and an evaluation of broadband prices. - <a href="https://arstechnica.com/?p=1956502">link</a></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Mass extinction event 260 million years ago resulted from climate change, studies say</strong> - Ocean stagnation, ecosystem collapses, and volcano eruptions all played a role. - <a href="https://arstechnica.com/?p=1956409">link</a></p></li>
</ul>
<h1 data-aos="fade-right" id="from-jokes-subreddit">From Jokes Subreddit</h1>
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<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Did you hear they arrested the devil?</strong> - <!-- SC_OFF --></p>
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Yeah, they got him on possession.
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"> submitted by <a href="https://www.reddit.com/user/Different-Tie-1085"> /u/Different-Tie-1085 </a> <br/> <span><a href="https://www.reddit.com/r/Jokes/comments/159z6y2/did_you_hear_they_arrested_the_devil/">[link]</a></span> <span><a href="https://www.reddit.com/r/Jokes/comments/159z6y2/did_you_hear_they_arrested_the_devil/">[comments]</a></span></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>I got in line to watch Oppenheimer around lunchtime, but I realized it was three hours long and I was starving.</strong> - <!-- SC_OFF --></p>
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So I went to the Barbie queue instead.
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"> submitted by <a href="https://www.reddit.com/user/KairuSmairukon"> /u/KairuSmairukon </a> <br/> <span><a href="https://www.reddit.com/r/Jokes/comments/159algc/i_got_in_line_to_watch_oppenheimer_around/">[link]</a></span> <span><a href="https://www.reddit.com/r/Jokes/comments/159algc/i_got_in_line_to_watch_oppenheimer_around/">[comments]</a></span></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>I recently joined a nudist colony..</strong> - <!-- SC_OFF --></p>
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The first few days were the hardest.
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"> submitted by <a href="https://www.reddit.com/user/sexxc"> /u/sexxc </a> <br/> <span><a href="https://www.reddit.com/r/Jokes/comments/159vm39/i_recently_joined_a_nudist_colony/">[link]</a></span> <span><a href="https://www.reddit.com/r/Jokes/comments/159vm39/i_recently_joined_a_nudist_colony/">[comments]</a></span></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>One day a young man and woman were in their bedroom making love. All of a sudden a bumble bee entered the bedroom window. As the young lady parted her legs the bee entered her vagina. The woman started screaming “Oh my god, help me, theres a bee in my vagina!”</strong> - <!-- SC_OFF --></p>
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The husband immediately took her to the local doctor and explained the situation. The doctor thought for a moment and said “Hmm, tricky situation. But I have a solution to the problem if young sir would permit.” The husband being very concerned agreed that the doctor could use whatever method to get the bee out of his wifes vagina. The doctor said “OK, what Im gonna do is rub some honey over the top of my penis and insert it into your wifes vagina. When I feel the bee getting closer to the tip of my penis I shall withdraw it and the bee should hopefully follow my penis out of your wifes vagina. The husband nodded and gave his approval. The young lady said”Yes, Yes, whatever, just get on with it." So the doctor, after covering the tip of his penis with honey, inserted it into the young ladys vagina. After a few gentle strokes, the doctor said, “I dont think the bee has noticed the honey yet. Perhaps I should go a bit deeper.” So the doctor went deeper and deeper. After a while the doctor began shafting the young lady very hard indeed. The young lady began to quiver with excitement. She began to moan and groan aloud. The doctor, concentrating very hard, looked like he was enjoying himself, he then put his hands on the young ladys breasts and started making loud noises. The husband at this point suddenly became very annoyed and shouted, “Now wait a minute! What the Hell do you think youre doing?” The doctor, still concentrating, replied, “Change of plan. Im gonna drown the bastard!”
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"> submitted by <a href="https://www.reddit.com/user/YZXFILE"> /u/YZXFILE </a> <br/> <span><a href="https://www.reddit.com/r/Jokes/comments/159hajb/one_day_a_young_man_and_woman_were_in_their/">[link]</a></span> <span><a href="https://www.reddit.com/r/Jokes/comments/159hajb/one_day_a_young_man_and_woman_were_in_their/">[comments]</a></span></p></li>
<li><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>One of my All-Time favorites (long):</strong> - <!-- SC_OFF --></p>
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A priest is fishing with one of his flock, an avid fisherman, and catches a whopper of a fish. The parishioner, forgetting himself for a moment, exclaims, “Look at the size of that Fucker!”
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The priest responds sternly and so the parishioner, quick-thinking as he his, explains, “Oh … no Father, thats the name of the fish!” The priest is surprised, but knowing his flock wouldnt lie to him, he happily carries on.
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That afternoon, he returns to the church, hands a nun a fish and asks, “Sister, can you clean and cook this Fucker?”
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“Father!”, she gasps, but the priest responds with a chuckle, “No Sister, thats the name of the fish.” The nun is surprised, but knowing the priest wouldnt lie, she happily carries on.
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That evening, the Pope has come for dinner at the small church with the priest and the nun. Theyre enjoying the meal, and the Pope remarks, “This fish is delicious!”
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The priest proudly responds, “I caught the Fucker!” The nun adds, “I cleaned and cooked the Fucker!”
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The Pope is slightly taken aback but regains himself, looks at the priest and the nun, then grins, “You know something? … you fuckers are alright!”
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"> submitted by <a href="https://www.reddit.com/user/JaRiSh117"> /u/JaRiSh117 </a> <br/> <span><a href="https://www.reddit.com/r/Jokes/comments/159sa1r/one_of_my_alltime_favorites_long/">[link]</a></span> <span><a href="https://www.reddit.com/r/Jokes/comments/159sa1r/one_of_my_alltime_favorites_long/">[comments]</a></span></p></li>
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