Showing papers by "University of Connecticut published in 2021"
Stanford University1, University of Idaho2, Wageningen University and Research Centre3, Shanghai Jiao Tong University4, Conservation International5, Harvard University6, University of Stirling7, Oregon State University8, University of Connecticut9, Stockholm Resilience Centre10, Royal Swedish Academy of Sciences11
TL;DR: A review of the development of aquaculture from 1997 to 2017 can be found in this article, where the authors highlight the integration of aqua-culture in the global food system and the potential for molluscs and seaweed to support global nutritional security.
Abstract: The sustainability of aquaculture has been debated intensely since 2000, when a review on the net contribution of aquaculture to world fish supplies was published in Nature. This paper reviews the developments in global aquaculture from 1997 to 2017, incorporating all industry sub-sectors and highlighting the integration of aquaculture in the global food system. Inland aquaculture—especially in Asia—has contributed the most to global production volumes and food security. Major gains have also occurred in aquaculture feed efficiency and fish nutrition, lowering the fish-in–fish-out ratio for all fed species, although the dependence on marine ingredients persists and reliance on terrestrial ingredients has increased. The culture of both molluscs and seaweed is increasingly recognized for its ecosystem services; however, the quantification, valuation, and market development of these services remain rare. The potential for molluscs and seaweed to support global nutritional security is underexploited. Management of pathogens, parasites, and pests remains a sustainability challenge industry-wide, and the effects of climate change on aquaculture remain uncertain and difficult to validate. Pressure on the aquaculture industry to embrace comprehensive sustainability measures during this 20-year period have improved the governance, technology, siting, and management in many cases. The volume of global aquaculture production has tripled since 2000 with positive trends in environmental performance, but the sector faces mounting challenges including pathogen management, pollution, climate change, and increasing dependence on land-based resource systems.
618 citations
TL;DR: Wagner et al. as discussed by the authors found that more than half of all amphibians are imperiled and more than 80% of all vertebrate species are in danger of extinction over the next few decades.
Abstract: Nature is under siege. In the last 10,000 y the human population has grown from 1 million to 7.8 billion. Much of Earth’s arable lands are already in agriculture (1), millions of acres of tropical forest are cleared each year (2, 3), atmospheric CO2 levels are at their highest concentrations in more than 3 million y (4), and climates are erratically and steadily changing from pole to pole, triggering unprecedented droughts, fires, and floods across continents. Indeed, most biologists agree that the world has entered its sixth mass extinction event, the first since the end of the Cretaceous Period 66 million y ago, when more than 80% of all species, including the nonavian dinosaurs, perished.
Ongoing losses have been clearly demonstrated for better-studied groups of organisms. Terrestrial vertebrate population sizes and ranges have contracted by one-third, and many mammals have experienced range declines of at least 80% over the last century (5). A 2019 assessment suggests that half of all amphibians are imperiled (2.5% of which have recently gone extinct) (6). Bird numbers across North America have fallen by 2.9 billion since 1970 (7). Prospects for the world’s coral reefs, beyond the middle of this century, could scarcely be more dire (8). A 2020 United Nations report estimated that more than a million species are in danger of extinction over the next few decades (9), but also see the more bridled assessments in refs. 10 and 11.
Although a flurry of reports has drawn attention to declines in insect abundance, biomass, species richness, and range sizes (e.g., refs. 12⇓⇓⇓⇓⇓–18; for reviews see refs. 19 and 20), whether the rates of declines for insects are on par with or exceed those for other groups remains unknown. There are still too …
[↵][1]1To whom correspondence may be addressed. Email: david.wagner{at}uconn.edu.
[1]: #xref-corresp-1-1
609 citations
European Bioinformatics Institute1, Newcastle upon Tyne Hospitals NHS Foundation Trust2, Newcastle University3, Oregon Health & Science University4, University of Genoa5, Istituto Giannina Gaslini6, King Edward Memorial Hospital7, University of Western Australia8, American College of Medical Genetics9, Anschutz Medical Campus10, Johns Hopkins University11, Ludwig Maximilian University of Munich12, Children's Hospital of Philadelphia13, Austrian Academy of Sciences14, University of Connecticut15, French Institute of Health and Medical Research16, Lawrence Berkeley National Laboratory17, University of Michigan18, University of Freiburg19, University of Luxembourg20, Oregon State University21, Chestnut Hill College22, Medical University of Graz23, Queen Mary University of London24, Hebrew University of Jerusalem25, University of Pennsylvania26
TL;DR: Recent major extensions of the Human Phenotype Ontology for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas are presented and new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease are presented.
Abstract: The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.
503 citations
University of Paris1, Northwestern University2, University College London3, Flanders Institute for Biotechnology4, Katholieke Universiteit Leuven5, Ludwig Maximilian University of Munich6, University of Connecticut7, University of Rome Tor Vergata8, Chiesi Farmaceutici S.p.A.9, University of Antwerp10, University of Cambridge11, Janssen Pharmaceutica12, McGill University13, Eisai14, French Institute of Health and Medical Research15
TL;DR: BACE1 concentrations and rates of activity are increased in AD brains and body fluids, thereby supporting the hypothesis that BACE1 plays a critical role in AD pathophysiology, and is a prime drug target for slowing down Aβ production in early AD.
275 citations
Idaho State University1, Texas A&M University2, University of Zagreb3, California State University, Los Angeles4, College of William & Mary5, Thomas Jefferson National Accelerator Facility6, Istituto Nazionale di Fisica Nucleare7, Louisiana Tech University8, Mississippi State University9, University of Manitoba10, University of Virginia11, State University of New York System12, Carnegie Mellon University13, University of Connecticut14, Hampton University15, University of Massachusetts Amherst16, Old Dominion University17, Temple University18, Indiana University19, Ohio University20, Syracuse University21, Duquesne University22, University of Winnipeg23, Veer Kunwar Singh University24, Virginia Tech25, Argonne National Laboratory26, Yerevan Physics Institute27, University of Mainz28, Christopher Newport University29, Shandong University30
TL;DR: In this paper, the parity-violating asymmetry in the elastic scattering of longitudinally polarized electrons from 208 Pb was measured, leading to an extraction of the neutral weak form factor F = 0.0036(exp)±0.0013(theo)
Abstract: We report a precision measurement of the parity-violating asymmetry A_{PV} in the elastic scattering of longitudinally polarized electrons from ^{208}Pb. We measure A_{PV}=550±16(stat)±8(syst) parts per billion, leading to an extraction of the neutral weak form factor F_{W}(Q^{2}=0.00616 GeV^{2})=0.368±0.013. Combined with our previous measurement, the extracted neutron skin thickness is R_{n}-R_{p}=0.283±0.071 fm. The result also yields the first significant direct measurement of the interior weak density of ^{208}Pb: ρ_{W}^{0}=-0.0796±0.0036(exp)±0.0013(theo) fm^{-3} leading to the interior baryon density ρ_{b}^{0}=0.1480±0.0036(exp)±0.0013(theo) fm^{-3}. The measurement accurately constrains the density dependence of the symmetry energy of nuclear matter near saturation density, with implications for the size and composition of neutron stars.
239 citations
Allen Institute for Brain Science1, Harvard University2, University of California, San Diego3, Salk Institute for Biological Studies4, University of Washington5, Cold Spring Harbor Laboratory6, Leiden University Medical Center7, J. Craig Venter Institute8, United States Department of Veterans Affairs9, University of Maryland, Baltimore10, University of Maryland, College Park11, Ludwig Institute for Cancer Research12, Discovery Institute13, University of Connecticut14, Karolinska Institutet15, Washington University in St. Louis16, Icahn School of Medicine at Mount Sinai17, Delft University of Technology18, Harborview Medical Center19, University of California, Los Angeles20, Broad Institute21, La Jolla Institute for Allergy and Immunology22, McGovern Institute for Brain Research23, Massachusetts Institute of Technology24
TL;DR: The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals using high-throughput transcriptomic and epigenomic profiling of more than 450k single nuclei in humans, marmoset monkeys and mice as mentioned in this paper.
Abstract: The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.
219 citations
TL;DR: In this paper, the authors conclude that the spread and intensification of agriculture during the past half century is directly related to these losses, and that a stable (and almost certainly lower) human population, sustainable levels of consumption, and social justice that empowers the less wealthy people and nations of the world, where the vast majority of us live, will be necessary.
Abstract: Major declines in insect biomass and diversity, reviewed here, have become obvious and well documented since the end of World War II. Here, we conclude that the spread and intensification of agriculture during the past half century is directly related to these losses. In addition, many areas, including tropical mountains, are suffering serious losses because of climate change as well. Crops currently occupy about 11% of the world's land surface, with active grazing taking place over an additional 30%. The industrialization of agriculture during the second half of the 20th century involved farming on greatly expanded scales, monoculturing, the application of increasing amounts of pesticides and fertilizers, and the elimination of interspersed hedgerows and other wildlife habitat fragments, all practices that are destructive to insect and other biodiversity in and near the fields. Some of the insects that we are destroying, including pollinators and predators of crop pests, are directly beneficial to the crops. In the tropics generally, natural vegetation is being destroyed rapidly and often replaced with export crops such as oil palm and soybeans. To mitigate the effects of the Sixth Mass Extinction event that we have caused and are experiencing now, the following will be necessary: a stable (and almost certainly lower) human population, sustainable levels of consumption, and social justice that empowers the less wealthy people and nations of the world, where the vast majority of us live, will be necessary.
218 citations
Fred Hutchinson Cancer Research Center1, Stanford University2, University of Cincinnati3, Vanderbilt University Medical Center4, Vanderbilt University5, Harvard University6, Broad Institute7, University of Lausanne8, University of Hawaii9, University of Colorado Denver10, Thomas Jefferson University11, Mayo Clinic12, Loyola University Medical Center13, Houston Methodist Hospital14, Emory University15, Beth Israel Deaconess Medical Center16, University of Florida17, McGill University Health Centre18, University of California, San Diego19, Case Western Reserve University20, St. Elizabeth Healthcare21, Icahn School of Medicine at Mount Sinai22, University of Kentucky23, Brown University24, Tufts Medical Center25, University of Michigan26, Henry Ford Health System27, Intermountain Healthcare28, George Washington University29, Cleveland Clinic30, Duke University31, Montefiore Medical Center32, Columbia University33, University of Connecticut34, Mount Auburn Hospital35, University of Kansas36, University of California, San Francisco37, Baylor College of Medicine38, Cancer Treatment Centers of America39, Ohio State University40, Penn State Cancer Institute41, University of Texas Health Science Center at San Antonio42, Loma Linda University43, University of California, Davis44, Medical University of South Carolina45, University of North Carolina at Chapel Hill46, Rutgers University47, Washington University in St. Louis48, LSU Health Sciences Center New Orleans49, University of Miami50
TL;DR: In this article, the authors analyzed a cohort of patients with cancer and coronavirus 2019 (COVID-19) reported to the COVID19 and Cancer Consortium (CCC19) to identify prognostic clinical factors, including laboratory measurements and anticancer therapies.
185 citations
TL;DR: Using administrative data on phone calls to the helpline for domestic violence in Peru, it is found that the incidence rate of the calls increased by 48 percent between April and July 2020, with effects increasing over time.
179 citations
TL;DR: In this paper, the authors provide a brief overview of mechanisms of siRNA action, physiological barriers to its delivery and activity, and the most common chemical modifications and delivery platforms used to overcome these barriers.
165 citations
St. Jude Children's Research Hospital1, University of Colorado Denver2, Stanford University3, Duke University4, Children's Mercy Hospital5, University of Missouri–Kansas City6, NorthShore University HealthSystem7, Indiana University8, Geneva College9, Vanderbilt University Medical Center10, University of Connecticut11, University of Florida12, Mental Health Research Institute13, Cincinnati Children's Hospital Medical Center14, University of Adelaide15
TL;DR: In this article, the authors provide therapeutic recommendations for the use of CYP2D6 genotype results for prescribing codeine and tramadol and describe the limited and/or weak data for CYP 2D6 and hydrocodone, oxycodone, and methadone for clinical use.
Abstract: Opioids are mainly used to treat both acute and chronic pain. Several opioids are metabolized to some extent by CYP2D6 (codeine, tramadol, hydrocodone, oxycodone, and methadone). Polymorphisms in CYP2D6 have been studied for an association with the clinical effect and safety of these drugs. Other genes that have been studied for their association with opioid clinical effect or adverse events include OPRM1 (mu receptor) and COMT (catechol-O-methyltransferase). This guideline updates and expands the 2014 Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for CYP2D6 genotype and codeine therapy and includes a summation of the evidence describing the impact of CYP2D6, OPRM1, and COMT on opioid analgesia and adverse events. We provide therapeutic recommendations for the use of CYP2D6 genotype results for prescribing codeine and tramadol and describe the limited and/or weak data for CYP2D6 and hydrocodone, oxycodone, and methadone, and for OPRM1 and COMT for clinical use.
TL;DR: Age and sex appear to be risk factors associated with a poorer prognosis in COVID-19 patients with cancer, and these factors are associated with increased risk of severe events in patients without cancer.
Abstract: BACKGROUND: Previous studies have indicated Coronavirus disease 2019 (COVID-19) patients with cancer have a high fatality rate. METHODS: We conducted a systematic review of studies that reported fatalities in COVID-19 patients with cancer. A comprehensive meta-analysis that assessed the overall case fatality rate and associated risk factors was performed. Using individual patient data, univariate and multivariate logistic regression analyses were used to estimate odds ratios (OR) for each variable with outcomes. RESULTS: We included 15 studies with 3019 patients, of which 1628 were men; 41.0% were from the UK and Europe, followed by the USA and Canada (35.7%) and Asia (China, 23.3%). The overall case fatality rate of COVID-19 patients with cancer measured 22.4% (95% confidence interval [CI] = 17.3% to 28.0%). Univariate analysis revealed age (odds ratio [OR] = 3.57; 95% CI = 1.80 to 7.06), male (OR = 2.10; 95% CI = 1.07 to 4.13), and comorbidity (OR = 2.00; 95% CI = 1.04 to 3.85) were associated with increased risk of severe events (defined as the individuals being admitted to the intensive care unit, or requiring invasive ventilation, or death). In multivariate analysis, only age greater than 65 years (OR = 3.16; 95% CI = 1.45 to 6.88) and being male (OR = 2.29; 95% CI = 1.07 to 4.87) were associated with increased risk of severe events. CONCLUSION: Our analysis demonstrated that COVID-19 patients with cancer have a higher fatality rate when compared with that of COVID-19 patients without cancer. Age and gender appear to be risk factors associated with a poorer prognosis.
TL;DR: In this paper, a cactus-like NiCo2S4@NiFe LDH hollow sphere was constructed by one-dimensional NiFeLDH nanowires and two-dimensional (2D) NiFe LDh nanosheets on the NiCo 2S4 hollow spheres by a facile hydrothermal method.
Abstract: The high-performance non-precious electrocatalysts for both oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) are crucial to the practical application of fuel cells and metal-air batteries. Herein, a novel cactus-like NiCo2S4@NiFe LDH hollow sphere assembled by one-dimensional (1D) NiFe LDH nanowires and two-dimensional (2D) NiFe LDH nanosheets on the NiCo2S4 hollow spheres is prepared by a facile hydrothermal method. The outer NiFe LDH nanowires and NiFe LDH nanosheets can effectively suppress the collapse and corrosion of inner NiCo2S4 hollow structure during long-term stability tests. The integration of the effective OER electrocatalyst NiFe LDH into NiCo2S4 to form heterostructures, as well as the strong electronic interaction between NiCo2S4 and NiFe LDH, can greatly boost both ORR and OER activities. Due to the above merits, the NiCo2S4@NiFe LDH achieves remarkably a small potential gap (ΔE = Ej=10-E1/2) of only 0.667 V. This work offers a facile strategy to design efficient catalysts with heterostructures.
TL;DR: In this article, a review of metal oxide based non-enzymatic glucose detection with a focus on electrochemical techniques is presented, followed by a discussion of future trends in developing advanced nonenzymatically glucose sensors.
University of Nottingham1, Suffolk University2, University of Dundee3, Medway School of Pharmacy4, University of Innsbruck5, University of Bristol6, University of Edinburgh7, Stanford University8, Tel Aviv University9, Northeastern University10, Ludwig Maximilian University of Munich11, Aston University12, University of Washington13, University of Birmingham14, Tufts University15, University of California, San Francisco16, University of Ferrara17, Nanyang Technological University18, University of California, Irvine19, University of Ulm20, Ariel University21, University of Illinois at Chicago22, University of Copenhagen23, Yale University24, University of Lausanne25, University of Strathclyde26, University College London27, University of Queensland28, University of Virginia29, University of Pennsylvania30, University of Oxford31, University of British Columbia32, University of Texas Health Science Center at Houston33, University of California, Davis34, Catholic University of Leuven35, University of Michigan36, University of Connecticut37
TL;DR: The Concise Guide to PHARMACOLOGY 2021/22 as mentioned in this paper provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands.
Abstract: The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes over 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/bph.15539. Ion channels are one of the six major pharmacological targets into which the Guide is divided, with the others being: G protein-coupled receptors, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2021, and supersedes data presented in the 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.
Lamont–Doherty Earth Observatory1, University of St Andrews2, University of Arizona3, Naval Postgraduate School4, University of Texas at Austin5, University of California, Los Angeles6, Federal University of Paraná7, Pusan National University8, Bureau of Meteorology9, Indian Institute of Tropical Meteorology10, Ocean University of China11, Nanjing Normal University12, Stanford University13, University of Connecticut14, National Taiwan University15, University of Reading16, Sun Yat-sen University17, Chinese Academy of Sciences18
TL;DR: This article provided a review on past monsoon changes and their primary drivers, the projected future changes and key physical processes, and discuss challenges of the present and future modeling and outlooks.
Abstract: Monsoon rainfall has profound economic and societal impacts for more than two-thirds of the global population. Here we provide a review on past monsoon changes and their primary drivers, the projected future changes and key physical processes, and discuss challenges of the present and future modeling and outlooks. Continued global warming and urbanization over the past century has already caused a significant rise in the intensity and frequency of extreme rainfall events in all monsoon regions (high confidence). Observed changes in the mean monsoon rainfall vary by region with significant decadal variations. NH land monsoon rainfall as a whole declined from 1950 to 1980 and rebounded after the 1980s, due to the competing influences of internal climate variability and radiative forcing from GHGs and aerosol forcing (high confidence); however, it remains a challenge to quantify their relative contributions. The CMIP6 models simulate better global monsoon intensity and precipitation over CMIP5 models, but common biases and large intermodal spreads persist. Nevertheless, there is high confidence that the frequency and intensity of monsoon extreme rainfall events will increase, alongside an increasing risk of drought over some regions. Also, land monsoon rainfall will increase in South Asia and East Asia (high confidence) and northern Africa (medium confidence), and decrease in North America and unchanged in Southern Hemisphere. Over Asian-Australian monsoon region the rainfall variability is projected to increase on daily to decadal scales. The rainy season will likely be lengthened in the Northern Hemisphere due to late retreat (especially over East Asia), but shortened in the Southern Hemisphere due to delayed onset.
TL;DR: In this article, a ligand core rebalances the in-plane and out-of-plane interactions that define anisotropic crystal growth, and a family of 2D π-conjugated metal-organic frameworks (MOFs) is derived from large single crystals of sizes up to 200 µm.
Abstract: Electrically conducting 2D metal–organic frameworks (MOFs) have attracted considerable interest, as their hexagonal 2D lattices mimic graphite and other 2D van der Waals stacked materials. However, understanding their intrinsic properties remains a challenge because their crystals are too small or of too poor quality for crystal structure determination. Here, we report atomically precise structures of a family of 2D π-conjugated MOFs derived from large single crystals of sizes up to 200 μm, allowing atomic-resolution analysis by a battery of high-resolution diffraction techniques. A designed ligand core rebalances the in-plane and out-of-plane interactions that define anisotropic crystal growth. We report two crystal structure types exhibiting analogous 2D honeycomb-like sheets but distinct packing modes and pore contents. Single-crystal electrical transport measurements distinctively demonstrate anisotropic transport normal and parallel to the π-conjugated sheets, revealing a clear correlation between absolute conductivity and the nature of the metal cation and 2D sheet packing motif. Two-dimensional MOFs can possess porosity and electrical conductivity but are difficult to grow as single crystals. Here, by balancing in-plane and out-of-plane interactions, single crystals of sizes up to 200 µm are grown, allowing in-plane transport measurements and atomic-resolution analysis.
Norwegian University of Science and Technology1, Chang'an University2, African Institute for Mathematical Sciences3, Stellenbosch University4, Universidade Federal de Ouro Preto5, Lalit Narayan Mithila University6, University of Idaho7, Indian Institute of Technology Roorkee8, Sonoma State University9, Indian Institute of Technology Guwahati10, University of KwaZulu-Natal11, Federation University Australia12, University of Bologna13, Ohio University14, Wuhan University of Technology15, China University of Mining and Technology16, University of Connecticut17, University of Technology, Sydney18, University of New South Wales19, University of Agder20, Sun Yat-sen University21, Indian Institute of Science22, Texas A&M University–Kingsville23, Virginia Tech24, University of Florida25
TL;DR: In this article, the authors examined individual mobility patterns for all transport modes (walk, bicycle, motorcycle, car driven alone and car driven in company, bus, subway, tram, train, airplane) before and during the restrictions adopted in ten countries on six continents: Australia, Brazil, China, Ghana, India, Iran, Italy, Norway, South Africa and United States.
Abstract: The restrictive measures implemented in response to the COVID-19 pandemic have triggered sudden massive changes to travel behaviors of people all around the world. This study examines the individual mobility patterns for all transport modes (walk, bicycle, motorcycle, car driven alone, car driven in company, bus, subway, tram, train, airplane) before and during the restrictions adopted in ten countries on six continents: Australia, Brazil, China, Ghana, India, Iran, Italy, Norway, South Africa and the United States. This cross-country study also aims at understanding the predictors of protective behaviors related to the transport sector and COVID-19. Findings hinge upon an online survey conducted in May 2020 (N = 9,394). The empirical results quantify tremendous disruptions for both commuting and non-commuting travels, highlighting substantial reductions in the frequency of all types of trips and use of all modes. In terms of potential virus spread, airplanes and buses are perceived to be the riskiest transport modes, while avoidance of public transport is consistently found across the countries. According to the Protection Motivation Theory, the study sheds new light on the fact that two indicators, namely income inequality, expressed as Gini index, and the reported number of deaths due to COVID-19 per 100,000 inhabitants, aggravate respondents' perceptions. This research indicates that socio-economic inequality and morbidity are not only related to actual health risks, as well documented in the relevant literature, but also to the perceived risks. These findings document the global impact of the COVID-19 crisis as well as provide guidance for transportation practitioners in developing future strategies.
TL;DR: The results show MolAICal can generate the various and novel ligands with good binding scores and appropriate XLOGP values, and it is believed that MolA ICal can use the advantages of deep learning model and classical programming for designing 3D drugs in protein pocket.
Abstract: Deep learning is an important branch of artificial intelligence that has been successfully applied into medicine and two-dimensional ligand design. The three-dimensional (3D) ligand generation in the 3D pocket of protein target is an interesting and challenging issue for drug design by deep learning. Here, the MolAICal software is introduced to supply a way for generating 3D drugs in the 3D pocket of protein targets by combining with merits of deep learning model and classical algorithm. The MolAICal software mainly contains two modules for 3D drug design. In the first module of MolAICal, it employs the genetic algorithm, deep learning model trained by FDA-approved drug fragments and Vinardo score fitting on the basis of PDBbind database for drug design. In the second module, it uses deep learning generative model trained by drug-like molecules of ZINC database and molecular docking invoked by Autodock Vina automatically. Besides, the Lipinski's rule of five, Pan-assay interference compounds (PAINS), synthetic accessibility (SA) and other user-defined rules are introduced for filtering out unwanted ligands in MolAICal. To show the drug design modules of MolAICal, the membrane protein glucagon receptor and non-membrane protein SARS-CoV-2 main protease are chosen as the investigative drug targets. The results show MolAICal can generate the various and novel ligands with good binding scores and appropriate XLOGP values. We believe that MolAICal can use the advantages of deep learning model and classical programming for designing 3D drugs in protein pocket. MolAICal is freely for any nonprofit purpose and accessible at https://molaical.github.io.
Lea Berrang-Ford1, A. R. Siders2, Alexandra Lesnikowski3, Alexandra Paige Fischer4 +147 more•Institutions (87)
TL;DR: In this article, the authors present a systematic and comprehensive global stocktake of implemented human adaptation to climate change and identify eight priorities for global adaptation research: assess the effectiveness of adaptation responses, enhance the understanding of limits to adaptation, enable individuals and civil society to adapt, include missing places, scholars and scholarship, understand private sector responses, improve methods for synthesizing different forms of evidence, assess the adaptation at different temperature thresholds, and improve the inclusion of timescale and the dynamics of responses.
Abstract: Assessing global progress on human adaptation to climate change is an urgent priority. Although the literature on adaptation to climate change is rapidly expanding, little is known about the actual extent of implementation. We systematically screened >48,000 articles using machine learning methods and a global network of 126 researchers. Our synthesis of the resulting 1,682 articles presents a systematic and comprehensive global stocktake of implemented human adaptation to climate change. Documented adaptations were largely fragmented, local and incremental, with limited evidence of transformational adaptation and negligible evidence of risk reduction outcomes. We identify eight priorities for global adaptation research: assess the effectiveness of adaptation responses, enhance the understanding of limits to adaptation, enable individuals and civil society to adapt, include missing places, scholars and scholarship, understand private sector responses, improve methods for synthesizing different forms of evidence, assess the adaptation at different temperature thresholds, and improve the inclusion of timescale and the dynamics of responses. Determining progress in adaptation to climate change is challenging, yet critical as climate change impacts increase. A stocktake of the scientific literature on implemented adaptation now shows that adaptation is mostly fragmented and incremental, with evidence lacking for its impact on reducing risk.
TL;DR: In this paper, the authors examined in-hospital mortality with intermediate- compared to prophylactic-dose anticoagulation, and separately with aspirin compared to no antiplatelet therapy, in a large, retrospective study of 2785 hospitalized adult COVID-19 patients.
Abstract: Thrombotic complications occur at high rates in hospitalized patients with COVID-19, yet the impact of intensive antithrombotic therapy on mortality is uncertain. We examined in-hospital mortality with intermediate- compared to prophylactic-dose anticoagulation, and separately with in-hospital aspirin compared to no antiplatelet therapy, in a large, retrospective study of 2785 hospitalized adult COVID-19 patients. In this analysis, we established two separate, nested cohorts of patients (a) who received intermediate- or prophylactic-dose anticoagulation ("anticoagulation cohort", N = 1624), or (b) who were not on home antiplatelet therapy and received either in-hospital aspirin or no antiplatelet therapy ("aspirin cohort", N = 1956). To minimize bias and adjust for confounding factors, we incorporated propensity score matching and multivariable regression utilizing various markers of illness severity and other patient-specific covariates, yielding treatment groups with well-balanced covariates in each cohort. The primary outcome was cumulative incidence of in-hospital death. Among propensity score-matched patients in the anticoagulation cohort (N = 382), in a multivariable regression model, intermediate- compared to prophylactic-dose anticoagulation was associated with a significantly lower cumulative incidence of in-hospital death (hazard ratio 0.518 [0.308-0.872]). Among propensity-score matched patients in the aspirin cohort (N = 638), in a multivariable regression model, in-hospital aspirin compared to no antiplatelet therapy was associated with a significantly lower cumulative incidence of in-hospital death (hazard ratio 0.522 [0.336-0.812]). In this propensity score-matched, observational study of COVID-19, intermediate-dose anticoagulation and aspirin were each associated with a lower cumulative incidence of in-hospital death.
TL;DR: In this article, the authors briefly describe the PCR and antigen tests and then focus mainly on existing antibody tests and their limitations including inaccuracies and possible causes of unreliability False negatives in antibody immunoassays can arise from assay formats, selection of viral antigens and antibody types, diagnostic testing windows, individual variance, and fluctuation in antibody levels.
Abstract: COVID-19, caused by the SARS-CoV-2 virus, has developed into a global health crisis, causing over 2 million deaths and changing people's daily life the world over Current main-stream diagnostic methods in the laboratory include nucleic acid PCR tests and direct viral antigen tests for detecting active infections, and indirect human antibody tests specific to SARS-CoV-2 to detect prior exposure In this Perspective, we briefly describe the PCR and antigen tests and then focus mainly on existing antibody tests and their limitations including inaccuracies and possible causes of unreliability False negatives in antibody immunoassays can arise from assay formats, selection of viral antigens and antibody types, diagnostic testing windows, individual variance, and fluctuation in antibody levels Reasons for false positives in antibody immunoassays mainly involve antibody cross-reactivity from other viruses, as well as autoimmune disease The spectrum bias has an effect on both the false negatives and false positives For assay developers, not only improvement of assay formats but also selection of viral antigens and isotopes of human antibodies need to be carefully considered to improve sensitivity and specificity For clinicians, the factors influencing the accuracy of assays must be kept in mind to test patients using currently imperfect but available tests with smart tactics and realistic interpretation of the test results
TL;DR: Artificial intelligence-based polyp detection systems during colonoscopy increase detection of small, non-advanced adenomas and polyps, but not advancedAdenomas, according to a systematic review and meta-analysis of prospective trials.
Abstract: Background Artificial intelligence (AI)-based polyp detection systems are used during colonoscopy with the aim of increasing lesion detection and improving colonoscopy quality Patients and methods: We performed a systematic review and meta-analysis of prospective trials to determine the value of AI-based polyp detection systems for detection of polyps and colorectal cancer We performed systematic searches in MEDLINE, EMBASE, and Cochrane CENTRAL Independent reviewers screened studies and assessed eligibility, certainty of evidence, and risk of bias We compared colonoscopy with and without AI by calculating relative and absolute risks and mean differences for detection of polyps, adenomas, and colorectal cancer Results Five randomized trials were eligible for analysis Colonoscopy with AI increased adenoma detection rates (ADRs) and polyp detection rates (PDRs) compared to colonoscopy without AI (values given with 95 %CI) ADR with AI was 296 % (222 % – 370 %) versus 193 % (127 % – 259 %) without AI; relative risk (RR] 152 (131 – 177), with high certainty PDR was 454 % (411 % – 498 %) with AI versus 306 % (265 % – 346 %) without AI; RR 148 (137 – 160), with high certainty There was no difference in detection of advanced adenomas (mean advanced adenomas per colonoscopy 003 for each group, high certainty) Mean adenomas detected per colonoscopy was higher for small adenomas (≤ 5 mm) for AI versus non-AI (mean difference 015 [012 – 018]), but not for larger adenomas (> 5 – ≤ 10 mm, mean difference 003 [001 – 005]; > 10 mm, mean difference 001 [000 – 002]; high certainty) Data on cancer are unavailable Conclusions AI-based polyp detection systems during colonoscopy increase detection of small nonadvanced adenomas and polyps, but not of advanced adenomas
01 Mar 2021
TL;DR: Fourier ptychography (FP) as mentioned in this paper is an imaging approach that addresses the intrinsic trade-off between resolution and field of view in optical systems and provides computational correction of optical aberrations.
Abstract: The competition between resolution and the imaging field of view is a long-standing problem in traditional imaging systems — they can produce either an image of a small area with fine details or an image of a large area with coarse details. Fourier ptychography (FP) is an approach for tackling this intrinsic trade-off in imaging systems. It takes the challenge of high-throughput and high-resolution imaging from the domain of improving the physical limitations of optics to the domain of computation. It also enables post-measurement computational correction of optical aberrations. We present the basic concept of FP, compare it to related imaging modalities and then discuss experimental implementations, such as aperture-scanning FP, macroscopic camera-scanning FP, reflection mode, single-shot set-up, X-ray FP, speckle-scanning scheme and deep-learning-related implementations. Various applications of FP are discussed, including quantitative phase imaging in 2D and 3D, digital pathology, high-throughput cytometry, aberration metrology, long-range imaging and coherent X-ray nanoscopy. A collection of datasets and reconstruction codes is provided for readers interested in implementing FP themselves. Fourier ptychography is an imaging approach that addresses the intrinsic trade-off between resolution and field of view in optical systems and provides computational correction of optical aberrations. This Technical Review surveys its implementations and applications.
National Institutes of Health1, University of California, San Diego2, Saint Petersburg State University3, University of Washington4, University of California, Berkeley5, Johns Hopkins University6, University of Connecticut7, University of California, Santa Cruz8, University of Geneva9, Stowers Institute for Medical Research10, Harvard University11, Wellcome Trust Sanger Institute12, University of Cambridge13, Howard Hughes Medical Institute14, Washington University in St. Louis15, University of Tennessee Health Science Center16, Yale University17, Pacific Biosciences18, University of Düsseldorf19, National Institute of Standards and Technology20, Max Planck Society21, Baylor College of Medicine22, University of California, Davis23, Institute for Systems Biology24, Duke University25, University of Pittsburgh26, Russian Academy of Sciences27
TL;DR: The T2T-CHM13 reference as mentioned in this paper contains gapless assemblies for all 22 autosomes plus Chromosome X, corrected numerous errors, and introduced nearly 200 million bp of novel sequence containing 2,226 paralogous gene copies, 115 of which are predicted to be protein coding.
Abstract: In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics. While these drafts and the updates that followed effectively covered the euchromatic fraction of the genome, the heterochromatin and many other complex regions were left unfinished or erroneous. Addressing this remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium has finished the first truly complete 3.055 billion base pair (bp) sequence of a human genome, representing the largest improvement to the human reference genome since its initial release. The new T2T-CHM13 reference includes gapless assemblies for all 22 autosomes plus Chromosome X, corrects numerous errors, and introduces nearly 200 million bp of novel sequence containing 2,226 paralogous gene copies, 115 of which are predicted to be protein coding. The newly completed regions include all centromeric satellite arrays and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies for the first time.
TL;DR: A comprehensive overview of human mobility open data is provided to guide researchers and policymakers in conducting data-driven evaluations and decision-making for the COVID-19 pandemic and other infectious disease outbreaks.
Abstract: The COVID-19 pandemic poses unprecedented challenges around the world. Many studies have applied mobility data to explore spatiotemporal trends over time, investigate associations with other variables, and predict or simulate the spread of COVID-19. Our objective was to provide a comprehensive overview of human mobility open data to guide researchers and policymakers in conducting data-driven evaluations and decision-making for the COVID-19 pandemic and other infectious disease outbreaks. We summarized the mobility data usage in COVID-19 studies by reviewing recent publications on COVID-19 and human mobility from a data-oriented perspective. We identified three major sources of mobility data: public transit systems, mobile operators, and mobile phone applications. Four approaches have been commonly used to estimate human mobility: public transit-based flow, social activity patterns, index-based mobility data, and social media-derived mobility data. We compared mobility datasets' characteristics by assessing data privacy, quality, space-time coverage, high-performance data storage and processing, and accessibility. We also present challenges and future directions of using mobility data. This review makes a pivotal contribution to understanding the use of and access to human mobility data in the COVID-19 pandemic and future disease outbreaks.
TL;DR: In this article, a corrugated-wall dual-type membrane reactor is proposed as an emerging alternative for CO2 hydrogenation to value-added products, with key pathways that dictate catalyst activity and selectivity of the most promising materials described.
University of Jena1, Wellcome Trust Sanger Institute2, Centre national de la recherche scientifique3, European Bioinformatics Institute4, Technische Universität München5, ETH Zurich6, National University of Luján7, Robert Koch Institute8, University of Marburg9, Free University of Berlin10, University of Virginia11, Greifswald University Hospital12, Max Planck Society13, Albert Einstein College of Medicine14, University of Hasselt15, University of Connecticut16, University of Edinburgh17, University of Copenhagen18, University of Los Andes19, University of Glasgow20, Katholieke Universiteit Leuven21, University of Victoria22
TL;DR: Bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies are reviewed.
Abstract: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.
TL;DR: The utility of lncRNAs as biomarkers of cancer progression, and their potential use as therapeutic targets for treatment of cancer are discussed.