bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global, regional, and national estimates of target population sizes for COVID-19 vaccination
Authors: Wang Wei , Wu Qianhui , Yang Juan , Dong Kaige , Chen Xinghui , Bai Xufang , Chen Xinhua , Chen Zhiyuan , Viboud Cécile , Ajelli Marco , Yu Hongjie 
Published: October 2020

AbstractBackgroundCOVID-19 vaccine prioritization and allocation strategies that maximize health benefit through efficient use of limited resources are urgently needed. We aimed to provide global, regional, and national estimates of target population sizes for COVID-19 vaccination to inform country-specific immunization strategies on a global scale.MethodsBased on a previous study of international allocation for pandemic COVID-19 vaccines, we classified the entire world population into eleven priority groups. Information on priority groups was derived from a multi-pronged search of official websites, media sources and academic journal articles. The sizes of different priority groups were projected for 194 countries globally.ResultsOverall, the size of COVID-19 vaccine recipient population varied markedly by goals of the vaccination program and geography. The general population aged <60 years without any underlying condition accounts for the majority of the total population (5.2 billion people, 68%), followed by 2.3 billion individuals at risk of severe disease, and 246.9 million essential workers which are critical to maintaining a functional society. Differences in the demographic structure, presence of underlying conditions, and number of essential workers led to highly variable estimates of target populations both at the WHO region and country level. In particular, Europe has the highest share of essential workers (6.8%) and the highest share of individuals with underlying conditions (37.8%), two priority categories to maintain societal functions and reduce severe burden. In contrast, Africa has the highest share of healthy adults, school-age individuals, and infants (77.6%), which are the key groups to target to reduce community transmission.InterpretationThe sizeable distribution of target groups on a country and regional bases underlines the importance of equitable and efficient vaccine prioritization and allocation globally. The direct and indirect benefits of COVID-19 vaccination should be balanced by considering local differences in demography and health.
Seroprevalence and Risk Factors of SARS CoV-2 in Health Care Workers of Tertiary-Care Hospitals in the Province of Khyber Pakhtunkhwa, Pakistan
Authors: Haq Mohsina , Rehman Asif , Noor Muhammad , Ahmad Jawad , Ahmad Junaid , Irfan Muhammad , Anwar Saeed , Ahmad Sajjad , Amin Said , Rahim Fawad , Haq Najib Ul 
Published: October 2020

AbstractBackgroundHigh number of SARS-CoV-2 infected patients has overburdened healthcare delivery system, particularly in low-income countries. In the recent past many studies from the developed countries have been published on the prevalence of SARS CoV-2 antibodies and the risk factors of COVID-19 in healthcare-workers but little is known from developing countries.MethodsThis cross-sectional study was conducted on prevalence of SARS-CoV-2 antibody and risk factors for seropositivity in HCWs in tertiary-care hospitals of Peshawar city, Khyber Pakhtunkhwa province Pakistan.ResultsThe overall seroprevalence of SARS CoV-2 antibodies was 30·7% (CI, 27·8–33·6) in 1011 HCWs. Laboratory technicians had the highest seropositivity (50·0%, CI, 31·8–68·1).Risk analysis revealed that wearing face-mask and observing social-distancing within a family could reduce the risk (OR:0·67. p<0·05) and (OR:0·73. p<0·05) while the odds of seropositivity were higher among those attending funeral and visiting local-markets (OR:1·83. p<0·05) and (OR:1·66. p<0·01). In Univariable analysis, being a nursing staff and a paramedical staff led to higher risk of seropositivity (OR:1.58. p< 0·05), (OR:1·79. p< 0·05). Fever (OR:2·36, CI, 1·52– 3·68) and loss of smell (OR:2·95, CI: 1·46–5·98) were significantly associated with increased risk of seropositivity (p<0.01). Among the seropositive HCWs, 165 (53·2%) had no symptoms at all while 145 (46·8%) had one or more symptoms.ConclusionThe high prevalence of SARS-CoV-2 antibodies in HCWs warrants for better training and use of protective measure to reduce their risk. Early detection of asymptomatic HCWs may be of special importance because they are likely to be potential threat to others during the active phase of viremia.
The Health Effects of Climate Change: An Overview of Systematic Reviews
Authors: Rocque Rhéa , Beaudoin Caroline , Ndjaboue Ruth , Cameron Laura , Bergeron Louann Poirier , Poulin-Rheault Rose-Alice , Fallon Catherine , Tricco Andrea C. , Witteman Holly O. 
Published: October 2020

AbstractBackgroundAlthough many studies have explored the health impacts of climate change, a broader overview of research is needed to guide future research and action to mitigate and adapt to the health impacts of climate change.MethodsWe conducted an overview of systematic reviews of health impacts of climate change. We systematically searched the literature using a predefined search strategy, inclusion, and exclusion criteria. We included systematic reviews that explored at least one health impact of climate change. We organized systematic reviews according to their key characteristics, including geographical regions, year of publication and authors’ affiliations. We mapped the climate effects and health outcomes being studied and synthesized major findings.FindingsWe included ninety-four systematic reviews. Most were published after 2015 and approximately one fifth contained meta-analyses. Reviews synthesized evidence about five categories of climate impacts; the two most common were meteorological and extreme weather events. Reviews covered ten health outcome categories; the three most common were 1) infectious diseases, 2) mortality, and 3) respiratory, cardiovascular, cardiopulmonary or neurological outcomes. Most reviews suggested a deleterious impact of climate change on multiple adverse health outcomes, although the majority also called for more research.InterpretationOverall, most systematic reviews suggest that climate change is associated with worse human health. Future research could explore the potential explanations between these associations to propose adaptation and mitigation strategies and could include psychological and broader social health impacts of climate change.FundingCanadian Institutes of Health Research FDN-148426
PD-L1 lncRNA splice promotes lung adenocarcinoma progression via enhancing c-Myc activity
Authors: Qu Shuang , Jiao Zichen , Lu Geng , Yao Bing , Wang Ting , Rong Weiwei , Xu Jiahan , Fan Ting , Sun Xinlei , Yang Rong , Wang Jun , Yao Yongzhong , Xu Guifang , Yan Xin , Wang Tao , Liang Hongwei , Zen Ke 
Published: October 2020

ABSTRACTAlthough blockade of programmed death-ligand 1 (PD-L1) to enhance T cell immune responses shows great promise in tumor immunotherapy, the efficacy of such immune-checkpoint inhibition strategy is limited for patients with solid tumors. The mechanism underlying the limited efficacy of PD-L1 inhibitors remains unclear. Here, we show that human lung adenocarcinoma, regardless of PD-L1 protein positive or negative, all produce a long non-coding RNA isoform of PD-L1 (PD-L1-lnc) via alternative splicing, which promotes lung adenocarcinoma proliferation and metastasis. PD-L1-lnc in various lung adenocarcinoma cells is significantly upregulated by IFNγ in a manner similar to PD-L1 mRNA. Bothin vitroandin vivostudies demonstrate that PD-L1-lnc increases proliferation and invasion but decreases apoptosis of lung adenocarcinoma cells. Mechanistically, PD-L1-lnc directly binds to c-Myc and enhances c-Myc transcriptional activity downstream in lung adenocarcinoma cells. Our results provide targeting PD-L1-lnc−c-Myc axis as a novel strategy for lung cancer therapy.
Nebulosarecovers single cell gene expression signals by kernel density estimation
Authors: Alquicira-Hernandez Jose , Powell Joseph E. 
Published: October 2020

AbstractSummaryData sparsity in single-cell experiments prevents an accurate assessment of gene expression when visualised in a low-dimensional space. Here, we introduceNebulosa, an R package that uses weighted kernel density estimation to recover signals lost through drop-out or low expression.Availability and implementationNebulosacan be easily installed fromwww.github.com/powellgenomicslab/Nebulosa
Allele-specific antisense oligonucleotide therapy for dominantly inherited hearing impairment DFNA9
Authors: de Vrieze Erik , Peijnenborg Jolien , Martin Jorge Cañas , Martens Aniek , Oostrik Jaap , van der Heuvel Simone , Neveling Kornelia , Pennings Ronald , Kremer Hannie , van Wijk Erwin 
Published: October 2020

AbstractThe c.151C>T founder mutation inCOCHis a frequent cause of late onset, dominantly inherited hearing impairment and vestibular dysfunction (DFNA9) in the Dutch/Belgian population. The initial clinical symptoms only manifest between the 3rd and 5th decade of life, which leaves ample time for therapeutic intervention. The dominant inheritance pattern and established non-haploinsufficiency disease mechanism indicate that suppressing translation of mutantCOCHtranscripts has high therapeutic potential. Single-Molecule Real-Time (SMRT) sequencing resulted in the identification of 11 variants with a low population-frequency (< 10%), that are specific to the c.151C>T mutantCOCHallele. Proof of concept was obtained that gapmer antisense oligonucleotides (AONs), directed against the c.151C>T mutation or mutant allele-specific intronic variants, are able to specifically induce mutantCOCHtranscript degradation when delivered to transgenic cells expressingCOCHminigenes. Sequence optimization of the AONs against the c.151C>T mutation resulted in a lead molecule that reduced the levels of mutantCOCHtranscripts by ~60% in a transgenic cell model, without affecting wildtypeCOCHtranscript levels. With the proven safety of AONs in humans, and rapid advancements in inner ear drug delivery, our in-vitro studies indicate that AONs offer a promising treatment modality for DFNA9.
New insights into large tropical tree mass and structure from direct harvest and terrestrial lidar
Authors: Burt A. , Vicari M. Boni , da Costa A. C. L. , Coughlin I. , Meir P. , Rowland L. , Disney M. 
Published: October 2020

AbstractA large portion of the terrestrial vegetation carbon stock is stored in the above-ground biomass (AGB) of tropical forests, but the exact amount remains uncertain, partly due to the lack of measurements. To date, accessible peer-reviewed data are available for just 10 large tropical trees in the Amazon that have been harvested and directly measured entirely via weighing. Here, we harvested four large tropical rainforest trees (stem diameter: 0.6–1.2m, height: 30–46m, AGB: 3960–18 584 kg) in intact old-growth forest in East Amazonia, and measured above-ground green mass, moisture content and woody tissue density. We first present rare ecological insights provided by these data, including unsystematic intra-tree variations in density, with both height and radius. We also found the majority of AGB was usually found in the crown, but varied from 42–62%. We then compare non-destructive approaches for estimating the AGB of these trees, using both classical allometry, and new lidar-based methods. Terrestrial lidar point clouds were collected pre-harvest, on which we fitted cylinders to model woody structure, enabling retrieval of volume-derived AGB. Estimates from this approach were more accurate than allometric counterparts (mean tree-scale relative error: 3% vs. 15%), and error decreased when up-scaling to the cumulative AGB of the four trees (1% vs. 15%). Further, whilst allometric error increased four-fold with tree size over the diameter range, lidar error remained constant. This suggests error in these lidar-derived estimates is random and additive. Were these results transferable across forest scenes, terrestrial lidar methods would reduce uncertainty in stand-scale AGB estimates, and therefore advance our understanding of the role of tropical forests in the global carbon cycle.
Reprogramming Epiblast Stem Cells into Pre-Implantation Blastocyst Cell-like Cells
Authors: Tomoda Kiichiro , Hu Haiming , Sahara Yoshiki , Sanyal Hashimita , Takasato Minoru , Kime Cody 
Published: October 2020

ABSTRACTRecently, a new wave of synthetic embryo systems (SESs) have been established from cultured cells toward efficient and ethical embryonic development research. We recently reported our epiblast stem cell (EPISC) reprogramming SES that generates numerous blastocyst (BC)-like hemispheres (BCLH) with pluripotent and extraembryonic cell features detected microscopically. Here, we further explored the system over key time points with unprecedented single-cell RNA sequencing (scRNA-seq) analysis and revealed broad induction of the 2C-like reporterMERVLand RNA velocity diverging three major population regions with genetic expression resembling pluripotent epiblast (EPI), primitive endoderm (PE), and trophectoderm (TE). Enrichment of those three BC-like cell fates involved key regulons, zygotic genome activation (ZGA) related genes, specific RNA splicing, and select cells meaningfully distinguished critical regulons of model cells. This analysis confirms the induction of the extraembryonic cell populations during the reprogramming and we anticipate that our unique BCLH SES and rich data may uncover new facets of cell potency, improve developmental biology, and help biomedicine advance.
Nonself-recognition-based self-incompatibility can alternatively promote or prevent introgression
Authors: Harkness Alexander , Brandvain Yaniv 
Published: October 2020

1SummaryTraditionally, we expect that self-incompatibility alleles (S-alleles), which prevent self-fertilization, should benefit from negative-frequency dependent selection and rise to high frequency when introduced to a new population through gene flow. However, the most taxonomically widespread form of self-incompatibility, the ribonuclease-based system ancestral to the core eudicots, functions through nonself-recognition, which drastically alters the process of S-allele diversification.We analyze a model of S-allele evolution in two populations connected by migration, focusing on comparisons among the fates of S-alleles originally unique to each population and those shared among populations.We find that both shared and unique S-alleles originating from the population with more unique S-alleles were usually fitter than S-alleles from the population with fewer. Resident S-alleles were often driven extinct and replaced by migrant S-alleles, though this outcome could be averted by pollen limitation or biased migration.Nonself-recognition-based self-incompatibility will usually either disfavor introgression of S-alleles or result in the whole-sale replacement of S-alleles from one population with those from another.
Using neural networks to mine text and predict metabolic traits for thousands of microbes
Authors: Hackmann Timothy J. 
Published: October 2020

AbstractMicrobes can metabolize more chemical compounds than any other group of organisms. As a result, their metabolism is of interest to investigators across biology. Despite the interest, information on metabolism of specific microbes is hard to access. Information is buried in text of books and journals, and investigators have no easy way to extract it out. Here we investigate if neural networks can extract out this information and predict metabolic traits. For proof of concept, we predicted two traits: whether microbes carry one type of metabolism (fermentation) or produce one metabolite (acetate). We collected written descriptions of 7,021 species of bacteria and archaea from Bergey’s Manual. We read the descriptions and manually identified (labeled) which species were fermentative or produced acetate. We then trained neural networks to predict these labels. In total, we identified 2,364 species as fermentative, and 1,009 species as also producing acetate. Neural networks could predict which species were fermentative with 97.3% accuracy. Accuracy was even higher (98.6%) when predicting species also producing acetate. We used these predictions to draw phylogenetic trees of species with these traits. The resulting trees were close to the actual trees (drawn using labels). Previous counts of fermentative species are 4-fold lower than our own. For acetate-producing species, they are 100-fold lower. This undercounting confirms past difficulty in extracting metabolic traits from text. Our approach with neural networks can extract information efficiently and accurately. It paves the way for putting more metabolic traits into databases, providing easy access of information by investigators.
Biomechanical characterization of endothelial cells exposed to shear stress using acoustic force spectroscopy
Authors: Silvani Giulia , Romanov Valentin , Cox Charles D. , Martinac Boris 
Published: October 2020

AbstractCharacterizing mechanical properties of cells is important for understanding many cellular processes, such as cell movement, shape, and growth, as well as adaptation to changing environments. In this study, we explore mechanical properties of endothelial cells that form the biological barrier lining blood vessels, whose dysfunction leads to development of many cardiovascular disorders. Stiffness and contractile prestress of living endothelial cells were determined byAcousticForceSpectroscopy (AFS) focusing on the displacement of functionalized microspheres located at the cell-cell periphery. The specific configuration of the acoustic microfluidic channel allowed us to develop a long-term dynamic culture protocol exposing cells to laminar flow, reaching shear stresses in the physiological range (i.e. 8 dyne cm-2) within 48 hours of barrier function maturation. A staircase-like sequence of increasing force steps, ranging from 186 pN to 3.5 nN, was applied in a single measurement revealing a force-dependent apparent stiffness in the kPa range. Moreover, our results show that different degrees of stiffening, defining the elastic behavior of the cell under different experimental conditions, i.e. static and dynamic, are caused by different levels of contractile prestress in the cytoskeleton, and are modulated by shear stress-mediated junction development and stabilization at cell borders. These results demonstrate that the AFS is capable of fast and high-throughput force measurements of adherent cells under conditions mimicking their native microenvironment, and thus revealing the shear stress dependence of mechanical properties of neighbouring endothelial cells.
Consequences of Mismatch, Misalignment and Rotation of Toric Intraocular Lenses in Refractive Cataract Surgery Part 2. Avoiding Flip Flops
Authors: I Sayegh Samir 
Published: October 2020

AbstractPurposeTo show current approaches for overcorrecting astigmatism and “flipping” its axis need be reconsidered in light of methods we introduce that take into account both mismatch and misalignment of the toric intraocular lens (tIOL) with respect to the astigmatism to be corrected at the time of cataract surgery.SettingPrivate Practice and Research Center. The EYE Center. Champaign, IL, USA.DesignFormal Analytical StudyMethodsIn the most common surgical situation where both mismatch and misalignment exist, we present an analysis of the point at which overcorrection and undercorrection residuals coincide, yielding a simple but powerful methodology to predict the optimal degree of overcorrection with a tIOL. The method is illustrated for tIOLs used in surgical practice.ResultsThe minimum astigmatism appropriate to overcorrect with a tIOL is given by, ,where m is the midpoint threshold used by “split-the-difference” algorithms and χ is the estimate of tIOL misalignment due to all causes. Correspondingly, the maximum overcorrection, Ωmax, that should be attempted is where is the dioptric step at the corneal plane, with σ = H − B, where H = n σ is the cylinder of the overcorrecting tIOL and B = (n − 1)σ is the cylinder of the undercorrecting tIOL, both at the IOL plane, τis the toricity ratio and γ relates to the angle of misalignment χ by which can be approximated by . Ω maxfactors elegantly in the product of , the (ideal) midpoint correction for perfect alignment, by the bracketed term, representing the percent reduction of the ideal value in a realistic surgical situation with estimated misalignment χ. To illustrate: an eye of average dimensions and tIOLs from major manufacturers , with A = 2.35 D dictating n = 5. For a misalignment of 10°Ωmax≅ 0.10 D is the maximum overcorrection that should be accepted, significantly smaller than the midpoint D, recommended by many current tIOL calculators.ConclusionAn optimal method is presented for the selection of an overcorrecting tIOL at the time of refractive cataract surgery with improvement over current tIOL calculators’ methods.
Life cycle of arabidopsis in the international space station - Growth direction of the inflorescence stems in the presence of light under microgravity
Authors: Yashiro Umi , Karahara Ichirou , Yano Sachiko , Tamaoki Daisuke , Tanigaki Fumiaki , Shimazu Toru , Masuda Daisuke , Kasahara Haruo , Kamisaka Seiichiro 
Published: October 2020

ABSTRACTIn the “Space Seed” experiment performed in Kibo module of the International Space Station, growth direction of the inflorescence stem of arabidopsis was examined under space 1G, μG, and ground 1Gconditions in the presence of light. The stems grew almost upright (vertical to the surface of seedbed) under ground 1G. Although the stems were primarily upright both under space 1Gand μG, they tilted slightly. The tilting of the stems under space 1Gwas indicated to be due to tilting of the artificial gravitational acceleration vectors produced on the centrifuge. The tilting of the stems under μGwas suggested to be due to the pressure of directional airflow produced by ventilation.