bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of symptom profile and risk of death associated with infection by SARS-CoV-2 and its variants in Hong Kong
Authors: Kwok Kin On , Wei Wan In , Mcneil Edward B. , Tang Arthur , Tang Julian Wei Tze , Wong Samuel Yeung Shan , Yeoh Eng Kiong 
Published: May 2023

ABSTRACTIntroductionThe recurrent multi-wave nature of COVID-19 necessitates updating its symptomatology. Before the omicron era, Hong Kong was relatively unscathed and had a low vaccine uptake rate among the old-old, giving us an opportunity to study the intrinsic severity of SARS-CoV-2 variants. A comparison of symptom patterns across variants and vaccination status in Hong Kong has yet to be undertaken. The intrinsic severity of variants and symptoms predictive of severe outcomes are also understudied as COVID-19 evolves. We therefore aim to characterize the effect of variants on symptom presentation, identify the symptoms predictive and protective of death, and quantify the effect of vaccination on symptom development.MethodsWith the COVID-19 case series in Hong Kong from inception to 25 August 2022, an iterative multi-tier text-matching algorithm was developed to identify symptoms from free text. Cases were fully vaccinated if they completed two doses. Multivariate regression was used to measure associations between variants, symptom development, death and vaccination status. A least absolute shrinkage and selection operator technique was used to identify a parsimonious set of symptoms jointly associated with death.ResultsOverall, 70.9% (54450/76762) of cases were symptomatic. We identified a wide spectrum of symptoms (n=102), with cough, fever, runny nose and sore throat being the most common (8.16-47.0%). Intrinsically, the wild-type and delta variant caused similar symptoms, with runny nose, sore throat, itchy throat and headache more frequent in the delta cohort; whereas symptoms were heterogeneous between the wild-type and omicron variant, with seven symptoms (fatigue, fever, chest pain, runny nose, sputum production, nausea/vomiting and sore throat) more frequent in the omicron cohort. With full vaccination, omicron was still more likely than delta to cause fever. Fever, blocked nose and shortness of breath were robustly jointly predictive of death as the virus evolved. Number of vaccine doses required for reduction in occurrence varied by symptoms.DiscussionThis is the first large-scale study to evaluate the changing symptomatology by COVID-19 variants and vaccination status using free-text reporting by patients. We substantiate existing findings that omicron has a different clinical presentation compared to previous variants. Syndromic surveillance can be bettered with reduced reliance on symptom-based case identification, increased weighing on symptoms robustly predictive of mortality in outcome prediction, strengthened infection control in care homes through universal individual-based risk assessment to enable early risk stratification, adjusting the stockpile of medicine to tally with the changing symptom profiles across vaccine doses, and incorporating free-text symptom reporting by patients.
The distribution of global tidal marshes from earth observation data
Authors: Worthington Thomas A. , Spalding Mark , Landis Emily , Maxwell Tania L. , Navarro Alejandro , Smart Lindsey S. , Murray Nicholas J. 
Published: May 2023

ABSTRACTAimTidal marsh ecosystems are heavily impacted by human activities, highlighting a pressing need to address gaps in our knowledge of their distribution. To better understand the global distribution and changes in tidal marsh extent, and identify opportunities for their conservation and restoration, it is critical to develop a spatial knowledge base of their global occurrence. Here, we develop a globally consistent tidal marsh distribution map for the year 2020 at 10-m resolution.LocationGlobalTime period2020Major taxa studiedTidal marshesMethodsTo map the location of the world’s tidal marshes we applied a random forest classification model to earth observation data from the year 2020. We trained the classification model with a reference dataset developed to support distribution mapping of coastal ecosystems, and predicted the spatial distribution of tidal marshes between 60°N to 60°S. We validated the tidal marsh map using standard accuracy assessment methods, with our final map having an overall accuracy score of 0.852.ResultsWe estimate the global extent of tidal marshes in 2020 to be 52,880 km2(95% CI: 32,030 to 59,780 km2) distributed across 120 countries and territories. Tidal marsh distribution is centred in temperate and Arctic regions, with nearly half of the global extent of tidal marshes occurring in the temperate Northern Atlantic (45%) region. At the national scale, over a third of the global extent (18,510 km2; CI: 11,200 – 20,900) occurs within the USA.Main conclusionsOur analysis provides the most detailed spatial data on global tidal marsh distribution to date and shows that tidal marshes occur in more countries and across a greater proportion of the world’s coastline than previous mapping studies. Our map fills a major knowledge gap regarding the distribution of the world’s coastal ecosystems and provides the baseline needed for measuring changes in tidal marsh extent and estimating their value in terms of ecosystem services
A predatory gastrula leads to symbiosis-independent settlement inAiptasia
Authors: Maegele Ira , Rupp Sebastian , Özbek Suat , Guse Annika , Hambleton Elizabeth A. , Holstein Thomas W. 
Published: May 2023

AbstractThe planulae larvae of cnidarians (jellyfish, hydras, anemones, corals) have attracted interest since Haeckels 150-year-old postulation of the gastrula developmental stage of sponges and corals as the terminal lifeform of primitive multicellular metazoans. Widely viewed as primarily particle feeders, the planulae larvae of the anemone Exaiptasia pallida (commonly Aiptasia) have not been reported to undergo settlement and metamorphosis to adult morphology, and the lack of a closed lifecycle has been a major obstacle in this increasingly popular model system for coral-dinoflagellate endosymbiosis. Here we studied Aiptasia larvae feeding behavior and show its indispensability to trigger the first reports of settlement and metamorphosis in the system, finally closing the Aiptasia lifecycle. Surprisingly, the young gastrula-like planulae at just two days post fertilization actively feed on living crustacean nauplii, preferentially to heat-killed ones. Predation is dependent on functional stinging cells (nematocytes), indicative of complex neuronal control. Larvae fed daily dramatically increase in size and at 14 days post fertilization begin to morphologically change prior to settlement at high efficiency. Strikingly, dinoflagellate endosymbionts are neither required for larval growth nor measurably affect settlement dynamics, but are essential for spawning of the mature adult polyps. Our data show for the first time that gastrula-like planulae were capable of prey capture, suggesting carnivory in addition to filter feeding as a common strategy of this terminal life form. These data are discussed in the context of recent revelations on the evolution of basal metazoans.
Hypoxia Bi-directionally Regulates Gut Vascular Barrier through HIF-1α-dependent Mechanismin vitro
Authors: Liu Ping , Dai Wen , Du Jing , Zhou Yingshan , Wang Xiaodu , Song Houhui 
Published: May 2023

AbstractObjectiveThe gut vascular barrier (GVB) is the key checkpoint for pathogens to enter the blood circulation through the intestine, which is crucial for maintaining the intestinal barrier function. However, the effect and molecular mechanism of hypoxia on GVB remains unclear. Here, we show a role of the transcription factor hypoxia inducible factor-1α (HIF-1α) in hypoxia-induced bi-directional regulation of GVB.Approach and ResultsAnin vitroGVB model composed of rat intestinal microvascular endothelial cells was studied. Evans blue-albumin efflux assay showed that the experimentally severe hypoxia induced by cobalt chloride (500 μM, 24 h) markedly disrupted the GVBin vitro, while mild hypoxia induced by cobalt chloride (500 μM, 6 h) evidently enhanced the GVB, revealing hypoxia-induced bi-directional regulation of the GVB for the first-time. Importantly, knockdown of HIF-1α largely abolished the bi-directional changes of GVB caused by hypoxia. Furthermore, experimentally severe hypoxia exacerbated the inflammatory GVB disruption induced by LPS or TNF-α, while the mild hypoxia promoted the repair.ConclusionCollectively, our data indicate that hypoxia bi-directionally regulates GVB in a HIF-1α-dependent manner.
Adaptation at the edge: Patterns of local adaptation and genetic variation during a contemporary range expansion
Authors: Clark Eliza I. , Bean Dan W. , Bitume Ellyn V. , Stahlke Amanda R. , Hohenlohe Paul A. , Hufbauer Ruth A. 
Published: May 2023

AbstractDuring range expansion, differences can evolve between populations at the core and expanding edge of a range. While theory and experimental work has focused on range expansions across uniform environments, natural range expansions often occur over environmental gradients, which present novel selection pressures. We seek to understand how genetic variation expressed in different environments may constrain adaptation during range expansion across environmental gradients, by testing whether long-established populations are better adapted to their local environments than newly established populations in the expanding edge. We study the timing of winter dormancy in a beetle introduced for biological control (Diorhabda carinulata), expanding from areas with cold winters to areas with milder, shorter winters. In a reciprocal environment experiment, core populations showed a pattern of local adaptation, but only some edge populations showed a similar pattern, indicating these populations vary in their degree of adaptation. Expressed genetic variation of dormancy timing in a core population was high in a local (core) environment but disappeared in a novel (edge) environment. These results show that adaptive evolution has been rapid, likely fueled by high heritability, but long-distance movement may hinder adaptation by reducing the heritable genetic variation on which selection can act.
A turning point in COVID-19 severity and fatality during the pandemic: A national cohort study in Qatar
Authors: Chemaitelly Hiam , Ayoub Houssein H. , Faust Jeremy Samuel , Coyle Peter , Tang Patrick , Hasan Mohammad R. , Yassine Hadi M. , Al-Khatib Hebah A. , Al Thani Asmaa A. , Al-Kanaani Zaina , Al-Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed Ghaith , Butt Adeel A. , Al-Romaihi Hamad Eid , Al-Thani Mohamed H. , Al-Khal Abdullatif , Bertollini Roberto , Abu-Raddad Laith J. 
Published: May 2023

AbstractBackgroundThis study assessed the evolution of COVID-19 severity and fatality by utilizing rigorous and standardized criteria that were consistently applied throughout the pandemic in Qatar.MethodsA national cohort study was conducted on Qataris, using data on COVID-19 acute-care and ICU hospitalizations, as well as severe, critical, and fatal COVID-19 cases classified according to the World Health Organization criteria.ResultsThe cumulative incidence of severe, critical, or fatal COVID-19 after 3.14 years of follow-up was 0.45% (95% CI: 0.43-0.47%). The incidence rate for severe, critical, or fatal COVID-19 throughout the pandemic was 1.43 (95% CI: 1.35-1.50) per 1,000 person-years. In the pre-omicron phase, first omicron wave, and combined phases, it was 2.01 (95% CI: 1.90-2.13), 3.70 (95% CI: 3.25-4.22), and 2.18 (95% CI: 2.07-2.30) per 1,000 person-years, respectively. The post-first omicron phase saw a drastic drop to 0.10 (95% CI: 0.08-0.14) per 1,000 person-years, a 95.4% reduction. Among all severe, critical, and fatal cases, 99.5% occurred during the primary infection. The cumulative incidence of fatal COVID-19 was 0.042% (95% CI: 0.036-0.050%), with an incidence rate of 0.13 (95% CI: 0.11-0.16) per 1,000 person-years. In the post-first omicron phase, the incidence rate of fatal COVID-19 decreased by 90.0% compared to earlier stages. Both severity and fatality exhibited an exponential increase with age and a linear increase with the number of coexisting conditions.ConclusionsThe conclusion of the first omicron wave was a turning point in the severity of the pandemic. While vaccination and enhanced case management reduced severity gradually, the rapid accumulation of natural immunity during the initial omicron wave appears to have played the crucial role in driving this shift in severity.
Mobile-linked point-of-care diagnostics in community-based healthcare: A scoping review of user experiences
Authors: Nxele Siphesihle R. , Moetlhoa Boitumelo , Dlangalala Thobeka , Maluleke Kuhlula , Kgarosi Kabelo , Theberge Ashleigh B. , Mashamba-Thompson Tivani 
Published: May 2023

AbstractBackgroundWhile mobile-linked point-of-care diagnostics may circumvent geographical and temporal barriers to efficient communication, the use of such technology in community settings will depend on user experience. We conducted a scoping review to systematically map evidence on user experiences of mobile-linked point-of-care diagnostics in community healthcare settings.MethodologyWe conducted a comprehensive search of the following electronic databases: Scopus, Web of Science, and EBSCOhost (Medline, CINAHL, Africa-wide, Academic Search Complete). The inter-reviewer agreement was determined using Cohen’s kappa statistic. Data quality was appraised using the mixed method appraisal tool version 2018, and the results were reported according to the preferred reporting items for systematic reviews and meta-analyses for scoping reviews (PRISMA-ScR).ResultsFollowing the abstract and full article screening, nine articles were found eligible for inclusion in data extraction. Following the quality appraisal, one study scored 72.5%, one study scored 95%, and the remaining seven studies scored 100%. Inter-rater agreement was 83.54% (Kappa statistic = 0.51, p < 0.05). Three themes emerged from the articles: approaches to implementing mobile-linked point-of-care diagnostics, user engagement in community-based healthcare settings, and limited user experiences in mobile-linked point-of-care diagnostics. User experiences are key to the sustainable implementation of mobile-linked point-of-care diagnostics. User experiences have been evaluated in small community healthcare settings. There is limited evidence of research aimed at evaluating the usability of mobile-linked diagnostics at the community level.ConclusionMore studies are needed to assess the user experience of mobile-linked diagnostics in larger communities. This scoping review revealed gaps that need to be addressed to improve user experiences of mobile-linked diagnostics, including language barriers, privacy issues, and clear instructions.
Balancing Memorization and Generalization in RNNs for High Performance Brain-Machine Interfaces
Authors: Costello Joseph T. , Temmar Hisham , Cubillos Luis H. , Mender Matthew J. , Wallace Dylan M. , Willsey Matthew S. , Patil Parag G. , Chestek Cynthia A. 
Published: May 2023

AbstractBrain-machine interfaces (BMIs) can restore motor function to people with paralysis but are currently limited by the accuracy of real-time decoding algorithms. Recurrent neural networks (RNNs) using modern training techniques have shown promise in accurately predicting movements from neural signals but have yet to be rigorously evaluated against other decoding algorithms in a closed-loop setting. Here we compared RNNs to other neural network architectures in real-time, continuous decoding of finger movements using intracortical signals from nonhuman primates. Across one and two finger online tasks, LSTMs (a type of RNN) outperformed convolutional and transformer-based neural networks, averaging 18% higher throughput than the convolution network. On simplified tasks with a reduced movement set, RNN decoders were allowed to memorize movement patterns and matched able-bodied control. Performance gradually dropped as the number of distinct movements increased but did not go below fully continuous decoder performance. Finally, in a two-finger task where one degree-of-freedom had poor input signals, we recovered functional control using RNNs trained to act both like a movement classifier and continuous decoder. Our results suggest that RNNs can enable functional real-time BMI control by learning and generating accurate movement patterns.
Enhanced specificity ofBacillusmetataxonomics using atuf-targeted amplicon sequencing approach
Authors: Xu Xinming , Nielsen Lasse Johan Dyrbye , Song Lijie , Maróti Gergely , Strube Mikael Lenz , Kovács Ákos T. 
Published: May 2023

AbstractBacillusspecies are ubiquitous in nature and have tremendous application potential in agriculture, medicine, and industry. However, the individual species of this genus vary widely in both ecological niches and functional phenotypes, which, hence, requires accurate classification of these bacteria when selecting them for specific purposes. Although analysis of the 16S gene has been widely used to disseminate the taxonomy of most bacterial species, this gene fails proper classification ofBacillusspecies. To circumvent this restriction, we designed novel primers and optimized them to allow exact species resolution ofBacillusspecies in both synthetic and natural communities using high-throughput amplicon sequencing. The primers designed for thetufgene were not only specific for theBacillusgenus but also sufficiently discriminated species bothin silicoandin vitroin a mixture of 11 distinctBacillusspecies. Investigating the primers using a natural soil sample, 13 dominant species were detected includingBacillus badius,Bacillus velezensis, andBacillus mycoidesas primary members, neither of which could be distinguished with 16S sequencing. In conclusion, a set of high-throughput primers were developed which allows unprecedented species-level identification ofBacillusspecies, including agriculturally important species.
Study of Glucometer Precision and Antimalarial Therapy Interference on Glucose Readings in Nigeria
Authors: Ugochukwu Ezinwanne Jane , Mosanaya Adaobi Uchenna , Nweze Victor Nnanna , Chukwu Marydith Ifeoma , Ubaka Chukwuemeka Michael , Alawami Mohammed 
Published: May 2023

ABSTRACTMalaria-infected diabetic (MID) patients have become one of the highest diabetic population with comorbidities in Nigeria. While the artemisinin-based combination therapy (ACT) are used for malaria treatment, glucometers are used to monitor their blood glucose levels. However, some drugs are known to interfere with the accuracy of glucose readings leading to misdiagnosis. In this study, we investigated the interferences of artemether and lumefantrine as well as other known drug interferents on the accuracy of glucose readings in three different glucometers commonly used in Nigeria(Accu-Answer®, VivaChek® and GlucoDr®). Blood sample was collected from a healthy volunteer, aliquots of the blood with pure samples of artemether and lumefantrinepowders as well as other known drug interferents were prepared in normal and low pools. The precision study on the glucometers were determined. We find that Accu-Answer®was the only precise glucometer considering its coefficient of variation. The influence of the artemether and lumefantrine was mild in two glucometers andthe predicted binding affinities showed possible binding interactions that may have caused their interferences.
The Genetic Landscape of a Metabolic Interaction
Authors: Nguyen Thuy N. , Ingle Christine , Thompson Samuel , Reynolds Kimberly A. 
Published: May 2023

AbstractEnzyme abundance, catalytic activity, and ultimately sequence are all shaped by the need of growing cells to maintain metabolic flux while minimizing accumulation of deleterious intermediates. While much prior work has explored the constraints on protein sequence and evolution induced by physical protein-protein interactions, the sequence-level constraints emerging from non-binding functional interactions in metabolism remain unclear. To quantify how variation in the activity of one enzyme constrains the biochemical parameters and sequence of another, we focused on dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), a pair of enzymes catalyzing consecutive reactions in folate metabolism. We used deep mutational scanning to quantify the growth rate effect of 2,696 DHFR single mutations in 3 TYMS backgrounds under conditions selected to emphasize biochemical epistasis. Our data are well-described by a relatively simple enzyme velocity to growth rate model that quantifies how metabolic context tunes enzyme mutational tolerance. Together our results reveal the structural distribution of epistasis in a metabolic enzyme and establish a foundation for the design of multi-enzyme systems.
Tracking the Metabolic Fate of Exogenous Arachidonic Acid in Ferroptosis Using Dual-Isotope Labeling Lipidomics
Authors: Reimers Noelle , Do Quynh , Zhang Rutan , Guo Angela , Ostrander Ryan , Shoji Alyson , Vuong Chau , Xu Libin 
Published: May 2023

ABSTRACTLipid metabolism is implicated in a variety of diseases, including cancer, cell death, and inflammation, but lipidomics has proven to be challenging due to the vast structural diversity over a narrow range of mass and polarity of lipids. Isotope labeling is often used in metabolomics studies to follow the metabolism of exogenously added labeled compounds because they can be differentiated from endogenous compounds by the mass shift associated with the label. The application of isotope labeling to lipidomics has also been explored as a method to track the metabolism of lipids in various disease states. However, it can be difficult to differentiate a single isotopically labeled lipid from the rest of the lipidome due to the variety of endogenous lipids present over the same mass range. Here we report the development of a dual-isotope deuterium labeling method to track the metabolic fate of exogenous polyunsaturated fatty acids, e.g, arachidonic acid (AA), in the context of ferroptosis using hydrophilic interaction-ion mobility-mass spectrometry (HILIC-IM-MS). Ferroptosis is a type of cell death that is dependent on lipid peroxidation. The use of two isotope labels rather than one enables the identification of labeled species by a signature doublet peak in the resulting mass spectra. A Python-based software, D-Tracer, was developed to efficiently extract metabolites with dual-isotope labels. The labeled species were then identified withLipydomicsbased on their retention times, collision cross section, andm/zvalues. Changes in exogenous AA incorporation in the absence and presence of a ferroptosis inducer were elucidated.Table of Contents
α-Synuclein oligomers form by secondary nucleation
Authors: Xu Catherine K , Meisl Georg , Andrzejewska Ewa , Krainer Georg , Dear Alexander J , Cruz Marta Castellana , Turi Soma , Jacquat Raphael , Arter William E , Vendruscolo Michele , Linse Sara , Knowles Tuomas PJ 
Published: May 2023

AbstractOligomeric species arising during aggregation of α-synuclein are proposed to be a major source of toxicity in Parkinson’s disease, and thus a major potential drug target. However, their mechanism of formation and role in aggregation are largely unresolved. Here we first show that, at physiological pH, α-synuclein aggregates by secondary nucleation, rather than fragmentation, and that this process is enhanced by agitation. Moreover, using a combination of single molecule and bulk level techniques, we identify secondary nucleation on the surfaces of existing fibrils, rather than formation directly from monomers, as the dominant source of oligomers. Our results highlight secondary nucleation as not only the key source of oligomers, but also the main mechanism of aggregate formation, and show that these processes take place under physiologically relevant conditions.