bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting COVID-19 outbreak using open mobility data for minimal disruption on the country’s economy
Authors: Morales-Fajardo Héctor , Rodríguez-Arce Jorge 
Published: February 2022

AbstractCOVID-19 is an infectious disease caused by the SARS-COV-2 coronavirus, which was discovered in late 2019. Within a few months, COVID-19 was declared a global pandemic by the WHO. Several countries adopted social distancing measures, such as self-quarantine, workplace and mobility restrictions, reducing the probability of contact between non-infected and infected people. In general, these measures have a negative impact on low-income economies and small and medium businesses. During the outbreak, several predictive models have been proposed in order to assess the level of saturation that health services might have. Nevertheless, none of them considers information on the people’s mobility to assess the effectiveness of the social distancing policies. In this study, the authors propose a prediction method based on people’s open mobility data from Apple© and Google© databases to project potential scenarios and monitor case growth. The proposed method shows the importance of monitoring daily case increase for the first 4-6 weeks of the pandemic wave. Active monitoring is crucial to determine the reduction in mobility and proper actions. The results can contribute to health authorities for making timely decisions, preventing the spread of viruses while balancing the reduction of mobility with minimal disruption in people’s economies in future outbreaks.
Next-generation intranasal Covid-19 vaccine: a polymersome-based protein subunit formulation that provides robust protection against multiple variants of concern and early reduction in viral load of the upper airway in the golden Syrian hamster model
Authors: Lam Jian Hang , Shivhare Devendra , Chia Teck Wan , Chew Suet Li , Sinsinbar Gaurav , Aw Ting Yan , Wong Siamy , Venkatraman Shrinivas , Lim Francesca Wei Inng , Vandepapeliere Pierre , Nallani Madhavan 
Published: February 2022

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease 2019 (Covid-19), an ongoing global public health emergency. Despite the availability of safe and efficacious vaccines, achieving herd immunity remains a challenge due in part to rapid viral evolution. Multiple variants of concern (VOCs) have emerged, the latest being the heavily mutated Omicron, which exhibits the highest resistance to neutralizing antibodies from past vaccination or infection. Currently approved vaccines generate robust systemic immunity, yet poor immunity at the respiratory tract. We have demonstrated that a polymersome-based protein subunit vaccine with wild type (WT) spike protein and CpG adjuvant induces robust systemic immunity (humoral and T cell responses) in mice. Both antigen and adjuvant are encapsulated in artificial cell membrane (ACM) polymersomes – synthetic, nanoscale vesicles that substantially enhance the immune response through efficient delivery to dendritic cells. In the present study, we have formulated a vaccine candidate with the spike protein from Beta variant and assessed its immunogenicity in golden Syrian hamsters. Two doses of ACM-Beta spike vaccine administered via intramuscular (IM) injection evoke modest serum neutralizing titers that are equally efficacious towards WT and Beta viruses. In contrast, the ACM-WT spike vaccine induces a predominantly WT-specific serum neutralizing response with pronounced reduction in potency towards the Beta variant. Remarkably, immunogenicity of the ACM-Beta spike vaccine is greatly enhanced through intranasal (IN) administration. Following IN challenge with the Beta variant, IM-immunized hamsters are fully protected from disease but not infection, displaying similar peak viral RNA loads in oral swabs as non-vaccinated controls. In contrast, hamsters IN vaccinated with ACM-Beta spike vaccine are protected from disease and infection, exhibiting a ∼100-fold drop in total and subgenomic RNA load as early as day 2 post challenge. We further demonstrate that nasal washes from IN-but not IM-immunized animals possess virus neutralizing activity that is broadly efficacious towards Delta and Omicron variants. Altogether, our results show IN administration of ACM-Beta spike vaccine to evoke systemic and mucosal antibodies that cross-neutralize multiple SARS-CoV-2 VOCs. Our work supports IN administration of ACM-Beta spike vaccine for a next-generation vaccination strategy that not only protects against disease but also an infection of the respiratory tract, thus potentially preventing asymptomatic transmission.
Quantitative fate mapping: Reconstructing progenitor field dynamics via retrospective lineage barcoding
Authors: Fang Weixiang , Bell Claire M. , Sapirstein Abel , Asami Soichiro , Leeper Kathleen , Zack Donald J. , Ji Hongkai , Kalhor Reza 
Published: February 2022

AbstractNatural and induced somatic mutations that accumulate in the genome during development record the phylogenetic relationships of cells; however, whether these lineage barcodes can capture the dynamics of complex progenitor fields remains unclear. Here, we introduce quantitative fate mapping, an approach to simultaneously map the fate and quantify the commitment time, commitment bias, and population size of multiple progenitor groups during development based on a time-scaled phylogeny of their descendants. To reconstruct time-scaled phylogenies from lineage barcodes, we introduce Phylotime, a scalable maximum likelihood clustering approach based on a generalizable barcoding mutagenesis model. We validate these approaches using realistically-simulated barcoding results as well as experimental results from a barcoding stem cell line. We further establish criteria for the minimum number of cells that must be analyzed for robust quantitative fate mapping. Overall, this work demonstrates how lineage barcodes, natural or synthetic, can be used to obtain quantitative fate maps, thus enabling analysis of progenitor dynamics long after embryonic development in any organism.
Rapid Knowledgebase Construction and Hypotheses Generation Using Extractive Literature Search
Authors: Launer-Wachs Shaked , Taub-Tabib Hillel , Goldberg Yoav , Shamay Yosi 
Published: February 2022

AbstractAs knowledgebases become increasingly important for structuring vast amounts of scientific knowledge and making it accessible to researchers, their construction entails expensive multi-year projects involving teams of bio-curators, computer scientists, or both. This restricts the coverage of existing knowledgebases to a limited set of popular topics, leaving a long tail of more specialized interests uncovered.We present a methodology and a supporting tool to allow individual researchers or small teams, without background in bio-curation or computer science, to mine the scientific literature and construct ad-hoc, personalized, and literature-anchored knowledgebases, that are tailored around their specific research interests and support their scientific goals. The time investment involved in creating a knowledgebase ranges from a few hours to a few weeks, depending on the desired coverage and accuracy.We demonstrate the methodology by constructing knowledgebases for different purposes: a high-level overview of challenges and controversies in a field (the cancer frontiers knowledgebase); a mapping of main concepts and interactions in a field, to support lab-internal hypothesis generation (tissue engineering and regeneration, cancer surgery and radiotherapy knowledgebases); and a comprehensive and accurate knowledgebase designated as an online up-to-date resource for the wider research community (the cell specific drug delivery knowledgebase). In each case we show how the structured knowledgebase, coupled with effective visualizations, facilitates effective data exploration, hypothesis generation and meta-analysis.We implement the method as part of an open source web-based platform for knowledgebase construction, available publicly and freely at https://spike-kbc.apps.allenai.org.
PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish
Authors: Barbara Rani , Kantharaju Madhu Nagathihalli , Haruvi Ravid , Harrington Kyle , Kawashima Takashi 
Published: February 2022

AbstractUnderstanding how neurons interact across the brain to control animal behaviors is one of the central goals in neuroscience. Recent developments in fluorescent microscopy and genetically-encoded calcium indicators led to the establishment of whole-brain imaging methods in zebrafish, which records neural activity across a brain-wide volume with single-cell resolution. Pioneering studies of whole-brain imaging used custom light-sheet microscopes, and their operation relied on commercially developed and maintained software that is not available globally. Hence it has been challenging to disseminate and develop the technology in the research community. Here, we present PyZebrascope, an open-source Python platform designed for neural activity imaging in zebrafish using light-sheet microscopy. PyZebrascope has intuitive user interfaces and implements essential features for whole-brain imaging, such as two orthogonal excitation beams and eye damage prevention. Its modular architecture allows the inclusion of advanced algorithms for microscope control and image processing. As a proof of concept, we implemented an automatic algorithm for maximizing the image resolution in the brain by precisely aligning the excitation beams to the image focal plane. PyZebrascope enables whole-brain neural activity imaging in fish behaving in a virtual reality environment with a stable high data throughput and low CPU and memory consumption. Thus, PyZebrascope will help disseminate and develop light-sheet microscopy techniques in the neuroscience community and advance our understanding of whole-brain neural dynamics during animal behaviors.
The V-type H+-ATPase is targeted in anti-diuretic hormone control of the Malpighian ‘renal’ tubules
Authors: Sajadi Farwa , Vergara-Martínez María Fernanda , Paluzzi Jean-Paul V. 
Published: February 2022

AbstractLike other insects, secretion by mosquito Malpighian tubules (MTs) is driven by the V-type H+-ATPase (VA) localized in the apical membrane of principal cells. InAedes aegypti, the anti-diuretic neurohormone CAPA inhibits secretion by MTs stimulated by select diuretic hormones; however, the cellular effectors of this inhibitory signaling cascade remain unclear. Herein, we demonstrate that the VA inhibitor bafilomycin selectively inhibits serotonin (5HT)- and calcitonin-related diuretic hormone (DH31)-stimulated secretion. VA activity increases in DH31-treated MTs, whereas CAPA abolishes this increase through a NOS/cGMP/PKG signaling pathway. A critical feature of VA activation involves the reversible association of the cytosolic (V1) and membrane (Vo) complexes. Indeed, higher V1protein abundance was found in membrane fractions of DH31-treated MTs whereas CAPA significantly decreased V1abundance in membrane fractions while increasing it in cytosolic fractions. V1immunolocalization was observed strictly in the apical membrane of DH31treated MTs whereas immunoreactivity was dispersed following CAPA treatment. VA complexes colocalized apically in female MTs shortly after a blood-meal consistent with the peak and post-peak phases of diuresis. Comparatively, V1immunoreactivity in MTs was more dispersed and did not colocalize with the Vocomplex in the apical membrane at 3 hours post blood-meal, representing a timepoint after the late phase of diuresis has concluded. Therefore, CAPA inhibition of MTs involves reducing VA activity and promotes complex dissociation hindering secretion. Collectively, these findings reveal a key target in hormone-mediated inhibition of MTs countering diuresis that provides a deeper understanding of this critical physiological process necessary for hydromineral balance.Significance StatementThe V-type H+ATPase (VA), or proton pump, provides the driving force for transepithelial ion and fluid secretion in insect Malpighian tubules (MTs). While studies have shown diuretic stimulation activates various signaling pathways, including cAMP and downstream effectors promoting increased VA activity, our understanding of anti-diuretic signaling and its potential regulation of the VA remains rudimentary. Herein, we show that CAPA neuropeptide acts through the NOS/cGMP/PKG pathway to inhibit DH31-stimulated VA activity, supporting the notion that the anti-diuretic regulation is achieved through dissociation of the VA complexes. These results demonstrate a critical role of VA inhibition and trafficking necessary for anti-diuretic signaling and advances our understanding of the complex neuroendocrine control of the MTs in this important human disease-vector mosquito.
Users’ Reactions on Announced Vaccines against COVID-19 Before Marketing in France: Analysis of Twitter posts
Authors: Dupuy-Zini Alexandre , Audeh Bissan , Gagneux-Brunon Amandine , Bousquet Cedric 
Published: February 2022

AbstractBackgroundWithin a few months, the COVID-19 pandemic has spread to many countries and has been a real challenge for health systems all around the world. This unprecedented crisis has led to a surge of online discussions about potential cures for the disease. Among them, vaccines have been at the heart of the debates, and have faced lack of confidence before marketing in France.ObjectiveThis study aims to identify and investigate the opinion of French Twitter users on the announced vaccines against COVID-19 through sentiment analysis.MethodsThis study was conducted in two phases. First, we filtered a collection of tweets related to COVID-19 from February to August 2020 with a set of keywords associated with vaccine mistrust using word embeddings. Second, we performed sentiment analysis using deep learning to identify the characteristics of vaccine mistrust. The model was trained on a hand labeled subset of 4,548 tweets.ResultsA set of 69 relevant keywords were identified as the semantic concept of the word “vaccin” (vaccine in French) and focus mainly on conspiracies, pharmaceutical companies, and alternative treatments. Those keywords enabled to extract nearly 350k tweets in French. The sentiment analysis model achieved a 0.75 accuracy. The model then predicted 16% of positive tweets, 41% of negative tweets and 43% of neutral tweets. This allowed to explore the semantic concepts of positive and negative tweets and to plot the trends of each sentiment. The main negative rhetoric identified from users’ tweets was that vaccines are perceived as having a political purpose, and that COVID-19 is a commercial argument for the pharmaceutical companies.ConclusionsTwitter might be a useful tool to investigate the arguments of vaccine mistrust as it unveils a political criticism contrasting with the usual concerns on adverse drug reactions. As the opposition rhetoric is more consistent and more widely spread than the positive rhetoric, we believe that this research provides effective tools to help health authorities better characterize the risk of vaccine mistrust.
Diagnostic Accuracy of Commercially Available Tests for Respiratory Syncytial Virus: A Scoping Literature Review in the COVID-19 Era
Authors: Bernstein David I. , Mejias Asuncion , Rath Barbara , Woods Christopher W. , Deeter Jamie Phillips 
Published: February 2022

ABSTRACTBackgroundNon-pharmaceutical interventions to prevent the spread of coronavirus disease 2019 also decreased the spread of respiratory syncytial virus (RSV) and influenza. Viral diagnostic testing in patients with respiratory tract infections (RTI) is a necessary tool for patient management; therefore, sensitive and specific tests are required. This scoping literature review evaluated the analytical validity of commercially available sample-to- answer RSV diagnostic tests in different contexts.ContentPubMed and Embase were queried for studies reporting on the analytical validity of tests for RSV in patients with RTI (published January 2005–January 2021). Sensitivity and specificity of RSV tests and information on study design, patient, and setting characteristics were extracted from 77 studies that met predefined inclusion criteria. A literature gap was identified for studies of RSV tests conducted in adult-only populations (5.3% of total sub- records), and in outpatient (7.5%) or household (0.8%) settings. Overall, RSV tests with analytical time >30 min had higher sensitivity (62.5–100%) versus RSV tests with analytical time ≤ 30 min (25.7–100%), this sensitivity range could be partially attributed to the different modalities (antigen versus molecular) used. Molecular-based rapid RSV tests had higher sensitivity (66.7–100%) and specificity (94.3–100%) than antigen-based RSV tests (25.7– 100%; 80.3–100%).SummaryMolecular-based RSV tests should be considered for first-line use when possible, given their high sensitivity and specificity and that adults with RTI typically have low viral load, necessitating a highly sensitive test. This review benefits healthcare professionals by summarizing the diagnostic accuracy data available for commercially available RSV tests.IMPACT STATEMENTViral diagnostic testing in patients with respiratory tract infection is a powerful tool for patient management. This scoping literature review included 77 studies reporting the analytical validity of commercially available respiratory syncytial virus (RSV) diagnostic tests (published January 2005–January 2021) and examined the characteristics of such studies. The data suggest that molecular-based RSV tests have higher sensitivity and specificity than antigen-based tests, thus should be considered for first-line use for timely diagnosis and to detect infections in adults with low level viral load. Future studies should investigate the diagnostic accuracy of RSV tests in adults and in outpatient/household settings.
Pilotins are mobile T3SS components involved in assembly and substrate specificity of the bacterial type III secretion system
Authors: Wimmi Stephan , Fleck Moritz , Helbig Carlos , Brianceau Corentin , Langenfeld Katja , Szymanski Witold G. , Angelidou Georgia , Glatter Timo , Diepold Andreas 
Published: February 2022

AbstractIn animal pathogens, assembly of the type III secretion system injectisome requires the presence of so-called pilotins, small lipoproteins that assist the formation of the secretin ring in the outer membrane. Using a combination of functional assays, interaction studies, proteomics, and live-cell microscopy, we determined the contribution of the pilotin to the assembly, function, and substrate selectivity of the T3SS and identified potential new downstream roles of pilotin proteins. In absence of its pilotin SctG,Yersinia enterocoliticaforms few, largely polar injectisome sorting platforms and needles. In line, most export apparatus subcomplexes are mobile in these strains, suggesting the absence of fully assembled injectisomes. Remarkably, while absence of the pilotin all but prevents export of early T3SS substrates, such as the needle subunits, it has little effect on secretion of late T3SS substrates, including the virulence effectors. We found that pilotins transiently interact with other injectisome components such as the secretin in the outer membrane, but mostly form transient mobile clusters in the bacterial membrane, which do not colocalize with assembled injectisomes. Together, these findings provide a new view on the role of pilotins during and after assembly of type III secretion injectisomes.
The impact of the soluble protein fraction and kernel hardness on wheat flour starch digestibility
Authors: Wu Jia , Warren Frederick J. 
Published: February 2022

AbstractWheat is the staple crop for 35% of the world’s population, providing a major source of calories for much of the world’s population. Starch is the main source of energy in wheat flour, but the digestibility of wheat starch varies greatly between different flours and wheat products. This has relevance from a health perspective because wheat starch products that are rapidly digested and elicit large post-prandial glucose peaks are associated with a host of cardiac and metabolic disorders. In this study, we investigate the impact of protein on starch digestion in three commercially sourced flours with different grain hardness. Grain hardness impacted on flour particle size, but not significantly on starch digestion. A soluble extract of wheat proteins was found to dramatically reduce starch digestion, even following gastric proteolysis. Proteomic analysis revealed that this soluble extract was enriched in proteinaceous α-amylase inhibitors which were partially degraded during gastric proteolysis. Therefore, we conclude that the soluble proteins of wheat flour have a significant contribution towards retarding starch digestion, even following gastric digestion.
Climate Change Impacts on Broussenetia papyrifera Pollens - Metabolome Investigations and Prospects of Allergy Prevalence
Authors: Humayun Muhammad , Naseem Saadia , Goodman Richard E. , Ali Zahid 
Published: February 2022

AbstractBroussonetia papyrifera (B. papyrifera) is an allergenic plant in the mulberry family that grows at varied elevations and climatic conditions worldwide. In northern Pakistan, B. papyrifera is abundant and it produces a substantial amount of pollen that disperses in the air causing allergies in some humans. Climate change affects pollen production. To investigate potential changes in pollens development and potential allergenicity, B. papyrifera pollens were collected in summer and in spring from different regions in Pakistan. Study samples were subjected to morphological analysis, Fourier Transform Infrared Spectroscopy (FTIR) analysis for biochemical differences, and Liquid Chromatography-Mass Spectrometry (LCMS) for metabolome analysis. Morphological studies of the dried pollen by light microscopy showed seasonal and regional differences in pollens size and exine morphology. FTIR analysis showed inter-regional and inter-seasonal differences in the metabolome of the pollen. Differences in lipid and protein functional groups of pollen from different regions showed variation in the FTIR spectra. These differences in FTIR spectra correlated with the changing climatic conditions. Metabolome analysis of targeted pollen samples identified 33 organic compounds of seven different groups. Four unsaturated fatty acids were identified that have a potential role in allergic responses. The findings in this study are unique in demonstrating climatic variables that effect B. papyrifera pollen physiology (FTIR analysis) which also confirms differences in pollen-associated lipid metabolites identified by LCMS analysis. These results demonstrate information that may be used to predict potential changes in allergy risks from pollens of B. papyrifera in the future. The findings may provide a model for predicting variation in pollen structure and associated allergies in response to climate changes for other species.