bluuebunny/crossref_metadata_2025_split huggingface dataset:
Curating, collecting, and cataloguing global COVID-19 datasets for the aim of predicting personalized risk
Authors: Khatami Sepehr Golriz , Russo Maria Francesca , Domingo-Fernández Daniel , Zaliani Andrea , Mubeen Sarah , Gadiya Yojana , Sargsyan Astghik , Karki Reagon , Gebel Stephan , Ruppa Surulinathan Ram Kumar , Lage-Rupprecht Vanessa , Archipovas Saulius , Mingrone Geltrude , Jacobs Marc , Claussen Carsten , Hofmann-Apitius Martin , Kodamullil Alpha Tom ,   the COPERIMOplus consortium
Published: November 2021

AbstractThe COVID-19 data catalogue is a repository that provides a landscape view of COVID-19 studies and datasets as a putative source to enable researchers to develop personalized COVID-19 predictive risk models. The COVID-19 data catalogue currently contains over 400 studies and their relevant information collected from a wide range of global sources such as global initiatives, clinical trial repositories, publications and data repositories. Further, the curated content stored in this data catalogue is complemented by a web application, providing visualizations of these studies, including their references, relevant information such as measured variables, and the geographical locations of where these studies were performed. This resource is one of the first to capture, organize and store studies, datasets and metadata in the area of COVID-19 in a comprehensive repository. We are convinced that our work will facilitate future research and development of personalized predictive risk models of COVID-19.
Continued Effectiveness of COVID-19 Vaccination among Urban Healthcare Workers during Delta Variant Predominance
Authors: Lan Fan-Yun , Sidossis Amalia , Iliaki Eirini , Buley Jane , Nathan Neetha , Bruno-Murtha Lou Ann , Kales Stefanos N. 
Published: November 2021

AbstractBackgroundData on COVID-19 vaccine effectiveness (VE) among healthcare workers (HCWs) during periods of delta variant predominance are limited.MethodsWe followed a population of urban Massachusetts HCWs (45% non-White) subject to epidemiologic surveillance. We accounted for covariates such as demographics and community background infection incidence, as well as information bias regarding COVID-19 diagnosis and vaccination status.Results and DiscussionDuring the study period (December 16, 2020 to September 30, 2021), 4615 HCWs contributed to a total of 1,152,486 person-days at risk (excluding 309 HCWs with prior infection) and had a COVID-19 incidence rate of 5.2/10,000 (114 infections out of 219,842 person-days) for unvaccinated person-days and 0.6/10,000 (49 infections out of 830,084 person-days) for fully vaccinated person-days, resulting in an adjusted VE of 82.3% (95% CI: 75.1–87.4%). For the secondary analysis limited to the period of delta variant predominance in Massachusetts (i.e., July 1 to September 30, 2021), we observed an adjusted VE of 76.5% (95% CI: 40.9–90.6%). Independently, we found no re-infection among those with prior COVID-19, contributing to 74,557 re-infection-free person-days, adding to the evidence base for the robustness of naturally acquired immunity.
Details of “conversion therapy” practices and concordance with legislative definition: Findings from a non-probability community-based survey in Canada, 2020
Authors: Salway Travis , Tiwana Amrit , Schillaci-Ventura Julia , Watt Sarah , Muse Erika , Ashley Florence 
Published: November 2021

AbstractBackground“Conversion therapy” practices (CTP) refer to a heterogeneous set of treatments and activities that share the common goal of suppressing, “repairing,” or otherwise preventing expressions of transgender, lesbian, gay, bisexual, or queer identities. This study aimed to elicit details from those with direct experience and assess concordance between CTP experiences and the definition of CTP included in federal legislation aiming to deter CTP.MethodsWe conducted an anonymous online survey of adults (>18 years) in Canada between August 18 and December 2, 2020. Participants were recruited through social media, CTP survivor networks, and word-of-mouth.ResultsOf 51 respondents with direct experience of CTP, 16 were transgender, 34 were cisgender. Most respondents lived in Alberta, British Columbia, Ontario, or Quebec. 49% experienced CTP in a licensed healthcare provider office, 45% at a faith-based organization, and 36% at an unlicensed counselor office (categories not mutually exclusive). Age at first CTP experience ranged from 2 to 44 years of age (mean: 17.8 years; median: 17 years). Respondents experienced CTP for <1 year to 33 years (mean: 4.6 years; median: 2 years). Fifty percent of those with direct experience of CTP indicated that the proposed legislative definition of CTP did not fully encompass their personal experience.InterpretationResults from this Canadian survey of adults with experience of CTP indicate that legislative attempts to ban CTP must be expanded (e.g., to include adults and practices that do not concord with previously drafted definitions) and paired with other prevention efforts.
Schema support for forming inferences in the human brain
Authors: Paulus J.P. , Vignali C. , Coutanche M.N. 
Published: November 2021

AbstractAssociative inference, the process of drawing novel links between existing knowledge to rapidly integrate associated information, is supported by the hippocampus and neocortex. Within the neocortex, the medial prefrontal cortex (mPFC) has been implicated in the rapid cortical learning of new information that is congruent with an existing framework of knowledge, or schema. How the brain integrates associations to form inferences, specifically how inferences are represented, is not well understood. In this study, we investigate how the brain uses schemas to facilitate memory integration in an associative inference paradigm (A-B-C-D). We conducted two event-related fMRI experiments in which participants retrieved previously learned direct (AB, BC, CD) and inferred (AC, AD) associations between word pairs for items that are schema congruent or incongruent. Additionally, we investigated how two factors known to affect memory, a delay with sleep, and reward, modulate the neural integration of associations within, and between, schema. Schema congruency was found to benefit the integration of associates, but only when retrieval immediately follows learning. RSA revealed that neural patterns of inferred pairs (AC) in the PHc, mPFC, and posHPC were more similar to their constituents (AB and BC) when the items were schema congruent, suggesting that schema facilitates the assimilation of paired items into a single inferred unit containing all associated elements. Furthermore, a delay with sleep, but not reward, impacted the assimilation of inferred pairs. Our findings reveal that the neural representations of overlapping associations are integrated into novel representations through the support of memory schema.Significance StatementOur ability to draw novel links between pieces of existing knowledge allows us to understand how information in memory is related. Existing knowledge (memory ‘schema’) can facilitate learning, and then integration, of new related information. We ask how the human brain uses schema to form links between related pieces of information, and how sleep and reward affect this process. Our results suggest that memory schema helps pieces of knowledge become a single inferred unit in the brain’s memory systems. A delay with sleep between learning and retrieval, though not reward, is important for how schema achieve this.
Mutagenic distinction between the receptor-binding and fusion subunits of the SARS-CoV-2 spike glycoprotein and its upshot
Authors: Penner Robert 
Published: November 2021

AbstractWe observe that a residue R of the spike glycoprotein of SARS-CoV-2 which has mutated in one or more of the current Variants of Concern or Interest or under Monitoring rarely participates in a backbone hydrogen bond if R lies in the S1 subunit and usually participates in one if R lies in the S2 subunit. A partial explanation for this based upon free energy is explored as a potentially general principle in the mutagenesis of viral glycoproteins. This observation could help target future vaccine cargos for the evolving coronavirus as well as more generally. A study of the Delta and Omicron variants suggests that Delta was an energetically necessary intermediary in the evolution from Wuhan-Hu-1 to Omicron.
Lytic phages displayed protective effects against soft rot-causing Pectobacterium sp.
Authors: Parena Aeron Jade S. , Silva Benji Brayan I. , Mercado Rae Mark L. , Sendon Adelbert Adrian A. , Signabon Freddiewebb B. , Balidion Johnny F. , Encabo Jaymee R. 
Published: November 2021

AbstractSoft rot caused by Pectobacterium sp. is responsible for significant losses in vegetable production worldwide. Methods for the effective control of soft rot are limited and are primarily based on good agricultural practices. The use of bacteriophages as biocontrol agents appears to be a promising alternative to combat phytopathogens. In this study, we investigated the efficacy of lytic phages recovered from symptomatic tissues and environmental samples against soft rot caused by Pectobacterium carotovorum subsp. carotovorum. Three bacteriophage isolates, designated as vB_PcaP-A3, vB_PcaM-D1, and vB_PcaM-J3, were observed to effectively lyse P. carotovorum subsp. carotovorum. Phage vB_PcaP-A3 exhibited virion morphology similar to the members of the podovirus group, while phages vB_PcaM-D1 and vB_PcaM-J3 showed myovirus morphology based on transmission electron microscopy. The optimal multiplicity of infection (MOI) differed greatly among the three phages. All three phages survived incubations at 30°C, 40°C and 50°C and pH conditions ranging from 3.0 to 9.0, but were all inactivated at 60°C and at pH 12. Both monophage and cocktail preparations were effective in inhibiting the growth of P. carotovorum subsp. carotovorum in the in vitro challenge tests. In the semi-in planta assays, while treatment with cocktail preparations completely inhibited the development of soft rot in tissue slices, monophage treatments not only resulted in significant reduction of tissue maceration in slices, but also showed protective effect against soft rot in tubers. Overall, these results demonstrate the efficacy of phages vB_PcaP-A3, vB_PcaM-D1, and vB_PcaM-J3 for the biocontrol of soft rot caused by P. carotovorum subsp. carotovorum.
PPAR-delta acts as a metabolic master checkpoint for metastasis in pancreatic cancer
Authors: Parejo-Alonso Beatriz , Barneda David , Trabulo Sara , Courtois Sarah , Compte-Sancerni Sara , Ruiz-Cañas Laura , Zheng Quan , Tang Jiajia , Chen Minchun , Guo Zhenyang , Schmitz Ulf , Irún Pilar , Penin-Peyta Laure , Crusz Shanthini M. , Cano-Galiano Andres , Lopez-Escalona Sergio , Jagust Petra , Espiau-Romera Pilar , Yuneva Mariia , Lin Meng-Lay , Lanas Angel , Sainz Bruno , Heeschen Christopher , Sancho Patricia 
Published: November 2021

SummaryIn pancreatic cancer, emerging evidence suggests that PPAR-δ overexpression is associated with tumor progression and metastasis, but a mechanistic link is still missing. Here we now show that PPAR-δ acts as the integrating upstream regulator for the metabolic rewiring, which is preceding the subsequent initiation of an invasive/metastatic program. Specifically, paracrine and metabolic cues regularly found in the metastasis-promoting tumor stroma consistently enhance, via induction of PPAR-δ activity, the glycolytic capacity and reserve of pancreatic cancer cells, respectively, accompanied by decreased mitochondrial oxygen consumption. Consequently, genetic or pharmacological inhibition of PPAR-δ results in reduced invasiveness and metastasis. Mechanistically, PPAR-δ acts by shifting the MYC/PGC1A balance towards MYC, enhancing metabolic plasticity. Targeting MYC similarly prevents the metabolic switch and subsequent initiation of invasiveness. Therefore, our data demonstrate that PPAR-δ is a key initiator for the metabolic reprogramming in pancreatic cancer, thereby acting as a checkpoint for the phenotypic change towards invasiveness. These findings provide compelling evidence for a novel treatment strategy to combat pancreatic cancer progression.
Telomerase and Alternative Lengthening of Telomeres coexist in the regenerating zebrafish caudal fins
Authors: Martínez-Balsalobre Elena , Anchelin-Flageul Monique , Alcaraz-Pérez Francisca , García-Castillo Jesús , Hernández-Silva David , Mione Maria C , Mulero Victoriano , Cayuela María L. 
Published: November 2021

ABSTRACTTelomeres are essential for chromosome protection and genomic stability, and telomerase function is critical to organ homeostasis. Zebrafish has become a useful vertebrate model for understanding the cellular and molecular mechanisms of regeneration. The regeneration capacity of the caudal fin of wild-type zebrafish is not affected by repetitive amputation, but the behavior of telomeres during this process has not yet been studied. In this study, the regeneration process was characterized in a telomerase deficient zebrafish model. Moreover, the regenerative capacity after repetitive amputations and at different ages was studied. Regenerative efficiency decreases with aging in all genotypes and surprisingly, telomere length is maintained even in telomerase deficient genotypes. Our results suggest that telomere length can be maintained by the regenerating cells through the recombination-mediated Alternative Lengthening of Telomeres (ALT) pathway, which is likely to support high rates of cell proliferation during the tailfin regeneration process. As far as we know, this is the first animal model to study ALT mechanism in regeneration, which opens a wealth of possibilities to study new treatments of ALT dependent processes.
Nascent adhesions differentially regulate lamellipodium velocity and persistence
Authors: Carney Keith R. , Khan Akib M. , Samson Shiela C. , Mittal Nikhil , Han Sangyoon J. , Mendoza Michelle C. , Bidone Tamara C. 
Published: November 2021

AbstractCell migration is essential to physiological and pathological biology. Migration is driven by the motion of a leading edge, in which actin polymerization pushes against the edge and adhesions transmit traction to the substrate while membrane tension increases. How the actin and adhesions synergistically control edge protrusion remains elusive. We addressed this question by developing a computational model in which the Brownian ratchet mechanism governs actin filament polymerization against the membrane and the molecular clutch mechanism governs adhesion to the substrate (BR-MC model). Our model predicted that actin polymerization is the most significant driver of protrusion, as actin had a greater effect on protrusion than adhesion assembly. Increasing the lifetime of nascent adhesions also enhanced velocity, but decreased the protrusion’s motional persistence, because filaments maintained against the cell edge ceased polymerizing as membrane tension increased. We confirmed the model predictions with measurement of adhesion lifetime and edge motion in migrating cells. Adhesions with longer lifetime were associated with faster protrusion velocity and shorter persistence. Experimentally increasing adhesion lifetime increased velocity but decreased persistence. We propose a mechanism for actin polymerization-driven, adhesion-dependent protrusion in which balanced nascent adhesion assembly and lifetime generates protrusions with the power and persistence to drive migration.
Live imaging of the co-translational recruitment of XBP1 mRNA to the ER and its processing by diffuse, non-polarized IRE1α
Authors: Gómez-Puerta Silvia , Ferrero Roberto , Hochstoeger Tobias , Zubiri Ivan , Chao Jeffrey A. , Aragón Tomás , Voigt Franka 
Published: November 2021

AbstractEndoplasmic reticulum (ER) to nucleus homeostatic signalling, known as the unfolded protein response (UPR), relies on the non-canonical splicing of XBP1 mRNA. The molecular switch that initiates splicing is the oligomerization of the ER stress sensor and UPR endonuclease IRE1α. While IRE1α can form large clusters that have been proposed to function as XBP1 processing centers on the ER, the actual oligomeric state of active IRE1α complexes as well as the targeting mechanism that recruits XBP1 to IRE1α oligomers, remain unknown.Here, we used a single molecule imaging approach to directly monitor the recruitment of individual XBP1 transcripts to the ER surface. We confirmed that stable ER association of unspliced XBP1 mRNA is established through HR2-dependent targeting and relies on active translation. In addition, we show that IRE1α-catalyzed splicing mobilizes XBP1 mRNA from the ER membrane in response to ER stress. Surprisingly, we find that XBP1 transcripts are not recruited into large IRE1α clusters, which only assemble upon overexpression of fluorescently-tagged IRE1α during ER stress. Our findings support a model where ribosome-engaged, ER-poised XBP1 mRNA is processed by functional IRE1α assemblies that are homogenously distributed throughout the ER membrane.
Generating weighted and thresholded gene coexpression networks using signed distance correlation
Authors: Pardo-Diaz Javier , Poole Philip S. , Beguerisse-Díaz Mariano , Deane Charlotte M. , Reinert Gesine 
Published: November 2021

AbstractEven within well-studied organisms, many genes lack useful functional annotations. One way to generate such functional information is to infer biological relationships between genes or proteins, using a network of gene coexpression data that includes functional annotations. Signed distance correlation has proved useful for the construction of unweighted gene coexpression networks. However, transforming correlation values into unweighted networks may lead to a loss of important biological information related to the intensity of the correlation. Here introduce a principled method to constructweightedgene coexpression networks using signed distance correlation. These networks contain weighted edges only between those pairs of genes whose correlation value is higher than a given threshold. We analyse data from different organisms and find that networks generated with our method based on signed distance correlation are more stable and capture more biological information compared to networks obtained from Pearson correlation. Moreover, we show that signed distance correlation networks capture more biological information than unweighted networks based on the same metric. While we use biological data sets to illustrate the method, the approach is general and can be used to construct networks in other domains.Data and code availabilityhttps://github.com/javier-pardodiaz/sdcorGCN
Nieman-Pick Type C2 proteins in Aedes aegypti: Their Structure-Function relationships and Expression in Uninfected versus Virus-infected Mosquitos
Authors: Thambi Prathigna Jaishankar , Modahl Cassandra M. , Kini R. Manjunatha 
Published: November 2021

AbstractAedes aegypti is a major vector that transmits arboviruses through the saliva injected into the host. Salivary proteins help in uninterrupted blood intake and enhance the transmission of pathogens. We studied Nieman-Pick Type C2 (NPC2) proteins, a superfamily of saliva proteins that play important role in arbovirus infections. In vertebrates, a single conserved gene encodes for the NPC2 protein that functions in cholesterol trafficking. Arthropods, in contrast, have several genes that encode for divergent NPC2 proteins. We compared the sequences of 20 A. aegypti NPC2 proteins to the cholesterol-binding residues of human and bovine, and fatty acid-binding residues of ant NPC2 proteins. We identified four and one mosquito NPC2 proteins as potential sterol- and fatty acid-binding proteins, respectively. From the published data, we analysed the expression of NPC2 genes in various tissues and their differential expression in midgut and salivary gland post-arbovirus infections. NPC2 genes are downregulated rather than upregulated in virus-infected tissues. Interestingly, AAEL012064 is the only gene that is downregulated in both the midgut and salivary gland in all virus infections. In addition, AAEL001650 is downregulated in the salivary gland infected with CHIKV, DENV2 or ZIKV. This gene in the midgut is downregulated infected with DENV1 but upregulated with DENV2. We studied the variation in cis elements in the promoter regions of two groups of closely related NPC2 genes and the expression of relevant transcription factors (TFs). In the midgut infected with DENV1 or DENV2, six TFs (CRE-BP1, AP1, c-Jun, c-Fos, Odd, and NF-kB) appear to play an opposing role in the expression of AAEL006854. Two TFs (RXR-beta/alpha and USF) have a potential role in the downregulation of AAEL009556 in CHIKV-infected midgut and salivary gland. Similarly, two TFs (COUP and Ftz) may have a key role in the downregulation of AAEL009555 and AAEL009556 in DENV2-infected salivary gland.
Detection of insect health with deep learning on near-infrared sensor data
Authors: Bick Emily , Edwards Sam , De Fine Licht Henrik H. 
Published: November 2021

AbstractConventional monitoring methods for disease vectors, pollinators or agricultural pests require time-consuming trapping and identification of individual insects. Automated optical sensors that detect backscattered near-infrared modulations created by flying insects are increasingly used to identify and count live insects, but do not inform about the health status of individual insects. Here we show that deep learning in trained convolutional neural networks in conjunction with sensors is a promising emerging method to detect infected insects. Health status was correctly determined in 85.6% of cases as early as two days post infection with a fungal pathogen. The ability to monitor insect health in real-time potentially has wide-reaching implications for preserving pollinator biodiversity and the rapid assessment of disease carrying individuals in vector populations.One sentence summaryAutomated optical sensors distinguish between fungus-infected and healthy insects.
Learning a new class of multisensory associations: High-density electrophysiological mapping of the temporal course of audio-visual object processing
Authors: Vercillo Tiziana , Freedman Edward G. , Ewen Joshua B. , Molholm Sophie , Foxe John J. 
Published: November 2021

ABSTRACTMultisensory objects that are frequently encountered in the natural environment lead to strong associations across a distributed sensory cortical network, with the end result experience of a unitary percept. Remarkably little is known, however, about the cortical processes sub-serving multisensory object formation and recognition. To advance our understanding in this important domain, the present study investigated the brain processes involved in learning and identification of novel visual-auditory objects. Specifically, we introduce and test a rudimentary three-stage model of multisensory object-formation and processing. Thirty adults were remotely trained for a week to recognize a novel class of multisensory objects (3D shapes paired to complex sounds), and high-density event related potentials (ERPs) were recorded to the corresponding unisensory (shapes or sounds only) and multisensory (shapes and sounds) stimuli, before and after intensive training. We identified three major stages of multisensory processing: 1) an early, multisensory, automatic effect (<100 ms) in occipital areas, related to the detection of simultaneous audiovisual signals and not related to multisensory learning 2) an intermediate object-processing stage (100-200 ms) in occipital and parietal areas, sensitive to the learned multisensory associations and 3) a late multisensory processing stage (>250 ms) that appears to be involved in both object recognition and possibly memory consolidation. Results from this study provide support for multiple stages of multisensory object learning and recognition that are subserved by an extended network of cortical areas.