bluuebunny/crossref_metadata_2025_split huggingface dataset:
ONE ASSAY TO TEST THEM ALL: COMPARING MULTIPLEX ASSAYS FOR EXPANSION OF RESPIRATORY VIRUS SURVEILLANCE
Authors: Boukli Narjis , Flamand Claude , Chea Kim Lay , Heng Leangyi , Keo Seangmai , Sour Kimhoung , In Sophea , Chhim Panha , Chhor Bunthea , Kruy Lomor , Feenstra Jelena D M , Gandhi Manoj , Okafor Obiageli , Ulekliev Camilla , Auerswald Heidi , Horm Viseth Srey , Karlsson Erik A 
Published: January 2023

ABSTRACTBackgroundMolecular multiplex assays (MPAs) for simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza and respiratory syncytial virus (RSV) in a single RT-PCR reaction reduce time and increase efficiency to identify multiple pathogens with overlapping clinical presentation but different treatments or public health implications.MethodsClinical performance of XpertXpress®SARS-CoV-2/Flu/RSV (Cepheid, GX), TaqPath™ COVID-19, FluA/B, RSV Combo kit (Thermo Fisher Scientific, TP), and PowerChek™ SARS-CoV-2/Influenza A&B/RSV Multiplex RT-PCR kit II (KogeneBiotech, PC) was compared to individual Standards of Care (SoC). Thirteen isolates of SARS-CoV-2, human seasonal influenza, and avian influenza served to assess limit of detection (LoD). Then, positive and negative residual nasopharyngeal specimens, collected under public health surveillance and pandemic response served for evaluation. Subsequently, comparison of effectiveness was assessed.ResultsThe three MPAs confidently detect all lineages of SARS-CoV-2 and influenza viruses. MPA-LoDs vary from 1-2 Log10 differences from SoC depending on assay and strain. Clinical evaluation resulted in overall agreement between 97% and 100%, demonstrating a high accuracy to detect all targets. Existing differences in costs, testing burden and implementation constraints influence the choice in primary or community settings.ConclusionTP, PC and GX, reliably detect SARS-CoV-2, influenza and RSV simultaneously, with reduced time-to-results and simplified workflows. MPAs have the potential to enhancediagnostics, surveillance system, and epidemic response to drive policy on prevention and control of viral respiratory infections.IMPORTANCEViral respiratory infections represent a major burden globally, weighed down by the COVID-19 pandemic, and threatened by spillover of novel zoonotic influenza viruses. Since respiratory infections share clinical presentations, identification of the causing agent for patient care and public health measures requires laboratory testing for several pathogens, including potential zoonotic spillovers. Simultaneous detection of SARS-CoV-2, influenza, and RSV in a single RT-PCR accelerates time from sampling to diagnosis, preserve consumables, and streamline human resources to respond to other endemic or emerging pathogens. Multiplex assays have the potential to sustain and even expand surveillance systems, can utilize capacity/capability developed during the COVID-19 pandemic worldwide, thereby strengthening epidemic/pandemic preparedness, prevention, and response.
Evidence against a cortical module for processing communicative gaze
Authors: Görner Marius , Dicke Peter W , Thier Peter 
Published: January 2023

AbstractWhere we look lets others know what we are interested in and allows them to join our focus of attention. In several studies our group investigated the neuronal basis of gaze following behavior in humans and macaques and described agaze following patch(GFP) in the posterior temporal cortex as being of central importance for this function. To our knowledge, this makes the GFP the most promising neurobiological correlate of Simon Baron-Cohen’seye direction detector(EDD), an integral part of hismindreading system. With the latter, Baron-Cohen proposed a set of domain-specific neurocognitive modules implementing a functional framework he suggested to be necessary to establish a Theory of Mind - the attribution of mental states to others. The tenet of domain-specificity requires that the EDD processes exclusively eye-like stimuli. In this preregistered fMRI study, we aimed to critically test if the GFP fulfills this criterion. Contrary to previous studies, the present results clearly demonstrate that GFP activity is not exclusively correlated with the perception of other people’s gaze direction and thus does not fulfill the criterion of domain-specificity. Furthermore, we show that it cannot be functionally dissociated from the MT+ complex, with which it overlaps anatomically. In the context of our previous studies which were specifically designed to capture the full behavioral relevance of active gaze following and to reveal the EDD, the results of the present study provide evidence that such a domain specific module does not exist. Therefore, the plausibility of Baron-Cohen’smindreading modelas a set of domain-specific modules is put into question.Significance statement.The presented results demonstrate that a brain area previously thought to be a domain-specific cortical module specialized in processing other people’s focus of visual attention is, in fact, domain-general. More specifically, we show that it is indistinguishable from cortical areas involved in the processing of visual motion. These findings add to a growing body of evidence arguing against domain-specific accounts in social neuroscience which posit that the functional building blocks of social behaviors are facilitated by dedicated neurocognitive modules.
Vascular and neural transcriptomics reveal stage-dependent pathways to inflammation and cognitive dysfunction in a rat model of hypertension
Authors: Ulbrich Philipp , Morton Lorena , Briese Michael , Lämmlin Naomi , Mattern Hendrik , Hasanuzzaman Md. , Westhues Melina , Khoshneviszadeh Mahsima , Appenzeller Silke , Gündel Daniel , Toussaint Magali , Brust Peter , Kniess Torsten , Oelschlegel Anja , Goldschmidt Jürgen , Meuth Sven , Heinze Hans-Jochen , Debska-Vielhaber Grazyna , Vielhaber Stefan , Becker Axel , Dityatev Alexander , Jandke Solveig , Sendtner Michael , Dunay Ildiko , Schreiber Stefanie 
Published: January 2023

AbstractChronic arterial hypertension causes cerebral microvascular dysfunction and doubles dementia risk in aging. However, cognitive health preservation by therapeutic blood pressure lowering alone is limited and depends on disease duration, the degree of irreversible tissue damage and whether microvascular function can be restored. This study aimed to understand molecular and cellular temporo-spatial pathomechanisms in the course of hypertension. We investigated the effects of initial, early chronic and late chronic hypertension in the frontal brain of rats by applying behavioral tests, histopathology, immunofluorescence, FACS, microvascular/neural tissue RNA sequencing as well as18F-FDG PET imaging. Chronic hypertension caused frontal brain-specific behavioral deficits. Our results highlight stage-dependent responses to continuous microvascular stress and wounding by hypertension. Early responses included a fast recruitment of activated microglia to the blood vessels, immigration of peripheral immune cells, blood-brain-barrier leakage and an energy-demanding hypermetabolic state. Vascular adaptation mechanisms were observed in later stages and included angiogenesis and vessel wall strengthening by upregulation of cellular adhesion molecules and extracellular matrix. Additionally, we identified late chronic accumulation of Igfbp-5 in the brains of hypertensive rats, which is also a signature of Alzheimer’s dementia and attenuates protective Igf-1 signaling. Our study advances the knowledge of involved pathomechanisms and highlights the stage-dependent nature of hypertensive pathobiology. This groundwork might be helpful for basic and clinical research to identify stage-dependent markers in the human disease course, investigate stage-dependent interventions besides blood pressure lowering and better understand the relationship between poor vascular health and neurodegenerative diseases.
Mitochondrial Genome Analysis and Phylogeny and Divergence Time Evaluation of theStrix aluco
Authors: Wang Yeying , Zhan Haofeng , Zhang Yu , Long Zhengmin , Yang Xiaofei 
Published: January 2023

ABSTRACTIn this study, a complete mitochondrial genome of theStrix alucowas reported for the first time, with a total length of 18,632 bp. There were 37 genes, including 22 tRNAs, 2 rRNAs, 13 protein-coding genes (PCGs), and 2 non-coding control regions (D-loop). The second-generation sequencing of the complete mitochondrial genome of theS. alucowas conducted using the Illumina platform, and then Tytoninae was used as the out-group, PhyloSuite software was applied to build the ML-tree and BI-tree of the Strigiformes, and finally, the divergence time tree was constructed using Beast2.6.7 software, the age ofMiosurnia diurnafossil-bearing sediments (6.0-9.5 Ma) was set as the internal correction point. The common ancestor of theStrixwas confirmed to have diverged during the Pleistocene(2.59~0.01Ma). The dramatic uplift of the Qinling Mountains in the Middle Pleistocene and the climate oscillation of the Pleistocene together causedStrixdivergence between the northern and southern parts of mainland China. The isolation of glacial-interglacial rotation and glacier refuge was the main reason for the divergence of the common ancestor of theStrix uralensisand theS. alucoduring this period. This study provides a reference for the evolution history of theStrix.Summary statementThis study was the first time to assemble the complete mitochondrial genome ofStrix aluco, and report the divergence time ofStrix. A full discussion was made, and it was inferred that the uplift of the Qinling Mountains and the glacial refuge led to the differentiation of this genus.
PyriculariaPopulations are Mostly Host-Specialized with Limited Reciprocal Cross-Infection Between Wheat and Endemic Grasses in Minas Gerais, Brazil
Authors: Ascari João P. , Cazón Luis I. , Rahnama Mostafa , Lamour Kurt , Fernandes José M. C. , Farman Mark L. , Del Ponte Emerson M. 
Published: January 2023

AbstractWheat blast, caused byPyricularia oryzaeTriticum (PoT), is an emergent threat to wheat production. Current understanding of the evolution and population biology of the pathogen and epidemiology of the disease has been based on phylogenomic studies that compared the wheat blast pathogen with isolates collected from grasses that were invasive to Brazilian wheat fields. Genetic similarity between isolates from wheat and grasses lead to the conclusion that significant cross-infection occurs, especially on signalgrass (Urochloa spp.); and this in turn prompted speculation that its widespread use as forage is a key driver of the disease’s epidemiology. We reanalyzed data from those studies and found that all but one of the isolates from non-wheat hosts were members of PoT and the relatedLolium-adapted lineage (PoL1), which meant that thePyriculariapopulations typically found on endemic grasses had not yet been sampled. To address this shortcoming, we performed a comprehensive sampling of blast lesions in wheat crops and endemic grasses found in and away from wheat fields in Minas Gerais. A total 1,368 diseased samples were collected (976 leaves of wheat and grasses and 392 wheat heads) which yielded a working collection of 564Pyriculariaisolates. We show that, contrary to earlier implications, PoT was rarely found on endemic grasses and, conversely, members of grass-adapted populations were rarely found on wheat. Instead, most populations were host-specialized with constituent isolates usually grouping according to their host-of-origin. With regard to the dominant role proposed for signalgrass in wheat blast epidemiology, we found only one PoT member in 67 isolates collected from signalgrass grown away from wheat fields, and only three members ofUrochloa-adapted populations among hundreds of isolates from wheat. Cross-inoculation assays on wheat and a signalgrass used in pastures (U. brizantha) suggested that the limited cross-infection observed in the field may be due to innate compatibility differences. Whether or not the observed level of cross-infection would be sufficient to provide an inoculum reservoir, or serve as a bridge between wheat growing regions, is questionable and, therefore, deserves further investigation.
Improving genome quality through artificial truncating purifying selection using heat shock: case of carps
Authors: Kuzmin Aleksandr , Evgenii Vinogradov , Balashov Dmitrii , Kozenkova Elena , Iliushchenko Dmitrii , Mikhailova Alina G. , Patlay Nataliya , Ekaterina Zakharenko , Ivan Kozenkov , Ivan Ptashnik , Timonina Valeriia , Tretiakov Evgenii , Galimov Yan , Haag Christoph , Efimenko Bogdan , Gunbin Konstantin , Mizgirev Igor , Mugue Nikolai , Popadin Konstantin 
Published: January 2023

AbstractThe process of domestication is associated with decrease in effective population size, which in turn leads to accumulation of slightly-deleterious mutations due to genetic drift. To maintain genome quality at a high level, we propose to use a stress-induced strong purifying selection, which based on negative epistasis, can effectively eliminate organisms with an excess of deleterious variants. Here, to identify stress factors, which interact with the effect of deleterious mutations we performed a proof-of-principle experiment with several regimes of a heat shock. We observed that fitness of mutated versus wild-type carp lines drops stronger after heat shock, which is a signature of a negative epistasis. Although the observed trend is promising, the effect of the epistasis is weak and unstable from family to family. Thus, more deep tuning of heat shock regimes is needed to uncover the most efficient combination of factors (absolute temperature, duration, stage of the embryo development) aggravating the burden of deleterious mutations and thus exposing them to the selection.
A vocalization-processing network in marmosets
Authors: Jafari Azadeh , Dureux Audrey , Zanini Alessandro , Menon Ravi S. , Gilbert Kyle M. , Everling Stefan 
Published: January 2023

AbstractVocalizations play an important role in the daily life of primates and likely form the basis of human language. Functional imaging studies have demonstrated that listening to language or reading activates a left-lateralized fronto-temporal language network in human participants. Here we acquired whole-brain ultrahigh field (9.4 Tesla) fMRI in awake marmosets (Callithrix jacchus) and demonstrate that these highly vocal small New World primates possess a similar fronto-temporal network, including subcortical regions, that is activated by the presentation of conspecific vocalizations. The findings suggest that the human language network has evolved from an ancestral vocalization network that predates the separation of New and Old World primates.
Texture-Based Image Analysis For the Assessment of Soybeans
Authors: Lee Alexander , Hoffseth Kevin 
Published: January 2023

AbstractAt 4.44 billion bushels worth an estimated $57.7 billion dollars, soybeans are one of the most produced crops in the United States and are appraised using a standard grading system set by the USDA(NASS, 2022). The grading and inspection process is based on twenty factors, including six that are visual based (USDA, 2020). The aim of this research is to apply texture-based image analysis to assess visual indicators of damage in soybeans and demonstrate potential use in increasing efficiency and consistency in soybean grading. Surface texture is one of the characteristics that is examined by inspectors as part of assessing soybean damage, while “image texture” is a calculated set of parameters that are used in image processing and analysis to quantify the apparent actual texture captured in an image. In this study, texture analysis using Haralick textural features is performed on sets of soybean images to assess damage types (as defined by the USDA inspection handbook and visual reference images) and improve soybean classification.
Decomposing intraspecific phenotypic variation: implications for species and functional diversity
Authors: Worthy Samantha J. , Umaña María N. , Zhang Caicai , Lin Luxiang , Cao Min , Swenson Nathan G. 
Published: January 2023

AbstractResearchers have a history of seeking explanation for and understanding of diversity patterns. High-dimensional trait-based trade-offs have been hypothesized as important for maintaining species and functional diversity. These relationships have primarily been investigated at the community-level, despite the importance of intraspecific variation to diversity maintenance. The goal of this research is to determine if alternative phenotypes are present within species and the impacts of this on diversity in a tropical seedling community in China. We ask 1) do trait combinations found across species, at the community-level, also exist within species?; 2) how consistent are alternative phenotypes and their contributions to growth across species?; and 3) how do findings align with species co-occurrence patterns? We model species-specific growth with individual-level trait measurements, environmental data, and their interactions, allowing for identification of intraspecific alternative phenotypes and quantification of the contribution of variables to growth. We find that two of three species have intraspecific alternative phenotypes. Specifically, individuals within these species share a trait combination, but how they combine the traits differs depending on the type and level of soil nutrients. Furthermore, we find that similarity among species in alternative phenotypes and variables that contribute most to growth may lead to negative spatial co-occurrence of species. Overall, we find that multiple traits or interactions between traits and the environment drive species-specific strategies for growth. These results highlight how individuals are highly variable, with phenotypically different individuals having similar growth performance, and suggest how high species and functional diversity can be maintained in communities.
VRPG: an interactive visualization framework for reference-projected pangenome graph
Authors: Miao Zepu , Yue Jia-Xing 
Published: January 2023

AbstractWith the increasing availability of high-quality genome assemblies, pangenome graph is emerging as a new paradigm in the genomics field for identifying, encoding, and interpreting genomic variation landscape at both population and species levels. However, it remains a major challenge in understanding and interpretating pangenome graph via biologically informative visualization. To facilitate a better examination of pangenome graph towards novel biological insights, here we present VRPG, a web-based interactive visualization framework of pangenome graph. VRPG provides dynamic and efficient supports for exploring and annotating pangenome graphs along a reference-based coordinate system. Moreover, VRPG shines with its unique features in highlighting the directed path of any graph-constitutive assembly as well as in denoting copy number variation of genomic segments represented by graph-constitutive nodes, which are highly valuable in genome comparison and variant analysis. Additionally, VRPG enables side-by-side visualization between pangenome graph and reference-based annotation features, bridging the graph and linear genome context. To further demonstrate its features and scalability, we applied VRPG to the cutting-edge yeast and human reference pangenome graphs derived from hundreds of high-quality genome assemblies via a dedicated website (https://www.evomicslab.org/app/vrpg/).Contact:yuejiaxing@gmail.comKey pointsDeveloped an intuitive visualization framework for pangenome graph.Empowered graph-based feature highlighting and variant visualization.Enabled connecting reference-based annotation features in the context of pangenome graph.
Preterm birth accelerates the maturation of spontaneous and resting activity in the visual cortex
Authors: Witteveen Isabelle F. , McCoy Emily , Holsworth Troy D. , Shen Catherine Z. , Chang Winnie , Nance Madelyn G. , Belkowitz Allison R. , Dougald Avery , Puglia Meghan H. , Ribic Adema 
Published: January 2023

AbstractPrematurity is among the leading risks for poor neurocognitive outcomes. The brains of preterm infants show alterations in structure and electrical activity, but the underlying circuit mechanisms are unclear. To address this, we performed a cross-species study of the electrophysiological activity in the visual cortices of prematurely born infants and mice. Using electroencephalography (EEG) in a sample of healthy preterm (N=29) and term (N=28) infants, we found that the maturation of the aperiodic EEG component was accelerated in the preterm cohort, with a significantly flatter 1/f slope when compared to the term infants. The flatter slope was a result of decreased spectral power in the theta and alpha bands and was correlated with the degree of prematurity. To determine the circuit and cellular changes that potentially mediate the changes in 1/f slope after preterm birth, we usedin vivoelectrophysiology in preterm mice and found that, similar to infants, preterm birth results in a flattened 1/f slope. We analyzed neuronal activity in the visual cortex of preterm mice (N=6 preterm and 9 term mice) and found suppressed spontaneous firing of neurons. Using immunohistochemistry, we further found an accelerated maturation of inhibitory circuits. In both preterm mice and infants, the functional maturation of the cortex was accelerated, underscoring birth as a critical checkpoint in cortical maturation. Our study points to a potential mechanism of preterm birth-related changes in resting neural activity, highlighting the utility of a cross-species approach in studying the neural circuit mechanisms of preterm birth-related neurodevelopmental conditions.
Developing a robust technique for denoising and extracting speech and breath sounds in voice recordings from asthmatic patients
Authors: Sayed Sania Fatima , Rezwan Faisal I. 
Published: January 2023

AbstractAuscultation and processing cough, voice and breath sounds play an important role in diagnosis of several pulmonary ailments. There have been a number of studies using machine learning algorithms on such sound files to build classification and prediction algorithms. Since these studies used specialized microphones in controlled environments, it is difficult to test and deploy these algorithms in real-life settings. Recorded speech files consist of breath and wheeze sounds and it is challenging to extract from this single sound file. Hence, several audio processing and editing software are used to demarcate these sounds. The proposed technique uses a combination of a denoiser and an extraction technique to overcome these drawbacks. The developed pipeline ensures that the audio files are free of any environmental and background noises, and the audio can be recorded through any kind of microphone and environmental settings. The extraction technique further is the result of combinations of filters to output the speech and breath sounds as individual sound files, ready for processing and eliminating the need of audio editing and processing software.