bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of a new dengue 3 controlled human infection model for use in the evaluation of candidate dengue vaccines
Authors: Pierce KK , Whitehead SS , Diehl SA , Naro G , Carmolli MC , He H , Tibery CM , Sabundayo BP , Kirkpatrick BD , Durbin AP 
Published: June 2023

AbstractAll four serotypes of dengue virus (DENV) cause the full spectrum of disease. Therefore, vaccines must protect against all serotypes. To evaluate candidate vaccines, a human challenge model of dengue serotype 3 (rDEN30Δ30) was developed. All challenge virus recipients safely met the primary endpoint of viremia and secondary endpoints of rash and seroconversion to DENV-3.
Night-time neuronal activation of Cluster N in a North American songbird
Authors: Rudolf Jennifer , Philipello Natalie , Fleihan Tamara , Dickman J. David , Delmore Kira E. 
Published: June 2023

AbstractNight-migrating songbirds utilize the Earth’s magnetic field to help navigate to and from their breeding sites each year. A region of the avian forebrain called Cluster N has been shown to be activated during night migratory behavior and it has been implicated in processing geomagnetic information. Previous studies with night-migratory European songbirds have shown that neuronal activity at Cluster N is higher at night than during the day. Comparable work in North American migrants has only been performed in one species of swallows, so extension of examination for Cluster N in other migratory birds is needed. In addition, it is unclear if Cluster N activation is lateralized and the full extent of its boundaries in the forebrain have yet to be described. We used sensory-driven gene expression based on ZENK and the Swainson’s thrush, a night-migratory North American songbird, to fill these knowledge gaps. We found elevated levels of gene expression in night-vs. day-active thrushes and no evidence for lateralization in this region. We further examined the anatomical extent of neural activation in the forebrain using 3D reconstruction topology. Our findings demonstrate that Swainson’s thrushes possess an extensive bilateral night-activated Cluster N region in the forebrain similar to other European avian species, suggesting that Cluster N is highly conserved in nocturnal migrants.
DS4DH at MEDIQA-Chat 2023: Leveraging SVM and GPT-3 Prompt Engineering for Medical Dialogue Classification and Summarization
Authors: Zhang Boya , Mishra Rahul , Teodoro Douglas 
Published: June 2023

AbstractThis paper presents the results of the Data Science for Digital Health (DS4DH) group in the MEDIQA-Chat Tasks at ACL-ClinicalNLP 2023. Our study combines the power of a classical machine learning method, Support Vector Machine, for classifying medical dialogues, along with the implementation of oneshot prompts using GPT-3.5. We employ dialogues and summaries from the same category as prompts to generate summaries for novel dialogues. Our findings exceed the average benchmark score, offering a robust reference for assessing performance in this field.
Intra-lineage microevolution ofWolbachialeads to the emergence of new cytoplasmic incompatibility patterns
Authors: Namias Alice , Ngaku Annais , Makoundou Patrick , Unal Sandra , Sicard Mathieu , Weill Mylène 
Published: June 2023

AbstractMosquitoes of theCulex pipienscomplex are worldwide vectors of arbovirus, filarial nematode, and avian malaria agents. In these hosts, the endosymbiotic bacteriaWolbachiainduce cytoplasmic incompatibility (CI), that is, reduced embryo viability in so-called incompatible crosses.WolbachiainfectingCulex pipiens(wPip) cause CI patterns of unparalleled complexity, associated with the amplification and diversification ofcidAandcidBgenes, with up to six different gene copies described in a singlewPip genome. By repeating crosses betweenCulexisofemale lines over 17 years, we documented the emergence of a new compatibility type. Using a new sequencing method adapted to multigene families to acquirecidgenes, we showed that somewPip genomes lost specificcidAgene copies, thus giving rise to several sub-lineages segregating in the same cage. By linking phenotypic changes to their underlying genotypic bases, we showed that gene copies that are key for CI phenotypes originated from recombinations, not point mutations. We revealed how new CI patterns could emerge as part of a two-step process: first, local changes take place in the CI repertoires while maintaining compatibility with the surrounding mosquitoes, and then migration and secondary contact occur with the incompatible lines.
Intraspecific scaling of home range size and its bioenergetic dependence
Authors: Byrnes Evan E. , Hounslow Jenna L. , Heim Vital , White Clemency E. , Smukall Matthew J. , Beatty Stephen J. , Gleiss Adrian C. 
Published: June 2023

AbstractHome range size and metabolic rate of animals are expected to scale with body mass at similar rates; with home ranges expanding to meet increased metabolic requirements. This expectation has widely been tested using lab-derived estimates of basal metabolic rate as proxies for field energy requirements, however, it is unclear if existing theory aligns with patterns of home range scaling observed in the field. Here, we conduct the first direct field test of the relationship between home range and metabolic rate allometry. Using acoustic telemetry, we simultaneously measured the individual home range size and field metabolic rate of lemon sharks(Negaprion brevirostris)spanning one order of magnitude in body mass. Although scaling rates of field metabolic rate were consistent with standard metabolic rate, home range size scaled at shallower rates than metabolic rates. This is evidence for strong top-down controls on home range scaling rates, likely a result of predation pressure placing constraints on home range expansions. Consequently, direct resource competition can lead to decreased home range scaling rates. We highlight inconsistencies with theory on the effects of population density and competition on home range scaling and propose that the influence of diverse types of competition should be examined.
Autoencoder Model for Translating Omics Signatures
Authors: Meimetis Nikolaos , Pullen Krista M. , Zhu Daniel Y. , Nilsson Avlant , Hoang Trong Nghia , Magliacane Sara , Lauffenburger Douglas A. 
Published: June 2023

AbstractThe development of effective therapeutics and vaccines for human diseases requires a systematic understanding of human biology. While animal and in vitro culture models have successfully elucidated the molecular mechanisms of diseases in many studies, they yet fail to adequately recapitulate human biology as evidenced by the predominant likelihood of failure in clinical trials. To address this broadly important problem, we developed AutoTransOP, a neural network autoencoder framework to map omics profiles from designated species or cellular contexts into a global latent space, from which germane information can be mapped between different contexts. This approach performs as well or better than extant machine learning methods and can identify animal/culture-specific molecular features predictive of other contexts, without requiring homology matching. For an especially challenging test case, we successfully apply our framework to a set of inter-species vaccine serology studies, where no 1-1 mapping between human and non-human primate features exists.
Modelling the probability of meeting IUCN Red List criteria to support reassessments
Authors: Henry Etienne Georges , Santini Luca , Butchart Stuart , Gonzalez-Suarez Manuela , Lucas Pablo Miguel , Benitez-Lopez Ana , Mancini Giordano , Jung Martin , Cardoso Pedro , Zizka Alexander , Meyer Carsten , Akcakaya H. Resit , Berryman Alex , Cazalis Victor , Di Marco Moreno 
Published: June 2023

AbstractComparative extinction risk analysis - which predicts species extinction risk from correlation with traits or geographical characteristics - has gained research attention as a promising tool to support extinction risk assessment in the IUCN Red List of Threatened Species. However, its uptake has been very limited so far, possibly because these models only predict a species’ Red List category, without indicating which Red List criteria may be triggered by which such approaches cannot easily be used in Red List assessments. We overcome this implementation gap by developing models that predict the probability of species meeting individual Red List criteria. Using data on the world’s birds, we evaluated the predictive performance of our criterion-specific models and compared it with the typical criterion-blind modelling approach. We compiled data on biological traits (e.g., range size, clutch size) and external drivers (e.g., change in canopy cover) often associated with extinction risk. For each specific criterion, we modelled the relationship between extinction risk predictors and species’ Red List category under that criterion using ordinal regression models. We found criterion-specific models were better at predicting threatened species compared to a criterion-blind model (higher sensitivity), but less good at predicting not threatened species (lower specificity). As expected, different covariates were important for predicting threat status under different criteria, for example change in annual temperature was important to predict criteria related to population trends, while clutch size was important for criteria related to restricted area of occupancy or small population size. Our criteria-specific method can support Red List assessors by producing outputs that identify species likely to meet specific criteria, and which are the most important predictors: these species can be prioritised for re-evaluation. We expect this new approach to increase the uptake of extinction risk models in Red List assessments, bridging a long-standing research-implementation gap.
Twilight length alters growth and flowering time in Arabidopsis via LHY/CCA1
Authors: Mehta Devang , Scandola Sabine , Kennedy Curtis , Lummer Christina , Rodriguez Gallo Maria Camila , Grubb Lauren E. , Tan Maryalle , Scarpella Enrico , Uhrig R. Glen 
Published: June 2023

AbstractThe plant circadian clock governs growth and development by syncing biological processes to periodic environmental changes. Decades of research has shown how the clock enables plants to respond to two environmental variables that change at different latitudes and over different seasons: photoperiod and temperature. However, a third variable, twilight length, has so far gone unstudied. The duration of twilight changes across the planet, lengthening with latitude and changing across seasons, and yet most circadian experiments are performed in lab environments with no twilight. Here, using controlled growth setups, we show that twilight length impacts plant growth and changes flowering time via the LHY/CCA1 morning module of the Arabidopsis circadian clock. Using a series of progressively truncated no-twilight photoperiods, we also found that plants are more sensitive to twilight length compared to equivalent changes in solely photoperiod. Further, transcriptome and proteome analyses indicated that twilight length alters the regulation of proteins involved in reactive oxygen species metabolism, photosynthesis, and carbon metabolism. Genetic analyses also implicated a twilight sensing pathway from phytochromes D and E, the morning elements of the circadian clock and modulating flowering time through theGI-FTpathway. Overall, our findings call for more nuanced models of daylength perception in plants and posit that twilight length is an important determinant of plant growth, development, and circadian function.
PlotS: web-based application for data visualization and analysis
Authors: Jajo Ringyao , Kansal Shivani , Balyan Sonia , Raghuvanshi Saurabh 
Published: June 2023

AbstractBackgroundData visualisation technique has greatly improved as technology has advanced. While representing the data through graph, it has made the underlying data structure become more transparent and interpretable. However, the informational scope of freely available generic visualisation tools is still limited since they only support descriptive statistics as well as no metainformation can be incorporated. Additionally, there is a need to promote the use of accepted scientific standards when performing and reporting statistical analysis.ResultPlotS is a visualization centric web-based application that allows the integration of statistical analysis into a single workflow. The current version has eight types of graphs (bar, box, density, frequency polygon, histogram, line, scatter and violin plot) and four statistical methods (T-test, ANOVA, Wilcoxon test and Krushkal-Wallis test). It is an interactive application that provide many useful customization options for data analysis-focused visualization. It support incorporation of metainformation in the graph and multivariate data analysis by adding layer with or without secondary y-axis, side graphs, inset graph or through faceting. It can handle variety of data formats with or without replicates and inferential statistical analysis can be incorporated in the graph. Necessary statistical results are explicitly displayed for inferences and reporting.ConclusionPlotS is freely available athttps://plots-application.shinyapps.io/plots/. We hope it will be a useful tool for data visualisation and analysis that will also encourage the widespread use of proper statistical methods in research and teaching.
CHPF boosts proliferation and invasion of clear cell renal cell carcinoma
Authors: Zhang Yaoyu , Li Xiaowei , Ran Shu , Zhao Youguang , Huang Yuanshun , Zhou Tingting , Wang Qiwu , Liu Jiwen , Zhang Qimin , Li Xiaodong , Leng Taiping , Luo Yihang , Li Shadan 
Published: June 2023

AbstractBackgroundClear cell renal cell carcinoma (ccRCC) is a malignant tumor most commonly seen in the urinary system, featuring quick progression, invasive behavior, frequent recrudesce, and bad prognosis, whereas Chondroitin polymerizing factor (CHPF) is an essential glycosyl transferase of biosynthesis involved chondroitin sulphate. But the relationship between the two has not been fully understood so far. The present research will probe into the relationship between CHPF and ccRCC.MethodsExplore the CHPF expression level in renal ccRCC tissues through bioinformatics analysis of The Cancer Genome Atlas (TCGA) and the real-time quantitative polymerase chain reaction detection system (qPCR); acquire relevant clinical data from the TCGA data-base and use Kaplan-Meier survival analysis to verify the relevance of CHPF expression to the clinical prognosis of ccRCC patients; then, effectively silence CHPF in ccRCC 786-O cells by a lentivirus-mediated approach; next, observe the effects of CHPF on tumor cell proliferation, cell cycle progression, and apoptosis.ResultsIn ccRCC tissues, CHPF expression has been significantly upregulated; the higher expression, the shorter survival of ccRCC patients. CHPF downregulation in the 786-O cell can effectively hold back the proliferation, apoptosis and cycle of cancer cells.ConclusionBased on the above results, we arrive at a conclusion that CHPF expression contributes markedly to the development of human ccRCC cells. Therefore, CHPF may act as a potential prognostic marker of ccRCC and provide a new target for ccRCC treatment.Simple SummaryChondroitin polymerizing factor (CHPF) is an important glycosyltransferase involved in the biosynthesis of chondroitin sulfate, which is thought to have some pro-carcinogenic effects. However, the role and mechanism of CHPF in clear cell renal cell carcinoma (ccRCC) have not been reported. The aim of this study was to investigate the relationship between CHPF and ccRCC. In this study, we found that CHPF was highly expressed in ccRCC and knocking out CHPF can greatly inhibit the proliferation and cell cycle progression of ccRCC and accelerate its apoptosis, suggesting that CHPF can predict the prognosis of ccRCC and a potential target for treatment.
Plasmodium falciparumtransmission in the highlands of Ethiopia is driven by closely related and clonal parasites
Authors: Holzschuh Aurel , Ewnetu Yalemwork , Carlier Lise , Lerch Anita , Gerlovina Inna , Baker Sarah Cate , Yewhalaw Delenasaw , Haileselassie Werissaw , Berhane Nega , Lemma Wossenseged , Koepfli Cristian 
Published: June 2023

ABSTRACTMalaria cases are frequently recorded in the Ethiopian highlands even at altitudes above 2,000 m. The epidemiology of malaria in the Ethiopian highlands, and in particular the role of importation by human migration from the highly endemic lowlands is not well understood. We characterized the parasite population structure and genetic relatedness by sequencing 159P. falciparumsamples from Gondar and an additional 28 samples from Ziway using a highly multiplexed droplet digital PCR (ddPCR)-based amplicon deep sequencing method targeting 35 microhaplotypes and drug resistance loci. Diversity was moderate (mean HE: 0.54), and infection complexity was low (74.9% single clone infections). A significant percentage of infections shared genomic haplotypes, even across transmission seasons, indicating persistent local and focal transmission. Multiple clusters of clonal or near-clonal infections were identified, highlighting the overall high genetic relatedness. Frequently, infections from travelers were the earliest observed cases, suggesting that parasites may have been imported and then transmitted locally. We observed population structure between Gondar and Ziway, although some haplotypes were shared between sites. 31.1% of infections carriedpfhrp2deletions and 84.4%pfhrp3deletions, and 28.7%pfhrp2/pfhrp3double deletions. Parasites withpfhrp2/3deletions and wild-type parasites were genetically distinct. Mutations associated with resistance to sulfadoxine-pyrimethamine and lumefantrine were observed at near-fixation, but no mutations inpfk13were found. In conclusion, genomic data corroborates local transmission and the importance of intensified control in the Ethiopian highlands.
Alteration of DNMT1/DNMT3A by eribulin elicits global DNA methylation changes with potential therapeutic implications for triple-negative breast cancer
Authors: Bagheri Meisam , Lee Min Kyung , Muller Kristen E. , Miller Todd W. , Pattabiraman Diwakar R. , Christensen Brock C. 
Published: June 2023

AbstractTriple-negative breast cancer (TNBC) is an aggressive disease subtype with limited treatment options. Eribulin is a chemotherapeutic approved for the treatment of advanced breast cancer that has been shown to elicit epigenetic changes. We investigated the effect of eribulin treatment on genome-scale DNA methylation patterns in TNBC cells. Following repeated treatment, The results showed that eribulin-induced changes in DNA methylation patterns evident in persister cells. Eribulin also affected the binding of transcription factors to genomic ZEB1 binding sites and regulated several cellular pathways, including ERBB and VEGF signaling and cell adhesion. Eribulin also altered the expression of epigenetic modifiers including DNMT1, TET1, and DNMT3A/B in persister cells. Data from primary human TNBC tumors supported these findings: DNMT1 and DNMT3A levels were altered by eribulin treatment in human primary TNBC tumors. Our results suggest that eribulin modulates DNA methylation patterns in TNBC cells by altering the expression of epigenetic modifiers. These findings have clinical implications for using eribulin as a therapeutic agent.
RBD-based high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways
Authors: Gagne Matthew , Flynn Barbara J. , Honeycutt Christopher Cole , Flebbe Dillon R. , Andrew Shayne F. , Provost Samantha J. , McCormick Lauren , Van Ry Alex , McCarthy Elizabeth , Todd John-Paul M. , Bao Saran , Teng I-Ting , Marciano Shir , Rudich Yinon , Li Chunlin , Pessaint Laurent , Dodson Alan , Cook Anthony , Lewis Mark G. , Andersen Hanne , Zahradník Jiří , Nason Martha C. , Foulds Kathryn E. , Kwong Peter D. , Roederer Mario , Schreiber Gideon , Seder Robert A. , Douek Daniel C. 
Published: June 2023

AbstractSARS-CoV-2 has the capacity to evolve mutations to escape vaccine-and infection-acquired immunity and antiviral drugs. A variant-agnostic therapeutic agent that protects against severe disease without putting selective pressure on the virus would thus be a valuable biomedical tool. Here, we challenged rhesus macaques with SARS-CoV-2 Delta and simultaneously treated them with aerosolized RBD-62, a protein developed through multiple rounds ofin vitroevolution of SARS-CoV-2 RBD to acquire 1000-fold enhanced ACE2 binding affinity. RBD-62 treatment gave equivalent protection in upper and lower airways, a phenomenon not previously observed with clinically approved vaccines. Importantly, RBD-62 did not block the development of memory responses to Delta and did not elicit anti-drug immunity. These data provide proof-of-concept that RBD-62 can prevent severe disease from a highly virulent variant.
Microbiome Features Associated with Performance Measures in Non-Athletic and Athletic Individuals
Authors: Humińska-Lisowska Kinga , Zielińska Kinga , Mieszkowski Jan , Sawczyn Monika Michałowska- , Cięszczyk Paweł , Łabaj Paweł P , Wasąg Bartosz , Frączek Barbara , Grzywacz Anna , Kochanowicz Andrzej , Kosciolek Tomasz 
Published: June 2023

AbstractThe influence of human gut microbiota on health and disease is now well established. Therefore, it is not surprising that microbiome research has found applications within the sports community, hoping to improve health and optimize performance. Every comparison study found new species or pathways that were more enriched in elites than in sedentary controls. In addition, sport-specific and performance-level-specific microbiome features have been identified. However, the results remain inconclusive and indicate the need for further assessment. In our study, we conducted two interventions, anaerobic (Wingate Anaerobic Tests (WAnTs)) and aerobic (Bruce Treadmill Test), on fit non-athletic but physically active controls and athletic strength (training professional sports which increase anaerobic efforts such as weightlifting, powerlifting, and bodybuilding) and endurance (training professional sports which increase aerobic efforts such as race walking, long-distance running, or ski running) individuals to compare sport-specific and training-specific responses. While we did not identify any differences in alpha and beta diversity or significant differential abundance of microbiome components at baseline, we noted that one-third of the species identified were unique to either group. Longitudinal analysis of samples (pre- and post-intervention) revealed an abundance ofAlistipes communisin the strength group during the WAnT intervention and 88 species with notable differences between groups during the Bruce Test intervention. SparCC recognizedBifidobacterium longumandBifidobacterium adolescentis, short-chain fatty acid producers with probiotic properties, as species strongly associated with VO2max. Ultimately, we identified several taxa with different baseline abundances and longitudinal changes when comparing individuals based on their VO2max, average power, and maximal power parameters. Our results confirmed the health status of the individuals involved in the study, based on previous assumptions about microbiome health. Furthermore, our findings indicate that microbiome features are associated with better performance measures previously identified in elite athletes.