bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mondo: Unifying diseases for the world, by the world
Authors: Vasilevsky Nicole A , Matentzoglu Nicolas A , Toro Sabrina , Flack Joseph E , Hegde Harshad , Unni Deepak R , Alyea Gioconda F , Amberger Joanna S , Babb Larry , Balhoff James P , Bingaman Taylor I , Burns Gully A , Buske Orion J , Callahan Tiffany J , Carmody Leigh C , Cordo Paula Carrio , Chan Lauren E , Chang George S , Christiaens Sean L , Dumontier Michel , Failla Laura E , Flowers May J , Garrett H. Alpha , Goldstein Jennifer L , Gration Dylan , Groza Tudor , Hanauer Marc , Harris Nomi L , Hilton Jason A , Himmelstein Daniel S , Hoyt Charles Tapley , Kane Megan S , Köhler Sebastian , Lagorce David , Lai Abbe , Larralde Martin , Lock Antonia , López Santiago Irene , Maglott Donna R , Malheiro Adriana J , Meldal Birgit H M , Munoz-Torres Monica C , Nelson Tristan H , Nicholas Frank W , Ochoa David , Olson Daniel P , Oprea Tudor I , Osumi-Sutherland David , Parkinson Helen , Pendlington Zoë May , Rath Ana , Rehm Heidi L , Remennik Lyubov , Riggs Erin R , Roncaglia Paola , Ross Justyne E , Shadbolt Marion F , Shefchek Kent A , Similuk Morgan N , Sioutos Nicholas , Smedley Damian , Sparks Rachel , Stefancsik Ray , Stephan Ralf , Storm Andrea L , Stupp Doron , Stupp Gregory S , Sundaramurthi Jagadish Chandrabose , Tammen Imke , Tay Darin , Thaxton Courtney L , Valasek Eloise , Valls-Margarit Jordi , Wagner Alex H , Welter Danielle , Whetzel Patricia L , Whiteman Lori L , Wood Valerie , Xu Colleen H , Zankl Andreas , Zhang Xingmin Aaron , Chute Christopher G , Robinson Peter N , Mungall Christopher J , Hamosh Ada , Haendel Melissa A 
Published: April 2022

AbstractThere are thousands of distinct disease entities and concepts, each of which are known by different and sometimes contradictory names. The lack of a unified system for managing these entities poses a major challenge for both machines and humans that need to harmonize information to better predict causes and treatments for disease. The Mondo Disease Ontology is an open, community-driven ontology that integrates key medical and biomedical terminologies, supporting disease data integration to improve diagnosis, treatment, and translational research. Mondo records the sources of all data and is continually updated, making it suitable for research and clinical applications that require up-to-date disease knowledge.
Hair concentrations of Δ-9-tetrahydrocannabinol (THC) and cannabidiol (CBD) in cannabis consumers psychiatric patients
Authors: Barguil Yann , Chiaradia Laura , Southwell Guy , Charlot Jean-Yves 
Published: April 2022

AbstractAmong young consumers of cannabis, a brief psychotic disorder (BPD) can be either the clinical manifestation of acute cannabis psychosis (ACP) or an announcement of schizophrenia’s onset. Clinicians are faced with the difficulty of making a differential diagnosis between disorders of the schizophrenic field and disorders induced by cannabis. To date, no clinical or even less paraclinical criteria have made it possible to differentiate syndromes whose prognoses and management are different. Since 2010, we measured delta-9 tetrahydrocannabinol (THC) and cannabidiol (CBD) concentrations in head hair among New Caledonian patients, all cannabis consumers (n = 256). We wanted to determine if these patients, cannabis users, suffering from different mental pathologies, present particular phenotypes of capillary cannabinoid concentrations (THC and CBD). At the time of initial psychiatric consultation, a sample of 3 cm proximal length of head hair was prepared for analysis, and THC and CBD were then assayed by Gas Chromatography coupled with Mass Spectrometry (Limit Of Quantitation: 0.05 ng/mg). At the end of the 6 months medico-psychologic follow-up from the initial evaluation, four groups of cannabis users were identified according to the final psychiatric diagnosis: control, acute cannabis psychosis (ACP), chronic psychosis (CP), and other personality disorders (OPD) groups. In this study, a high hair level of THC detected (> 0.7 ng/mg) associated with a low hair CBD/THC ratio (< 0.26) are two parameters that taken together could be good markers of CP development. For OPD and ACP, hair CBD/THC ratios were higher in the ACP group (> 0.43) than in the OPD group (< 0.32). This study highlights, once again, the protective role of CBD against the deleterious effects of THC. In association with clinical evaluation, this toxicological approach could be helpful for psychiatric diagnosis and would allow early management of BPD in cannabis consumers. For a consumer who does not present with a psychiatric disorder, it could give an information about the possibility of belonging to a group of patients at high risk of psychiatric decompensation. This provides an additional argument for efforts to control cannabis consumption by patients.
Expression quantitative trait methylation analysis elucidates gene regulatory effects of DNA methylation: The Framingham Heart Study
Authors: Keshawarz Amena , Bui Helena , Joehanes Roby , Ma Jiantao , Liu Chunyu , Huan Tianxiao , Hwang Shih-Jen , Tejada Brandon , Sooda Meera , Courchesne Paul , Munson Peter J. , Demirkale Cumhur Y. , Yao Chen , Heard-Costa Nancy L. , Pitsillides Achilleas N. , Lin Honghuan , Liu Ching-Ti , Wang Yuxuan , Peloso Gina M. , Lundin Jessica , Haessler Jeffrey , Du Zhaohui , Cho Michael , Hersh Craig P. , Castaldi Peter , Raffield Laura M. , Wen Jia , Li Yun , Reiner Alexander P. , Feolo Mike , Sharopova Nataliya , Vasan Ramachandran S. , Silverman Edwin K. , DeMeo Dawn L. , Carson April P. , Kooperberg Charles , Levy Daniel 
Published: April 2022

BackgroundExpression quantitative trait methylation (eQTM) analysis identifies DNA CpG sites at which methylation is associated with gene expression and may reveal molecular mechanisms of disease. The present study describes an eQTM resource of CpG-transcript pairs.MethodsDNA methylation was measured in blood samples from 1,045 Framingham Heart Study (FHS) participants using the Illumina 450K BeadChip and in 1,070 FHS participants using the Illumina EPIC array. Blood gene expression data were collected from all 2,115 participants using RNA sequencing (RNA-seq). The association between DNA methylation and gene expression was quantified for all cis (i.e., within 1Mb) and trans (>1Mb) CpG-transcript pairs. Significant results (p<1E-7 for cis and <1E-14 for trans) were subsequently tested for enrichment of biological pathways and of clinical traits.ResultsWe identified 70,047 significant cis CpG-transcript pairs where the top most significant eGenes (i.e., gene transcripts associated with a CpG) were enriched in biological pathways related to cell signaling, and for 1,208 clinical traits (enrichment false discovery rate [FDR] ≤ 0.05). We also identified 246,667 significant trans CpG-transcript pairs where the top most significant eGenes were enriched in biological pathways related to activation of the immune response, and for 1,191 clinical traits (enrichment FDR ≤ 0.05). Using significant cis CpG-transcript pairs, we identified significant mediation of the association between CpG sites and cardiometabolic traits through gene expression and identified shared genetic regulation between CpGs and transcripts associated with these cardiometabolic traits.ConclusionsWe developed a robust and powerful resource of eQTM CpG-transcript pairs that can help inform future functional studies that seek to understand the molecular basis of disease.
Parent-reported assessment scores reflect ASD severity in 2- to 7- year-old children
Authors: Jagadeesan Priyanka , Kabbani Adam , Vyshedskiy Andrey 
Published: April 2022

AbstractWe investigated the relationship between parent-reported assessments and autism spectrum disorder (ASD) severity. Parents evaluated 9573 children with ASD on five subscales: combinatorial receptive language, expressive language, sociability, sensory awareness, and health using Autism Treatment Evaluation Checklist (ATEC) and Mental Synthesis Evaluation Checklist (MSEC). Scores in every subscale improved with age and there were clear differences between the three diagnostic categories. The differences between mild and moderate ASD as well as between moderate and severe ASD reached statistical significance in each subscale and in every age group in children 3 years of age and older. These findings demonstrate a consistent relationship between children’s diagnoses and their assessments.
Combined effects of 12-week yoga warm-up on athletic performance in male high school track and field athletes
Authors: Wei Danyang 
Published: April 2022

AbstractBackgroundPracticing yoga could improve balance and flexibility, but its positive significance as a long-term warm-up for formal training was uncertain. We hypothesized that practicing yoga during warm-up might positively affect balance, flexibility, and speed performance in male high school track and field athletes.MethodsOver a 12-week period, athletes in a yoga group (YG) (n=10) practiced yoga for 15 min 4 times a week during warm-up, while athletes in a dynamic stretching group (DSG) (n=10) practiced 15 min of dynamic stretching. Except for the warm-up activities, the training content of the two groups of students was the same. we tested performance indicators immediately before and after the intervention, including lower extremity flexibility test (right hip active flexion range), lower extremity balance test [using surface electromyography (sEMG) to measure right leg tibialis anterior (TA) activation during one-leg stance (OLS) with eyes closed], and speed performance test (100-meter and 800-meter tests).ResultsWe performed between-group and within-group comparisons for indicators of two groups by using SPSS (version 26.0). Within-group comparisons showed a significant improvement in flexibility (P=0.002) and balance (P=0.003) in YG, but no significant change in DSG, after the 12-week intervention. In addition, speed performance of both YG (100m, P=0.026; 800m, P=0.045) and DSG (100m, P=0.029; 800m, P=0.006) was significantly improved. Between-group comparison showed that YG had a significant advantage in 800m (P=0.045) and flexibility (P=0.031).ConclusionsThese data suggested that practicing yoga as a long-term warm-up could help male high school track and field athletes improve lower body flexibility and 800m speed. In addition, yoga had a certain positive effect on balance, but it was not significant overall.
Optimal gap-affine alignment in O(s) space
Authors: Marco-Sola Santiago , Eizenga Jordan M. , Guarracino Andrea , Paten Benedict , Garrison Erik , Moreto Miquel 
Published: April 2022

AbstractMotivationPairwise sequence alignment remains a fundamental problem in computational biology and bioinformatics. Recent advances in genomics and sequencing technologies demand faster and scalable algorithms that can cope with the ever-increasing sequence lengths. Classical pairwise alignment algorithms based on dynamic programming are strongly limited by quadratic requirements in time and memory. The recently proposed wavefront alignment algorithm (WFA) introduced an efficient algorithm to perform exact gap-affine alignment in O(ns) time, where s is the optimal score and n is the sequence length. Notwithstanding these bounds, WFA’s O(s2) memory requirements become computationally impractical for genome-scale alignments, leading to a need for further improvement.ResultsIn this paper, we present the bidirectional WFA algorithm (BiWFA), the first gap-affine algorithm capable of computing optimal alignments in O(s) memory while retaining WFA’s time complexity of O(ns). As a result, this work improves the lowest known memory bound O(n) to compute gap-affine alignments. In practice, our implementation never requires more than a few hundred MBs aligning noisy Oxford Nanopore Technologies reads up to 1 Mbp long while maintaining competitive execution times.AvailabilityAll code is publicly available at https://github.com/smarco/BiWFA-paperContactsantiagomsola@gmail.com
High genetic diversity in the pelagic deep-sea fauna of the Atacama Trench revealed by environmental DNA
Authors: Ramírez-Flandes Salvador , González Carolina E. , Aldunate Montserrat , Poulain Julie , Wincker Patrick , Glud Ronnie N. , Escribano Rubén , Haond Sophie Arnaud , Ulloa Osvaldo 
Published: April 2022

AbstractA current paradigm in marine biodiversity states that faunal richness decreases with depth. However, the deep-ocean ecosystem has been significantly under-sampled, hindering a complete view of its biodiversity. This situation is accentuated in ultra-deep waters, where the remote and extreme conditions unfit the traditional sampling methods. Using environmental DNA, we assessed the pelagic metazoan diversity of the Atacama Trench from the high-productive near-surface level down to ~8000 m depth. Our results show that waters deeper than 4000 m contributed up to 50% of the overall genetic diversity. These findings contrast with similar observations in the less-productive Kermadec Trench, where the diversity in deep waters was lower than in shallower waters. Moreover, both deep pelagic ecosystems exhibited some unknown phylogenetic clades within the dominant taxonomic groups: hydrozoans and copepods. The deep-ocean biota may thus contribute to global biodiversity far more than hitherto suggested, especially in zones influenced by high primary production. Our results underline the need for increased effort to study these remote ecosystems and improve our understanding of their contribution to the ecology and biogeochemistry of the deep-sea pelagic and benthic realms.
Toward Evaluation of Disseminated Effects of Medications for Opioid Use Disorder within Provider-Based Clusters Using Routinely-Collected Health Data
Authors: Buchanan Ashley L. , Sun Tianyu , Wu Jing , Aroke Hilary , Bratberg Jeffrey , Rich Josiah , Kogut Stephen , Hogan Joseph 
Published: April 2022

AbstractRoutinely-collected health data can be employed to emulate a target trial when randomized trial data are not available. Patients within provider-based clusters likely exert and share influence on each other’s treatment preferences and subsequent health outcomes and this is known as dissemination or spillover. Extending a framework to replicate an idealized two-stage randomized trial using routinely-collected health data, an evaluation of disseminated effects within provider-based clusters is possible. In this paper, we propose a novel application of causal inference methods for dissemination to retrospective cohort studies in administrative claims data and evaluate the impact of the normality of the random effects distribution for the cluster-level propensity score on estimation of the causal parameters. An extensive simulation study was conducted to study the robustness of the methods under different distributions of the random effects. We applied these methods to evaluate baseline prescription for medications for opioid use disorder among a cohort of patients diagnosed opioid use disorder and adjust for baseline confounders using information obtained from an administrative claims database. We discuss future research directions in this setting to better address unmeasured confounding in the presence of disseminated effects.
Cell-free Protein Crystallization for Nanocrystal Structure Determination
Authors: Abe Satoshi , Tanaka Junko , Kojima Mariko , Kanamaru Shuji , Hirata Kunio , Yamashita Keitaro , Kobayashi Ayako , Ueno Takafumi 
Published: April 2022

AbstractIn-cell protein crystallization (ICPC) has attracted attention as a next-generation structural biology tool because it does not require multistep purification processes and large-scale crystallization screenings. However, significant issues remain to be solved in context of obtaining various protein crystals in sufficient amounts and quality for structure determination by ICPC. Here, we report the development of cell-free protein crystallization (CFPC), a direct protein crystallization technique which uses cell-free protein synthesis. The most crucial advantages of CFPC are that the reaction scale and time can be minimized and that various reagents can be added during the reaction. We obtained high-quality nano-sized polyhedra crystals, which are produced in insect cells by infection with cytoplasmic polyhedrosis virus, at a 200 μL reaction scale within 6 h. We applied this technology to structure determination of crystalline inclusion protein A (CipA) by suppressing twin crystal formation with addition of an inhibitor to the reaction solution. We succeeded in determining a 2.11 Å resolution structure from the nanocrystals of CipA. This technology, which integrates in-cell and in vitro crystallizations significantly expands the tools available for high throughput protein structure determination, particularly in context of unstable, low-yield, or substrate-binding proteins, which are difficult to analyze by conventional methods.
Impact of sequencing technologies on long non-coding RNA computational identification
Authors: Chiquitto Alisson G. , Silva Lucas Otávio L. , Oliveira Liliane Santana , Domingues Douglas S. , Paschoal Alexandre R. 
Published: April 2022

AbstractThe correct annotation of non-coding RNAs, especially long non-coding RNAs (lncRNAs), is still an important critial challenge in genome analyses. One crucial issue in lncRNA transcript annotation is the transcriptome resource that supports lncRNA loci. Long-read technologies now bring the potential to improve the quality of transcriptome annotation. Consequently, long non-coding RNAs (lncRNA) are probably the most benefited class of transcripts that would have improved annotation using this novel technology. However, there is a gap regarding benchmarking studies that highlighted if the direct use of lncRNA predictors in long-reads makes more precise identification of these transcripts. Considering that these lncRNA tools were not trained with these reads, we want to address: how is the performance of these tools? Are they also able to efficiently identify lncRNAs? We could provide evidence of where and how to make potential better approaches for the lncRNA annotation by understanding these issues. Keywords: Non-coding RNAs, high-throughput sequencing technologies, coding, methods, benchmarking, tools, NGS, transcripts
Rye: genetic ancestry inference at biobank scale
Authors: Conley Andrew B. , Rishishwar Lavanya , Ahmad Maria , Sharma Shivam , Norris Emily T. , Jordan I. King , Mariño-Ramírez Leonardo 
Published: April 2022

ABSTRACTBiobank projects around the world are generating genomic data for many thousands and even millions of individuals. Computational methods are needed to handle these massive data sets, including tools for genetic ancestry (GA) inference. Current methods for GA inference are generally accurate, but they are slow and do not scale to biobank-size genomic datasets. Here we present Rye – a new algorithm for GA inference at biobank scale. We compare the accuracy and runtime performance of Rye to the widely used RFMix and ADMIXTURE programs, and we apply it to a dataset of 488,221 genome-wide variant samples from the UK Biobank. Rye infers GA based on principal component analysis (PCA) of genomic variant samples from ancestral reference populations and query individuals. The algorithm’s accuracy is powered by Metropolis-Hastings optimization and its speed is provided by non-negative least squares (NNLS) regression. Rye produces highly accurate GA estimates for three-way admixed populations – African, European, and Native American – compared to RFMix and ADMIXTURE (R2 = 0.998 – 1.00), and shows 50x runtime improvement compared to ADMIXTURE on the UK Biobank dataset. Rye analysis of UK Biobank samples demonstrates how it can be used to infer GA at different levels of relatedness. We discuss user consideration and options for the use of Rye; the program and its documentation are distributed on the GitHub repository: https://github.com/healthdisparities/rye.
A revised calcium-dependent model of theta-burst transcranial magnetic stimulation
Authors: Ma K. , Rothwell J. C. , Goetz S. M. 
Published: April 2022

AbstractCalcium dependency is presently an essential assumption in modelling the neuromodulatory effects of transcranial magnetic stimulation (TMS). Among the various neuromodulatory TMS protocols, theta-burst stimulation (TBS) at present is the fastest intervention to generate strong effects. A decade ago, Y.Z. Huang et al. developed a first neuromodulation model to explain the bidirectional effects of TBS based on postsynaptic intracellular calcium concentration elevation. We discover, however, that the published computer code is not consistent with the model formulations in the corresponding paper. Further analysis confirms that the computer model with an index confusion was used for fitting the experimental results, running the simulation, and plotting the corresponding figures in the original publication. This paper intends to fix the computer code and additionally create a non-convex optimisation solution for re-calibrating the model. After re-calibration, the revised model outperforms the initial model in accuracy describing the MEP amplitudes of TBS-induced after-effects under specific situations.
Prostaglandin EP3 receptor-expressing preoptic neurons bidirectionally control body temperature via tonic GABAergic signaling
Authors: Nakamura Yoshiko , Yahiro Takaki , Kataoka Naoya , Hioki Hiroyuki , Nakamura Kazuhiro 
Published: April 2022

SUMMARYThe circuit mechanism of the thermoregulatory center in the preoptic area (POA) is unknown. Using rats, here we show prostaglandin EP3 receptor-expressing POA neurons (POAEP3R neurons) as a pivotal bidirectional controller in the central thermoregulatory mechanism. POAEP3R neurons are activated in response to elevated ambient temperature, but inhibited by prostaglandin E2, a pyrogenic mediator. Chemogenetic stimulation of POAEP3R neurons at room temperature reduces body temperature by enhancing heat dissipation, whereas inhibition of them elicits hyperthermia involving brown fat thermogenesis, mimicking fever. POAEP3R neurons innervate sympathoexcitatory neurons in the dorsomedial hypothalamus (DMH) via tonic inhibitory signaling. Although many POAEP3R neuronal cell bodies express a glutamatergic mRNA marker, paradoxically, their axons in the DMH predominantly contain terminals with GABAergic presynaptic proteins, which are increased by chronic heat exposure. These findings indicate that tonic GABAergic inhibitory signaling from POAEP3R neurons is a fundamental determinant of body temperature for thermal homeostasis and fever.
Phylogenomic patterns of divergence and gene flow detail the evolution of reinforcement and hybrid speciation inPhloxwildflowers
Authors: Garner Austin G. , Goulet-Scott Benjamin E. , Hopkins Robin 
Published: April 2022

SummaryThe tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standingPhlox, appear to be hotspots of hybridization. In this group there are two cases of reinforcement and nine hypothesized hybrid species. Given the historical importance of this group for our understanding of plant speciation, the relationships of these taxa and the role of hybridization and gene flow in their diversification require genomic validation.Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standingPhloxand test hypotheses about if and how hybridization and gene flow were creative forces in their diversification.Our results provide novel resolution of the phylogenetic relationships in this group, including well-supported paraphyly across some species. We identify gene flow during one of two cases of reinforcement and find support for one of the five hypothesized homoploid hybrid speciation events. Additionally, we infer the ancestries of four allotetraploid hybrid species.Hybridization has contributed to diverse evolutionary outcomes within thisPhloxgroup; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in confirming hypothesized histories of non-model systems and adds to the growing evidence of interspecific genetic exchange in the generation of biodiversity.