bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting Parkinson’s disease and its cognitive phenotypes via automated semantic analyses of action stories
Authors: García Adolfo M. , Escobar-Grisales Daniel , Vásquez Correa Juan Camilo , Bocanegra Yamile , Moreno Leonardo , Carmona Jairo , Orozco-Arroyave Juan Rafael 
Published: November 2022

AbstractAction-concept outcomes are useful targets to identify Parkinson’s disease (PD) patients and differentiate between those with and without mild cognitive impairment (PD-MCI, PD-nMCI). Yet, most approaches employ burdensome examiner-dependent tasks, limiting their utility. We introduce a framework capturing action-concept markers automatically in natural speech. Patients from both subgroups and controls retold an action-laden and a non-action-laden text (AT, nAT). In each retelling, we weighed action and non-action concepts through our automated Proximity-to-Reference-Semantic-Field (P-RSF) metric, for analysis via ANCOVAs (controlling for cognitive dysfunction) and support vector machines. Patients were differentiated from controls based on AT (but not nAT) P-RSF scores. The same occurred in PD-nMCI patients. Conversely, PD-MCI patients exhibited reduced P-RSF scores for both texts. Direct discrimination between patient subgroups was not systematic, but it yielded best outcomes via AT scores. Our approach outperformed classifiers based on corpus-derived embeddings. This framework opens scalable avenues to support PD diagnosis and phenotyping.
Functional analysis of structural variants in single cells using Strand-seq
Authors: Jeong Hyobin , Grimes Karen , Rauwolf Kerstin K. , Bruch Peter-Martin , Rausch Tobias , Hasenfeld Patrick , Benito Eva , Roider Tobias , Sabarinathan Radhakrishnan , Porubsky David , Herbst Sophie A. , Erarslan-Uysal Büşra , Jann Johann-Christoph , Marschall Tobias , Nowak Daniel , Bourquin Jean-Pierre , Kulozik Andreas E. , Dietrich Sascha , Bornhauser Beat , Sanders Ashley D. , Korbel Jan O. 
Published: November 2022

AbstractSomatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations.
Year-round trace gas measurements in the central Arctic during the MOSAiC expedition
Authors: Angot Hélène , Blomquist Byron , Howard Dean , Archer Stephen , Bariteau Ludovic , Beck Ivo , Boyer Matthew , Crotwell Molly , Helmig Detlev , Hueber Jacques , Jacobi Hans-Werner , Jokinen Tuija , Kulmala Markku , Lan Xin , Laurila Tiia , Madronich Monica , Neff Donald , Petäjä Tuukka , Posman Kevin , Quéléver Lauriane , Shupe Matthew D. , Vimont Isaac , Schmale Julia 
Published: November 2022

AbstractDespite the key role of the Arctic in the global Earth system, year-round in-situ atmospheric composition observations within the Arctic are sparse and mostly rely on measurements at ground-based coastal stations. Measurements of a suite of in-situ trace gases were performed in the central Arctic during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition. These observations give a comprehensive picture of year-round near-surface atmospheric abundances of key greenhouse and trace gases, i.e., carbon dioxide, methane, nitrous oxide, ozone, carbon monoxide, dimethylsulfide, sulfur dioxide, elemental mercury, and selected volatile organic compounds (VOCs). Redundancy in certain measurements supported continuity and permitted cross-evaluation and validation of the data. This paper gives an overview of the trace gas measurements conducted during MOSAiC and highlights the high quality of the monitoring activities. In addition, in the case of redundant measurements, merged datasets are provided and recommended for further use by the scientific community.
TractoInferno - A large-scale, open-source, multi-site database for machine learning dMRI tractography
Authors: Poulin Philippe , Theaud Guillaume , Rheault Francois , St-Onge Etienne , Bore Arnaud , Renauld Emmanuelle , de Beaumont Louis , Guay Samuel , Jodoin Pierre-Marc , Descoteaux Maxime 
Published: November 2022

AbstractTractoInferno is the world’s largest open-source multi-site tractography database, including both research- and clinical-like human acquisitions, aimed specifically at machine learning tractography approaches and related ML algorithms. It provides 284 samples acquired from 3 T scanners across 6 different sites. Available data includes T1-weighted images, single-shell diffusion MRI (dMRI) acquisitions, spherical harmonics fitted to the dMRI signal, fiber ODFs, and reference streamlines for 30 delineated bundles generated using 4 tractography algorithms, as well as masks needed to run tractography algorithms. Manual quality control was additionally performed at multiple steps of the pipeline. We showcase TractoInferno by benchmarking the learn2track algorithm and 5 variations of the same recurrent neural network architecture. Creating the TractoInferno database required approximately 20,000 CPU-hours of processing power, 200 man-hours of manual QC, 3,000 GPU-hours of training baseline models, and 4 Tb of storage, to produce a final database of 350 Gb. By providing a standardized training dataset and evaluation protocol, TractoInferno is an excellent tool to address common issues in machine learning tractography.
Biochemical characterization of Dimocarpus longan polyphenol oxidase provides insights into its catalytic efficiency
Authors: Ruckthong Leela , Pretzler Matthias , Kampatsikas Ioannis , Rompel Annette 
Published: November 2022

AbstractThe “dragon-eye” fruits produced by the tropical longan tree are rich in nutrients and antioxidants. They suffer from post-harvest enzymatic browning, a process for which mainly the polyphenol oxidase (PPO) family of enzymes is responsible. In this study, two cDNAs encoding the PPO have been cloned from leaves of Dimocarpus longan (Dl), heterologously expressed in Escherichia coli and purified by affinity chromatography. The prepro-DlPPO1 contains two signal peptides at its N-terminal end that facilitate transportation of the protein into the chloroplast stroma and to the thylakoid lumen. Removal of the two signal peptides from prepro-DlPPO1 yields pro-DlPPO1. The prepro-DlPPO1 exhibited higher thermal tolerance than pro-DlPPO1 (unfolding at 65 °C vs. 40 °C), suggesting that the signal peptide may stabilize the fold of DlPPO1. DlPPO1 can be classified as a tyrosinase because it accepts both monophenolic and diphenolic substrates. The pro-DlPPO1 exhibited the highest specificity towards the natural diphenol (–)-epicatechin (kcat/KM of 800 ± 120 s−1 mM−1), which is higher than for 4-methylcatechol (590 ± 99 s−1 mM−1), pyrogallol (70 ± 9.7 s−1 mM−1) and caffeic acid (4.3 ± 0.72 s−1 mM−1). The kinetic efficiencies of prepro-DlPPO1 are 23, 36, 1.7 and 4.7-fold lower, respectively, than those observed with pro-DlPPO1 for the four aforementioned diphenolic substrates. Additionally, docking studies showed that (–)-epicatechin has a lower binding energy than any other investigated substrate. Both kinetic and in-silico studies strongly suggest that (–)-epicatechin is a good substrate of DlPPO1 and ascertain the affinity of PPOs towards specific flavonoid compounds.
Slowing down x-ray photons in a vibrating recoilless resonant absorber
Authors: Khairulin I. R. , Radeonychev Y. V. , Kocharovskaya Olga 
Published: November 2022

AbstractRecently, an observation of acoustically induced transparency (AIT) of a stainless-steel foil for resonant 14.4-keV photons from a radioactive 57Co Mössbauer source due to collective uniform oscillations of atomic nuclei was reported [Phys Rev Lett 124,163602, 2020]. In this paper, we propose to use the steep resonant dispersion of the absorber within the AIT spectral window to dramatically reduce a propagation velocity of γ-ray and x-ray photons. In particular, we show that a significant fraction (more than 40%) of a 97-ns γ-ray single-photon wave packet from a 57Co radioactive source can be slowed down up to 3 m/s and delayed by 144 ns in a 57Fe-enriched stainless-steel foil at room temperature. We also show that a similarly significant slowing down up to 24 m/s and a delay by 42 ns can be achieved for more than 70% of the 100-ns 14.4-keV x-ray single-photon pulse from a synchrotron Mössbauer source available at European Synchrotron Radiation Facility (ESRF) and Spring-8 facility. The propagation velocity can be widely controlled by changing the absorber vibration frequency. Achieving the propagation velocity on the order of 1–50 m/s would set a record in the hard x-ray range, comparable to what was obtained in the optical range.
Tobacco use and risk of COVID-19 infection in the Finnish general population
Authors: Peña Sebastián , Ilmarinen Katja , Kestilä Laura , Parikka Suvi , Kärkkäinen Sanna , Caspersen Ida Henriette , Shaaban Ahmed Nabil , Magnus Per , Galanti Maria Rosaria , Karvonen Sakari 
Published: November 2022

AbstractEmpirical evidence, primarily based on hospital-based or voluntary samples, suggests that current smokers have a lower risk of COVID-19 infection than never smokers. In this study, we used nationally representative data to examine the association between tobacco use and the risk of having a confirmed COVID-19 case. We explored several forms of tobacco use, contributing to separate the role of nicotine from smoking. We used data from 44,199 participants from three pooled national health surveys in Finland (FinSote 2018–2020). The primary outcome was a confirmed COVID-19 case. We examined current smoking, moist smokeless tobacco (snus), e-cigarettes with and without nicotine and nicotine replacement therapy products. Current daily smokers had a relative risk of 1.12 of a confirmed COVID-19 case (95% CI 0.65; 1.94) in fully adjusted models compared with never smokers. Current snus use was associated with a 68% higher risk of a confirmed COVID-19 case (RR 1.68, 95% CI 1.02; 2.75) than never users. We did not find conclusive evidence of associations between e-cigarettes with and without nicotine and nicotine replacement therapy products and the risk of confirmed COVID-19 cases. Our findings suggest that nicotine might not have a protective role in the risk of COVID-19 as previously hypothesized.
The mu opioid receptor and the orphan receptor GPR151 contribute to social reward in the habenula
Authors: Allain Florence , Carter Michelle , Dumas Sylvie , Darcq Emmanuel , Kieffer Brigitte L. 
Published: November 2022

AbstractThe mu opioid receptor (MOR) and the orphan GPR151 receptor are inhibitory G protein coupled receptors that are enriched in the habenula, a small brain region involved in aversion processing, addiction and mood disorders. While MOR expression in the brain is widespread, GPR151 expression is restricted to the habenula. In a previous report, we created conditional ChrnB4-Cre × Oprm1fl/fl (so-called B4MOR) mice, where MORs are deleted specifically in Chrnb4-positive neurons restricted to the habenula, and shown a role for these receptors in naloxone aversion. Here we characterized the implication of habenular MORs in social behaviors. B4MOR−/− mice and B4MOR+/+ mice were compared in several social behavior measures, including the chronic social stress defeat (CSDS) paradigm, the social preference (SP) test and social conditioned place preference (sCPP). In the CSDS, B4MOR−/− mice showed lower preference for the social target (unfamiliar mouse of a different strain) at baseline, providing a first indication of deficient social interactions in mice lacking habenular MORs. In the SP test, B4MOR−/− mice further showed reduced sociability for an unfamiliar conspecific mouse. In the sCPP, B4MOR−/− mice also showed impaired place preference for their previous familiar littermates after social isolation. We next created and tested Gpr151−/− mice in the SP test, and also found reduced social preference compared to Gpr151+/+ mice. Altogether our results support the underexplored notion that the habenula regulates social behaviors. Also, our data suggest that the inhibitory habenular MOR and GPR151 receptors normally promote social reward, possibly by dampening the aversive habenula activity.
The adaptive significance of human scleral brightness: an experimental study
Authors: Wacewicz Slawomir , Perea-García Juan Olvido , Lewandowski Zdzisław , Danel Dariusz P. 
Published: November 2022

AbstractHomogeneously depigmented sclerae have long been proposed to be uniquely human—an adaptation to enable cooperative behaviour by facilitating interpersonal coordination through gaze following. However, recent evidence has shown that deeply pigmented sclerae also afford gaze following if surrounding a bright iris. Furthermore, while current scleral depigmentation is clearly adaptive in modern humans, it is less clear how the evolutionarily intermediate stages of scleral pigmentation may have been adaptive. In sum, it is unclear why scleral depigmentation became the norm in humans, while not so in sister species like chimpanzees, or why some extant species display intermediate degrees of pigmentation (as our ancestors presumably did at some point). We created realistic facial images of 20 individually distinct hominins with diverse facial morphologies, each face in the (i) humanlike bright sclera and (ii) generalised apelike dark sclera version. Participants in two online studies rated the bright-sclera hominins as younger, healthier, more attractive and trustworthy, but less aggressive than the dark-sclera hominins. Our results support the idea that the appearance of more depigmented sclerae promoted perceived traits that fostered trust, increasing fitness for those individuals and resulting in depigmentation as a fixed trait in extant humans.
Preparation of a cellulose acetate membrane using cigarette butt recycling and investigation of its efficiency in removing heavy metals from aqueous solution
Authors: Torkashvand Javad , Saeedi-Jurkuyeh Alireza , Rezaei Kalantary Roshanak , Gholami Mitra , Esrafili Ali , Yousefi Mahmood , Farzadkia Mahdi 
Published: November 2022

AbstractThis study investigated the recycling of freshly-smoked cigarette butts (FCBs) and unsmoked cigarette filters (UCFs) into a cellulose acetate (CA) membrane. The both samples were prepared by means of a combination of seven cigarette brands, and the phase inversion method was used to recycle each sample into a membrane using N-methyl-2-pyrrolidone. The efficiency of the prepared membranes for the removal of chromium, cadmium, and lead from an aqueous solution in a forward osmosis reactor was investigated. The results showed that the both membranes had a smooth surface and macrovoids. The flux of the prepared membranes from the UCFs and FCBs recycling were 14.8 and 13.2 LMH, respectively. The porosity and reverse salt of the UCFs membrane were 61% and 3.5 gMH, while those for FCBs membrane were 58% and 3.9 gMH. The observed metal removal efficiency of the both membranes was in the range of 85 to 90%. However, increasing the concentration of metals up to five times caused a slight decrease in the removal efficiency (less than 5%).
In vitro model of predicting metastatic ability using tumor derived extracellular vesicles; beyond seed soil hypothesis
Authors: Bhadresha Kinjal , Upadhyay Vinal , Brahmbhatt Jpan , Mughal Muhammad Jameel , Jain Nayan , Rawal Rakesh 
Published: November 2022

AbstractLung cancer progression is often driven by metastasis, which has resulted in a considerable increase in lung cancer-related deaths. Cell-derived extracellular vesicles (EVs), particularly exosomes, serve key roles in cellular signal transmission via microenvironment, however, their biological relevance in cancer development and metastasis still needs to be clear. Here, we demonstrate that extracellular vesicles (EVs) derived from lung cancer bone metastatic patients exhibited a great capacity to promote the progression of lung cancer cells. We carried out a comprehensive meta-analysis to identify the gene expression profile of bone metastases using publicly available microarray datasets. Furthermore, mRNA expression of six identified genes was quantified by real time PCR in lung cancer with and without bone metastasis and healthy individual derived EVs. In addition, we utilized a very novel approach by to study how lung cancer cells uptake EVs by co-culturing EVs with lung cells. We observed that EVs obtained from bone metastases patients were efficiently ingested by lung cancer cells. Morevore, integration and uptake of these EVs lead to increased lung cancer cell proliferation, migration, invasion, and sphere formation. We discovered that EV uptake increase the expression of SPP1, CD44, and POSTN genes in lung cancer cells. The data obtained from this study, support to the possibility that circulating EVs play a significant role in the formation of the pre-metastatic niche, eventually leading to metastasis.
Nuclear factor (erythroid-derived 2)-like 2 counter-regulates thymosin beta-4 expression and primary cilium formation for HeLa cervical cancer cell survival
Authors: Lee Jae-Wook , Thuy Pham Xuan , Koo Ja Hyun , Moon Eun-Yi 
Published: November 2022

AbstractWe investigated the function of thymosin beta-4 (TB4) expression and primary cilium (PC) formation via the underlying Nrf2-dependent mechanism for cervical cancer cell (CC) survival under conditions of serum deprivation (SD). TB4 silencing was achieved using RNA interference. The percentage of PC formation was analyzed by immunofluorescence staining. Nrf2 expression was modified by the preparation of stable Nrf2-knockdown cells with shNrf2 and the overexpression of Nrf2 with pcDNA-Nrf2 plasmids. Gene expression was measured using reverse-transcription PCR, Gaussia luciferase assay, and western blotting. Cell viability was assessed using the MTT assay or CellTiter Glo assay. Reactive oxygen species (ROS) were detected with flow cytometry. CCs incubated in SD without fetal bovine serum remained viable, and SD increased PC formation and TB4 transcription. CC viability was further decreased by treatment with ciliobrevin A to inhibit PC formation or TB4-siRNA. SD increased ROS, including H2O2. N-acetylcysteine inhibited ROS production following H2O2 treatment or SD, which also decreased PC formation and TB4 transcription. Meanwhile, H2O2 increased PC formation, which was attenuated in response to TB4 siRNA. Treatment with H2O2 increased Nrf2 expression, antioxidant responsive element (ARE) activity, and PC formation, which were inhibited by the Nrf2 inhibitor clobestasol propionate. Nrf2 knockdown via expression of Tet-On shNrf2 enhanced ROS production, leading to increased PC formation and decreased TB4 expression; these effects were counteracted by Nrf2 overexpression. Our data demonstrate that Nrf2 counter-regulates TB4 expression and PC formation for CC survival under conditions of SD, suggesting cervical CC survival could be upregulated by PC formation via Nrf2 activation and TB4 expression.
Whole genome DNA and RNA sequencing of whole blood elucidates the genetic architecture of gene expression underlying a wide range of diseases
Authors: Liu Chunyu , Joehanes Roby , Ma Jiantao , Wang Yuxuan , Sun Xianbang , Keshawarz Amena , Sooda Meera , Huan Tianxiao , Hwang Shih-Jen , Bui Helena , Tejada Brandon , Munson Peter J. , Demirkale Cumhur Y. , Heard-Costa Nancy L. , Pitsillides Achilleas N. , Peloso Gina M. , Feolo Michael , Sharopova Nataliya , Vasan Ramachandran S. , Levy Daniel 
Published: November 2022

AbstractTo create a scientific resource of expression quantitative trail loci (eQTL), we conducted a genome-wide association study (GWAS) using genotypes obtained from whole genome sequencing (WGS) of DNA and gene expression levels from RNA sequencing (RNA-seq) of whole blood in 2622 participants in Framingham Heart Study. We identified 6,778,286 cis-eQTL variant-gene transcript (eGene) pairs at p < 5 × 10–8 (2,855,111 unique cis-eQTL variants and 15,982 unique eGenes) and 1,469,754 trans-eQTL variant-eGene pairs at p < 1e−12 (526,056 unique trans-eQTL variants and 7233 unique eGenes). In addition, 442,379 cis-eQTL variants were associated with expression of 1518 long non-protein coding RNAs (lncRNAs). Gene Ontology (GO) analyses revealed that the top GO terms for cis-eGenes are enriched for immune functions (FDR < 0.05). The cis-eQTL variants are enriched for SNPs reported to be associated with 815 traits in prior GWAS, including cardiovascular disease risk factors. As proof of concept, we used this eQTL resource in conjunction with genetic variants from public GWAS databases in causal inference testing (e.g., COVID-19 severity). After Bonferroni correction, Mendelian randomization analyses identified putative causal associations of 60 eGenes with systolic blood pressure, 13 genes with coronary artery disease, and seven genes with COVID-19 severity. This study created a comprehensive eQTL resource via BioData Catalyst that will be made available to the scientific community. This will advance understanding of the genetic architecture of gene expression underlying a wide range of diseases.