bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database
Authors: Zelenova Maria , Ivanova Anna , Semyonov Semyon , Gankin Yuriy 
Published: August 2021

AbstractBackgroundThe 31st of December 2019 was when the World Health Organization received a report about an outbreak of pneumonia of unknown etiology in the Chinese city of Wuhan. The outbreak was the result of the novel virus labeled as SARS-CoV-2, which spread to about 220 countries and caused approximately 3,311,780 deaths, infecting more than 159,319,384 people by May 12th, of 2021. The virus caused a worldwide pandemic leading to panic, quarantines, and lockdowns – although none of its predecessors from the coronavirus family have ever achieved such a scale. The key to understanding the global success of SARS-CoV-2 is hidden in its genome.Materials and MethodsWe retrieved data for 329,942 SARS-CoV-2 records uploaded to the GISAID database from the beginning of the pandemic until the 8th of January 2021. To process the data, a Python variant detection script was developed, using pairwise2 from the BioPython library. Pandas, Matplotlib, and Seaborn, were applied to visualize the data. Genomic coordinates were obtained from the UCSC Genome Browser (https://genome.ucsc.edu/). Sequence alignments were performed for every gene separately. Genomes less than 26,000 nucleotides long were excluded from the research. Clustering was performed using HDBScan.ResultsHere, we addressed the genetic variability of SARS-CoV-2 using 329,942 worldwide samples. The analysis yielded 155 genome variations (SNPs and deletions) in more than 0.3% of the sequences. Nine common SNPs were present in more than 20% of the samples. Clustering results suggested that a proportion of people (2.46%) were infected with a distinct subtype of the B.1.1.7 variant. The subtype may be characterized by four to six additional mutations, with four being a more frequent option (G28881A, G28882A, and G28883С in the N gene, A23403G in S, A28095T in ORF8, G25437T in ORF3a). Two clusters were formed by mutations in the samples uploaded predominantly by Denmark and Australia, which may indicate the emergence of “Danish” and “Australian” variants. Five clusters were linked to increased/decreased age, shifted gender ratio, or both. According to a correlation coefficient matrix, 69 mutations correlate with at least one other mutation (correlation coefficient greater than 0.7). We also addressed the completeness of the GISAID database, where between 77% and 93% of the fields were either left blank or filled incorrectly. Metadata mining analysis has led to a hypothesis about gender inequality in medical care in certain countries. Finally, we found ORF6 and E as the most conserved genes (96.15% and 94.66% of the sequences totally match the reference, respectively), making them potential targets for vaccines and treatment. Our results indicate areas of the SARS-CoV-2 genome that researchers can focus on for further structural and functional analysis.
Probing the stability of the SpCas9-DNA complex after cleavage
Authors: Aldag Pierre , Welzel Fabian , Jakob Leonhard , Schmidbauer Andreas , Rutkauskas Marius , Fettes Fergus , Grohmann Dina , Seidel Ralf 
Published: August 2021

ABSTRACTCRISPR-Cas9 is a ribonucleoprotein complex that sequence-specifically binds and cleaves double-stranded DNA. Wildtype Cas9 as well as its nickase and cleavage-incompetent mutants have been used in various biological techniques due to their versatility and programmable specificity. Cas9 has been shown to bind very stably to DNA even after cleavage of the individual DNA strands, inhibiting further turnovers and considerably slowing down in-vivo repair processes. This poses an obstacle in genome editing applications. Here, we employed single-molecule magnetic tweezers to investigate the binding stability of different S. pyogenes Cas9 variants after cleavage by challenging them with supercoiling. We find that different release mechanisms occur depending on which DNA strand is cleaved. After non-target strand cleavage, supercoils are immediately but slowly released by swiveling of the non-target strand around the DNA with friction. Consequently, Cas9 and its non-target strand nicking mutant stay stably bound to the DNA for many hours even at elevated torsional stress. After target-strand cleavage, supercoils are only removed after the collapse of the R-loop. We identified several states with different stabilities of the R-loop. Most importantly, we find that the post-cleavage state of Cas9 exhibits a higher stability compared to the pre-cleavage state. This suggests that Cas9 has evolved to remain tightly bound to its cut target.
Dataset on Emotion with Naturalistic Stimuli (DENS) on Indian Samples
Authors: Mishra Sudhakar , Asif Mohammad , Srinivasan Narayanan , Tiwary Uma Shanker 
Published: August 2021

ABSTRACTEmotions are constructed and emerge through the dynamic interaction of multiple components. It is difficult to capture the dynamics using static or artificial stimuli. Hence, there is a need for an experiment paradigm using ecologically valid film stimuli. The data set described in this work results from an attempt to capture felt emotional experience at a particular point in time using physiological measures like EEG, ECG and EMG as well as self-reported scales. Sixteen emotional film stimuli were used from the film stimuli dataset validated in the Indian population. Participants self-reported the felt emotional category. Both the raw and pre-processed data are provided along with the pre-processing pipeline. The paradigm we have adopted is new which we have termed as Emotional Event Marker Paradigm (EEMP). Hence, the dataset has unique information about temporal markers of emotional experiences while watching the film stimuli, which is not available with any data to date. It is the first EEG data with emotional film stimuli on the Indian population. This data can be utilized to study dynamic activation and connectivity in a whole-brain source localization study, understand the mutual interactions between the central and autonomic nervous system, understand temporal hierarchy using multi-resolution tools, and perform machine learning-based classification and complex networks analysis associated with emotions.
AATF/Che-1, a new component of paraspeckles, controls R-loops formation and Interferon activation in Multiple Myeloma
Authors: Bruno Tiziana , Corleone Giacomo , Cortile Clelia , Nicola Francesca De , Catena Valeria , Fabretti Francesca , Gumenyuk Svitlana , Pisani Francesco , Mengarelli Andrea , Passananti Claudio , Fanciulli Maurizio 
Published: August 2021

AbstractMultiple myeloma (MM) is a hematological neoplasm of plasma cells characterized by abnormal production of immunoglobulins. Che-1/AATF (Che-1) is an RNA binding protein involved in transcription regulation and is highly expressed in this malignancy. Here we experimentally show that Che-1 interacts with paraspeckle components, including the lncRNA NEAT1_2 (NEAT1), which serves as the seed for the maintenance of these structures. Che-1 and NEAT1 localize on R-loops, three-stranded RNA:DNA hybrids structures involved in DNA transcription and repair. Depletion of Che-1 produces a marked accumulation of RNA:DNA hybrids sustaining activation of a systemic inflammatory response. We provide evidence that high levels of Unfolded Protein Response (UPR) in MM cells induces RNA:DNA hybrids and an interferon (IFN) gene signature. We found that MM patients exhibit elevated R-loops levels and paraspeckle genes mRNAs increase linearly to MM progression. Strikingly, patients showing elevated IFN genes signature are associated with a marked poor prognosis. Overall, these findings delineate that elevated R-loops accumulation and inflammatory signaling may contribute to MM progression and that Che-1/NEAT1 plays an essential role in maintaining R-loops homeostasis by preventing excessive inflammatory signaling.
Perturbation of transmembrane 6 superfamily member 2 expression alters lipid metabolism in a human liver cell line
Authors: Pant Asmita , Chen Yue , Kuppa Annapurna , Du Xiaomeng , Halligan Brian D , Speliotes Elizabeth K 
Published: August 2021

AbstractBackgroundNonalcoholic fatty liver disease (NAFLD) is caused by accumulation of excess lipids in hepatocytes. Genome wide association studies have identified strong association of NAFLD with non-synonymous E167K amino acid mutation in transmembrane 6 superfamily member 2 (TM6SF2) protein. The E167K mutation affects TM6SF2 stability and its carriers display increased hepatic lipids levels and lower serum triglycerides. While similar phenotype is evident in mice with TM6SF2 knockdown, effects of TM6SF2 on hepatic lipid metabolism is not completely understood.MethodsHere, we overexpressed wild-type or E167K variant of TM6SF2 or knocked down TM6SF2 expression in lipid-treated Huh-7 cells and used biochemical assays, untargeted lipidomic analysis, RNAseq transcriptome analysis and high-throughput fluorescent imaging to determine changes in lipid metabolism.ResultsBoth knockdown and E167K overexpression increased acylglyceride levels which was decreased by wild-type TM6SF2 overexpression. Further, mean intensity of individual lipid droplets was increased by E167K overexpression and knockdown while wild-type TM6SF2 had no effects. We also observed lipid chain remodeling for acylglycerides by TM6SF2 knockdown leading to a relative increase in species with shorter and more saturated side chains. RNA sequencing revealed differential expression of several lipid metabolizing genes, including genes belonging to AKR1 family and lipases, primarily in cells with TM6SF2 knockdown.ConclusionTaken together, our data shows that overexpression of TM6SF2 gene or its loss-of-function changes hepatic lipid species composition and expression of lipid metabolizing genes. Further, overexpression of E167K variant and TM6SF2 knockdown similarly increased hepatic lipid accumulation and lipid droplets profile further confirming a loss-of-function effect for variant.
A Self-Limiting Circuit Regulates Mammary Cap Cell Plasticity Through TGF-beta Signaling
Authors: Le Guelte Armelle , Macara Ian G. 
Published: August 2021

SUMMARYThe organization and maintenance of complex tissues requires emergent properties driven by self-organizing and self-limiting cell-cell interactions. We examined these interactions in the murine mammary gland. Luminal and myoepithelial subpopulations of the postnatal mammary gland arise from unipotent progenitors, but the destiny of cap cells, which enclose terminal end buds (TEB) in pubertal mice, remains controversial. Using a transgenic strain (Tg11.5kb-GFP) that specifically marks cap cells, we found ~50% of these cells undergo divisions perpendicular to the TEB surface, suggesting they might contribute to the underlying luminal cell population. To address their stemness potential we developed a lineage tracing mouse driven from the s-SHIP (11.5 kb) promoter. Induction of tdTomato (tdTom) from this promoter in vivo demonstrated that all cap cell progeny are myoepithelial, with no conversion to luminal lineage. Organoid cultures also exhibited unipotency. However, isolated cap cells cultured as mammospheres generated mixed luminal/myoepithelial spheres. Moreover, ablation of luminal cells in vivo using diphtheria toxin triggered repopulation by progeny of tdTom+ cap cells. A signaling inhibitor screen identified the TGFβ pathway as a potential regulator of multipotency. TGFβR inhibitors or gene deletion blocked conversion to the luminal lineage, consistent with an autocrine loop in which cap cells secrete TGFβ to activate the receptor and promote luminal transdifferentiation. Ductal tree regeneration in vivo from isolated cap cells was much more efficient when they were pre-treated with inhibitor, consistent with more cells retaining cap cell potential prior to transplantation. Notably, in vitro transdifferentiation of cap cells was blocked by co-culture with luminal cells. Overall, these data reveal a self-limiting cell circuit through which mammary luminal cells suppress cap cell conversion to the luminal lineage.
Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling
Authors: Rossi Federico , Crnjar Alessandro , Comitani Federico , Feliciano Rodrigo , Jahn Leonie , Malim George , Southgate Laura , Kay Emily , Oakey Rebecca , Buggs Richard , Moir Andy , Kistler Logan , Mateos Ana Rodriguez , Molteni Carla , Schulz Reiner 
Published: August 2021

AbstractTree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus spp.) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.
IMMMUNE MEDIATORS IN IDIOPATHIC UVEITIS
Authors: Errera Marie-Hélène , Pratas Ana , Fisson Sylvain , Manicom Thomas , Boubaya Marouane , Sedira Neila , Héron Emmanuel , Merabet Lilia , Kobal Alfred , Levy Vincent , Warnet Jean-Michel , Chaumeil Christine , Brignole-Baudouin Françoise , Sahel José-Alain , Goldschmidt Pablo , Bodaghi Bahram , Bloch-Queyrat Coralie 
Published: August 2021

ABSTRACTTo investigate which cytokines, chemokines and growth factors are involved in the immunopathogenesis of idiopathic uveitis, and whether cytokine profiles are associated with. Serum and aqueous humor (AH) samples of 75 patients with idiopathic uveitis were analyzed by multiplex immunoassay. Infectious controls consisted of 16 patients with ocular toxoplasmosis all confirmed by intraocular fluid analyses. Noninfectious controls consisted of 7 patients with Behçet disease related uveitis and 15 patients with sarcoidosis related uveitis. The control group consisted of AH and serum samples from 47 noninflammatory control patients with age-related cataract. In each sample, 27 immune mediators ± IL-21 and IL-23 were measured. In idiopathic uveitis, 13 of the 29 mediators, including most proinflammatory and vascular mediators such as IL-6, IL-8, IL-12, G-CSF, GM-CSF, MCP-1, IP-10, TNF-α and VEGF, were significantly elevated in the aqueous humor when compared to all controls. Moreover, IL-17, IP-10, and IL-21, were significantly elevated in the serum when compared to all controls. We clustered 4 subgroups of idiopathic uveitis using a statistical analysis of hierarchical unsupervised classification, characterized by the order of magnitude of concentrations of intraocular cytokines. The pathogenesis of idiopathic uveitis is characterized by the presence of predominantly proinflammatory cytokines and chemokines and vascular endothelial growth factor with high expression levels as compared to other causes of uveitis. There are indications for obvious Th-1/ IL21-Th17 pathways but also IL9-Th9 and increased IFN-γ-inducing cytokine (IL12) and IFN-γ-inducible CXC chemokine (IP-10). The combined data suggest that immune mediator expression is different among idiopathic uveitis. This study suggests various clusters among the idiopathic uveitis group rather than one specific uveitis entity.
Gender identity and sexual experience affect mating behaviour and chemical profile in the lesser mealworm,Alphitobius diaperinus(Coleoptera: Tenebrionidae)
Authors: Calla-Quispe Erika , Martel Carlos , Ibañez Alfredo J. 
Published: August 2021

AbstractAlphitobius diaperinus(Coleoptera: Tenebrionidae), the lesser mealworm, is one of the most significant pests of the poultry industry worldwide. These insects cause structural damage in poultry houses and transmit several diseases, impacting chickens’ productivity and rearing costs. Although semiochemicals may offer alternative insect pest management strategies, basic information regarding pheromone identity and their role on the behavioural ecology according to their circadian pattern of sexual behaviour ofA. diaperinusis essentially lacking. This study is aimed to analyse the relation of gender identity and sexual experience of adults ofA. diaperinuson their mating behaviour and whether this response is related to their CHC profiles secreted. The following steps were taken to achieve the study’s goal. First, the circadian pattern of their sexual activity was observed in newly emerged pairs for at least twenty-one days (virgin adults) and experienced adults collected from the field to identify a difference based on their sexual experience and achieve the optimal mating season to develop the following assays. Subsequently, Y-tube olfactometer bioassays were conducted to evaluate their odour bouquet attraction based on gender and sexual experience. Additionally, mating behaviour bioassays were conducted to evaluate the two factor effects. Finally, cuticular analysis was performed using gas chromatography-mass spectrometry to evaluate possible chemical differences based on the two factors. With statistical and multivariate analysis, we found that behavioural, mating and chemical responses are different based on their sexual experience. The mating sequences were described into precopulatory, copulatory and postcopulatory phases. This finding gives us a deeper understanding of the sexual communication during mating. In summary, our findings provide new insights into the mating system and chemical ecology ofA. diaperinus. The results presented here may serve as a base for further studies to develop strategies for managing this pest.
The complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) and its phylogenetic position in Decapoda
Authors: Zhu Longqiang , Zhu Zhihuang , Zhu Leiyu , Wang Dingquan , Wang Jianxin , Lin Qi 
Published: August 2021

AbstractIn this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (−0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. We compared the order of genes of Decapoda ancestor and found that the positions of the two tRNAs genes (trnA and trnR) of the L. vittata were translocated. The phylogenetic tree showed that L. vittata was an independent clade, namely Hippolytidae.
The role of artificial photo backgrounds of shelter dogs on pet profile clicking and the perception of sociability
Authors: Lamb F , Andrukonis A , Protopopova A 
Published: August 2021

AbstractWith the increasing prevalence of technology, the internet is often the first step for potential pet owners searching for an adoptable dog. However, best practices for the online portrayal of shelter and foster dogs remain unclear. Different online photo backgrounds appearing on adoption websites for shelter dogs may impact adoption speed by influencing viewer interest. Online clicking behaviour on pet profiles and human-directed sociability, broadly defined, has been previously linked to increased adoption likelihood. Therefore, the objective of this study was to determine the relationship between photo backgrounds of shelter dogs and online clicking as well as perceived human-directed sociability. In a virtual experiment, 680 participants were asked to rank the sociability and friendliness of four different adoptable dogs on a scale from 0-10. The photo background of each dog was digitally altered and randomly assigned to four experimental background conditions: 1) outdoor, 2) home indoor, 3) in-kennel indoor, and 4) plain coloured. As a proxy for adoption interest, a link to the dog’s adoption profile was presented on each slide and the clicking behaviour of participants on this link was recorded. Mixed logistic regression and poisson models revealed that background did not affect participants’ link-clicking behaviour (chisq = 3.55, df = 3, p = .314) nor perceptions of sociability (statistic = 6.19, df = 3, p = .103). Across all backgrounds, only 4.74% of presented slides culminated in participant link-clicking. Sociability scores also did not predict link clicking. Assessment of participant-related factors and dog ID revealed that link-clicking and sociability scores of photographs were influenced by differences between dogs themselves and unaffected by participants’ awareness of study hypotheses. We conclude that artificial background types did not affect participant responses. The results demonstrate the importance of empirical data in making marketing decisions in animal shelters. Understanding which aspects of online marketing materials impact viewer interest will provide guidance for both animal shelter personnel and foster families to improve speed of adoption of the animals in their care.
Reaching articular limits can negatively impact embodiment in virtual reality
Authors: Porssut Thibault , Blanke Olaf , Herbelin Bruno , Boulic Ronan 
Published: August 2021

AbstractProviding Virtual Reality(VR) users with a 3D representation of their body complements the experience of immersion and presence in the virtual world with the experience of being physically located and more personally involved. A full-body avatar representation is known to induce a Sense of Embodiment (SoE) for this virtual body, which is associated with improvements in task performance, motivation and motor learning. Recent experimental research on embodiment provides useful guidelines, indicating the extent of discrepancy tolerated by users and, conversely, the limits and disruptive events that lead to a break in embodiment (BiE). Based on previous works on the limit of agency under movement distortion, this paper describes, studies and analyses the impact of a very common yet overlooked embodiment limitation linked to articular limits when performing a reaching movement. We demonstrate that perceiving the articular limit when fully extending the arm provides users with an additional internal proprioceptive feedback which, if not matched in the avatar’s movement, leads to the disruptive realization of an incorrect posture mapping. This study complements previous works on self-contact and visuo-haptic conflicts and emphasizes the risk of disrupting the SoE when distorting users’ movements or using a poorly-calibrated avatar.