bluuebunny/crossref_metadata_2025_split huggingface dataset:
Best BLAST hit alone cannot be used as evidence of fraud
Authors: Díaz-Arce Natalia , Rodríguez-Ezpeleta Naiara 
Published: November 2021

AbstractIn a recent study, Blanco-Fernandez, et al. 1 applied molecular tools to authenticate fish products and conclude evidence of “worrying international fraud”. They revealed mislabeling in recognizable and unrecognizable fish products labeled as anchovy, hake and tuna commercialized by European companies. Their analyses consisted on extracting DNA from the fish product to be authenticated followed by amplification and sequencing of a suite of DNA markers and on comparing the resulting sequences to the GenBank sequence database using BLAST (Basic Tool Alignment Search Tool) (https://blast.ncbi.nlm.nih.gov/Blast.cgi). By carefully reanalyzing their data, we identify errors in their species identification and conclude that best BLAST hit alone cannot be used as evidence of fraud.
FastQTLmapping: an ultra-fast package for mQTL-like analysis
Authors: Gao Xingjian , Li Jiarui , Liu Xinxuan , Peng Qianqian , Jing Han , Wang Sijia , Liu Fan 
Published: November 2021

AbstractSummaryHere we describe fastQTLmapping, a C++ package that is computationally efficient not only for mQTL-like analysis but as a generic solver also for conducting exhaustive linear regressions involving extraordinarily large numbers of dependent and explanatory variables allowing for covariates. Compared to the state-of-the-art MatrixEQTL, fastQTLmapping was an order of magnitude faster with much lower peak memory usage. In a large dataset consisting of 3,500 individuals, 8 million SNPs, 0.8 million CpGs and 20 covariates, fastQTLmapping completed the mQTL analysis in 7 hours with 230GB peak memory usage.Availability and ImplementationFastQTLmapping is implemented in C++ and released under a GPL license. FastQTLmapping can be downloaded from https://github.com/TianTTL/xQTLmapping.Contactliufan@big.ac.cn
The evolution of genomic, transcriptomic, and single-cell protein markers of metastatic upper tract urothelial carcinoma
Authors: Ohara Kentaro , Figueiredo Rendeiro André , Bhinder Bhavneet , Eng Kenneth Wha , Ravichandran Hiranmayi , Pisapia David , Vosoughi Aram , Fernandez Evan , Shohdy Kyrillus S. , Manohar Jyothi , Beg Shaham , Wilkes David , Robinson Brian D. , Khani Francesca , Bareja Rohan , Tagawa Scott T. , Sboner Andrea , Elemento Olivier , Faltas Bishoy M. , Mosquera Juan Miguel 
Published: November 2021

AbstractThe molecular characteristics of metastatic upper tract urothelial carcinoma (UTUC) are unknown. The genomic and transcriptomic differences between primary and metastatic UTUC is not well described either. We combined whole-exome sequencing, RNA-sequencing, and Imaging Mass Cytometry™ (IMC™) of 44 tumor samples from 28 patients with high-grade primary and metastatic UTUC. IMC enables spatially resolved single-cell analyses to examine the evolution of cancer cell, immune cell, and stromal cell markers using mass cytometry with lanthanide metal-conjugated antibodies. We discovered that actionable genomic alterations are frequently discordant between primary and metastatic UTUC tumors in the same patient. In contrast, molecular subtype membership and immune depletion signature were stable across primary and matched metastatic UTUC. Molecular and immune subtypes were consistent between bulk RNA-sequencing and mass cytometry of protein markers from 340,798 single-cells. Molecular subtyping at the single cell level was highly conserved between primary and metastatic UTUC tumors within the same patient.
Identification, analysis, and confirmation of seed storability-related loci in Dongxiang wild rice (Oryza rufipogon Griff.)
Authors: Zhao Minmin , Hu Biaolin , Fan Yuanwei , Ding Gumu , Yang Wanling , Chen Yong , Chen Yanhong , Xie Jiankun , Zhang Fantao 
Published: November 2021

AbstractDongxiang wild rice (Oryza rufipogon Griff.) (DXWR) has strong seed storability and identifying its elite gene resources may facilitate genetic improvements in rice seed storability. In this study, we developed two backcross inbred lines (BILs) populations, with DXWR as a common donor parent and two rice varieties (F6 and R974) as recipient parents. Bulked segregant analysis via whole genome sequencing (BSA-seq) was used to identify seed storability-related loci in the DXWR and F6 population. Two main genomic regions containing 18,550,000–20,870,000 bp on chromosome 4 and 7,860,000–9,780,000 bp on chromosome 9 were identified as candidate loci of DXWR seed storability; these overlapped partially with seed storability-related quantitative trait loci (QTLs) discovered in previous studies, suggesting that these loci may provide important regions for isolating the responsible genes. In total, 448 annotated genes were predicted within the identified regions, of which 274 and 82 had nonsynonymous and frameshift mutations, respectively. We detected extensive metabolic activities and cellular processes during seed storability and confirmed the effects of the seed storability-related candidate loci using four BILs from DXWR and R974. These results may facilitate the cloning of DXWR seed storability-related genes, thereby elucidating rice seed storability and its improvement potential.
The sleep EEG envelope: a novel, neuronal firing-based human biomarker
Authors: Ujma Péter P. , Dresler Martin , Simor Péter , Fabó Dániel , Ulbert István , Erőss Loránd , Bódizs Róbert 
Published: November 2021

AbstractSleep EEG reflects instantaneous voltage differences relative to a reference, while its spectrum reflects the degree to which it is comprised of oscillations at various frequencies. In contrast, the envelope of the sleep EEG reflects the instantaneous amplitude of oscillations at specific frequencies, and its spectrum reflects the rhythmicity of the occurrence of these oscillations. The ordinary sleep EEG and its spectrum have been extensively studied and its individual stability and relationship to various demographic characteristics, psychological traits and pathologies is well known. In contrast, the envelope spectrum has not been extensively studied before. In two studies, we explored the generating mechanisms and utility of studying the envelope of the sleep EEG. First, we used human invasive data from cortex-penetrating microelectrodes and subdural grids to demonstrate that the sleep EEG envelope spectrum reflects local neuronal firing. Second, we used a large database of healthy volunteers to demonstrate that the scalp EEG envelope spectrum is highly stable within individuals, especially in NREM sleep, and that it is affected by age and sex. Multivariate models based on a learning algorithm could predict both age (r=0.6) and sex (r=0.5) with considerable accuracy from the EEG envelope spectrum. With age, oscillations characteristically shifted from a 4-5 second rhythm to higher rhythms. The envelope spectrum was not associated with general cognitive ability (IQ). Our results demonstrate that the sleep envelope spectrum is a promising, neuronal firing-based biomarker of various demographic and disease-related phenotypes.
Transcriptome network analysis implicates CX3CR1-positive type 3 dendritic cells in non-infectious uveitis
Authors: Hiddingh S. , Pandit A. , Verhagen F.H. , Rijken R. , Servaas N. H. , Wichers C.G.K. , Dam-van Loon N.H. ten , Imhof S.M. , Radstake T.R.D.J. , de Boer J.H. , Kuiper J.J.W. 
Published: November 2021

ABSTRACTBackgroundType I interferons (IFNs) promote the expansion of subsets of CD1c+ conventional dendritic cells (CD1c+ DCs), but the molecular basis of CD1c+ DCs involvement in conditions not associated without elevated type I IFNs remains unclear.MethodsWe analyzed CD1c+ DCs from two cohorts of non-infectious uveitis patients and healthy donors using RNA-sequencing followed by high-dimensional flow cytometry to characterize the CD1c+ DC populations.ResultsWe report that the CD1c+ DCs pool from patients with non-infectious uveitis is skewed towards a gene module with the chemokine receptorCX3CR1as the key hub gene. We confirmed these results in an independent case-control cohort and show that the disease-associated gene module is not mediated by type I IFNs. An analysis of peripheral blood using flow cytometry revealed that CX3CR1+ DC3s were diminished, whereas CX3CR1-DC3s were not. Stimulated CX3CR1+ DC3s secrete high levels of inflammatory cytokines, including TNF-alpha, and CX3CR1+ DC3-like cells can be detected in inflamed eyes of patients.ConclusionsThese results show that CX3CR1+ DC3s are implicated in non-infectious uveitis and can secrete proinflammatory mediators implicated in its pathophysiology.FundingThe presented work is supported by UitZicht (project number #2014-4, #2019-10, an #2021-4). The funders had no role in the design, execution, interpretation, or writing of the study.
Influence network model uncovers relations between biological processes and mutational signatures
Authors: Amgalan Bayarbaatar , Wojtowicz Damian , Kim Yoo-Ah , Przytycka Teresa M. 
Published: November 2021

AbstractThere has been a growing appreciation recently that mutagenic processes can be studied through the lenses of mutational signatures, which represent characteristic mutation patterns attributed to individual mutagens. However, the causal link between mutagens and observed mutation patterns remains not fully understood, limiting the utility of mutational signatures. To gain insights into these relationships, we developed a network-based method, named GeneSigNetthat constructs a directed network among genes and mutational signatures. The approach leverages a sparse partial correlation among other statistical techniques to uncover dominant influence relations between the activities of network nodes. Applying GeneSigNetto cancer data sets, we uncovered important relations between mutational signatures and several cellular processes that can shed light on cancer related mutagenic processes. Our results are consistent with previous findings such as the impact of homologous recombination deficiency on a clustered APOBEC mutations in breast cancer. The network identified by GeneSigNetalso suggest an interaction between APOBEC hypermutation and activation of regulatory T Cells (Tregs) and a relation between APOBEC mutations and changes in DNA conformation. GeneSigNetalso exposed a possible link between the SBS8 signature of unknown aetiology and the nucleotide excision repair pathway. GeneSigNetprovides a new and powerful method to reveal the relation between mutational signatures and gene expression.GeneSigNetis freely available athttps://github.com/ncbi/GeneSigNet.
Trajectory Recording and Analysis System for Cockroach Robot
Authors: Huai Ruituo , Zhu Haoran , Yang Shuo , Yu Zhihao , Wang Hui , Yang Junqing , Zhang Pingqiu , Shi Yong , Yan Rui 
Published: November 2021

ABSTRACTIn this study, We design a trajectory recording and analysis system to record and analysis the changes in the movement behavior of the cockroach robot after stimulation. The external hardware of this system is an infrared touchpad as the experimental platform for the cockroach robot to crawl freely, and the infrared matrices densely distributed in the X and Y directions of the infrared touchpad are used to detect and locate the position of the cockroach robot. The cockroach robot’s movement trajectory is displayed visually through the projector’s interface projection on the infrared touchpad. The system software consists of three main parts: the electrical signal parameter setting module, the movement trajectory recording module, and the data analysis module. The electrical signal parameter setting module sets the stimulation parameters and configures the corresponding serial port to independently stimulate the left and right antenna and cercus of the cockroach; the trajectory recording module is used to record the trajectory of the cockroach robot through the coordinate positioning method. The data analysis module explores the change of motion behavior of the cockroach robot with time after receiving the stimulus by using the stage analysis method, and explores the change of motion of the cockroach robot with different voltage stimulus by using the module analysis method. The system is tested in experiments and the results demonstrated its applicability to the recording and analysis of the cockroach robot’s trajectories.
Adversarial domain translation networks for fast and accurate integration of large-scale atlas-level single-cell datasets
Authors: Zhao Jia , Wang Gefei , Ming Jingsi , Lin Zhixiang , Wang Yang ,   The Tabula Microcebus Consortium, Wu Angela Ruohao , Yang Can 
Published: November 2021

AbstractThe rapid emergence of large-scale atlas-level single-cell RNA-seq datasets presents remarkable opportunities for broad and deep biological investigations through integrative analyses. However, harmonizing such datasets requires integration approaches to be not only computationally scalable, but also capable of preserving a wide range of fine-grained cell populations. We created Portal, a unified framework of adversarial domain translation to learn harmonized representations of datasets. With innovation in model and algorithm designs, Portal achieves superior performance in preserving biological variation during integration, while achieving integration of millions of cells in minutes with low memory consumption. We show that Portal is widely applicable to integrating datasets across samples, platforms and data types (including scRNA-seq, snRNA-seq and scATAC-seq). Finally, we demonstrate the power of Portal by applying it to the integration of cross-species datasets with limited shared information among them, elucidating biological insights into the similarities and divergences in the spermatogenesis process among mouse, macaque and human.
Reduced Incidence of Long-COVID Symptoms Related to Administration of COVID-19 Vaccines Both Before COVID-19 Diagnosis and Up to 12 Weeks After
Authors: Simon Michael A. , Luginbuhl Ryan D. , Parker Richard 
Published: November 2021

AbstractBoth clinical trials and studies leveraging real-world data have repeatedly confirmed the three COVID-19 vaccines authorized for use by the Food and Drug Administration are safe and effective at preventing infection, hospitalization, and death due to COVID-19 and a recent observational study of self-reported symptoms provides support that vaccination may also reduce the probability of developing long-COVID. As part of a federated research study with the COVID-19 Patient Recovery Alliance, Arcadia.io performed a retrospective analysis of the medical history of 240,648 COVID-19-infected persons to identity factors influencing the development and progression of long-COVID. This analysis revealed that patients who received at least one dose of any of the three COVID vaccines prior to their diagnosis with COVID-19 were 7-10 times less likely to report two or more long-COVID symptoms compared to unvaccinated patients. Furthermore, unvaccinated patients who received their first COVID-19 vaccination within four weeks of SARS-CoV-2 infection were 4-6 times less likely to report multiple long-COVID symptoms, and those who received their first dose 4-8 weeks after diagnosis were 3 times less likely to report multiple long-COVID symptoms compared to those who remained unvaccinated. This relationship supports the hypothesis that COVID-19 vaccination is protective against long-COVID and that effect persists even if vaccination occurs up to 12 weeks after COVID-19 diagnosis. A critical objective of this study was hypothesis generation, and the authors intend to perform further studies to substantiate the findings and encourage other researchers to as well.
C-reactive protein and lactate dehydrogenase as prognostic indicators in COVID-2019 outpatients
Authors: Suzuki Keiko , Ichikawa Takaya , Suzuki Satoshi , Tanino Yoko , Kakinoki Yasutaka 
Published: November 2021

AbstractBackgroundIt is critical for clinicians seeing outpatients with coronavirus disease 2019 (COVID-19) to identify those who will require oxygen therapy after the hospital visit. Although studies on biomarkers predicting mortality or ventilator requirement in hospitalized patients with COVID-19 have been conducted, research on biomarkers predicting the need for oxygen therapy in outpatients is sparse.MethodsPatients with COVID-19 who visited Asahikawa City Hospital on an outpatient basis were included in the study. In total, 287 new outpatients visited between April 2021 and September 2021, and 142 underwent blood testing. All blood tests were performed before any treatments for COVID-19 were started. Demographic information, laboratory data, and clinical treatment information were extracted from the electronic medical records. Risk factors associated with oxygen therapy were explored.ResultsIn total, 40 of 142 patients who underwent blood testing required oxygen therapy within 7 days after blood samples were taken, and all other patients recovered without oxygen therapy. C-reactive protein (CRP) and lactate dehydrogenase (LDH) levels were significantly higher in patients who required oxygen therapy, and their cutoffs were 36 mg/L (sensitivity, 0.802; specificity, 0.725) and 267 U/L (sensitivity, 0.713; specificity, 0.750), respectively. Multivariate logistic regression identified age, body mass index, CRP ≥ 36 mg/L, and LDH ≥ 267 U/L as significant risk factors for oxygen therapy requirement. This study suggests that elevated CRP and LDH levels are independent risk factors for oxygen therapy in outpatients with COVID-19. Further confirmatory studies are needed.
The output of interneurons in the primary visual cortex is best reflected by pre-synaptic activity, not somatic activity
Authors: Vroman Rozan , McKay Lawrie 
Published: November 2021

AbstractRecent advances in 2-photon calcium-imaging in awake mice have made it possible to study the effect of different behavioural states on cortical circuitry. Many studies assume that somatic activity can be used as a measure for neuronal output. We set out to test the validity of this assumption by comparing somatic activity with the pre-synaptic activity of VIP (Vasoactive intestinal peptide)- and SST (Somatostatin)-positive interneurons in layer 2/3 of the primary visual cortex (V1). We used mice expressing genetically encoded calcium indicators in VIP/SST-interneurons across the whole cell (VIP/SST:GCaMP6f) or confined to pre-synapses (VIP/SST:SyGCaMP5). Mice were exposed to a full-field visual stimulation protocol consisting of 60-second-long presentations of moving Gabor gratings (0.04 cpd, 2 Hz) alternated by 30 seconds of grey screen. During imaging, mice were placed on an air-suspended Styrofoam ball, allowing them to run voluntarily. We compared neural activity during three 4-second time-windows: Before visual stimulation (−4 to 0 sec), during the initial onset (1 to 5 sec) and at the end of the stimulation (56 to 60 sec.). These were further compared while the mice were stationary and while they were voluntarily locomoting. Unlike VIP-somas, VIP-pre-synapses showed strong suppressive responses to the visual stimulus. Furthermore, VIP-somas were positively correlated with locomotion, whereas in VIP-synapses we observed a split between positive and negative correlations. In addition, a similar but weaker distinction was found between SST-somas and pre-synapses. The excitatory effect of locomotion in VIP-somas increased over the course of the visual stimulus but this property was only shared with the positively correlated VIP-pre-synapses. The remaining negatively correlated pre-synapses showed no relation to the overall activity of the Soma. Our results suggest that when making statements about the involvement of interneurons in V1 layer 2/3 circuitry it is crucial to measure from synaptic terminals as well as from somas.
Esrrγa regulates nephron development and ciliogenesis by controlling prostaglandin synthesis and cooperation with Ppargc1a
Authors: Wesselman Hannah M. , Flores-Mireles Ana L. , Wingert Rebecca A. 
Published: November 2021

AbstractCilia are essential for the ontogeny and function of many tissues, including the kidney. In mammals, Esrrγ has been previously established as a significant determinant of renal health, with decreased expression linked to age related dysfunction, cyst formation, and kidney disease. Here, we report that the Esrrγ vertebrate ortholog estrogen related receptor gamma a (esrrγa) is essential for proper cell fate choice within kidney functional units (nephrons) as well as ciliogenesis. Deficiency of esrrγa resulted in nephrons with alterations in proximodistal segmentation and a decreased multiciliated epithelial cell populace. Surprisingly, esrrγa deficiency disrupted renal ciliogenesis and caused a similar abrogation within the developing node and otic vesicle—all defects that occurred independently of changes in cell polarity or basal body organization. These phenotypes were consistent with interruptions in prostaglandin signaling, and we found that ciliogenesis was rescued in esrrγa deficient embryos with exogenous PGE2 or through overexpression of the cyclooxygenase enzyme Ptgs1. Through genetic interaction studies, we found that peroxisome proliferator-activated receptor gamma, coactivator 1 alpha (ppargc1a), which acts upstream of Ptgs1-mediated prostaglandin synthesis, has a synergistic relationship with esrrγa in the ciliogenic pathway. These data position esrrγa as a novel link between ciliogenesis and nephrogenesis through regulation of prostaglandin signaling and cooperation with ppargc1a, and highlight esrrγa as a potential new target for future ciliopathic treatments.
MAPR origins reveal a new class of prokaryotic cytochrome b5 proteins and possible role in eukaryogenesis
Authors: Tamarit Daniel , Teakel Sarah , Marama Michealla , Aragão David , Gerdes Svetlana Y. , Forwood Jade K. , Ettema Thijs J. G. , Cahill Michael A. 
Published: November 2021

AbstractThe multiple functions of PGRMC1, the archetypal heme-binding eukaryotic MAPR family member, include steroidogenic regulation, membrane trafficking, and steroid responsiveness. The interrelationships between these functions are currently poorly understood. Previous work has shown that different MAPR subclasses were present early in eukaryotic evolution, and that tyrosine phosphorylated residues appeared in the eumetazoan ancestor, coincident with a gastrulation organizer. Here we show that MAPR proteins are related to a newly recognized class of prokaryotic cytochrome-b5 domain proteins. Our first solved structure of this new class exhibits shared MAPR-like folded architecture and heme-binding orientation. We also report that a protein subgroup from Candidate Phyla Radiation bacteria shares MAPR-like heme-interacting tyrosines. Our results support bacterial origins for both PGRMC1 and CYP51A, that catalyze the meiosis-associated 14-demethylation of the first sterol lanosterol from yeast to humans. We propose that eukaryotic acquisition of a membrane-trafficking function related to sterol metabolism was associated with the appearance of MAPR genes early in eukaryotic evolution.