bluuebunny/crossref_metadata_2025_split huggingface dataset:
Illuminating the Pre‐, Co‐, and Post‐Seismic Phases of the 2016 M7.8 Kaikōura Earthquake With 10 Years of Seismicity
Authors: Chamberlain C. J. , Frank W. B. , Lanza F. , Townend J. , Warren‐Smith E. 
Published: July 2021

AbstractThe 2016 M7.8 Kaikōura earthquake is one of the most complex earthquakes in recorded history, with significant rupture of at least 21 crustal faults. Using a matched‐filter detection routine, precise cross‐correlation pick corrections, and accurate location and relocation techniques, we construct a catalog of 33,328 earthquakes between 2009 and 2020 on and adjacent to the faults that ruptured in the Kaikōura earthquake. We also compute focal mechanisms for 1,755 of the earthquakes used as templates. Using this catalog we reassess the rupture pathway of the Kaikōura earthquake. In particular we show that: (a) the earthquake nucleated on the Humps Fault; (b) there is a likely linking offshore reverse fault between the southern fault system and the Papatea Fault, which could explain the anomalously high slip on the Papatea Fault; (c) the faults that ruptured in the 2013 Cook Strait sequence were reactivated by the Kaikōura earthquake and may have played a role in the termination of the earthquake; and (d) no seismicity on an underlying subduction interface is observed beneath almost all of the ruptured region suggesting that if deformation did occur on the plate interface then it occurred aseismically and did not play a significant role in generating co‐seismic ground motion.
Observations From NOAA's Newest Solar Proton Sensor
Authors: Kress B. T. , Rodriguez J. V. , Boudouridis A. , Onsager T. G. , Dichter B. K. , Galica G. E. , Tsui S. 
Published: July 2021

AbstractSpace weather instrumentation on board the National Oceanic and Atmospheric Administration's (NOAA's) newest Geostationary Operational Environmental Satellite (GOES)‐R series includes the Solar and Galactic Proton Sensor (SGPS), which has been collecting data since January 8, 2017. SGPS supports real‐time alerts of solar energetic particle events at the NOAA Space Weather Prediction Center (SWPC) and provides data to the space science community, advancing basic space science research and understanding of space weather effects on satellite systems. The first GOES‐R series spacecraft, GOES‐16, was launched on November 19, 2016. A series of solar particle events in September 2017 enabled cross‐calibration of GOES‐16 SGPS with the Energetic Particle Sensors on GOES‐13 and ‐15. This paper is intended as a resource for SGPS data users, including comparisons with legacy GOES energetic particle measurements, corrections applied to SGPS Level‐2 data, important caveats, background level fluxes, and measurements of trapped magnetospheric protons.
Exploring the genetic heterogeneity in major depression across diagnostic criteria
Authors: Jermy Bradley S. , Glanville Kylie P. , Coleman Jonathan R. I. , Lewis Cathryn M. , Vassos Evangelos 
Published: July 2021

AbstractMajor depressive disorder (MDD) is defined differently across genetic research studies and this may be a key source of heterogeneity. While previous literature highlights differences between minimal and strict phenotypes, the components contributing to this heterogeneity have not been identified. Using the cardinal symptoms (depressed mood/anhedonia) as a baseline, we build MDD phenotypes using five components—(1) five or more symptoms, (2) episode duration, (3) functional impairment, (4) episode persistence, and (5) episode recurrence—to determine the contributors to such heterogeneity. Thirty-two depression phenotypes which systematically incorporate different combinations of MDD components were created using the mental health questionnaire data within the UK Biobank. SNP-based heritabilities and genetic correlations with three previously defined major depression phenotypes were calculated (Psychiatric Genomics Consortium (PGC) defined depression, 23andMe self-reported depression and broad depression) and differences between estimates analysed. All phenotypes were heritable (h2SNP range: 0.102–0.162) and showed substantial genetic correlations with other major depression phenotypes (Rg range: 0.651–0.895 (PGC); 0.652–0.837 (23andMe); 0.699–0.900 (broad depression)). The strongest effect on SNP-based heritability was from the requirement for five or more symptoms (1.4% average increase) and for a long episode duration (2.7% average decrease). No significant differences were noted between genetic correlations. While there is some variation, the two cardinal symptoms largely reflect the genetic aetiology of phenotypes incorporating more MDD components. These components may index severity, however, their impact on heterogeneity in genetic results is likely to be limited.
A dimensional perspective on the genetics of obsessive-compulsive disorder
Authors: Strom Nora I. , Soda Takahiro , Mathews Carol A. , Davis Lea K. 
Published: July 2021

AbstractThis review covers recent findings in the genomics of obsessive-compulsive disorder (OCD), obsessive-compulsive symptoms, and related traits from a dimensional perspective. We focus on discoveries stemming from technical and methodological advances of the past five years and present a synthesis of human genomics research on OCD. On balance, reviewed studies demonstrate that OCD is a dimensional trait with a highly polygenic architecture and genetic correlations to multiple, often comorbid psychiatric phenotypes. We discuss the phenotypic and genetic findings of these studies in the context of the dimensional framework, relying on a continuous phenotype definition, and contrast these observations with discoveries based on a categorical diagnostic framework, relying on a dichotomous case/control definition. Finally, we highlight gaps in knowledge and new directions for OCD genetics research.
Contributing factors to advanced brain aging in depression and anxiety disorders
Authors: Han Laura K. M. , Schnack Hugo G. , Brouwer Rachel M. , Veltman Dick J. , van der Wee Nic J. A. , van Tol Marie-José , Aghajani Moji , Penninx Brenda W. J. H. 
Published: July 2021

AbstractDepression and anxiety are common and often comorbid mental health disorders that represent risk factors for aging-related conditions. Brain aging has shown to be more advanced in patients with major depressive disorder (MDD). Here, we extend prior work by investigating multivariate brain aging in patients with MDD, anxiety disorders, or both, and examine which factors contribute to older-appearing brains. Adults aged 18–57 years from the Netherlands Study of Depression and Anxiety underwent structural MRI. A pretrained brain-age prediction model based on >2000 samples from the ENIGMA consortium was applied to obtain brain-predicted age differences (brain PAD, predicted brain age minus chronological age) in 65 controls and 220 patients with current MDD and/or anxiety. Brain-PAD estimates were associated with clinical, somatic, lifestyle, and biological factors. After correcting for antidepressant use, brain PAD was significantly higher in MDD (+2.78 years, Cohen’sd = 0.25, 95% CI −0.10-0.60) and anxiety patients (+2.91 years, Cohen’sd = 0.27, 95% CI −0.08-0.61), compared with controls. There were no significant associations with lifestyle or biological stress systems. A multivariable model indicated unique contributions of higher severity of somatic depression symptoms (b = 4.21 years per unit increase on average sum score) and antidepressant use (−2.53 years) to brain PAD. Advanced brain aging in patients with MDD and anxiety was most strongly associated with somatic depressive symptomatology. We also present clinically relevant evidence for a potential neuroprotective antidepressant effect on the brain-PAD metric that requires follow-up in future research.
The combined detection of Amphiregulin, Cyclin A1 and DDX20/Gemin3 expression predicts aggressive forms of oral squamous cell carcinoma
Authors: Bourova-Flin Ekaterina , Derakhshan Samira , Goudarzi Afsaneh , Wang Tao , Vitte Anne-Laure , Chuffart Florent , Khochbin Saadi , Rousseaux Sophie , Aminishakib Pouyan 
Published: July 2021

AbstractBackgroundLarge-scale genetic and epigenetic deregulations enable cancer cells to ectopically activate tissue-specific expression programmes. A specifically designed strategy was applied to oral squamous cell carcinomas (OSCC) in order to detect ectopic gene activations and develop a prognostic stratification test.MethodsA dedicated original prognosis biomarker discovery approach was implemented using genome-wide transcriptomic data of OSCC, including training and validation cohorts. Abnormal expressions of silent genes were systematically detected, correlated with survival probabilities and evaluated as predictive biomarkers. The resulting stratification test was confirmed in an independent cohort using immunohistochemistry.ResultsA specific gene expression signature, including a combination of three genes,AREG, CCNA1andDDX20, was found associated with high-risk OSCC in univariate and multivariate analyses. It was translated into an immunohistochemistry-based test, which successfully stratified patients of our own independent cohort.DiscussionThe exploration of the whole gene expression profile characterising aggressive OSCC tumours highlights their enhanced proliferative and poorly differentiated intrinsic nature. Experimental targeting ofCCNA1in OSCC cells is associated with a shift of transcriptomic signature towards the less aggressive form of OSCC, suggesting that CCNA1 could be a good target for therapeutic approaches.
PPM1G promotes the progression of hepatocellular carcinoma via phosphorylation regulation of alternative splicing protein SRSF3
Authors: Chen Dawei , Zhao Zhenguo , Chen Lu , Li Qinghua , Zou Jixue , Liu Shuanghai 
Published: July 2021

AbstractEmerging evidence has demonstrated that alternative splicing has a vital role in regulating protein function, but how alternative splicing factors can be regulated remains unclear. We showed that the PPM1G, a protein phosphatase, regulated the phosphorylation of SRSF3 in hepatocellular carcinoma (HCC) and contributed to the proliferation, invasion, and metastasis of HCC. PPM1G was highly expressed in HCC tissues compared to adjacent normal tissues, and higher levels of PPM1G were observed in adverse staged HCCs. The higher levels of PPM1G were highly correlated with poor prognosis, which was further validated in the TCGA cohort. The knockdown of PPM1G inhibited the cell growth and invasion of HCC cell lines. Further studies showed that the knockdown of PPM1G inhibited tumor growth in vivo. The mechanistic analysis showed that the PPM1G interacted with proteins related to alternative splicing, including SRSF3. Overexpression of PPM1G promoted the dephosphorylation of SRSF3 and changed the alternative splicing patterns of genes related to the cell cycle, the transcriptional regulation in HCC cells. In addition, we also demonstrated that the promoter of PPM1G was activated by multiple transcription factors and co-activators, including MYC/MAX and EP300, MED1, and ELF1. Our study highlighted the essential role of PPM1G in HCC and shed new light on unveiling the regulation of alternative splicing in malignant transformation.
flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions
Authors: Hu Gang , Katuwawala Akila , Wang Kui , Wu Zhonghua , Ghadermarzi Sina , Gao Jianzhao , Kurgan Lukasz 
Published: July 2021

AbstractIdentification of intrinsic disorder in proteins relies in large part on computational predictors, which demands that their accuracy should be high. Since intrinsic disorder carries out a broad range of cellular functions, it is desirable to couple the disorder and disorder function predictions. We report a computational tool, flDPnn, that provides accurate, fast and comprehensive disorder and disorder function predictions from protein sequences. The recent Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment and results on other test datasets demonstrate that flDPnn offers accurate predictions of disorder, fully disordered proteins and four common disorder functions. These predictions are substantially better than the results of the existing disorder predictors and methods that predict functions of disorder. Ablation tests reveal that the high predictive performance stems from innovative ways used in flDPnn to derive sequence profiles and encode inputs. flDPnn’s webserver is available at http://biomine.cs.vcu.edu/servers/flDPnn/
A novel characteristic of a phytoplankton as a potential source of straight-chain alkanes
Authors: Harada Naomi , Hirose Yuu , Chihong Song , Kurita Hirofumi , Sato Miyako , Onodera Jonaotaro , Murata Kazuyoshi , Itoh Fumihiro 
Published: July 2021

AbstractBiosynthesis of hydrocarbons is a promising approach for the production of alternative sources of energy because of the emerging need to reduce global consumption of fossil fuels. However, the suitability of biogenic hydrocarbons as fuels is limited because their range of the number of carbon atoms is small, and/or they contain unsaturated carbon bonds. Here, we report that a marine phytoplankton, Dicrateria rotunda, collected from the western Arctic Ocean, can synthesize a series of saturated hydrocarbons (n-alkanes) from C10H22 to C38H78, which are categorized as petrol (C10–C15), diesel oils (C16–C20), and fuel oils (C21–C38). The observation that these n-alkanes were also produced by ten other cultivated strains of Dicrateria collected from the Atlantic and Pacific oceans suggests that this capability is a common characteristic of Dicrateria. We also identified that the total contents of the n-alkanes in the Arctic D. rotunda strain increased under dark and nitrogen-deficient conditions. The unique characteristic of D. rotunda could contribute to the development of a new approach for the biosynthesis of n-alkanes.
A wireless spinal stimulation system for ventral activation of the rat cervical spinal cord
Authors: Hogan Matthew K. , Barber Sean M. , Rao Zhoulyu , Kondiles Bethany R. , Huang Meng , Steele William J. , Yu Cunjiang , Horner Philip J. 
Published: July 2021

AbstractElectrical stimulation of the cervical spinal cord is gaining traction as a therapy following spinal cord injury; however, it is difficult to target the cervical motor region in a rodent using a non-penetrating stimulus compared with direct placement of intraspinal wire electrodes. Penetrating wire electrodes have been explored in rodent and pig models and, while they have proven beneficial in the injured spinal cord, the negative aspects of spinal parenchymal penetration (e.g., gliosis, neural tissue damage, and obdurate inflammation) are of concern when considering therapeutic potential. We therefore designed a novel approach for epidural stimulation of the rat spinal cord using a wireless stimulation system and ventral electrode array. Our approach allowed for preservation of mobility following surgery and was suitable for long term stimulation strategies in awake, freely functioning animals. Further, electrophysiology mapping of the ventral spinal cord revealed the ventral approach was suitable to target muscle groups of the rat forelimb and, at a single electrode lead position, different stimulation protocols could be applied to achieve unique activation patterns of the muscles of the forelimb.
Roux-en-Y gastric bypass potentially improved intestinal permeability by regulating gut innate immunity in diet-induced obese mice
Authors: Jin Zhangliu , Chen Kai , Zhou Zhe , Peng Weihui , Liu Wei 
Published: July 2021

AbstractRoux-en-Y gastric bypass (RYGB) has been demonstrated to be the most effective treatment for morbid obesity, yet the impact of RYGB on intestinal permeability is not fully known. In this work, we subjected obese mice to RYGB and sham operation procedures. Serum lipopolysaccharide (LPS) level, inflammatory cytokines and intestinal permeability were measured at 8 weeks post surgery. In contrast to sham surgery, RYGB reduced body weight, improved glucose tolerance and insulin resistance, and decreased serum levels of LPS, IL6 and TNFα. Intestinal permeability of the common limb and colon was significantly improved in the RYGB group compared to the sham group. The mRNA levels of IL1β, IL6, and TLR4 in the intestine were significantly decreased in the RYGB group compared with the sham group. The expression levels of intestinal islet-derived 3β (REG3β), islet-derived 3γ (REG3γ) and intestinal alkaline phosphatase (IAP) were higher in the RYGB group than in the sham group. In conclusion, in a diet-induced obesity (DIO) mouse model, both decreased intestinal permeability and attenuated systemic inflammation after RYGB surgery were associated with improved innate immunity, which might result from enhanced production of IAP and antimicrobial peptides.
Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice
Authors: Villacastin Anne J. , Adams Keeley S. , Boonjue Rin , Rushton Paul J. , Han Mira , Shen Jeffery Q. 
Published: July 2021

AbstractWRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system. We have identified prevalence of Group III WRKYs despite differences in breeding of cultivated and wild species. Same groups of WRKY genes tend to cluster together, suggesting recent, multiple duplication events. Duplications followed by divergence may result in neofunctionalizations of co-expressed WRKY genes that finely tune the regulation of target genes in a same metabolic or response pathway. WRKY genes have undergone recent rearrangements to form novel genes. Group Ib WRKYs, unique to AA genome type Oryza species, are derived from Group III genes dated back to 6.76 million years ago. Gene tree reconciliation analysis with the species tree revealed details of duplication and loss events in the 11 genomes. Selection analysis on single copy orthologs reveals the highly conserved nature of the WRKY domain and clusters of fast evolving sites under strong positive selection pressure. Also, the numbers of single copy orthologs under positive or negative selection almost evenly split. Our results provide valuable insights into the preservation and diversification of an important gene family under strong selective pressure for biotechnological improvements of the world’s most valued food crop.
Rasch analysis for development and reduction of Symptom Questionnaire for Visual Dysfunctions (SQVD)
Authors: Cantó-Cerdán Mario , Cacho-Martínez Pilar , Lara-Lacárcel Francisco , García-Muñoz Ángel 
Published: July 2021

AbstractTo develop the Symptom Questionnaire for Visual Dysfunctions (SQVD) and to perform a psychometric analysis using Rasch method to obtain an instrument which allows to detect the presence and frequency of visual symptoms related to any visual dysfunction. A pilot version of 33 items was carried out on a sample of 125 patients from an optometric clinic. Rasch model (using Andrich Rating Scale Model) was applied to investigate the category probability curves and Andrich thresholds, infit and outfit mean square, local dependency using Yen’s Q3 statistic, Differential item functioning (DIF) for gender and presbyopia, person and item reliability, unidimensionality, targeting and ordinal to interval conversion table. Category probability curves suggested to collapse a response category. Rasch analysis reduced the questionnaire from 33 to 14 items. The final SQVD showed that 14 items fit to the model without local dependency and no significant DIF for gender and presbyopia. Person reliability was satisfactory (0.81). The first contrast of the residual was 1.908 eigenvalue, showing unidimensionality and targeting was − 1.59 logits. In general, the SQVD is a well-structured tool which shows that data adequately fit the Rasch model, with adequate psychometric properties, making it a reliable and valid instrument to measure visual symptoms.
On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples
Authors: Sun Shan , Zhu Xiangzhu , Huang Xiang , Murff Harvey J. , Ness Reid M. , Seidner Douglas L. , Sorgen Alicia A. , Blakley Ivory C. , Yu Chang , Dai Qi , Azcarate-Peril M. Andrea , Shrubsole Martha J. , Fodor Anthony A. 
Published: July 2021

AbstractThe gut microbiota plays an important role in human health and disease. Stool, rectal swab and rectal mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. In this study, we report differences in stool, rectal swab and rectal mucosal tissue microbial communities with shotgun metagenome sequencing of 1397 stool, swab and mucosal tissue samples from 240 participants. The taxonomic composition of stool and swab samples was distinct, but less different to each other than mucosal tissue samples. Functional profile differences between stool and swab samples are smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or rectal swab gave broadly significantly correlated results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for determination of how inference can change for taxa and pathways depending on the choice of where to sample within the human gut.
Drug-associated cues and drug dosage contribute to increased opioid seeking after abstinence
Authors: Zanda Mary Tresa , Floris Gabriele , Daws Stephanie E. 
Published: July 2021

AbstractPatients with opioid use disorder experience high rates of relapse during recovery, despite successful completion of rehabilitation programs. A key factor contributing to this problem is the long-lasting nature of drug-seeking behavior associated with opioid use. We modeled this behavior in a rat drug self-administration paradigm in which drug-seeking is higher after extended abstinence than during the acute abstinence phase. The goal of this study was to determine the contribution of discrete or discriminative drug cues and drug dosage to time-dependent increases in drug-seeking. We examined heroin-seeking after 2 or 21 days of abstinence from two different self-administration cue-context environments using high or low doses of heroin and matched animals for their drug intake history. When lower dosages of heroin are used in discriminative or discrete cue protocols, drug intake history contributed to drug-seeking after abstinence, regardless of abstinence length. Incubation of opioid craving at higher dosages paired with discrete drug cues was not dependent on drug intake. Thus, interactions between drug cues and drug dosage uniquely determined conditions permissible for incubation of heroin craving. Understanding factors that contribute to long-lasting opioid-seeking can provide essential insight into environmental stimuli and drug-taking patterns that promote relapse after periods of successful abstinence.