bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic Profiling on Localized Gastric Cancer Identified CPLX1 as a Gene Promoting Malignant Phenotype of Gastric Cancer and a Predictor of Recurrence after Surgery and Subsequent Chemotherapy
Authors: Tanaka Haruyoshi , Kanda Mitsuro , Shimizu Dai , Tanaka Chie , Hattori Norifumi , Inokawa Yoshikuni , Hayashi Masamichi , Nakayama Goro , Kodera Yasuhiro 
Published: March 2021

AbstractLocalized gastric cancer (GC) becomes fatal once recurring. We still have room for improving their prognoses. Firstly, a transcriptomic analysis was done on surgically resected specimens of 16 patients with UICC stage III GC who underwent curative gastrectomy and adjuvant oral fluoropyrimidine monotherapy. Four of them were free from disease for longer than 5 years, and the others experienced 15 metachronous metastasis at either liver, peritoneum, or distant lymph nodes (n = 4 each) within 2 years after surgery. CPLX1 was identified as a novel oncogene candidate for recurrence among 57,749 genes. Secondary, we tested alteration of malignant phenotypes including drug resistance of gastric cancer cell lines by small interfering RNA-mediated CPLX1 knockdown. Inhibiting CPLX1 expression decreased the proliferation, motility, and invasiveness of GC cells, and increased apoptosis and sensitivity to fluorouracil. Thirdly, we validated the clinical significance of CPLX1 expression in GC by quantitative RT-PCR on 180 primary gastric cancer tissues of which patients underwent gastric resection for stage II and III GC without preoperative treatment between 2001 and 2014. Increased expression of CPLX1 mRNA in gastric cancer tissues correlated with worse prognoses and was an independent risk factor for peritoneal recurrence in subgroups receiving adjuvant chemotherapy. CPLX1 may represent a biomarker for recurrence of gastric cancer and a target for therapy.Brief descriptionTranscriptomic analysis identified CPLX1 gene as a novel oncogene candidate for gastric cancer. CPLX1 may promote epithelial-mesenchymal transition and evading apoptosis of gastric cancer cells even under a cytotoxic agent, and also be a predictor for recurrence after surgery for UICC Stage II-III gastric cancer.
Neurophysiological biomarkers of post-concussion syndrome: a scoping review
Authors: Mortaheb Sepehr , Filippini Maria Maddalena , Kaux Jean-François , Annen Jitka , Lejeune Nicolas , Martens Géraldine , Calderón Maria Antonia Fuentes , Laureys Steven , Thibaut Aurore 
Published: March 2021

AbstractBackground and objectivesPost-concussion syndrome (PCS) consists of neurologic and psychological complaints persisting after a mild traumatic brain injury (mTBI). It affects up to 50% of mTBI patients, causes long-term disability and reduces quality of life. The aim of this scoping review was to examine possible uses of different neuroimaging modalities in PCS.MethodsArticles from Pubmed database were screened to extract studies that investigated the relationship between any neuroimaging features and symptoms of PCS. Descriptive statistics were applied to report results.Results88 out of 939 papers were included in the final review. 12 examined conventional MRI (42% specificity), 27 diffusion weighted imaging (56% specificity), 25 functional MRI (84% specificity), 10 electro(magneto)encephalography (80% specificity), and 14 examined other techniques (71% specificity).ConclusionMRI was the most widely used technique, while functional techniques seem to be the most sensitive tools to evaluate PCS. Common patterns associated with symptoms of PCS were a decreased anticorrelation between the default mode network and the task positive network and reduced brain activity in specific areas (most often prefrontal cortex).SignificanceOur findings highlight the importance to use functional approaches which demonstrated a functional alternation in brain connectivity and activity in most studies assessing PCS.Highlightspost-concussion syndrome causes long term problems for up to 50% of patients after concussion.Among different neuroimaging techniques, fMRI and EEG show to be the most sensitive tools for PCS assessment.Heterogeneity of axonal injury, symptoms, and populations limits having a specific prognostic criteria for the PCS patients.
iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists
Authors: Vences Miguel , Miralles Aurélien , Brouillet Sophie , Ducasse Jacques , Fedosov Alexander , Kharchev Vladimir , Kostadinov Ivaylo , Kumari Sangeeta , Patmanidis Stefanos , Scherz Mark D. , Puillandre Nicolas , Renner Susanne S. 
Published: March 2021

AbstractWhile powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software specifically targeted at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and centered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The alpha version (iTaxoTools 0.1) distributed with this paper contains GUI versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files and tables; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses.
Tracking the rates and mechanisms of canopy damage and recovery following Hurricane Maria using multitemporal lidar data
Authors: Leitold Veronika , Morton Douglas C , Martinuzzi Sebastian , Paynter Ian , Uriarte Maria , Keller Michael , Ferraz António , Cook Bruce D , Corp Lawrence A , González Grizelle 
Published: March 2021

ABSTRACTHurricane Maria (Category 4) snapped and uprooted canopy trees, removed large branches, and defoliated vegetation across Puerto Rico. The magnitude of forest damages and the rates and mechanisms of forest recovery following Maria provide important benchmarks for understanding the ecology of extreme events. We used airborne lidar data acquired before (2017) and after Maria (2018, 2020) to quantify landscape-scale changes in forest structure along a 439-ha elevational gradient (100 to 800 m) in the Luquillo Experimental Forest. Damages from Maria were widespread, with 73% of the study area losing ≥1 m in canopy height (mean = −7.1 m). Taller forests at lower elevations suffered more damage than shorter forests above 600 m. Yet only 13% of the study area had canopy heights ≤2 m in 2018, a typical threshold for forest gaps, highlighting the importance of damaged trees and advanced regeneration on post-storm forest structure. Heterogeneous patterns of regrowth and recruitment yielded shorter and more open forests by 2020. Nearly 45% of forests experienced initial height loss (<-1 m, 2017-2018) followed by rapid height gain (>1 m, 2018-2020), whereas 21.6% of forests with initial height losses showed little or no height gain, and 17.8% of forests exhibited no structural changes >|1| m in either period. Canopy layers <10 m accounted for most increases in canopy height and fractional cover between 2018-2020, with gains split evenly between height growth and lateral crown expansion by surviving individuals. These findings benchmark rates of gap formation, crown expansion, and canopy closure following hurricane damage.MANUSCRIPT HIGHLIGHTSHurricane Maria gave forests a haircut by toppling trees and shearing branches.Regrowth after Maria was patchy, with equal areas of height gain and no change.3-D measures of forest recovery after hurricanes can improve ecosystem models.
Acute vagus nerve stimulation does not affect liking or wanting ratings of food in healthy participants
Authors: Müller Franziska K. , Teckentrup Vanessa , Kühnel Anne , Ferstl Magdalena , Kroemer Nils B. 
Published: March 2021

AbstractThe vagus nerve plays a vital role in the regulation of food intake and vagal afferent signals may help regulate food cue reactivity by providing negative homeostatic feedback. Despite strong evidence from preclinical studies on vagal afferent “satiety” signals in guiding food intake, evidence from human studies is largely inconclusive to date. Here, we investigated the acute effects of left or right transcutaneous auricular vagus nerve stimulation (taVNS) on subjective ratings of wanting and liking of various food and non-food items in 82 healthy participants (46 women, MBMI= 23.1 kg/m2). In contrast to previous reports in patients with depression, we found moderate to anecdotal evidence supporting the absence of taVNS-induced changes in food ratings. To test whether the absence of taVNS effects on food ratings is due to heterogeneity in the sample, we conducted post hoc subgroup analyses by splitting the data according to stimulation side and sex (between-subject factors) as well as caloric density, perceived healthiness, and flavor (sweet vs. savory) of the food (within-subject factors). This multiverse analysis largely supported the absence of taVNS-induced changes since the strongest subgroup effects provided only anecdotal evidence in favor of taVNS-induced changes. We conclude that acute taVNS only has a marginal effect on subjective ratings of food, suggesting that it is an unlikely mechanism for the reported long-term effects of VNS on body weight. In light of an absence of acute taVNS effects on food craving, our results call for future research on the correspondence between acute and chronic effects of vagal afferent stimulation.
Profiles of expressed mutations in single cells reveal subclonal expansion patterns and therapeutic impact of intratumor heterogeneity
Authors: Mehrabadi Farid Rashidi , Marie Kerrie L. , Pérez-Guijarro Eva , Malikić Salem , Azer Erfan Sadeqi , Yang Howard H. , Kızılkale Can , Gruen Charli , Robinson Welles , Liu Huaitian , Kelly Michael C. , Marcelus Christina , Burkett Sandra , Buluç Aydın , Ergün Funda , Lee Maxwell P. , Merlino Glenn , Day Chi-Ping , Sahinalp S. Cenk 
Published: March 2021

AbstractAdvances in single-cell RNA sequencing (scRNAseq) technologies uncovered an unexpected complexity in tumors, underlining the relevance of intratumor heterogeneity to cancer progression and therapeutic resistance. Heterogeneity in the mutational composition of cancer cells is a result of distinct (sub)clonal expansions, each with a distinct metastatic potential and resistance to specific treatments. Unfortunately, due to their low read coverage per cell, scRNAseq datasets are too sparse and noisy to be used for detecting expressed mutations in single cells. Additionally, the large number of cells and mutations present in typical scRNAseq datasets are too large for available computational tools to, e.g., infer distinct subclones, lineages or trajectories in a tumor. Finally, there are no principled methods to assess distinct subclones inferred through single-cell sequencing data and the genomic alterations that seed and potentially cause them. Here we presentTrisicell, a computational toolkit for scalable mutational intratumor heterogeneity inference and assessment from scRNAseq as well as single-cell genome or exome sequencing data.Trisicellallows reliable identification of distinct clonal lineages of a tumor, offering the ability to focus on the most important subclones and the genomic alterations that are associated with tumor proliferation. We comprehensively assessedTrisicellon a melanoma model by comparing distinct lineages and subclones it identifies on scRNAseq data, to those inferred using matching bulk whole exome (bWES) and transcriptome (bWTS) sequencing data from clonal sublines derived from single cells. Our results demonstrate that distinct lineages and subclones of a tumor can be reliably inferred and evaluated based on mutation calls from scRNAseq data through the use ofTrisicell. Additionally, they reveal a strong correlation between aggressiveness and mutational composition, both across the inferred subclones, and among human melanomas. We also appliedTrisicellto infer and evaluate distinct subclonal expansion patterns of the same mouse melanoma model after treatment with immune checkpoint blockade (ICB). After integratively analyzing our cell-specific mutation calls with their expression profiles, we observed that each subclone with a distinct set of novel somatic mutations is strongly associated with a specific developmental status. Moreover, each subclone had developed a unique ICB-resistance mechanism. These results demonstrate thatTrisicellcan robustly utilize scRNAseq data to delineate intratumor heterogeneity and help understand biological mechanisms underlying tumor progression and resistance to therapy.
Sensorimotor temporal recalibration: the contribution of motor-sensory and inter-sensory components
Authors: Arikan Belkis Ezgi , van Kemenade Bianca M. , Fiehler Katja , Kircher Tilo , Drewing Knut , Straube Benjamin 
Published: March 2021

AbstractAdaptation to delays between actions and sensory feedback is important for efficiently interacting with our environment. Adaptation may rely on predictions of action-feedback pairing (motor-sensory component), or predictions of tactile-proprioceptive sensation from the action and sensory feedback of the action (inter-sensory component). Reliability of temporal information might differ across sensory feedback modalities (e.g. auditory or visual), influencing adaptation. Here, we investigated the role of motor-sensory and inter-sensory components on sensorimotor temporal recalibration for motor-auditory events (button press-tone) and motor-visual events (button press-Gabor patch). In the adaptation phase of the experiment, the motor action-feedback event pairs were presented with systematic temporal delays (0ms or 150ms). In the subsequent test phase, sensory feedback of the action were presented with variable delays. The participants were then asked whether this delay could be detected. To disentangle motor-sensory from inter-sensory component, we varied movements (active button press or passive depression of button) at adaptation and test. Our results suggest that motor-auditory recalibration is mainly driven by motor-sensory component, whereas motor-visual recalibration is mainly driven by inter-sensory component. Recalibration transferred from vision to audition, but not from audition to vision. These results indicate that motor-sensory and inter-sensory components of recalibration are weighted in a modality-dependent manner.
SBGNview: Data Analysis, Integration and Visualization on All Pathways
Authors: Dong Xiaoxi , Vegesna Kovidh , Brouwer Cory , Luo Weijun 
Published: March 2021

AbstractPathway analysis is widely used in genomics and omics research, but the data visualization has been highly limited in function, pathway coverage and data format. Here we develop SBGNview a comprehensive solution to address these needs. By adopting the standard SBGN format, SBGNview greatly extend the coverage of pathway based analysis and data visualization to essentially all major pathway databases beyond KEGG, including 5200 reference pathways and over 3000 species. In addition, SBGNview substantially extends current tools in both design and function, including standard coherent input/output formats, high quality graphics convenient for both computational and manual analysis, and flexible and open-end workflow. In addition to pathway analysis and data visualization, SBGNview provides essential infrastructure for SBGN data manipulation and processing. SBGNview is available online:https://github.com/datapplab/SBGNview.
Rescue of aberrant huntingtin palmitoylation ameliorates mutant huntingtin-induced toxicity
Authors: Lemarié Fanny L. , Caron Nicholas S. , Sanders Shaun S. , Schmidt Mandi E. , Nguyen Yen T.N. , Ko Seunghyun , Xu Xiaohong , Pouladi Mahmoud A. , Martin Dale D.O. , Hayden Michael R. 
Published: March 2021

AbstractHuntington disease (HD) is a neurodegenerative disorder caused by a CAG expansion in theHTTgene that codes for an elongated polyglutamine tract in the huntingtin (HTT) protein. HTT is subject to multiple post-translational modifications (PTMs) that regulate its cellular function. Mutating specific PTM sites within mutant HTT (mHTT) in HD mouse models can modulate disease phenotypes, highlighting the key role of HTT PTMs in the pathogenesis of HD. These findings have led to increased interest in developing small molecules to modulate HTT PTMs in order to decrease mHTT toxicity. However, the therapeutic efficacy of pharmacological modulation of HTT PTMs in preclinical HD models remains largely unknown. HTT is palmitoylated at cysteine 214 by the huntingtin-interacting protein 14 (HIP14 or ZDHHC17) and 14-like (HIP14L or ZDHHC13) acyltransferases. Here, we assessed if HTT palmitoylation should be regarded as a therapeutic target to treat HD by (1) investigating palmitoylation dysregulation in rodent and human HD model systems, (2) measuring the impact of mHTT-lowering therapy on brain palmitoylation, and (3) evaluating if HTT palmitoylation can be pharmacologically modulate. We show that palmitoylation of mHTT and some HIP14/HIP14L-substrates is decreased early in multiple HD mouse models, and that aging further reduces HTT palmitoylation. Lowering mHTT in the brain of YAC128 mice is not sufficient to rescue aberrant palmitoylation. However, we demonstrate that mHTT palmitoylation can be normalized in COS-7 cells, in YAC128 cortico-striatal primary neurons and HD patient-derived lymphoblasts using an acyl-protein thioesterase (APT) inhibitor. Moreover, we show that modulating palmitoylation reduces mHTT aggregation and mHTT-induced cytotoxicity in COS-7 cells and YAC128 neurons.HighlightsPalmitoylation of mHTT is reduced in multiple transgenic HD mouse modelsHTT palmitoylation decreases with increasing polyQ length in HD patient cellsmHTT-lowering in mouse brains does not rescue aberrant palmitoylationmHTT palmitoylation in HD patient-derived cells can be rescued via APT inhibitionPromoting palmitoylation reduces mHTT aggregation and cytotoxicityin vitro
Little evidence that Eurasian jays (Garrulus glandarius) protect their caches by responding to cues about a conspecific’s desire and visual perspective
Authors: Amodio Piero , Farrar Benjamin G. , Krupenye Christopher , Ostojić Ljerka , Clayton Nicola S. 
Published: March 2021

ABSTRACTCorvids appear to be capable of adjusting their behaviour according to another’s perspective, knowledge and desire. For example, Eurasian jays have been found to employ a variety of cache protection strategies to minimise cache loss by responding to cues about the visual perspective or current desire of an observing conspecific. However, it is not known whether these jays (or any other corvid) can integrate multiple cues about different mental states and perform the optimal response accordingly. Across five experiments, we found little evidence that our Eurasian jays responded to either the visual perspective or current desire of another agent. In Experiments 1 and 2 we investigated whether Eurasian jays can limit the risk of cache loss by responding simultaneously to cues about the desire and perspective of a potential conspecific pilferer. Building on established paradigms, we used opaque and clear barriers to manipulate the observer’s visual access to cache locations, and specific satiety to manipulate the observer’s desire towards different types of food. Across both experiments the jays’ caching pattern provided no evidence that they could integrate information about the observer’s desire and perspective. Moreover, the results were also inconsistent with the previously reported effects that jays protect their caches by responding to either the visual access or specific satiety of the observer independently. To gain further insight into these unexpected results, we conducted three more experiments. In Experiments 3 and 4, we attempted to replicate the previous finding that Eurasian jays prefer to cache behind an opaque barrier over a clear barrier when observed by a conspecific than when caching in private. In Experiment 5, we further investigated the previous finding that jays preferentially cache a type of food that had been eaten to satiety by a conspecific over a food that had not been eaten by the conspecific. Experiments 3, 4 and 5 found no significant effects in the direction of the previously reported effects, questioning their robustness. We conclude by discussing the implications of our study for the field of corvid cognition and highlight several key issues that affect the reliability of comparative cognition research.
Sexual antagonism in haplodiploids
Authors: Hitchcock Thomas J. , Gardner Andy , Ross Laura 
Published: March 2021

AbstractFemales and males may face different selection pressures, such that alleles conferring a benefit in one sex may be deleterious in the other. Such sexual antagonism has received a great deal of theoretical and empirical attention, almost all of which has focused on diploids. However, a sizeable minority of animals display an alternative haplodiploid mode of inheritance, encompassing both arrhenotoky, whereby males develop from unfertilized eggs, and paternal genome elimination (PGE), whereby males receive but do not transmit a paternal genome. Alongside unusual genetics, haplodiploids often exhibit social ecologies that modulate the relative value of females and males. Here we develop a series of evolutionary-genetic models of sexual antagonism for haplodiploids, incorporating details of their molecular biology and social ecology. We find that: 1) PGE promotes female-beneficial alleles more than arrhenotoky, and to an extent determined by the timing of elimination – and degree of silencing of – the paternal genome; 2) sib-mating relatively promotes female-beneficial alleles, as do other forms of inbreeding, including limited male-dispersal, oedipal-mating, and the pseudo-hermaphroditism ofIcerya purchasi; 3) resource competition between related females relatively inhibits female-beneficial alleles; and 4) sexual antagonism foments conflicts between parents and offspring, endosymbionts and hosts, and maternal-origin and paternal-origin genes.
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs
Authors: Sibbesen Jonas A. , Eizenga Jordan M. , Novak Adam M. , Sirén Jouni , Chang Xian , Garrison Erik , Paten Benedict 
Published: March 2021

AbstractPangenomics is emerging as a powerful computational paradigm in bioinformatics. This field uses population-level genome reference structures, typically consisting of a sequence graph, to mitigate reference bias and facilitate analyses that were challenging with previous reference-based methods. In this work, we extend these methods into transcriptomics to analyze sequencing data using the pantranscriptome: a population-level transcriptomic reference. Our novel toolchain can construct spliced pangenome graphs, map RNA-seq data to these graphs, and perform haplotype-aware expression quantification of transcripts in a pantranscriptome. This workflow improves accuracy over state-of-the-art RNA-seq mapping methods, and it can efficiently quantify haplotype-specific transcript expression without needing to characterize a sample’s haplotypes beforehand.