bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations between sensory processing and electrophysiological and neurochemical measures in children with ASD: an EEG-MRS study
Authors: Pierce Sarah , Kadlaskar Girija , Edmondson David A. , McNally Keehn Rebecca , Dydak Ulrike , Keehn Brandon 
Published: January 2021

Abstract
Background
Autism spectrum disorder (ASD) is associated with hyper- and/or hypo-sensitivity to sensory input. Spontaneous alpha power, which plays an important role in shaping responsivity to sensory information, is reduced across the lifespan in individuals with ASD. Furthermore, an excitatory/inhibitory imbalance has also been linked to sensory dysfunction in ASD and has been hypothesized to underlie atypical patterns of spontaneous brain activity. The present study examined whether resting-state alpha power differed in children with ASD as compared to TD children, and investigated the relationships between alpha levels, concentrations of excitatory and inhibitory neurotransmitters, and atypical sensory processing in ASD.

Methods
Participants included thirty-one children and adolescents with ASD and thirty-one age- and IQ-matched typically developing (TD) participants. Resting-state electroencephalography (EEG) was used to obtain measures of alpha power. A subset of participants (ASD = 16; TD = 16) also completed a magnetic resonance spectroscopy (MRS) protocol in order to measure concentrations of excitatory (glutamate + glutamine; Glx) and inhibitory (GABA) neurotransmitters.

Results
Children with ASD evidenced significantly decreased resting alpha power compared to their TD peers. MRS estimates of GABA and Glx did not differ between groups with the exception of Glx in the temporal-parietal junction. Inter-individual differences in alpha power within the ASD group were not associated with region-specific concentrations of GABA or Glx, nor were they associated with sensory processing differences. However, atypically decreased Glx was associated with increased sensory impairment in children with ASD.

Conclusions
Although we replicated prior reports of decreased alpha power in ASD, atypically reduced alpha was not related to neurochemical differences or sensory symptoms in ASD. Instead, reduced Glx in the temporal-parietal cortex was associated with greater hyper-sensitivity in ASD. Together, these findings may provide insight into the neural underpinnings of sensory processing differences present in ASD.
Detection of unrecorded environmental challenges in high-frequency recorded traits, and genetic determinism of resilience to challenge, with an application on feed intake in lambs
Authors: Garcia-Baccino Carolina Andrea , Marie-Etancelin Christel , Tortereau Flavie , Marcon Didier , Weisbecker Jean-Louis , Legarra Andrés 
Published: January 2021

AbstractBackgroundResilient animals can remain productive under different environmental conditions. Rearing in increasingly heterogeneous environmental conditions increases the need of selecting resilient animals. Detection of environmental challenges that affect an entire population can provide a unique opportunity to select animals that are more resilient to these events. The objective of this study was two-fold: (1) to present a simple and practical data-driven approach to estimate the probability that, at a given date, an unrecorded environmental challenge occurred; and (2) to evaluate the genetic determinism of resilience to such events.MethodsOur method consists of inferring the existence of highly variable days (indicator of environmental challenges) via mixture models applied to frequently recorded phenotypic measures and then using the inferred probabilities of the occurrence of an environmental challenge in a reaction norm model to evaluate the genetic determinism of resilience to these events. These probabilities are estimated for each day (or other time frame). We illustrate the method by using an ovine dataset with daily feed intake (DFI) records.ResultsUsing the proposed method, we estimated the probability of the occurrence of an unrecorded environmental challenge, which proved to be informative and useful for inclusion as a covariate in a reaction norm animal model. We estimated the breeding values for sensitivity of the genetic potential for DFI of animals to environmental challenges. The level and slope of the reaction norm were negatively correlated (− 0.46 ± 0.21).ConclusionsOur method is promising and appears to be viable to identify unrecorded events of environmental challenges, which is useful when selecting resilient animals and only productive data are available. It can be generalized to a wide variety of phenotypic records from different species and used with large datasets. The negative correlation between level and slope indicates that a hypothetical selection for increased DFI may not be optimal depending on the presence or absence of stress. We observed a reranking of individuals along the environmental gradient and low genetic correlations between extreme environmental conditions. These results confirm the existence of a G $$\times$$× E interaction and show that the best animals in one environmental condition are not the best in another one.
SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model
Authors: Zheng Yan , Zhong Yuanke , Hu Jialu , Shang Xuequn 
Published: January 2021

Abstract
Background
Single-cell RNA sequencing (scRNA-seq) enables the possibility of many in-depth transcriptomic analyses at a single-cell resolution. It’s already widely used for exploring the dynamic development process of life, studying the gene regulation mechanism, and discovering new cell types. However, the low RNA capture rate, which cause highly sparse expression with dropout, makes it difficult to do downstream analyses.

Results
We propose a new method SCC to impute the dropouts of scRNA-seq data. Experiment results show that SCC gives competitive results compared to two existing methods while showing superiority in reducing the intra-class distance of cells and improving the clustering accuracy in both simulation and real data.

Conclusions
SCC is an effective tool to resolve the dropout noise in scRNA-seq data. The code is freely accessible at https://github.com/nwpuzhengyan/SCC.
CXCL9 secreted by tumor-associated dendritic cells up-regulates PD-L1 expression in bladder cancer cells by activating the CXCR3 signaling
Authors: Xiu Weigang , Luo Jingjing 
Published: January 2021

Abstract
Background
Tumor-associated dendritic cells (TADCs) can interact with tumor cells to suppress anti-tumor T cell immunity. However, there is no information on whether and how TADCs can modulate programmed death-ligand 1 (PD-L1) expression by cancer cells.

Methods
Human peripheral blood monocytes were induced for DCs and immature DCs were cultured alone, or co-cultured with bladder cancer T24 or control SV-HUC-1 cells, followed by stimulating with LPS for DC activation. The activation status of DCs was characterized by flow cytometry and allogenic T cell proliferation. The levels of chemokines in the supernatants of co-cultured DCs were measured by CBA-based flow cytometry. The impacts of CXCL9 on PD-L1, STAT3 and Akt expression and STAT3 and Akt phosphorylation in T24 cells were determined by flow cytometry and Western blot.

Results
Compared with the control DCs, TADCs exhibited immature phenotype and had significantly lower capacity to stimulate allogenic T cell proliferation, particularly in the presence of recombinant CXCL9. TADCs produced significantly higher levels of CXCL9, which enhanced PD-L1 expression in T24 cells. Pre-treatment with AMG487 abrogated the CXCL9-increased PD-L1 expression in T24 cells. Treatment with CXCL9 significantly enhanced STAT3 and Akt activation in T24 cells.

Conclusions
TADCs produced high levels of CXCL9 that increased PD-L1 expression in bladder cancer T24 cells by activating the CXCR3-related signaling. Our findings may shed new lights in understanding the regulatory roles of TADCs in inhibiting antitumor T cell responses and promoting tumor growth.
Comparison of gut microbiota structure and Actinobacteria abundances in healthy young adults and elderly subjects: a pilot study
Authors: Li Jun , Si Haiyan , Du Haitao , Guo Hongxia , Dai Huanqin , Xu Shiping , Wan Jun 
Published: January 2021

Abstract
Background
The aim was to determine the potential association of the gut microbiota composition, especially the abundance of Actinobacteria, as well as the differentiation of functional and resistance genes with age (young adults vs elderly subjects) in China.

Results
The patterns of relative abundance of all bacteria isolated from fecal samples differed between young adults and elderly subjects, but the alpha diversity (Chao1 P = 0.370, Shannon P = 0.560 and Simpson P = 0.270) and beta diversity (ANOSIM R = 0.031, P = 0.226) were not significantly different. There were 3 Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways (carbon metabolism, inositol phosphate metabolism, and sesquiterpenoid and triterpenoid biosynthesis) and 7 antibiotic resistant genes (ARGs) (macrolide lincosamide-streptogramin B (MLSB), tetracycline, aminoglycoside, sulfonamide, fosmidomycin, lincomycin, and vancomycin) that showed significant differences between the 2 groups (all P < 0.05). The abundance of Actinomycetes was enriched (about 2.4-fold) in young adults. Bifidobacteria dominated in both young adults and elderly subjects, with overall higher abundances in young adults (P > 0.05). Only the Bifidobacterium_dentium species showed significant differences between the 2 groups (P = 0.013), with a higher abundance in elderly subjects but absent in young adults.

Conclusions
The present study revealed that there were 3 KEGG metabolic pathways and 7 ARGs as well as enhanced Bifidobacterium_dentium species abundance in elderly compared to young subjects.
The NAC-type transcription factor CaNAC46 regulates the salt and drought tolerance of transgenic Arabidopsis thaliana
Authors: Ma Jing , Wang Li-yue , Dai Jia-xi , Wang Ying , Lin Duo 
Published: January 2021

Abstract
Background
The NAC (NAM, ATAF1/ATAF2, and CUC2) transcription factors belong to a large family of plant-specific transcription factors in monocot and dicot species. These transcription factors regulate the expression of stress tolerance-related genes that protect plants from various abiotic stresses, including drought, salinity, and low temperatures.

Results
In this study, we identified the CaNAC46 transcription factor gene in Capsicum annuum. Its open reading frame was revealed to comprise 921 bp, encoding a protein consisting of 306 amino acids, with an isoelectric point of 6.96. A phylogenetic analysis indicated that CaNAC46 belongs to the ATAF subfamily. The expression of CaNAC46 was induced by heat, cold, high salt, drought, abscisic acid, salicylic acid, and methyl jasmonate treatments. Thus, CaNAC46 may be important for the resistance of dry pepper to abiotic stresses. A subcellular localization analysis confirmed that CaNAC46 is localized in the nucleus. The overexpression of CaNAC46 improved the tolerance of transgenic Arabidopsis thaliana plants to drought and salt stresses. The CaNAC46-overexpressing lines had longer roots and more lateral roots than wild-type lines under prolonged drought and high salt stress conditions. Additionally, CaNAC46 affected the accumulation of reactive oxygen species (ROS). Moreover, CaNAC46 promoted the expression of SOD, POD, RD29B, RD20, LDB18, ABI, IAA4, and P5CS. The malondialdehyde contents were higher in TRV2-CaNAC46 lines than in wild-type plants in response to drought and salt stresses. Furthermore, the expression levels of stress-responsive genes, such as ABA2, P5CS, DREB, RD22, CAT, and POD, were down-regulated in TRV2-CaNAC46 plants.

Conclusions
Under saline and drought conditions, CaNAC46 is a positive regulator that activates ROS-scavenging enzymes and enhances root formation. The results of our study indicate CaNAC46 is a transcriptional regulator responsible for salinity and drought tolerance and suggest the abiotic stress-related gene regulatory mechanisms controlling this NAC transcription factor are conserved between A. thaliana and pepper.
Are activated B cells involved in the process of myocardial fibrosis after acute myocardial infarction? An in vivo experiment
Authors: Mo Fanrui , Luo Ying , Yan Yuluan , Li Juan , Lai Shayi , Wu Weifeng 
Published: January 2021

Abstract
Background
Inflammatory cells infiltrate into the ischemic and hypoxic myocardial tissue after myocardial infarction. B cells gather at the site of myocardial injury and secrete cytokines to regulate immune inflammation and fiber repair processes.

Methods
The animal experiment used ligation of the left anterior descending (LAD) artery of C57BL/6 mice to establish a mouse acute myocardial infarction (AMI) model to observe changes in activated B cells and cytokines at different time points. Twelve-week-old C57BL/6 male mice were randomly divided into the Sham group (24 mice) (thread under the LAD artery without ligation) and the AMI group (64 mice). In addition, C57BL/6 B-cell knockout (BKO) mice and C57BL/6 wild-type (WT) mice were used to establish AMI models to observe the expression levels of cardiomyocyte cytokines, such as TNF-α IL-1β, IL-6, TGF-β1, COL1-A1, COL3-AIII, TIMP, and MMP9. Moreover, pathological and collagen changes in the myocardium were analysed. One-way ANOVA and LSD method was used for comparisons of multiple and pairwise groups respectively. P < 0.05 indicated significant differences.

Results
An AMI model of C57BL/6 mice was established successfully. The ratio of activated B cells and the expression of TNF-α, IL-1β, IL-6, TGF-β1, and B cell activating factor (BAFF) in the 5-day subgroup were the highest in the myocardium, spleen and peripheral blood with the most obvious myocardial inflammatory cell infiltration. The cytokines mRNA expression levels in the 5-day subgroup of the BKO group were decreased compared with those in the WT group (P < 0.05). Among the 2-week subgroups of the Sham, WT and BKO groups, the the LVEDd and LVESd of the BKO group were lower than those of the WT group (P < 0.05), and the left ventricular ejection fraction was higher than that of the WT group (P < 0.05).

Conclusion
Activated B cells participate in the sustained state of myocardial inflammation and immune system activation after AMI, and may affect the metabolism of myocardial collagen after AMI by secreting cytokines. Moreover, B cells promote the expression of myocardial collagen Type I and Type III and damage the left ventricular ejection function.
Long-term prognosis of short QT interval in Korean patients: a multicenter retrospective cohort study
Authors: Kim Dae-Young , Uhm Jae-Sun , Kim Min , Kim In-Soo , Jin Moo-Nyun , Yu Hee Tae , Kim Tae-Hoon , Kim Jong-Youn , Joung Boyoung , Pak Hui-Nam , Lee Moon-Hyoung 
Published: January 2021

Abstract
Background
Short QT syndrome is a rare, inherited channelopathy associated with sudden cardiac arrest (SCA) but the characteristics and prognosis of short QT interval (SQTI) in Korean patients remain unclear. This study aimed to determine the clinical characteristics and outcomes of SQTI in a Korean population.

Methods
Consecutive patients with SQTI from January 1999 to March 2019 in three university hospitals in South Korea were recruited.
SQTI was defined as a Bazett’s formula-corrected QT interval (QTc) ≤ 340 ms in serial electrocardiograms. Age- and sex-matched patients with a normal QTc and without overt cardiovascular disease were included in a 1:4 ratio. Clinical and ECG features and outcomes were compared between patients with and without SQTI.

Results
34 patients with SQTI [age, 23.5 (21–30.5) years; 31 male] were followed up for 4.8 (2.0–7.8) years. Early repolarization, tall T wave, and U wave were significantly more frequent in patients with SQTI than in those without SQTI. QT dispersion [44.0 (28.0–73.0) vs. 20.0 (12.0–35.0) ms, P < 0.001] was significantly wider and heart rate [52.0 (47.0–58.0) vs. 70.0 (62.3–84.0)/min, P < 0.001] was significantly slower in patients with SQTI than in those without. Atrial fibrillation (AF, 11.8% vs. 2.2%, P = 0.030) and ventricular arrhythmia (VA)/SCA (8.7% vs. 0%, P = 0.007) were significantly more frequent in patients with SQTI than in those without. SQTI was significantly associated with AF [odds ratio, 5.911; 95% confidence interval, 1.257–27.808; P = 0.025] and VA/SCA.

Conclusions
In this subset of Korean population, SQTI was associated with AF and VA/SCA.
Berry syndrome: a case report and literature review
Authors: Bi Wen-jing , Xiao Yang-jie , Liu Yue-jia , Hou Yang , Ren Wei-dong 
Published: January 2021

Abstract
Background
Berry syndrome, a rare combination of cardiac anomalies, consists of aortopulmonary window (APW); aortic origin of the right pulmonary artery; interrupted aortic arch (IAA) or hypoplastic aortic arch or coarctation of the aorta; and an intact ventricular septum. There is lack of review articles that elucidate the clinical features, diagnosis, treatment, and outcomes of Berry syndrome. This publication systematically reviews the 89 cases published since 1982 on Berry syndrome.

Case presentation
A 38-year-old woman presented with a loud murmur and cyanosis. Transthoracic echocardiography demonstrated a severely dilated aorta and main pulmonary artery with a large intervening defect. Distal to the APW, the ascending aorta gave rise to the right pulmonary artery. Additionally, a type A IAA, an intact ventricular septum, and a large patent ductus arteriosus were revealed. Computed tomography angiography with 3-dimensional reconstruction confirmed above findings. This is the first report of a patient of this age with Berry syndrome who did not undergo surgery.

Conclusions
Berry syndrome is a rare but well-identified and surgically correctable anomaly. Patients with Berry syndrome should be followed up for longer periods to better characterize long-term outcomes.
Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms
Authors: Bi Siwei , Liu Ruiqi , He Linfeng , Li Jingyi , Gu Jun 
Published: January 2021

AbstractBackgroundAneurysm is a severe and fatal disease. This study aims to comprehensively identify the highly conservative co-expression modules and hub genes in the abdominal aortic aneurysm (AAA), thoracic aortic aneurysm (TAA) and intracranial aneurysm (ICA) and facilitate the discovery of pathogenesis for aneurysm.MethodsGSE57691, GSE122897, and GSE5180 microarray datasets were downloaded from the Gene Expression Omnibus database. We selected highly conservative modules using weighted gene co‑expression network analysis before performing the Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway and Reactome enrichment analysis. The protein–protein interaction (PPI) network and the miRNA-hub genes network were constructed. Furtherly, we validated the preservation of hub genes in three other datasets.ResultsTwo modules with 193 genes and 159 genes were identified as well preserved in AAA, TAA, and ICA. The enrichment analysis identified that these genes were involved in several biological processes such as positive regulation of cytosolic calcium ion concentration, hemostasis, and regulation of secretion by cells. Ten highly connected PPI networks were constructed, and 55 hub genes were identified. In the miRNA-hub genes network, CCR7 was the most connected gene, followed by TNF and CXCR4. The most connected miRNAs were hsa-mir-26b-5p and hsa-mir-335-5p. The hub gene module was proved to be preserved in all three datasets.ConclusionsOur study highlighted and validated two highly conservative co-expression modules and miRNA-hub genes network in three kinds of aneurysms, which may promote understanding of the aneurysm and provide potential therapeutic targets and biomarkers of aneurysm.
Risk factors of poor prognosis and impairment of activities of daily living in patients with hemorrhagic gastroduodenal ulcers
Authors: Arai Junya , Kato Jun , Toda Nobuo , Kurokawa Ken , Shibata Chikako , Kurosaki Shigeyuki , Funato Kazuyoshi , Kondo Mayuko , Takagi Kaoru , Kojima Kentaro , Ohki Takamasa , Seki Michiharu , Tagawa Kazumi 
Published: January 2021

Abstract
Background
Impairment of activities of daily living (ADL) due to hemorrhagic gastroduodenal ulcers (HGU) has rarely been evaluated. We analyzed the risk factors of poor prognosis, including mortality and impairment of ADL, in patients with HGU.

Methods
In total, 582 patients diagnosed with HGU were retrospectively analyzed. Admission to a care facility or the need for home adaptations during hospitalization were defined as ADL decline. The clinical factors were evaluated: endoscopic features, need for interventional endoscopic procedures, comorbidities, symptoms, and medications. The risk factors of outcomes were examined with multivariate analysis.

Results
Advanced age (> 75 years) was a significant predictor of poor prognosis, including impairment of ADL. Additional significant risk factors were renal disease (odds ratio [OR] 3.43; 95% confidence interval [CI] 1.44–8.14) for overall mortality, proton pump inhibitor (PPIs) usage prior to hemorrhage (OR 5.80; 95% CI 2.08–16.2), and heart disease (OR 3.05; 95% CI 1.11–8.43) for the impairment of ADL. Analysis of elderly (> 75 years) subjects alone also revealed that use of PPIs prior to hemorrhage was a significant predictor for the impairment of ADL (OR 8.24; 95% CI 2.36–28.7).

Conclusion
In addition to advanced age, the presence of comorbidities was a risk of poor outcomes in patients with HGU. PPI use prior to hemorrhage was a significant risk factor for the impairment of ADL, both in overall HGU patients and in elderly patients alone. These findings suggest that the current strategy for PPI use needs reconsideration.