bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insight of Transcriptional Regulators reveals the Tolerance Mechanism of Carpet-grass (Axonopus compressus) Against Drought
Authors: Nawaz Mohsin , Li Liao , Azeem Farrukh , Shabbir Samina , Zohaib Ali , Ashraf Umair , Yang Hubiao , Wang Zhiyong 
Published: October 2020

Abstract
Background: Carpet grass [Axonopus compressus (L.)] is an important warm-season perennial grass around the world and is known for its adaptability to varied environmental conditions. However, Carpet grass lacks enough data in public data banks, which confined our comprehension on the mechanisms of environmental adaptations, gene discovery and development of molecular markers. In current study, the DEGs (differentially expressed genes) in Axonopus compressus under drought stress (DS) were identified and compared with CK (control) by RNA-Seq. Results: A total of 263,835 unigenes were identified in Axonopus compressus, and 201,303 (also added to the numbers of the remaining 2 data bases) a sequence of unigenes significantly matched in at least one of the seven databases. A total of 153697 (58.25%) unigenes classified to 144 KEGG pathways, and 7,444 unigenes were expressed differentially between DS and CK, of which 4,249 were up-regulated and 3,195 were down-regulated unigenes. Of the 50 significantly enriched GO terms, 18, 6 and 14 items were related to BP, CC and MF respectively. Analysis of KEGG enrichment revealed 2569 DEGs involved in 143 different pathways, under drought stress. 2,747 DEGs were up-regulated and 2,502 DEGs were down-regulated. Moreover, we identified 352 transcription factors (TFs) in Axonopus compressus, of which 270 were differentially expressed between CK and DS. The qRT-PCR validation experiment also support the transcriptional response of Axonopus compressus against drought. Accuracy of transcriptome unigenes of Axonopus compressus was assessed with BLAST, which showed 3,300 sequences of Axonopus compressus in the NCBI.Conclusion: The 7,444 unigenes were found to be between DS and CK treatments which indicate that there is a strong mechanism of drought tolerance in Axonopus compressus. The current findings provide the first framework for further investigations for the particular roles of these unigenes in Axonopus compressus in response to drought.
Identification of Candidate Genes Controlling Fiber Quality Traits in Upland Cotton through Integration of Meta-QTL, Significant SNP and Transcriptomic Data
Authors: Shudi XU , Pan Zhenyuan , Yin Feifan , Yang Qingyong , Lin Zhongxu , Wen Tianwang , Zhu Longfu , Zhang Dawei , Nie Xinhui 
Published: October 2020

Abstract
Background: Meta-analysis of quantitative trait locus (QTL) is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies. The combination of meta-QTL intervals, significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.Results: In our study, 884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1, as a result, 74 meta-QTLs were identified, including 19 meta-QTLs for fiber length (FL); 18 meta-QTLs for fiber strength (FS); 11 meta-QTLs for fiber uniformity (FU); 11 meta-QTLs for fiber elongation (FE); and 15 meta-QTLs for micronaire (MIC). Combined with 8,589 significant SNPs associated with fiber quality traits collected from 15 studies, 297 candidate genes were identified in the meta-QTL intervals, 20 of which showed high expression specifically in the developing fibers. According to the function annotations, some of the 20 key candidate genes are associated with the fiber development.Conclusions: This study provides not only stable QTLs used for marker-assisted selection (MAS), but also candidate genes to uncover the molecular mechanisms for cotton fiber development.
Inhibition of pyruvate dehydrogenase kinase influence microbiota and metabolomic profile in pancreatic cancer xenograft mice
Authors: Adamberg Kaarel , Vilu Raivo , Pazienza Valerio 
Published: October 2020

Abstract
Objective: Despite recent advances in treatment options, pancreatic cancer remains the most deadly major cancer. Targeting metabolism represents an emerging anti-cancer strategy. Results: Metagenomic 16S analysis was employed to explore the effect of Dichloroacetate (DCA) on the composition of the fecal microbiota and metabolomic profile was assessed on in vivo pancreatic cancer mouse xenograft model. Pancreatic cancer xenograft mice displayed a shift of microbiota’ profile as compared to control mice without DCA treatment and a significant decrease of the purine bases inosine xanthine together with their metabolically-related compound hypoxanthine were observed in the DCA treated group as compared to the control group. Two aminoacids methionine and aspartic acid resulted decreased and increased respectively. DCA affects tumor environment and studies are needed in order to understand whether DCA supplementation could be supportive as synergistic approach to enhance the efficacy of existing cancer treatments in pancreatic cancer patients.
Effects of virtual reality training on occupational performance and self-efficacy of patients with stroke: a randomized controlled trial
Authors: Long Yi , Ouyang Rangge , Zhang Jiaqi 
Published: October 2020

Abstract
Background—Virtual reality (VR) has been broadly applied in post-stroke rehabilitation. However, studies on occupational performance and self-efficacy as primary outcomes of stroke rehabilitation using VR are lacking. Thus, this study aims to investigate the effects of VR training on occupational performance and self-efficacy in patients with stroke.Methods—This was an assessor-blinded, randomized controlled trial. Sixty participants with first-ever stroke (< 1-year onset) underwent rehabilitation in a single acute hospital. Participants were randomly assigned to either the VR group (n = 30) or control group (n = 30). Both groups received dose-matched conventional rehabilitation (i.e., 45 min, five times per week over 3 weeks). The VR group received additional 45-min VR training for five weekdays over 3 weeks. The primary outcome measures were the Canadian Occupational Performance Measure and Stroke Self-Efficacy Questionnaire. Secondary outcome measures included Modified Barthel Index, Fugl-Meyer Assessment-Upper Extremity, and Functional Test for the Hemiplegic Upper Extremity. The assessment was conducted at baseline and after the 3-week intervention.Results—A total of 52 participants (86.7%) completed the trial. Significant between-group differences in Stroke Self-Efficacy Questionnaire (Median Difference = 8, P = 0.043) and Modified Barthel Index (Median Difference = 10, P = 0.030) were found; however, no significant between-group differences in Canadian Occupational Performance Measure, Fugl-Meyer Assessment-Upper Extremity, and Functional Test for the Hemiplegic Upper Extremity were noted. No serious adverse reactions related to the program were reported.Conclusions—Additional VR training could help improve the self-efficacy and activities of daily living of patients with stroke; however, it was not superior to conventional training in the improvement of upper limb functions, occupational performance, and satisfaction. Nevertheless, VR could be integrated into conventional rehabilitation programs to enhance self-efficacy of patients after stroke.Trial Registration—This study was successfully registered under the title “Effects of virtual reality training on occupational performance and self-efficacy of patients with stroke” on October 13 2019 and could be located in http://www.chictr.org with the study identifier ChiCTR1900026550.
Integration of RNA-Seq and proteomics data identifies glioblastoma multiforme surfaceome signature
Authors: Syafruddin Saiful Effendi , Nazarie Wan Fahmi Wan Mohamad , Moidu Nurshahirah Ashikin , Soon Bee Hong , Mohtar M. Aiman 
Published: October 2020

Abstract
Background: Glioblastoma multiforme (GBM) is a highly lethal, stage IV brain tumour with a prevalence of approximately 2 per 10000 people globally. The cell surface proteins or surfaceome serve as an information gateway in many oncogenic signalling pathways and are important in modulating cancer phenotypes. Dysregulation of surfaceome expression and activity have been shown to promote tumorigenesis. The expression of GBM surfaceome is a case in point; OMICS screening in cell-based system identified that this sub-proteome is largely perturbed in GBM. Additionally, since these cell surface proteins have ‘direct’ access to drugs, they are appealing targets for cancer therapy. However, a comprehensive aberrant GBM surfaceome landscape has not been fully defined. Thus, this study aimed to define GBM-specific surfaceome genes and identify key cell-surface genes that could potentially be developed as novel GBM biomarkers for therapeutic purposes. Methods: We integrated the RNA-Seq data from TCGA GBM (n=166) and GTEx normal brain cortex (n=408) databases to identify the significantly dysregulated surfaceome in GBM. This was followed by integrative analysis that combines transcriptomics, proteomics and protein-protein interaction network data to prioritize the high-confidence GBM surfaceome signature. Results: Of the 2,381 significantly dysregulated genes in GBM, 395 genes were classified as surfaceome. Via the integrative analysis, we identified 6 high-confidence GBM molecular signature, HLA-DRA, CD44, SLC1A5, EGFR, ITGB2, PTPRJ, which were significantly upregulated in GBM. The expression of these genes were validated in an independent transcriptomics database, which confirmed their upregulated expression in GBM. Importantly, high expression of CD44, PTPRJ and HLA-DRA is significantly associated with poor disease-free survival. Last, using the Drugbank database, we identified several clinically-approved drugs targeting the GBM molecular signature suggesting potential drug repurposing. Conclusions: In summary, we identified and highlighted the key GBM surface-enriched repertoires that could be biologically relevant in supporting GBM pathogenesis. These genes could be further interrogated experimentally in future studies that could lead to efficient diagnostic/prognostic markers or potential treatment options for GBM.
Long-term target tracking combined with re-detection
Authors: Zhao ZengShun , Wang Juanjuan , Yang HaoRan , Xu Ning , Wu Chengqin , Zhang Jixiang , Wu Dapeng Oliver 
Published: October 2020

Abstract
The long-term visual tracking undergoes more challenges and is closer to realistic applications than short-term tracking. However, the performances of most existing methods have been limited in the long-term tracking tasks. In this work, we present a reliable yet simple long-term tracking method, which extends the state-of-the-art Learning Adaptive Discriminative Correlation Filters (LADCF) tracking algorithm with a re-detection component based on the SVM model. The LADCF tracking algorithm localizes the target in each frame and the re-detector is able to efficiently re-detect the target in the whole image when the tracking fails. We further introduce a robust confidence degree evaluation criterion that combines the maximum response criterion and the average peak-to correlation energy (APCE) to judge the confidence level of the predicted target. When the confidence degree is generally high, the SVM is updated accordingly. If the confidence drops sharply, the SVM re-detects the target. We perform extensive experiments on the OTB-2015 and UAV123 datasets. The experimental results demonstrate the effectiveness of our algorithm in long-term tracking.
Resuscitation fluid types in sepsis, surgical, and trauma patients: A Systematic review and sequential network meta-analyses
Authors: Tseng Chien-Hua , Chen Tzu-Tao , Wu Mei-Yi , Chan Ming-Cheng , Shih Ming-Chieh , Tu Yu-Kang 
Published: October 2020

Abstract
Background: Crystalloids and different component colloids, used for volume resuscitation, are sometimes associated with various adverse effects. Clinical trial findings for such fluid types in different patients’ conditions are conflicting. Whether the mortality benefit of balanced crystalloid than saline can be infer from sepsis to other patient group is uncertain, and adverse effect profile is not comprehensive. This study aims to compare the survival benefits and adverse effects of seven fluid types with network meta-analysis in sepsis, surgical, trauma, and traumatic brain injury patients.

Methods: Searched databases (PubMed, EMBASE, and Cochrane CENTRAL) and reference lists of relevant articles occurred from inception until January 2020. Studies on critically ill adults requiring fluid resuscitation were included. Intervention studies reported on balanced crystalloid, saline, iso-oncotic albumin, hyperoncotic albumin, low molecular weight hydroxyethyl starch (L-HES), high molecular weight HES, and gelatin. Network meta-analyses were conducted using random-effects model to calculate odds ratio (OR) and mean difference. Risk of Bias tool 2.0 was used to assess bias. CINeMA (Confidence in Network Meta-Analysis) web application was used to rate confidence in synthetic evidence.

Results: Fifty-eight trials (n=26,351 patients) were identified. Seven fluid types were evaluated. Among patients with sepsis and surgery, balanced crystalloids and albumin achieved better survival, fewer acute kidney injury, and smaller blood transfusion volumes than saline and L-HES. In those with sepsis, balanced crystalloids significantly reduced mortality more than saline (OR, 0.84; 95% CI 0.74 to 0.95) and L-HES (OR, 0.81; 95% CI 0.69 to 0.95) and reduced acute kidney injury more than L-HES (OR, 0.80; 95% CI 0.65 to 0.99). However, they required the greatest resuscitation volume among all fluid types, especially in trauma patients. In patients with traumatic brain injury, saline and L-HES achieved lower mortality than albumin and balanced crystalloids; especially saline was significantly superior to iso-oncotic albumin (OR, 0.55; 95% CI 0.35 to 0.87).

Conclusions: Our network meta-analysis found that balanced crystalloids and albumin decreased mortality more than L-HES and saline did in sepsis patients; however, saline or L-HES, is better than iso-oncotic albumin or balanced crystalloids in traumatic brain injury patients.
Characterization of the Materials and Techniques of a Birthday Inscribed Lacquer Plaque of the Qing Dynasty
Authors: Zheng Liping , Wang Liqin , Zhao Xing , Yang Jiali , Zhang Mengxia , Wang Yunfu 
Published: October 2020

Abstract
In this study, in order to analyze the materials and techniques used for the production of the inscribed plaques, multi-analytical scientific approach, including optical microscopy (OM), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), X-ray diffraction (XRD), micro-attenuated total reflection Fourier transform infrared spectroscopy (μ-ATR-FTIR), and micro-Raman spectroscopy (μ-Raman), were used to explore the materials and techniques utilized to create the “Chun Rong Xuan Mao” birthday inscribed plaque of the Qing Dynasty. The results showed that the plaque was made of cypress wood and decorative parts consisting of the surface lacquer layers, plaster lacquer layers and primer lacquer layers. Chinese lacquer was the principal material used in the surface lacquer layers; gypsum and Chinese lacquer were the materials used in the plaster lacquer layers; and the primer lacquer layers was composed of Chinese lacquer, calcite, and mixed pigments by cinnabar and minium. The surface lacquer layers of the inscribed plaque were lacquered black. Gypsum lacquer plaster has been commonly used in the ground layer of lacquerware in modern history. This study confirmed the existence of technology to make lacquerware using gypsum lacquer plaster in the Bashu area during the late Qing Dynasty. Moreover, this study not only provides new findings regarding the traditional production of inscribed plaques and offers technical support for the protection and restoration of such plaques but also has great significance to exploring the history of ancient techniques of lacquering and decorating lacquerware.
Target Vehicle Selection Algorithm Based on Lane-changing Intention of Preceding Vehicle for ACC
Authors: Yao Jun , Chen Guoying , Gao Zhenhai 
Published: October 2020

Abstract
In order to improve the ride comfort and safety of the traditional adaptive cruise control (ACC) system when the preceding vehicle changes lanes, this paper proposes a target vehicle selection algorithm based on the prediction of the lane-changing intention of the preceding vehicle. First, NGSIM dataset is used to train a lane-changing intention prediction algorithm based on sliding window SVM, and the lane-changing intent of the preceding vehicle in the current lane can be identified by lateral position offset. Secondly, according to the lane-changing intention and the collision threat of the preceding vehicle, the target vehicle selection algorithm is studied under three different conditions: safe lane-changing condition, dangerous lane-changing condition, and lane-changing cancellation condition. Finally, the effectiveness of the algorithm proposed in this paper is verified in the co-simulation platform. The simulation results show that the target vehicle selection algorithm proposed in this paper can ensure the smooth transfer of the target vehicle and effectively reduce the longitudinal acceleration fluctuation of the subject vehicle when the preceding vehicle changes lanes safely or cancels the lane change. In the case of a dangerous lane change, the target vehicle selection algorithm proposed in this paper can respond to the dangerous lane change in advance compared with the target vehicle selection method of the traditional ACC system, which can effectively avoid collisions and improve the safety of the subject vehicle.
Joint Topical Word Embedding for Detecting Drift in Social Media Text
Authors: J VIJAYARANI , T.V. Geetha 
Published: October 2020

Abstract
Social media texts like tweets and blogs are collaboratively created by human interaction. Fast change in trends leads to topic drift in the social media text. This drift is usually associated with words and hashtags. However, geotags play an important part in determining topic distribution with location context. Rate of change in the distribution of words, hashtags and geotags cannot be considered as uniform and must be handled accordingly. This paper builds a topic model that associates topic with a mixture of distributions of words, hashtags and geotags. Stochastic gradient Langevin dynamic model with varying mini-batch sizes is used to capture the changes due to the asynchronous distribution of words and tags. Topical word embedding with co-occurrence and location contexts are specified as hashtag context vector and geotag context vector respectively. These two vectors are jointly learned to yield topical word embedding vectors related to tags context. Topical word embeddings over time conditioned on hashtags and geotags predict, location-based topical variations effectively. When evaluated with Chennai and UK geolocated Twitter data, the proposed joint topical word embedding model enhanced by the social tags context, outperforms other methods.
Cutaneous Hyperpigmentation and Familial Gastrointestinal Stromal Tumor Associated with Germline KIT Mutation Treated with Imatinib
Authors: Yuan Wei , Huang Wen , Ren Lei , Xu Chen , Luan Lijuan , Huang Jie , Xue Anwei , Fang Yong , Gao Xiaodong , Shen Kuntang , Lv Jinghuan , Hou Yingyong 
Published: October 2020

Abstract
Background: Familial gastrointestinal stromal tumor (GIST) has been identified with multiple GISTs containing the mutations in germline KIT and PDGFRA. There are only 35 kindreds with germline KIT and 6 with PDGFRA mutations have been reported so far. Familial GIST is often characterized by a series of manifestations, such as multiple lesions, hyperpigmentation, mastocytosis, and dysphagia. Only some kindreds have response to imatinib treatment.Materials and Methods: A 25-year-old Chinese woman went to hospital because of the abdominal pain, and through the computed tomography (CT) scan showed us the multiple tumors in the small intestine. Her father had a history of multifocal GISTs, and referred to the hospital with abdominal pain and tumor recurrences last year. Immuhistochemical analysis of CD117 and DOG-1 were performed on tumor samples from the two patients, while KIT mutational analysis was carried out by direct sequencing on DNA from paraffin-embedded specimens and saliva sample.Results: Multiple GISTs associated with diffuse interstitial cells of Cajal (ICC) hyperplasia were illustrated in these two patients. These tumors were positive for CD117 and DOG-1. The germline mutation at codon 560 of exon 11 (p.V560G) of the KIT gene were found. The treatment with imatinib resulted in favorable responses in both tumor and cutaneous hyperpigmentation.Conclusions: It is difficult to make a correct diagnosis of familial GIST at first time for its rarity. This case was finally diagnosed as familial GIST depending on the combination of diffuse ICC hyperplasia, germline KIT mutation, hyperpigmentation and its family history.
Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment
Authors: Sommer Morten , Kang Kang , Imamovic Lejla , Misiakou Maria-Anna , Sørensen Maria Bornakke , Heshiki Yoshitaro , Ni Yueqiong , Zheng Tingting , Li Jun , Ellabaan Mostafa Mostafa Hashim , Colomer-Lluch Marta , Rode Anne A. , Bytzer Peter , Panagiotou Gianni 
Published: October 2020

Abstract
Background. Oral antibiotics are commonly prescribed to non-hospitalized adults. However, antibiotic-induced changes on the human gut microbiome are often investigated in cohorts with pre-existing health conditions and/or concomitant medication, leaving the effects of antibiotics not completely understood. Results. We used a combination of omic approaches to comprehensively assess the effects of antibiotics on the gut microbiota and particularly the gut resistome of a small cohort of healthy adults. We observed that 3 to 19 species per individual proliferated during antibiotic treatment and Gram-negative species expanded significantly in relative abundance. While the overall relative abundance of antibiotic resistance gene homologs did not significantly change, antibiotic-specific gene homologs with presumed resistance towards the administered antibiotics were common in proliferating species and significantly increased in relative abundance. Virome sequencing and plasmid analysis showed the expansion of antibiotic-specific resistance gene homologs even three months after antibiotic administration, while paired-end read analysis suggested their dissemination among different species. Conclusions. These results suggest that antibiotic treatment can lead to a persistent expansion of antibiotic resistance genes in the human gut microbiota and provide further data in support of good antibiotic stewardship.