bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viscoelastometry for detecting oral anticoagulants
Authors: Groene Philipp , Wagner Daniela , Kammerer Tobias , Kellert Lars , Giebl Andreas , Massberg Steffen , Schäfer Simon Thomas 
Published: March 2021

Abstract
Background
Determination of anticoagulant therapy is of pronounced interest in emergency situations. However, routine tests do not provide sufficient insight. This study was performed to investigate the impact of anticoagulants on the results of viscoelastometric assays using the ClotPro device.

Methods
This prospective, observational study was conducted in patients receiving dabigatran, factor Xa (FXa)-inhibitors, phenprocoumon, low molecular weight heparin (LMWH) or unfractionated heparin (UFH) (local ethics committee approval number: 17–525-4). Healthy volunteers served as controls. Viscoelastometric assays were performed, including the extrinsic test (EX-test), intrinsic test (IN-test) Russel’s viper venom test (RVV-test), ecarin test (ECA-test), and the tissue plasminogen activator test (TPA-test).

Results
70 patients and 10 healthy volunteers were recruited. Clotting time in the EX-test (CTEX-test) was significantly prolonged versus controls by dabigatran, FXa inhibitors and phenprocoumon. CTIN-test was prolonged by dabigatran, FXa inhibitors and UFH. Dabigatran, FXa inhibitors and UFH significantly prolonged CTRVV-test in comparison with controls (median 200, 207 and 289 vs 63 s, respectively; all p < 0.0005). Only dabigatran elicited a significant increase in CTECA-test compared to controls (median 307 vs 73 s; p < 0.0001). CTECA-test correlated strongly with dabigatran plasma concentration (measured by anti-IIa activity; r = 0.9970; p < 0.0001) and provided 100% sensitivity and 100% specificity for detecting dabigatran. Plasma concentrations (anti-XA activity) of FXa inhibitors correlated with CTRVV-test (r = 0.7998; p < 0.0001), and CTRVV-test provided 83% sensitivity and 64% specificity for detecting FXa inhibitors.

Conclusions
In emergency situations, ClotPro viscoelastometric assessment of whole-blood samples may help towards determining the presence and type of anticoagulant class that a patient is taking.

Trial registration
German clinical trials database ID: DRKS00015302.
Novel and recurrent BRCA1/BRCA2 germline mutations in patients with breast/ovarian cancer: a series from the south of Tunisia
Authors: Ben Ayed-Guerfali Dorra , Ben Kridis-Rejab Wala , Ammous-Boukhris Nihel , Ayadi Wajdi , Charfi Slim , Khanfir Afef , Sellami-Boudawara Tahia , Frikha Mounir , Daoud Jamel , Mokdad-Gargouri Raja 
Published: March 2021

AbstractBackgroundThe incidence of breast cancer (BC) and/or ovarian cancer (OC) is increasing in Tunisia especially in young women and mostly those with family history. However, the spectrum ofBRCAmutations remains little explored in Tunisian patients in particular in the southern region.MethodsWe sequenced the entire coding regions ofBRCA1andBRCA2genes using next generation sequencing (NGS) in 134 selected patients with BC and/or OC.ResultsAmong the 134 patients, 19 (14.17%) carried pathogenic mutations (10 areBRCA1mutation carriers and 9 areBRCA2mutation carriers) that are mainly frameshift index (76.9%). Interestingly, 5 out of the 13 variants (38.46%) were found at least twice in unrelated patients, as the c.1310-1313 delAAGA inBRCA2and the c.5030_5033 delCTAA that has been identified in 4/98 BC patients and in 3/15 OC patients from unrelated families with strong history of cancer. Besides recurrent mutations, 6 variant (4 inBRCA1and 2 inBRCA2) were not reported previously. Furthermore, 3 unrelated patients carried the VUS c.9976A > T, (K3326*) inBRCA2exon 27.BRCAcarriers correlated significantly with tumor site (p = 0.029) and TNBC cases (p = 0.008). In the groups of patients aged between 31 and 40, and 41–50 years,BRCA1mutations occurred more frequently in patients with OC than those with BC, and converselyBRCA2carriers are mostly affected with BC (p = 0.001, and p = 0.044 respectively).ConclusionsThe overall frequency of the BRCA germline mutations was 14.17% in patients with high risk of breast/ovarian cancer. We identified recurrent mutations as the c.1310_1313 delAAGA inBRCA2gene and the c.5030_5033 delCTAA inBRCA1gene that were found in 4% and 20% of familial BC and OC respectively. Our data will contribute in the implementation of genetic counseling and testing for families with high-risk of BC and/or OC.
The influence of powered prostheses on user perspectives, metabolics, and activity: a randomized crossover trial
Authors: Kim Jay , Wensman Jeffrey , Colabianchi Natalie , Gates Deanna H. 
Published: March 2021

Abstract
Background
Powered prosthetic ankles provide battery-powered mechanical push-off, with the aim of reducing the metabolic demands of walking for people with transtibial amputations. The efficacy of powered ankles has been shown in active, high functioning individuals with transtibial amputation, but is less clear in other populations. Additionally, it is unclear how use of a powered prosthesis influences everyday physical activity and mobility.

Methods

Individuals with unilateral transtibial amputations participated in a randomized clinical trial comparing their prescribed, unpowered prosthesis and the BiOM powered prosthesis. Participants’ metabolic costs and self-selected walking speeds were measured in the laboratory and daily step count, daily steps away from home, and walking speed were measured over two weeks of at-home prosthesis use. Participants also rated their perception of mobility and quality of life and provided free-form feedback. Dependent measures were compared between prostheses and the relationships between metabolic cost, perception of mobility, and characteristics of walking in daily life were explored using Pearson’s correlations.

Results
Twelve people were randomly allocated to the powered prosthesis first (n = 7) or unpowered prosthesis first (n = 5) and ten completed the full study. There were no differences in metabolic costs (p = 0.585), daily step count (p = 0.995), walking speed in-lab (p = 0.145) and in daily life (p = 0.226), or perception of mobility between prostheses (p ≥ 0.058). Changes varied across participants, however. There were several medium-sized effects for device comparisons. With the powered prosthesis, participants had increased self-reported ambulation (g = 0.682) and decreased frustration (g = 0.506).

Conclusions
There were no universal benefits of the powered prosthesis on function in the lab or home environment. However, the effects were subject-specific, with some reporting preference for power and improved mobility, and some increasing their activity and decreasing their metabolic effort. Additionally, self-reported preferences did not often correlate with objective measures of function. This highlights the need for future clinical research to include both perception and objective measures to better inform prosthetic prescription.
Trial registration: https://clinicaltrials.gov, #NCT02828982.
Registered 12 July 2016, https://clinicaltrials.gov/ct2/show/NCT02828982
Identification of key genes in hepatitis B associated hepatocellular carcinoma based on WGCNA
Authors: Liu Chang , Dai Qinghai , Ding Qian , Wei Min , Kong Xiaohong 
Published: March 2021

AbstractChronic Infection of Hepatitis B virus (HBV) is one risk factor of hepatocellular carcinoma (HCC). Much effort has been made to research the process of HBV-associated HCC, but its molecular mechanisms of carcinogenesis remain vague. Here, weighted gene co-expression network analysis (WGCNA) was employed to explore the co-expressed modules and hub/key genes correlated to HBV-associated HCC. We found that genes of the most significant module related to HBV-associated HCC were enriched in DNA replication, p53 signaling pathway, cell cycle, and HTLV-1 infection associated pathway; these cellular pathways played critical roles in the initiation and development of HCC or viral infections. Furthermore, seven hub/key genes were identified based on the topological network analysis, and their roles in HCC were verified by expression and Kaplan-Meier survival analysis. Protein-protein interaction and KEGG pathway analysis suggested that these key genes may stimulate cellular proliferation to promote the HCC progression. This study provides new perspectives to the knowledge of the key pathways and genes in the carcinogenesis process of HBV-associated HCC, and our findings provided potential therapeutic targets and clues of the carcinogenesis of HBV-associated HCC.
RASMA: a reverse search algorithm for mining maximal frequent subgraphs
Authors: Salem Saeed , Alokshiya Mohammed , Hasan Mohammad Al 
Published: March 2021

Abstract
Background
Given a collection of coexpression networks over a set of genes, identifying subnetworks that appear frequently is an important research problem known as mining frequent subgraphs. Maximal frequent subgraphs are a representative set of frequent subgraphs; A frequent subgraph is maximal if it does not have a super-graph that is frequent. In the bioinformatics discipline, methodologies for mining frequent and/or maximal frequent subgraphs can be used to discover interesting network motifs that elucidate complex interactions among genes, reflected through the edges of the frequent subnetworks. Further study of frequent coexpression subnetworks enhances the discovery of biological modules and biological signatures for gene expression and disease classification.

Results
We propose a reverse search algorithm, called RASMA, for mining frequent and maximal frequent subgraphs in a given collection of graphs. A key innovation in RASMA is a connected subgraph enumerator that uses a reverse-search strategy to enumerate connected subgraphs of an undirected graph. Using this enumeration strategy, RASMA obtains all maximal frequent subgraphs very efficiently. To overcome the computationally prohibitive task of enumerating all frequent subgraphs while mining for the maximal frequent subgraphs, RASMA employs several pruning strategies that substantially improve its overall runtime performance. Experimental results show that on large gene coexpression networks, the proposed algorithm efficiently mines biologically relevant maximal frequent subgraphs.

Conclusion
Extracting recurrent gene coexpression subnetworks from multiple gene expression experiments enables the discovery of functional modules and subnetwork biomarkers. We have proposed a reverse search algorithm for mining maximal frequent subnetworks. Enrichment analysis of the extracted maximal frequent subnetworks reveals that subnetworks that are frequent are highly enriched with known biological ontologies.
Caveolin-1 deficiency impairs synaptic transmission in hippocampal neurons
Authors: Koh Soulmee , Lee Wongyoung , Park Sang Myun , Kim Sung Hyun 
Published: March 2021

AbstractIn addition to providing structural support, caveolin-1 (Cav1), a component of lipid rafts, including caveolae, in the plasma membrane, is involved in various cellular mechanisms, including signal transduction. Although pre-synaptic membrane dynamics and trafficking are essential cellular processes during synaptic vesicle exocytosis/synaptic transmission and synaptic vesicle endocytosis/synaptic retrieval, little is known about the involvement of Cav1 in synaptic vesicle dynamics. Here we demonstrate that synaptic vesicle exocytosis is significantly impaired in Cav1–knockdown (Cav1–KD) neurons. Specifically, the size of the synaptic recycled vesicle pool is modestly decreased in Cav1–KD synapses and the kinetics of synaptic vesicle endocytosis are somewhat slowed. Notably, neurons rescued by triple mutants of Cav1 lacking palmitoylation sites mutants show impairments in both synaptic transmission and retrieval. Collectively, our findings implicate Cav1 in activity-driven synaptic vesicle dynamics—both exocytosis and endocytosis—and demonstrate that palmitoylation of Cav1 is important for this activity.
α1A-adrenaline receptors in dorsal horn inhibitory neurons have an inhibitory role in the regulation of chloroquine-induced itch in mice
Authors: Shiraishi Yuto , Koga Keisuke , Yamagata Ryo , Hatada Izuho , Shiratori-Hayashi Miho , Tsuda Makoto 
Published: March 2021

AbstractOur previous study showed the intrinsic ability of descending noradrenergic neurons projecting from the locus coeruleus to the spinal dorsal horn (SDH) to suppress itch-related behaviors. Noradrenaline and α1A-adrenaline receptor (α1A-AR) agonist increase inhibitory synaptic inputs onto SDH interneurons expressing gastrin-releasing peptide receptors, which are essential for itch transmission. However, the contribution of α1A-ARs expressed in SDH inhibitory interneurons to itch-related behavior remains to be determined. In this study, RNAscope in situ hybridization revealed that Adra1a mRNA is expressed in SDH inhibitory interneurons that are positive for Slc32a1 mRNA (known as vesicular GABA transporter). Mice with conditional knock-out of α1A-ARs in inhibitory interneurons (Vgat-Cre;Adra1aflox/flox mice) exhibited an increase in scratching behavior when induced by an intradermal injection of chloroquine, but not compound 48/80, which are known as models of histamine-independent and dependent itch, respectively. Furthermore, knockout of inhibitory neuronal α1A-ARs in the SDH using the CRISPR–Cas9 system also increased the scratching behavior elicited by chloroquine but not compound 48/80. Our findings demonstrated for the first time that α1A-ARs in SDH inhibitory interneurons contribute to the regulation of itch signaling with preference for histamine-independent itch.
Intranasal oxytocin administration ameliorates social behavioral deficits in a POGZWT/Q1038R mouse model of autism spectrum disorder
Authors: Kitagawa Kohei , Matsumura Kensuke , Baba Masayuki , Kondo Momoka , Takemoto Tomoya , Nagayasu Kazuki , Ago Yukio , Seiriki Kaoru , Hayata-Takano Atsuko , Kasai Atsushi , Takuma Kazuhiro , Hashimoto Ryota , Hashimoto Hitoshi , Nakazawa Takanobu 
Published: March 2021

AbstractAutism spectrum disorder (ASD) is a highly prevalent neurodevelopmental disorder characterized by core symptoms of impaired social behavior and communication. Recent studies have suggested that the oxytocin system, which regulates social behavior in mammals, is potentially involved in ASD. Mouse models of ASD provide a useful system for understanding the associations between an impaired oxytocin system and social behavior deficits. However, limited studies have shown the involvement of the oxytocin system in the behavioral phenotypes in mouse models of ASD. We have previously demonstrated that a mouse model that carries the ASD patient-derived de novo mutation in the pogo transposable element derived with zinc finger domain (POGZWT/Q1038R mice), showed ASD-like social behavioral deficits. Here, we have explored whether oxytocin (OXT) administration improves impaired social behavior in POGZWT/Q1038R mice and found that intranasal oxytocin administration effectively restored the impaired social behavior in POGZWT/Q1038R mice. We also found that the expression level of the oxytocin receptor gene (OXTR) was low in POGZWT/Q1038R mice. However, we did not detect significant changes in the number of OXT-expressing neurons between the paraventricular nucleus of POGZWT/Q1038R mice and that of WT mice. A chromatin immunoprecipitation assay revealed that POGZ binds to the promoter region of OXTR and is involved in the transcriptional regulation of OXTR. In summary, our study demonstrate that the pathogenic mutation in the POGZ, a high-confidence ASD gene, impairs the oxytocin system and social behavior in mice, providing insights into the development of oxytocin-based therapeutics for ASD.
LncRNA SPOCD1-AS from ovarian cancer extracellular vesicles remodels mesothelial cells to promote peritoneal metastasis via interacting with G3BP1
Authors: Wang Conghui , Wang Jiaying , Shen Xiameng , Li Mingyue , Yue Yongfang , Cheng Xiaodong , Lu Weiguo , Wang Xinyu , Xie Xing 
Published: March 2021

AbstractBackgroundMetastasis is the key cause of death in ovarian cancer patients. To figure out the biological nature of cancer metastasis is essential for developing effective targeted therapy. Here we investigate how long non-coding RNA (lncRNA) SPOCD1-AS from ovarian cancer extracellular vesicles (EVs) remodel mesothelial cells through a mesothelial-to-mesenchymal transition (MMT) manner and facilitate peritoneal metastasis.MethodsEVs purified from ovarian cancer cells and ascites of patients were applied to mesothelial cells. The MMT process of mesothelial cells was assessed by morphology observation, western blot analysis, migration assay and adhesion assay. Altered lncRNAs of EV-treated mesothelial cells were screened by RNA sequencing and identified by qRT-PCR. SPOCD1-AS was overexpressed or silenced by overexpression lentivirus or shRNA, respectively. RNA pull-down and RNA immunoprecipitation assays were conducted to reveal the mechanism by which SPOCD1-AS remodeled mesothelial cells. Interfering peptides were synthesized and applied. Ovarian cancer orthotopic implantation mouse model was established in vivo.ResultsWe found that ovarian cancer-secreted EVs could be taken into recipient mesothelial cells, induce the MMT phenotype and enhance cancer cell adhesion to mesothelial cells. Furthermore, SPOCD1-AS embedded in ovarian cancer-secreted EVs was transmitted to mesothelial cells to induce the MMT process and facilitate peritoneal colonization in vitro and in vivo. SPOCD1-AS induced the MMT process of mesothelial cells via interacting with G3BP1 protein. Additionally, G3BP1 interfering peptide based on the F380/F382 residues was able to block SPOCD1-AS/G3BP1 interaction, inhibit the MMT phenotype of mesothelial cells, and diminish peritoneal metastasis in vivo.ConclusionsOur findings elucidate the mechanism associated with EVs and their cargos in ovarian cancer peritoneal metastasis and may provide a potential approach for metastatic ovarian cancer therapeutics.
Identification of potential markers for differentiating epithelial ovarian cancer from ovarian low malignant potential tumors through integrated bioinformatics analysis
Authors: Hao Wende , Zhao Hongyu , Li Zhefeng , Li Jie , Guo Jiahao , Chen Qi , Gao Yan , Ren Meng , Zhao Xiaoting , Yue Wentao 
Published: March 2021

Abstract
Background
Epithelial ovarian cancer (EOC), as a lethal malignancy in women, is often diagnosed as advanced stages. In contrast, intermediating between benign and malignant tumors, ovarian low malignant potential (LMP) tumors show a good prognosis. However, the differential diagnosis of the two diseases is not ideal, resulting in delays or unnecessary therapies. Therefore, unveiling the molecular differences between LMP and EOC may contribute to differential diagnosis and novel therapeutic and preventive policies development for EOC.

Methods
In this study, three microarray data (GSE9899, GSE57477 and GSE27651) were used to explore the differentially expressed genes (DEGs) between LMP and EOC samples. Then, 5 genes were screened by protein–protein interaction (PPI) network, receiver operating characteristic (ROC), survival and Pearson correlation analysis. Meanwhile, chemical-core gene network construction was performed to identify the potential drugs or risk factors for EOC based on 5 core genes. Finally, we also identified the potential function of the 5 genes for EOC through pathway analysis.

Results
Two hundred thirty-four DEGs were successfully screened, including 81 up-regulated genes and 153 down-regulated genes. Then, 5 core genes (CCNB1, KIF20A, ASPM, AURKA, and KIF23) were identified through PPI network analysis, ROC analysis, survival and Pearson correlation analysis, which show better diagnostic efficiency and higher prognostic value for EOC. Furthermore, NetworkAnalyst was used to identify top 15 chemicals that link with the 5 core genes. Among them, 11 chemicals were potential drugs and 4 chemicals were risk factors for EOC. Finally, we found that all 5 core genes mainly regulate EOC development via the cell cycle pathway by the bioinformatic analysis.

Conclusion
Based on an integrated bioinformatic analysis, we identified potential biomarkers, risk factors and drugs for EOC, which may help to provide new ideas for EOC diagnosis, condition appraisal, prevention and treatment in future.
Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis
Authors: Yi Huiguang , Lin Yanling , Lin Chengqi , Jin Wenfei 
Published: March 2021

AbstractHere, we develop k -mer substring space decomposition (Kssd), a sketching technique which is significantly faster and more accurate than current sketching methods. We show that it is the only method that can be used for large-scale dataset comparisons at population resolution on simulated and real data. Using Kssd, we prioritize references for all 1,019,179 bacteria whole genome sequencing (WGS) runs from NCBI Sequence Read Archive and find misidentification or contamination in 6164 of these. Additionally, we analyze WGS and exome runs of samples from the 1000 Genomes Project.
A U.S. isolate of Theileria orientalis, Ikeda genotype, is transmitted to cattle by the invasive Asian longhorned tick, Haemaphysalis longicornis
Authors: Dinkel Kelcey D. , Herndon David R. , Noh Susan M. , Lahmers Kevin K. , Todd S. Michelle , Ueti Massaro W. , Scoles Glen A. , Mason Kathleen L. , Fry Lindsay M. 
Published: March 2021

Abstract
Background
Theileria orientalis is a tick-borne hemoparasite that causes anemia, ill thrift, and death in cattle globally. The Ikeda strain of T.orientalis is more virulent than other strains, leading to severe clinical signs and death of up to 5% of affected animals. Within the Asia–Pacific region, where it affects 25% of Australian cattle, T.orientalis Ikeda has a significant economic impact on the cattle industry. In 2017, T.orientalis Ikeda was detected in a cattle herd in Albermarle County, Virginia, United States. Months earlier, the U.S. was alerted to the invasion of the Asian longhorned tick, Haemaphysalis longicornis, throughout the eastern U.S. Abundant H.longicornis ticks were identified on cattle in the T.orientalis-affected herd in VA, and a subset of ticks from the environment were PCR-positive for T.orientalis Ikeda. A strain of T.orientalis from a previous U.S. outbreak was not transmissible by H.longicornis; however, H.longicornis is the primary tick vector of T.orientalis Ikeda in other regions of the world. Thus, the objective of this study was to determine whether invasive H.longicornis ticks in the U.S. are competent vectors of T.orientalis Ikeda.

Methods
Nymphal H.longicornis ticks were fed on a splenectomized calf infected with the VA-U.S.-T.orientalis Ikeda strain. After molting, a subset of adult ticks from this cohort were dissected, and salivary glands assayed for T.orientalis Ikeda via qPCR. The remaining adult ticks from the group were allowed to feed on three calves. Calves were subsequently monitored for T.orientalis Ikeda infection via blood smear cytology and PCR.

Results
After acquisition feeding on a VA-U.S.-T.orientalis Ikeda-infected calf as nymphs, a subset of molted adult tick salivary glands tested positive by qPCR for T.orientalis Ikeda. Adult ticks from the same cohort successfully transmitted T.orientalis Ikeda to 3/3 naïve calves, each of which developed parasitemia reaching 0.4–0.9%.

Conclusions
Our findings demonstrate that U.S. H.longicornis ticks are competent vectors of the VA-U.S.-T.orientalis Ikeda strain. This data provides important information for the U.S. cattle industry regarding the potential spread of this parasite and the necessity of enhanced surveillance and control measures.

Graphical Abstract