bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molecular mechanism of scale degeneration
Authors: Feng Xiu , Jia Yintao , Zhu Ren , Li Kemao , Guan Zhongzhi , Chen Yifeng 
Published: November 2020

Abstract
Background
The scale degeneration is thought to be related to the adaptation to the extreme environment with cold climate and high-altitude in schizothoracine fishes. Gymnocypris eckloni, a schizothoracine fish living in plateau waters with the elevation above 2500 m, is nearly esquamate and only covered with shoulder scales and anal scales, making it a good model species to study the molecular mechanism of scale degeneration.

Results
The transcriptomes of shoulder scaled skins (SSS), anal scaled skins (ASS) and scaleless skins (NSS) were sequenced and analyzed in G. eckloni at the age of 1 year. Histological examination showed that shoulder scale had completed its differentiation and anal scale just initiated the differentiation. A total of 578,046 unigenes were obtained from the transcriptomes, with 407,799 unigenes annotated in public databases. A total of 428 and 142 differentially expressed unigenes (DEUs) were identified between SSS and NSS, and between ASS and NSS, respectively, with 45 DEUs that were overlapped. Annotation analysis indicated that these DEUs were mainly enriched in Gene Ontology (GO) terms and KEGG pathways associated with bone and muscle formation, such as myofibril, contractile fiber, cytoskeletal protein binding, muscle structure development, cardiac muscle contraction, hypertrophic cardiomyopathy (HCM) and calcium signaling pathway.

Conclusions
Our results would provide insights into the molecular mechanisms of scale degeneration in G. eckloni and other congeneric fishes. In addition, the transcriptome data provides candidate genes and markers for future studies.
Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos
Authors: Aguilar-Marin Sandra Bibiana , Betancur-Murillo Claudia Lorena , Isaza Gustavo A. , Mesa Henry , Jovel Juan 
Published: November 2020

Abstract
Background
Ruminants burp massive amounts of methane into the atmosphere and significantly contribute to the deposition of greenhouse gases and the consequent global warming. It is therefore urgent to devise strategies to mitigate ruminant’s methane emissions to alleviate climate change. Ruminal methanogenesis is accomplished by a series of methanogen archaea in the phylum Euryarchaeota, which piggyback into carbohydrate fermentation by utilizing residual hydrogen to produce methane. Abundance of methanogens, therefore, is expected to affect methane production. Furthermore, availability of hydrogen produced by cellulolytic bacteria acting upstream of methanogens is a rate-limiting factor for methane production. The aim of our study was to identify microbes associated with the production of methane which would constitute the basis for the design of mitigation strategies.

Results
Moderate differences in the abundance of methanogens were observed between groups. In addition, we present three lines of evidence suggesting an apparent higher abundance of a consortium of Prevotella species in animals with lower methane emissions. First, taxonomic classification revealed increased abundance of at least 29 species of Prevotella. Second, metagenome assembly identified increased abundance of Prevotella ruminicola and another species of Prevotella. Third, metabolic profiling of predicted proteins uncovered 25 enzymes with homology to Prevotella proteins more abundant in the low methane emissions group.

Conclusions
We propose that higher abundance of ruminal Prevotella increases the production of propionic acid and, in doing so, reduces the amount of hydrogen available for methanogenesis. However, further experimentation is required to ascertain the role of Prevotella on methane production and its potential to act as a methane production mitigator.
Repeated centrifuging and washing concentrates bacterial samples in peritoneal dialysis for optimal culture: an original article
Authors: Tien Ni , You Bang-Jau , Lin Hsuan-Jen , Chang Chieh-Ying , Chou Che-Yi , Lin Hsiu-Shen , Chang Chiz-Tzung , Wang Charles C. N. , Chen Hung-Chih 
Published: November 2020

Abstract
Background
Bacterial cultures allow the identification of infectious disease pathogens. However, obtaining the results of conventional culture methods is time-consuming, taking at least two days. A more efficient alternative is the use of concentrated bacterial samples to accelerate culture growth. Our study focuses on the development of a high-yield sample concentrating technique.

Results
A total of 71 paired samples were obtained from patients on peritoneal dialysis (PD). The peritoneal dialysates were repeat-centrifuged and then washed with saline, namely the centrifuging and washing method (C&W method). The concentrated samples were Gram-stained and inoculated into culture plates. The equivalent unprocessed dialysates were cultured as the reference method. The times until culture results for the two methods were compared. The reference method yielded no positive Gram stain results, but the C&W method immediately gave positive Gram stain results for 28 samples (p < 0.001). The culture-negative rate was lower in the C&W method (5/71) than in the reference method (13/71) (p = 0.044). The average time for bacterial identification achieved with the C&W method (22.0 h) was shorter compared to using the reference method (72.5 h) (p < 0.001).

Conclusions
The C&W method successfully concentrated bacterial samples and superseded blood culture bottles for developing adequate bacterial cultures. The C&W method may decrease the culture report time, thus improving the treatment of infectious diseases.
Vestibular rehabilitation in multiple sclerosis: study protocol for a randomised controlled trial and cost-effectiveness analysis comparing customised with booklet based vestibular rehabilitation for vestibulopathy and a 12 month observational cohort study of the symptom reduction and recurrence rate following treatment for benign paroxysmal positional vertigo
Authors: Marsden J. , Pavlou M. , Dennett R. , Gibbon A. , Knight-Lozano R. , Jeu L. , Flavell C. , Freeman J. , Bamiou D. E. , Harris C. , Hawton A. , Goodwin E. , Jones B. , Creanor S. 
Published: November 2020

Abstract
Background
Symptoms arising from vestibular system dysfunction are observed in 49–59% of people with Multiple Sclerosis (MS). Symptoms may include vertigo, dizziness and/or imbalance. These impact on functional ability, contribute to falls and significant health and social care costs. In people with MS, vestibular dysfunction can be due to peripheral pathology that may include Benign Paroxysmal Positional Vertigo (BPPV), as well as central or combined pathology. Vestibular symptoms may be treated with vestibular rehabilitation (VR), and with repositioning manoeuvres in the case of BPPV. However, there is a paucity of evidence about the rate and degree of symptom recovery with VR for people with MS and vestibulopathy. In addition, given the multiplicity of symptoms and underpinning vestibular pathologies often seen in people with MS, a customised VR approach may be more clinically appropriate and cost effective than generic booklet-based approaches. Likewise, BPPV should be identified and treated appropriately.

Methods/ design
People with MS and symptoms of vertigo, dizziness and/or imbalance will be screened for central and/or peripheral vestibulopathy and/or BPPV. Following consent, people with BPPV will be treated with re-positioning manoeuvres over 1–3 sessions and followed up at 6 and 12 months to assess for any re-occurrence of BPPV. People with central and/or peripheral vestibulopathy will be entered into a randomised controlled trial (RCT). Trial participants will be randomly allocated (1:1) to either a 12-week generic booklet-based home programme with telephone support or a 12-week VR programme consisting of customised treatment including 12 face-to-face sessions and a home exercise programme. Customised or booklet-based interventions will start 2 weeks after randomisation and all trial participants will be followed up 14 and 26 weeks from randomisation. The primary clinical outcome is the Dizziness Handicap Inventory at 26 weeks and the primary economic endpoint is quality-adjusted life-years. A range of secondary outcomes associated with vestibular function will be used.

Discussion
If customised VR is demonstrated to be clinically and cost-effective compared to generic booklet-based VR this will inform practice guidelines and the development of training packages for therapists in the diagnosis and treatment of vestibulopathy in people with MS.

Trial registration
ISRCTN Number: 27374299
Date of Registration 24/09/2018
Protocol Version 15 25/09/2019
Routinely collected patient data in neurology research: a systematic mapping review
Authors: Biggin Fran , Emsley Hedley C. A. , Knight Jo 
Published: November 2020

AbstractBackgroundThis review focuses on neurology research which uses routinely collected data. The number of such studies is growing alongside the expansion of data collection. We aim to gain a broad picture of the scope of how routine healthcare data have been utilised.MethodsThis study follows a systematic mapping review approach which does not make a judgement on the quality of the papers included in the review, thereby enabling a complete overview of the field.ResultsOf 4481 publications retrieved, 386 met the eligibility criteria for this study. These publications covered a wide range of conditions, but the majority were based on one or only a small number of neurological conditions. In particular, publications concerned with three discrete areas of neurological practice - multiple sclerosis (MS), epilepsy/seizure and Parkinson’s disease - accounted for 60% of the total. MS was the focus of the highest proportion of eligible studies (35%), yet in the recent Global Burden of Neurological Disease study it ranks only 14th out of 15 neurological disorders for DALY rates. In contrast, migraine is the neurological disorder with the highest ranking of DALYs globally (after stroke) and yet it was represented by only 4% of eligible studies.ConclusionThis review shows that there is a disproportionately large body of literature pertaining to relatively rare disorders, and a correspondingly small body of literature describing more common conditions. Therefore, there is potential for future research to redress this balance.
Both EZH2 and JMJD6 regulate cell cycle genes in breast cancer
Authors: Biswas Antara , Mukherjee Geetashree , Kondaiah Paturu , Desai Kartiki V. 
Published: November 2020

Abstract
Background
Strong evidences support the critical role of Jumonji domain containing 6 (JMJD6) in progression of breast cancer. Here we explore potential partners that coregulate gene expression, to understand additional pathways that are activated by higher amounts of JMJD6.

Methods
We used Gene Set Enrichment Analysis (GSEA) data to identify factors that display gene expression similar to cells treated with JMJD6 siRNA. Using chromatin immunoprecipitations (ChIP) against genomic regions that bind JMJD6 identified by in house and public database Encyclopaedia of DNA Elements (ENCODE), we confirmed JMJD6 occupancy by ChIP PCR. We tested the association of co-regulated genes with patient prognosis using The Cancer Genome Atlas (TCGA) datasets.

Results
JMJD6 profiles overlapped with those of Enhancer of Zeste homolog 2 (EZH2) and together they appear to co-regulate a unique cassette of genes in both ER+ and ER- cells. 496 genes including aurora kinases, which are currently being tested as novel therapeutic targets in breast cancer were co-regulated in MDA MB 231 cells. JMJD6 and EZH2 neither inter-regulated nor physically interacted with one another. Since both proteins are chromatin modulators, we performed ChIP linked PCR analysis and show that JMJD6 bound in the neighbourhood of co-regulated genes, though EZH2 data did not show any peaks within 100 kb of these sites. Alignment of binding site sequences suggested that atleast two types of binding partners could offer their DNA binding properties to enrich JMJD6 at regulatory sites. In clinical samples, JMJD6 and EZH2 expression significantly correlated in both normal and tumor samples, however the strongest correlation was observed in triple-negative breast cancer (TNBC) subtype. Co-expression of JMJD6 and EZH2 imposed poorer prognosis in breast cancer.

Conclusions
JMJD6 and EZH2 regulate the same crucial cell cycle regulatory and therapeutic targets but their mechanisms appear to be independent of each other. Blocking of a single molecule may not axe cell proliferation completely and blocking both JMJD6 and EZH2 simultaneously may be more effective in breast cancer patients.
An aggressive systemic mastocytosis preceded by ovarian dysgerminoma
Authors: Tsutsumi Makiko , Miura Hiroki , Inagaki Hidehito , Shinkai Yasuko , Kato Asuka , Kato Takema , Hamada-Tsutsumi Susumu , Tanaka Makito , Kudo Kazuko , Yoshikawa Tetsushi , Kurahashi Hiroki 
Published: November 2020

Abstract
Background
Aggressive systemic mastocytosis (ASM) is a rare malignant disease characterized by disordered mast cell accumulation in various organs. We here describe a female ASM patient with a previous history of ovarian dysgerminoma.

Methods
Molecular cytogenomic analyses were performed to elucidate an etiological link between the ASM and dysgerminoma of the patient.

Results
This patient was affected by ovarian dysgerminoma which was treated by chemotherapy and surgical resection. Having subsequently been in complete remission for 2 years, she developed symptoms of ASM. A somatic D816A mutation in the KIT gene was detected in her bone marrow, which facilitated the diagnosis of ASM. Unexpectedly, this KIT D816A variant was also detected in the prior ovarian dysgerminoma sample. Whole-exome sequencing allowed us to identify a somatic nonsense mutation of the TP53 gene in the bone marrow, but not in the dysgerminoma. Microarray analysis of the patient’s bone marrow revealed a copy-number-neutral loss of heterozygosity at the TP53 locus, suggestive of the homozygous nonsense mutation in the TP53 gene. In addition, the loss of heterozygosity at the TP53 locus was also detected in the dysgerminoma.

Conclusions
These results indicated that either the mast cells causing the ASM in this case had originated from the preceding ovarian dysgerminoma as a clonal evolution of a residual tumor cell, which acquired the TP53 mutation, or that both tumors developed from a common cancer stem cell carrying the KIT D816A variation.
Phase II randomized trial of capecitabine with bevacizumab and external beam radiation therapy as preoperative treatment for patients with resectable locally advanced rectal adenocarcinoma: long term results
Authors:   on behalf of the Spanish Cooperative Group for the Treatment of Digestive Tumors (TTD), Salazar Ramón , Capdevila Jaume , Manzano Jose Luis , Pericay Carles , Martínez-Villacampa Mercedes , López Carlos , Losa Ferrán , Safont María José , Gómez-España Auxiliadora , Alonso-Orduña Vicente , Escudero Pilar , Gallego Javier , García-Paredes Beatriz , Palacios Amalia , Biondo Sebastiano , Grávalos Cristina , Aranda Enrique 
Published: November 2020

Abstract
Background
Preoperative chemoradiotherapy with capecitabine is considered as a standard of care for locally advanced rectal cancer. The “Tratamiento de Tumores Digestivos” group (TTD) previously reported in a randomized Ph II study that the addition of Bevacizumab to capecitabine-RT conferred no differences in the pre-defined efficacy endpoint (pathological complete response).
We present the follow-up results of progression-free survival, distant relapse-free survival, and overall survival data at 3 and 5 years.

Methods
Patients (pts) were randomized to receive 5 weeks of radiotherapy (45 Gy/25 fractions) with concurrent Capecitabine 825 mg/m2 twice daily, 5 days per week with (arm A) or without (arm b) bevacizumab (5 mg/kg once every 2 weeks).

Results
In our study, the addition of bevacizumab to capecitabine and radiotherapy in the neoadjuvant setting shows no differences in pathological complete response (15.9% vs 10.9%), distant relapse-free survival (81.0 vs 80.4 and 76.2% vs 78.2% at 3 and 5 years respectively), disease-free survival (75% vs 71.7 and 68.1% vs 69.57% at 3 and 5 years respectively) nor overall survival at 5-years of follow-up (81.8% vs 86.9%).

Conclusions
the addition of bevacizumab to capecitabine plus radiotherapy does not confer statistically significant advantages neither in distant relapse-free survival nor in disease-free survival nor in Overall Survival in the short or long term.

Trial registration
EudraCT number: 2009–010192-24.
Clinicaltrials.gov number: NCT01043484.
A novel TGF-β receptor II mutation (I227T/N236D) promotes aggressive phenotype of oral squamous cell carcinoma via enhanced EGFR signaling
Authors: Son Hwa-Kyung , Kim Dokyeong , Lim Yongwoon , Kim Jin , Park Iha 
Published: November 2020

AbstractBackgroundTransforming growth factor-β (TGF-β) signaling is a double-edged sword in cancer development and progression. TGF-β signaling plays a tumor suppressive role during the early stages of tumor development but promotes tumor progression in later stages. We have previously identified various mutations of TGF-β receptor II (TβRII) in human oral squamous cell carcinoma (OSCC) samples. In the present study we analyzed I227T/N236D mutation of TβRII, which was detected in the metastatic lymph node of an OSCC patient.MethodsThe effect of I227T/N236D TβRII mutation on transcriptional activities was measured using DR26 cells, which lack functional TβRII. HSC2 human OSCC cells stably expressing wild-type and I227T/N236D mutant TβRII were generated and used to examine the effect of I227T/N236D TβRII mutation on xenograft tumor growth, in vitro cell proliferation, apoptosis, migration, and invasion.ResultsThe I227T/N236D mutation of TβRII upregulated TGF-β signaling and promoted xenograft tumor growth when compared with the wild-type, without affecting the in vitro proliferative capacities. To delineate the differences in proliferative capacities in vivo and in vitro, the apoptotic and survival signals were analyzed following curcumin treatment. Concomitant with apoptotic induction, epidermal growth factor receptor (EGFR) activation was observed upon curcumin treatment, which was further activated in I227T/N236D mutant transfectant cells when compared with wild-type cells. Enhanced EGFR activation correlated with cell survival and apoptotic resistance. Enhanced migratory and invasive capabilities of I227T/N236D mutant cells also depended on EGFR signaling.ConclusionsThese results suggest that enhanced EGFR signaling via upregulated TGF-β signaling shifted the balance toward survival and promoted cell migration and invasion in I227T/N236D mutant cells, elucidating the role of I227T/N236D mutation of TβRII in OSCC progression.
Health behaviors in major chronic diseases patients: trends and regional variations analysis, 2008–2017, Korea
Authors: Jeon Young-Jee , Pyo Jeehee , Park Young-Kwon , Ock Minsu 
Published: November 2020

Abstract
Background
Improving the health behaviors of those with chronic diseases such as hypertension and diabetes is important for disease management. Few in-depth studies have been conducted in Korea on the health behaviors of chronic disease patients. This study examined the health behaviors of chronic disease patients over time and compared them with those of the general population.

Methods
Cross-sectional time-series data obtained from the Korea Community Health Survey from 2008 to 2017 were analyzed. Thirteen diseases were included in this analysis, namely, hypertension, diabetes, dyslipidemia, stroke, myocardial infarction, angina, osteoarthritis, osteoporosis, asthma, allergic rhinitis, atopic dermatitis, cataract, and depression. The current smoking rate, drinking rate, and the walking rate, which are leading health behaviors necessary for preventing chronic diseases, were analyzed by disease type. We compared patients’ health behaviors with those of the general population and identified regional variations.

Results
Although the current overall smoking rate was seemingly declining, the overall monthly drinking and high-risk drinking rates were increasing. In 2017, patients experiencing depression symptoms had a higher smoking rate than did the general population; hypertension and diabetes patients had a higher risk-drinking rate than did the latter. The general population’s walking rate was highest. There were considerable variations by region among chronic disease patients.

Conclusions
Chronic disease patients displayed worse health behaviors than those of the general population, in some instances. Rather than focusing only on chronic disease patients’ medication adherence, strategies must be devised to increase their smoking cessation rate, decrease their drinking rate, and increase their walking rate.
Clinical features of patients with hepatic portal venous gas
Authors: Fujii Manato , Yamashita Suguru , Tanaka Mayuko , Tashiro Jo , Takenaka Yoshiharu , Yamasaki Kazuki , Masaki Yukiyoshi 
Published: November 2020

AbstractBackgroundHepatic portal venous gas (HPVG) is a rare clinical condition that is caused by a variety of underlying diseases. However, the factors that would permit accurate identification of bowel ischemia, requiring surgery, in patients with HPVG have not been fully investigated.MethodsThirty patients that had been diagnosed with HPVG using computed tomography between 2010 and 2019 were allocated to two groups on the basis of clinical and intraoperative findings: those with (Group 1; n = 12 [40%]) and without (Group 2; n = 18 [60%]) bowel ischemia. Eleven patients underwent emergency surgery, and bowel ischemia was identified in eight of these (73%). Four patients in Group 1 were diagnosed with bowel ischemia, but treated palliatively because of their general condition. We compared the characteristics and outcomes of Groups 1 and 2 and identified possible prognostic factors for bowel ischemia.ResultsAt admission, patients in Group 1 more commonly showed the peritoneal irritation sign, had lower base excess, higher lactate, and higher C-reactive protein, and more frequently had comorbid intestinal pneumatosis. Of the eight bowel ischemia surgery patients, four (50%) died, mainly because of anastomotic leak following bowel resection and primary anastomosis (3/4, 75%). All except one patient in Group 2, who presented with aspiration pneumonia, responded better to treatment.ConclusionsEarlier identification and grading of bowel ischemia according to the findings at admission should benefit patients with HPVG by reducing the incidence of unnecessary surgery and increasing the use of safer procedures, such as prophylactic stoma placement.