bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrical pulse stimulation: an in vitro exercise model for the induction of human skeletal muscle cell hypertrophy. A proof‐of‐concept study
Authors: Tarum Janelle , Folkesson Mattias , Atherton Philip J. , Kadi Fawzi 
Published: September 2017

New Findings
What is the central question of this study?
Is electrical pulse stimulation (EPS) an in vitro exercise model able to elicit the hypertrophy of human muscle cells?

What is the main finding and its importance?
The addition of a restitution period of 8 h after EPS induces the enlargement of human muscle cells, a major physiological end‐point to resistance exercise. This is supported by downregulation of myostatin, a negative regulator of muscle mass, and increased phosphorylated mTOR and 4E‐BP1, key factors in the growth cascade. This proof‐of‐concept study provides a model of physiologically mediated muscle growth, which will be the basis for future studies aiming to depict molecular events governing the hypertrophy of human muscle cells.

Electrical pulse stimulation (EPS) of muscle cells has previously been used as an in vitro exercise model. The present study aimed to establish an EPS protocol promoting the hypertrophy of human muscle cells, which represents a major physiological end‐point to resistance exercise in humans. We hypothesized that adding a resting period after EPS would be crucial for the occurrence of the morphological change. Myoblasts obtained from human muscle biopsies (n = 5) were differentiated into multinucleated myotubes and exposed to 8 h of EPS consisting of 2 ms pulses at 12 V, with a frequency of 1 Hz. Myotube size was assessed using immunohistochemistry immediately, 4 and 8 h after completed EPS. Gene expression and phosphorylation status of selected markers of hypertrophy were assessed using RT‐PCR and Western blotting, respectively. Release of the myokine interleukin‐6 in culture medium was measured using enzyme‐linked immunosorbent assay. We demonstrated a significant increase (31 ± 14%; P = 0.03) in the size of myotubes when EPS was followed by an 8 h resting period, but not immediately or 4 h after completion of EPS. The response was supported by downregulation (P = 0.04) of the gene expression of myostatin, a negative regulator of muscle mass, and an increase in phosphorylated mTOR (P = 0.03) and 4E‐BP1 (P = 0.01), which are important factors in the cellular growth signalling cascade. The present work demonstrates that EPS is an in vitro exercise model promoting the hypertrophy of human muscle cells, recapitulating a major physiological end‐point to resistance exercise in human skeletal muscle.
Draft Genome Sequence of the Phytopathogenic FungusFusarium euwallaceae, the Causal Agent ofFusariumDieback
Authors: Ibarra-Laclette Enrique , Sánchez-Rangel Diana , Hernández-Domínguez Eric , Pérez-Torres Claudia-Anahí , Ortiz-Castro Randy , Villafán Emanuel , Alonso-Sánchez Alexandro , Rodríguez-Haas Benjamín , López-Buenfil Abel , García-Avila Clemente , Ramírez-Pool José-Abrahán 
Published: September 2017

ABSTRACTHere, we report the genome ofFusarium euwallaceaestrain HFEW-16-IV-019, an isolate obtained from Kuroshio shot hole borer (aEuwallaceasp.). These beetles were collected in Tijuana, Mexico, from elm trees showing typical symptoms ofFusariumdieback. The final assembly consists of 287 scaffolds spanning 48,274,071 bp and 13,777 genes.
Complete Genome Sequence of Lumpy Skin Disease Virus Isolate SERBIA/Bujanovac/2016, Detected during an Outbreak in the Balkan Area
Authors: Toplak Ivan , Petrović Tamaš , Vidanović Dejan , Lazić Sava , Šekler Milanko , Manić Marija , Petrović Miloš , Kuhar Urška 
Published: September 2017

ABSTRACT
The lumpy skin disease virus (LSDV) isolate SERBIA/Bujanovac/2016 consists of 150,661 nucleotides and has a 99.95% nucleotide identity with the Neethling Warmbaths LW strain isolated in South Africa in 1999. This is the first complete LSDV genome determined in Serbia and also in the Balkan area.
Whole-Genome Sequence of Bacillus cereus AR156, a Potential Biocontrol Agent with High Soilborne Disease Biocontrol Efficacy and Plant Growth Promotion
Authors: Jiang Chun-Hao , Chen Yun , Yan Fang , Fan Zhi-Hang , Guo Jian-Hua 
Published: September 2017

ABSTRACT

Bacillus cereus
AR156 was originally isolated from the forest soil of Zhenjiang, a city in China. To shed new light on the molecular mechanisms underlying the biological control of soilborne pathogens, the whole genome of this strain was sequenced. Here, we report the draft genome sequence of this strain, consisting of a single circularized contig measuring 5.66 Mb, with an average GC content of 35.5% and 5,367 open reading frames.
Draft Genome Sequences of the Oomycete
Pilasporangium apinafurcum
Strains JCM 30513 and JCM 30514, Formerly Classified as
Pythium apinafurcum
Authors: Uzuhashi Shihomi , Endoh Rikiya , Manabe Ri-ichiroh , Ohkuma Moriya 
Published: September 2017

ABSTRACT

Pilasporangium apinafurcum
, formerly classified as
Pythium apinafurcum
, is a unique oomycete that infects plants asymptomatically. Here, we present the draft genome sequences of two variants of
P. apinafurcum
, JCM 30513 and JCM 30514, isolated from uncultivated field soil in Wakayama Prefecture, Japan.
Whole-Genome Sequence and Methylome Analysis of the Freshwater Colorless Sulfur Bacterium
Thioflexothrix psekupsii
D3
Authors: Fomenkov Alexey , Vincze Tamas , Grabovich Margarita Y. , Dubinina Galina , Orlova Maria , Belousova Elena , Roberts Richard J. 
Published: September 2017

ABSTRACT

In this report, we announce the availability of a whole-genome sequence and methylome analysis of
Thioflexothrix psekupsii
strain D3.
High-Quality Draft Genome Sequences for Four Drug-Resistant or Outbreak-Associated Shigella sonnei Strains Generated with PacBio Sequencing and Whole-Genome Maps
Authors: Lindsey Rebecca L. , Batra Dhwani , Rowe Lori , N. Loparev Vladimir , Juieng Phalasy , Garcia-Toledo Lisley , Bicknese Amelia , Stripling Devon , Martin Haley , Chen Jessica , Strockbine Nancy , Trees Eija 
Published: September 2017

ABSTRACT

Drug-resistant
Shigella sonnei
poses a clinical and public health challenge. We report here the high-quality draft whole-genome sequences of four outbreak-associated
S. sonnei
isolates; three were resistant to two or more antibiotics, and one was resistant to streptomycin only.
Complete Genome Sequence of the Pathogenic Vibrio vulnificus Type Strain ATCC 27562
Authors: Rusch Douglas B. , Rowe-Magnus Dean A. 
Published: September 2017

ABSTRACT

Vibrio vulnificus
has the highest death rate and economic burden per case of any foodborne pathogen in the United States. A complete genome sequence of the type strain promotes comparative analyses with other clinical and environmental isolates, improving our understanding of this important human pathogen and successful environmental organism.
Complete Genome Sequence of
Nectarine stem pitting-associated virus
, Isolated from
Prunus persica
in Cheongdo County, South Korea
Authors: Igori Davaajargal , Baek Dasom , Kim San Yeong , Seo Euncheol , Lee Su-Heon , Jeong Rae-Dong , Yi Seung-In , Bong Jin-Jong , Moon Jae Sun 
Published: September 2017

ABSTRACT

We report here the first complete genome sequence of a South Korean isolate of
Nectarine stem pitting-associated virus
(NSPaV) from peach and compare it with previously described complete NSPaV genome sequences. The highest whole-genome nucleotide sequence identity was 95.3% with GenBank accession no. KT273409 (NSPaV) from the United States.
Complete Genome Sequence of Bacillus velezensis GQJK49, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity
Authors: Ma Jinjin , Liu Hu , Liu Kai , Wang Chengqiang , Li Yuhuan , Hou Qihui , Yao Liangtong , Cui Yanru , Zhang Tongrui , Wang Haide , Wang Beibei , Wang Yun , Ge Ruofei , Xu Baochao , Yao Gan , Xu Wenfeng , Fan Lingchao , Ding Yanqin , Du Binghai 
Published: September 2017

ABSTRACT

Bacillus velezensis
GQJK49 is a plant growth-promoting rhizobacterium with antifungal activity, which was isolated from
Lycium barbarum
L. rhizosphere. Here, we report the complete genome sequence of
B. velezensis
GQJK49. Twelve gene clusters related to its biosynthesis of secondary metabolites, including antifungal and antibacterial antibiotics, were predicted.
Genome Sequence of Rhizobium esperanzae Type Strain CNPSo 668, Isolated from Phaseolus vulgaris Nodules in Mexico
Authors: Helene Luisa Caroline Ferraz , Ribeiro Renan Augusto , Hungria Mariangela 
Published: September 2017

ABSTRACT

Rhizobium esperanzae
CNPSo 668
T
is a nitrogen-fixing symbiont of
Phaseolus vulgaris
isolated from Mexican soils. Its genome is estimated at 6,294,057 bp, with 6,219 coding sequences (CDSs) showing higher similarity (92.9%) with
Rhizobium etli
. Three copies of the regulatory
nodD
, in addition to other nodulation genes, should define its host specificity.
Comparative analysis of gender differences in outcomes after trauma in India and the USA: case for standardised coding of injury mechanisms in trauma registries
Authors: Dasari Mohini , David Siddarth D , Miller Elizabeth , Puyana Juan Carlos , Roy Nobhojit 
Published: September 2017

IntroductionWhile females generally have better outcomes than males after traumatic injury, higher mortality has been shown to occur in females after intentional trauma in lower-income countries. However, gender differences in trauma outcomes in different countries have not been previously compared. We conducted a two-country comparative analysis to characterise gender differences in mortality for different mechanisms of injury.MethodsTwo urban trauma databases were analysed from India and the USA for fall, motor vehicle collision (MVC) and assault patients between 2013 and 2015. Coarsened exact matching was used to match the two groups based on gender, age, injury severity score, Glasgow Coma Score and type of injury (blunt vs penetrating). The primary outcome of mortality was studied by using logistic regression to calculate the odds of death in the four country/gender subgroups.ResultsA total of 10 089 and 14 144 patients were included from the Indian and US databases, respectively. After matching on covariates, 7505 and 9448 patients were included in the logistic regression. Indian males had the highest odds of death compared with US males, US females and Indian females for falls, MVC and assaults. Indian females had over 7 times the odds of dying after falls, 5 times the odds of dying for MVC and 40 times the odds of dying after assaults when compared with US females.ConclusionThe high odds of death for Indian females compared with US females suggests that there are other injury and systemic factors that contribute to this discrepancy in mortality odds. This same mortality pattern and implication is seen for Indian males compared with all subgroups. Standardised coding of injury mechanism in trauma registries, in addition to intentionality of injury, can help further characterise discrepancies in outcomes by gender and country, to guide targeted injury prevention and care.
Development and validation of hospital information system-generated indicators of the appropriateness of oral anticoagulant prescriptions in hospitalised adults: the PACHA study protocol
Authors: Petit-Monéger Aurélie , Thiessard Frantz , Jouhet Vianney , Noize Pernelle , Berdaï Driss , Kret Marion , Sitta Rémi , Salmi Louis-Rachid , Saillour-Glénisson Florence 
Published: September 2017

IntroductionThe appropriateness of oral anticoagulant prescriptions is a major challenge to improve quality and safety of care. As indicators of the appropriateness of oral anticoagulant prescriptions are lacking, the aim of the study is to develop and validate a panel of such indicators, in hospitalised adults, from the hospital information system of two university hospitals in France.Methods and analysisThe study will be carried out in four steps: (1) a literature review to identify indicators of the appropriateness of oral anticoagulant prescriptions and their conditions of appropriateness; (2) a Delphi consensus method to assess the potential utility and operational implementation of the selected indicators; (3) techniques of medical data search to implement indicators from the hospital information system and; (4) a cross-sectional study to assess the ability of indicators to detect inappropriate oral anticoagulant prescriptions, performance of medical data search techniques for tracking or retrieving information and the ability of tools to be transferred into other institutions. The fourth step will include up to 80 patient hospital stays for each indicator, depending on the prevalence of inappropriate prescriptions estimated in interim analyses.Ethics and disseminationThis work addresses the current lack of quality indicators of the appropriateness of oral anticoagulant prescriptions. We aim to develop and validate such indicators for integrating them into hospital clinical practice, as part of a structured approach to improve quality and safety of care. As each hospital information system is different, we will propose tools transferable to other healthcare institutions to allow an automated construction of these indicators. The PACHA study protocol was approved by institutional review boards and ethics committees (CPP Sud-Ouest et Outre Mer III—DC 2016/119; CPP Ile-de-France II—CDW_2016_0014).Registration detailsClinical Trial.gov registration:NCT02898090.
Can more appropriate support and services be provided for people who attend the emergency department frequently? National Health Service staff views
Authors: Ablard Suzanne , Coates Elizabeth , Cooper Cindy , Parry Glenys , Mason Suzanne M 
Published: September 2017

BackgroundInterventions designed to help Emergency Department (ED) staff manage frequent attenders are labour-intensive and only benefit a small sample of frequent attenders. We aimed to use the in-depth knowledge of health professionals with experience of working with ED frequent attenders to understand the challenges of managing this group of patients and their opinions on providing more appropriate support.MethodsSemi-structured interviews were conducted with medical and nursing ED staff, mental health liaison nurses and general practitioners (GPs). Interviews covered the following: definitions and experiences of treating frequent attenders and thoughts on alternative service provision. Vignettes of frequent attenders were used to elicit discussions on these topics. Thematic analysis of transcribed interviews was undertaken.ResultsTwelve health professionals were interviewed. Three groups of frequent attenders were identified: people with long-term physical conditions, mental health problems and health-related anxiety. Underlying reasons for attendance differed between the groups, highlighting the need for targeted interventions. Suggested interventions included improving self-management of long-term physical conditions; creating a ‘go-to’ place away from the ED for patients experiencing a mental health crisis; increasing the provision of mental health liaison services; and for patients with health-related anxiety, the role of the GP in the patients’ care pathway was emphasised, as were the benefits of providing additional training for ED staff to help identify and support this group.ConclusionInterventions to address frequent attendance should focus on redirection to and liaison with more appropriate services, located on the hospital site or in the community, tailored to each identified patient group.
Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas
Authors: Lin De-Chen , Dinh Huy Q , Xie Jian-Jun , Mayakonda Anand , Silva Tiago Chedraoui , Jiang Yan-Yi , Ding Ling-Wen , He Jian-Zhong , Xu Xiu-E , Hao Jia-Jie , Wang Ming-Rong , Li Chunquan , Xu Li-Yan , Li En-Min , Berman Benjamin P , Phillip Koeffler H 
Published: September 2017

Objectives
Oesophageal squamous cell carcinoma (OSCC) and adenocarcinoma (OAC) are distinct cancers in terms of a number of clinical and epidemiological characteristics, complicating the design of clinical trials and biomarker developments. We analysed 1048 oesophageal tumour-germline pairs from both subtypes, to characterise their genomic features, and biological and clinical significance.

Design
Previously exome-sequenced samples were re-analysed to identify significantly mutated genes (SMGs) and mutational signatures. The biological functions of novel SMGs were investigated using cell line and xenograft models. We further performed whole-genome bisulfite sequencing and chromatin immunoprecipitation (ChIP)-seq to characterise epigenetic alterations.

Results

OSCC and OAC displayed nearly mutually exclusive sets of driver genes, indicating that they follow independent developmental paths. The combined sample size allowed the statistical identification of a number of novel subtype-specific SMGs, mutational signatures and prognostic biomarkers. Particularly, we identified a novel mutational signature similar to Catalogue Of Somatic Mutations In Cancer (COSMIC)signature 16, which has prognostic value in OSCC. Two newly discovered SMGs,
CUL3
and
ZFP36L2
, were validated as important tumour-suppressors specific to the OSCC subtype. We further identified their additional loss-of-function mechanisms.
CUL3
was homozygously deleted specifically in OSCC and other squamous cell cancers (SCCs). Notably,
ZFP36L2
is associated with super-enhancer in healthy oesophageal mucosa; DNA hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancer-associated SCC suppressor.

Conclusions
These data comprehensively contrast differences between OSCC and OAC at both genomic and epigenomic levels, and reveal novel molecular features for further delineating the pathophysiological mechanisms and treatment strategies for these cancers.
From Famine to Feast: Developing Early-Phase Combination Immunotherapy Trials Wisely
Authors: Day Daphne , Monjazeb Arta M. , Sharon Elad , Ivy S. Percy , Rubin Eric H. , Rosner Gary L. , Butler Marcus O. 
Published: September 2017

Abstract
Not until the turn of this century has immunotherapy become a fundamental component of cancer treatment. While monotherapy with immune modulators, such as immune checkpoint inhibitors, provides a subset of patients with durable clinical benefit and possible cure, combination therapy offers the potential for antitumor activity in a greater number of patients. The field of immunology has provided us with a plethora of potential molecules and pathways to target. This abundance makes it impractical to empirically test all possible combinations efficiently. We recommend that potential immunotherapy combinations be chosen based on sound rationale and available data to address the mechanisms of primary and acquired immune resistance. Novel trial designs may increase the proportion of patients receiving potentially efficacious treatments and, at the same time, better define the balance of clinical activity and safety. We believe that implementing a strategic approach in the early development of immunotherapy combinations will expedite the delivery of more effective therapies with improved safety and durable outcomes. Clin Cancer Res; 23(17); 4980–91. ©2017 AACR.
See all articles in this CCR Focus section, “Clinical Trial Design Considerations in the Immuno-oncology Era.”
Immuno-oncology Clinical Trial Design: Limitations, Challenges, and Opportunities
Authors: Baik Christina S. , Rubin Eric H. , Forde Patrick M. , Mehnert Janice M. , Collyar Deborah , Butler Marcus O. , Dixon Erica L. , Chow Laura Q.M. 
Published: September 2017

Abstract
Recent advances in immuno-oncology and regulatory approvals have been rapid and paradigm shifting in many difficult-to-treat malignancies. Despite immune checkpoint inhibitor therapy becoming the standard of care across multiple tumor types, there are many unanswered questions that need to be addressed before this therapeutic modality can be fully harnessed. Areas of limitations include treatment of patients not sufficiently represented in clinical trials, uncertainty of the optimal treatment dosing and duration, and lack of understanding regarding long-term immune related toxicities and atypical tumor responses. Patients such as those with autoimmune disease, chronic viral infections, limited performance status, and brain metastases were often excluded from initial trials due to concerns of safety. However, limited data suggest that some of these patients can benefit from therapy with manageable toxicities; thus, future studies should incorporate these patients to clearly define safety and efficacy. There are still controversies regarding the optimal dosing strategy that can vary from weight-based to flat dosing, with undefined treatment duration. Further elucidation of the optimal dosing approach and evaluation of predictive biomarkers should be incorporated in the design of future trials. Finally, there are long-term immune-mediated toxicities, atypical tumor responses such as pseudoprogression and endpoints unique to immuno-oncology that are not adequately captured by traditional trial designs; thus, novel study designs are needed. In this article, we discuss in detail the above challenges and propose needed areas of research for exploration and incorporation in the next generation of immuno-oncology clinical trials. Clin Cancer Res; 23(17); 4992–5002. ©2017 AACR.
See all articles in this CCR Focus section, “Clinical Trial Design Considerations in the Immuno-oncology Era.”
Signals from the Adipose Microenvironment and the Obesity–Cancer Link—A Systematic Review
Authors: Himbert Caroline , Delphan Mahmoud , Scherer Dominique , Bowers Laura W. , Hursting Stephen , Ulrich Cornelia M. 
Published: September 2017

Abstract
Obesity and its associated metabolic dysregulation are established risk factors for many cancers. However, the biologic mechanisms underlying this relationship remain incompletely understood. Given the rising rates of both obesity and cancer worldwide, and the challenges for many people to lose excess adipose tissue, a systematic approach to identify potential molecular and metabolic targets is needed to develop effective mechanism-based strategies for the prevention and control of obesity-driven cancer. Epidemiologic, clinical, and preclinical data suggest that within the growth-promoting, proinflammatory microenvironment accompanying obesity, crosstalk between adipose tissue (comprised of adipocytes, macrophages and other cells) and cancer-prone cells may occur via obesity-associated hormones, cytokines, and other mediators that have been linked to increased cancer risk and/or progression. We report here a systematic review on the direct “crosstalk” between adipose tissue and carcinomas in humans. We identified 4,641 articles with n = 20 human clinical studies, which are summarized as: (i) breast (n = 7); (ii) colorectal (n = 4); (iii) esophageal (n = 2); (iv) esophageal/colorectal (n = 1); (v) endometrial (n = 1); (vi) prostate (n = 4); and (vii) ear-nose-throat (ENT) cancer (n = 1). Findings from these clinical studies reinforce preclinical data and suggest organ-dependent crosstalk between adipose tissue and carcinomas via VEGF, IL6, TNFα, and other mechanisms. Moreover, visceral white adipose tissue plays a more central role, as it is more bioenergetically active and is associated with a more procancer secretome than subcutaneous adipose tissue. Efforts to eavesdrop and ultimately interfere with this cancer-enhancing crosstalk may lead to new targets and strategies for decreasing the burden of obesity-related cancers. Cancer Prev Res; 10(9); 494–506. ©2017 AACR.