bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Sequence of vB_AbaS_TRS1, a Viable Prophage Isolated from Acinetobacter baumannii Strain A118
Authors: Turner Dann , Wand Matthew E. , Sutton J. Mark , Centron Daniela , Kropinski Andrew M. , Reynolds Darren M. 
Published: October 2016

ABSTRACT

A novel temperate phage, vB_AbaS_TRS1, was isolated from cultures of
Acinetobacter baumannii
strain A118 that had been exposed to mitomycin C. Phage TRS1 belongs to the
Siphoviridae
family of bacteriophages and encapsulates a 40,749-bp genome encoding 70 coding sequences and a single tRNA.
Genome Sequences of Polyomaviruses from the Wild-Living Red Colobus (
Piliocolobus badius
) and Western Chimpanzee (Pan troglodytes
verus
)
Authors: Ben Salem Nicole , Leendertz Fabian H. , Ehlers Bernhard 
Published: October 2016

ABSTRACT

We identified with PCR and sequencing the full genomes of the recently discovered
Pan troglodytes
verus
polyomavirus 8 and
Piliocolobus badius
polyomavirus 2 in a western chimpanzee and a western red colobus free-ranging in Taï National Park of Côte d'Ivoire.
Draft Genome Sequences of Two Benthic Cyanobacteria,
Oscillatoriales
USR 001 and
Nostoc
sp. MBR 210, Isolated from Tropical Freshwater Lakes
Authors: Te Shu Harn , Tan Boon Fei , Thompson Janelle R. , Gin Karina Yew-Hoong 
Published: October 2016

ABSTRACT

Genomes of two filamentous benthic cyanobacteria were obtained from cocultures obtained from two freshwater lakes. The cultures were obtained by first growing cyanobacterial trichome on solid medium, followed by subculturing in freshwater media. Subsequent shotgun sequencing,
de novo
assembly, and genomic binning yielded almost complete genomes of
Oscillatoriales
USR 001 and
Nostoc
sp. MBR 210.
Complete Genome Sequence of a Brazil-Type
Avian coronavirus
Detected in a Chicken
Authors: Brandão Paulo E. , Ayres Giselle R. R. , Torres Carolina A. , Villarreal Laura Y. B. , Hora Aline S. , Taniwaki Sueli A. 
Published: October 2016

ABSTRACT

Avian coronavirus
is the causative agent of infectious bronchitis in chickens, leading to multisystemic disease that might be controlled if adequate vaccine strains are used. This paper reports the first complete genome sequence of a Brazil type of this virus (27,615 nucleotides [nt]) isolated from the kidneys of a chicken.
Genome Sequence of the Photoarsenotrophic Bacterium
Ectothiorhodospira
sp. Strain BSL-9, Isolated from a Hypersaline Alkaline Arsenic-Rich Extreme Environment
Authors: Hernandez-Maldonado Jaime , Stoneburner Brendon , Boren Alison , Miller Laurence , Rosen Michael , Oremland Ronald S. , Saltikov Chad W. 
Published: October 2016

ABSTRACT

The full genome sequence of
Ectothiorhodospira
sp. strain BSL-9 is reported here. This purple sulfur bacterium encodes an
arxA
-type arsenite oxidase within the
arxB2AB1CD
gene island and is capable of carrying out “photoarsenotrophy” anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb and has approximately 63% G+C content.
Complete Genome Sequences of Two Novel Isolates of Human Parainfluenza Virus 1 Associated with Acute Respiratory Infection
Authors: Denson J. L. , Kennedy J. L. , Dehority W. N. , Eickman M. M. , Schwalm K. S. , Stoner A. N. , Kincaid J. C. , Abramo T. J. , Thompson T. M. , Ulloa E. M. , Burchiel S. W. , Young S. A. , Dinwiddie D. L. 
Published: October 2016

ABSTRACT
Using target capture of viral nucleic acid and next-generation sequencing, we generated the complete genomes of two novel human parainfluenza virus 1 isolates. Isolates AR001 (accession no. KX570602) and NM001 (accession no. KX639498) were collected 3 months apart from pediatric patients with acute respiratory infection from Arkansas and New Mexico, respectively.
Draft Genome Sequence of
Arenibacter
sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment
Authors: Ito Kohei , Nakajima Nobuyoshi , Yamamura Shigeki , Tomita Masaru , Suzuki Haruo , Amachi Seigo 
Published: October 2016

ABSTRACT

Arenibacter
sp. strain C-21, isolated from surface marine sediment of Japan, accumulates iodine in the presence of glucose and iodide (I
-
). We report here the draft genome sequence of this strain to provide insight into the molecular mechanism underlying its iodine-accumulating ability.
Ageing with cerebral palsy; what are the health experiences of adults with cerebral palsy? A qualitative study
Authors: Mudge Suzie , Rosie Juliet , Stott Susan , Taylor Denise , Signal Nada , McPherson Kathryn 
Published: October 2016

ObjectiveTo enhance understanding of the experiences of ageing with cerebral palsy (CP) in adulthood with a particular focus on experiences with health services.DesignA qualitative descriptive methodology was applied to capture adults' views of ageing with CP and related interactions with health services. Semistructured interviews were undertaken with data systematically coded and interpreted by grouping information into categories. Themes that encompassed the categories were identified through thematic analysis.SettingAll healthcare settings.Participants28 adults (14 women) with CP, aged 37–70 years.Results5 themes covered the breadth of participants' experiences: (1) acceptance of change; (2) exploring identity: cerebral palsy as only one part of self; (3) taking charge of help; (4) rethinking the future and (5) interacting with health professionals. Being seen and being heard were the features described in positive healthcare interactions. Participants also valued health professionals who reflected on who holds the knowledge?; demonstrated a willingness to learn and respected participants' knowledge and experience.ConclusionsOur findings could, and arguably should, inform more responsive strategies for disabled people in health services and, indeed, all health consumers. Our study supports other findings that impairments related to CP change and, for many, severity of disabling impact increases with age. Increased interactions with health and rehabilitation professionals, as a consequence of these changes, have the potential to impact the person's healthcare experience either positively or negatively. A ‘listening health professional’ may bridge their knowledge gap and, in recognising the person's own expertise, may achieve three things: a more contextualised healthcare intervention; a better healthcare experience for the person with CP and positive impact on the person's sense of autonomy and identity by recognising their expertise. Future research should identify whether this approach improves the healthcare experience for adults living with CP.
The psychological health and well-being of emergency medicine consultants in the UK
Authors: Fitzgerald Katherine , Yates Philip , Benger Jonathan , Harris Adrian 
Published: October 2016

ObjectiveTo explore the experience of psychological distress and well-being in emergency medicine (EM) consultants.MethodsA qualitative, interpretative phenomenological analysis (IPA) study based on 1:1 semistructured interviews with EM consultants working full time in EDs across South West England. Eighteen EM consultants were interviewed across five EDs, the mean (SD) age of participants being 43.17 (5.8) years. The personal meanings that participants attached to their experiences were inductively analysed.ResultsThe analysis formed three superordinate themes: systemic pressures, physical and mental strain and managing the challenges. Pressures within the ED and healthcare system contributed to participants feeling undervalued and unsatisfied when working in an increasingly uncontrollable environment. Participants described working intensely to meet systemic demands, which inadvertently contributed to a diminishing sense of achievement and self-worth. Consultants perceived their experience of physical and emotional strain as unsustainable, as it negatively impacted; functioning at work, relationships, personal well-being and the EM profession. Participants described how sustainability as an EM consultant could be promoted by social support from consultant colleagues and the ED team, and the opportunity to develop new roles and support ED problem solving at an organisational level. These processes supported a stigma-reducing means of promoting psychological well-being.ConclusionsEM consultants experience considerable physical and mental strain. This strain is dynamically related to consultants' experiences of diminishing self-worth and satisfaction, alongside current sociopolitical demands on EM services. Recognising the psychological experiences and needs of EM consultants and promoting a sustainable EM consultant role could benefit individual psychological well-being and the delivery of emergency care.
Efficacy of Adoptive T-cell Therapy Is Improved by Treatment with the Antioxidant N-Acetyl Cysteine, Which Limits Activation-Induced T-cell Death
Authors: Scheffel Matthew J. , Scurti Gina , Simms Patricia , Garrett-Mayer Elizabeth , Mehrotra Shikhar , Nishimura Michael I. , Voelkel-Johnson Christina 
Published: October 2016

Abstract
Although adoptive transfer of autologous tumor antigen–specific T-cell immunotherapy can produce remarkable clinical efficacy, most patients do not achieve durable complete responses. We hypothesized that reducing susceptibility of T cells to activation-induced cell death (AICD), which increases during the rapid in vitro expansion of therapeutic T cells before their infusion, might improve the persistence of adoptively transferred cells. Our investigations revealed that repetitive stimulation of the T-cell receptor (TCR) induced AICD, as a result of activating the DNA damage response pathway through ATM-mediated Ser15 phosphorylation of p53. Activation of this DNA damage response pathway also occurred upon antigen-specific restimulation in TCR-transduced TIL1383I T cells prepared for adoptive transfer to patients as part of a clinical trial. Notably, treatment with the antioxidant N-acetyl cysteine (NAC) significantly reduced upregulation of the DNA damage marker γH2AX, subsequent ATM activation, and cell death. In the Pmel mouse model of melanoma, the presence of NAC during ex vivo T-cell expansion improved the persistence of adoptively transferred cells, reduced tumor growth, and increased survival. Taken together, our results offer a preclinical proof of concept for the addition of NAC to current therapeutic T-cell expansion protocols, offering immediate potential to improve the quality and therapeutic efficacy of adoptive T-cell therapeutics infused into patients. Cancer Res; 76(20); 6006–16. ©2016 AACR.
Novel Genetic Causes of Pituitary Adenomas
Authors: Caimari Francisca , Korbonits Márta 
Published: October 2016

AbstractRecently, a number of novel genetic alterations have been identified that predispose individuals to pituitary adenomas. Clinically relevant pituitary adenomas are relatively common, present in 0.1% of the general population. They are mostly benign monoclonal neoplasms that arise from any of the five hormone-secreting cell types of the anterior lobe of the pituitary gland, and cause disease due to hormonal alterations and local space-occupying effects. The pathomechanism of pituitary adenomas includes alterations in cell-cycle regulation and growth factor signaling, which are mostly due to epigenetic changes; somatic and especially germline mutations occur more rarely. A significant proportion of growth hormone- and adrenocorticotrophin-secreting adenomas have activating somatic mutations in the GNAS and USP8 genes, respectively. Rarely, germline mutations predispose to pituitary tumorigenesis, often in a familial setting. Classical tumor predisposition syndromes include multiple endocrine neoplasia type 1 (MEN1) and type 4 (MEN4) syndromes, Carney complex, and McCune-Albright syndrome. Pituitary tumors have also been described in association with neurofibromatosis type 1, DICER1 syndrome, and SDHx mutations. Pituitary adenomas with no other associated tumors have been described as familial isolated pituitary adenomas. Patients with AIP or GPR101 mutations often present with pituitary gigantism either in a familial or simplex setting. GNAS and GPR101 mutations that arise in early embryonic age can lead to somatic mosaicism involving the pituitary gland and resulting in growth hormone excess. Senescence has been suggested as the key mechanism protecting pituitary adenomas turning malignant in the overwhelming majority of cases. Here we briefly summarize the genetic background of pituitary adenomas, with an emphasis on the recent developments in this field. Clin Cancer Res; 22(20); 5030–42. ©2016 AACR.See all articles in this CCR Focus section, “Endocrine Cancers: Revising Paradigms.”
Adrenocortical Cancer: A Molecularly Complex Disease Where Surgery Matters
Authors: Payabyab Eden C. , Balasubramaniam Sanjeeve , Edgerly Maureen , Velarde Margarita , Merino Maria J. , Venkatesan Aradhana M. , Leuva Harshraj , Litman Thomas , Bates Susan E. , Fojo Tito 
Published: October 2016

Abstract
The development of new therapies has lagged behind for rare cancers without defined therapeutic targets. Adrenocortical cancer is no exception. Mitotane, an older agent considered “adrenolytic,” is used both to control symptoms in advanced disease and as adjuvant therapy after surgical resection. Molecular characterization of adrenocortical cancer has deepened our understanding of this genetically complex disease while identifying subgroups whose importance remains to be determined. Unfortunately, such studies have yet to demonstrate a therapeutic target for drug development, and to date, no targeted therapy has achieved meaningful outcomes. Consequently, first-line therapy for metastatic disease remains a combination regimen of etoposide, doxorubicin, and cisplatinum established in a randomized clinical trial. In addition to evaluating recent studies in adrenocortical cancer, we raise one critical clinical issue—the risk of peritoneal dissemination following laparoscopic resection of adrenocortical cancer. In a retrospective case series of 267 patients referred to the NCI for the treatment of recurrent or advanced adrenocortical cancer, we found extensive peritoneal dissemination in 25 of the 45 patients (55.6%) who had undergone laparoscopic resection, compared with only 7 of the 222 patients (3%) who had undergone an open resection (P &lt; 0.0001). Although this has been debated in the literature, our data argue for an end to laparoscopic resection of adrenocortical cancers to avoid peritoneal dissemination, a complication of laparoscopy that is uniformly fatal. Clin Cancer Res; 22(20); 4989–5000. ©2016 AACR.
See all articles in this CCR Focus section, “Endocrine Cancers: Revising Paradigms.”
Classical Hodgkin Lymphoma with Reduced β2M/MHC Class I Expression Is Associated with Inferior Outcome Independent of 9p24.1 Status
Authors: Roemer Margaretha G.M. , Advani Ranjana H. , Redd Robert A. , Pinkus Geraldine S. , Natkunam Yasodha , Ligon Azra H. , Connelly Courtney F. , Pak Christine J. , Carey Christopher D. , Daadi Sarah E. , Chapuy Bjoern , de Jong Daphne , Hoppe Richard T. , Neuberg Donna S. , Shipp Margaret A. , Rodig Scott J. 
Published: October 2016

Abstract
In classical Hodgkin lymphoma (cHL), malignant Hodgkin Reed–Sternberg (HRS) cells evade antitumor immunity by multiple mechanisms, including perturbed antigen presentation and enhanced PD-1 signaling. HRS cell expression of the PD-1 ligands is attributable, in part, to copy number alterations of 9p24.1/CD274(PD-L1)/PDCD1LG2(PD-L2). Amplification of PD-L1/PD-L2 is associated with advanced clinical stage and inferior progression-free survival (PFS) following first-line (induction) therapy. The relationships between altered expression of β2-microglobulin (β2M), MHC class I, and MHC class II by HRS cells, PD-L1/PD-L2 amplification, and clinical outcome in cHL are poorly defined. We assessed these variables in diagnostic biopsy specimens from 108 patients with cHL who received uniform treatment and had long-term follow-up and found decreased/absent expression of β2M/MHC class I in 79% (85/108) and decreased/absent expression of MHC class II in 67% (72/108) of cases. Patients with decreased/absent β2M/MHC class I had shorter PFS, independent of PD-L1/PD-L2 amplification and advanced stage. Decreased or absent MHC class II was unrelated to outcome. These results suggest that MHC class I–mediated antigen presentation by HRS cells is an important component of the biological response to standard chemo/radiotherapy. The paucity of β2M/MHC class I expression on HRS cells also prompts speculation regarding alternative mechanisms of action of PD-1 blockade in cHL. Cancer Immunol Res; 4(11); 910–6. ©2016 AACR.
Von Willebrand Factor, ADAMTS13, and the Risk of Mortality
Authors: Sonneveld Michelle A.H. , Franco Oscar H. , Ikram M. Arfan , Hofman Albert , Kavousi Maryam , de Maat Moniek P.M. , Leebeek Frank W.G. 
Published: October 2016

Objective—
Von Willebrand Factor (VWF) is a plasma protein that plays a major role in platelet adhesion and aggregation. Large VWF multimers are cleaved into smaller, less coagulant forms by the metalloprotease ADAMTS13 (A Disintegrin And Metalloprotease with ThromboSpondin motif repeats 13). Previous studies have shown that high VWF and low ADAMTS13 levels are associated with cardiovascular disease, but whether these factors are associated with mortality is unclear. Our aim is to establish the association between VWF antigen (VWF:Ag) levels, ADAMTS13 activity, and mortality.

Approach and Results—
We included 6130 participants of the Rotterdam study, a population-based cohort study among individuals aged ≥55 years. We determined the association between ADAMTS13 activity, VWF:Ag levels, and all-cause and cardiovascular mortality by Cox proportional hazard regression analysis. During a median follow-up time of 11.3 years and a total of 90 635 person years, 1868 of the 6130 individuals died (30.5%), of whom 442 (23.7%) died because of cardiovascular disease. In individuals with low ADAMTS13 activity, the risk of cardiovascular mortality (hazard ratio, 1.46; 95% confidence interval, 1.09–1.96) was higher than that in individuals with high ADAMTS13 activity. The risk of cardiovascular mortality (hazard ratio, 1.29; 95% confidence interval 0.98–1.70) was higher in individuals with the highest VWF:Ag levels than in those with the lowest levels. In individuals with both low ADAMTS13 activity and high VWF:Ag levels, the risk of cardiovascular mortality was even higher (hazard ratio, 1.73 95% confidence interval, 1.28–2.35).

Conclusions—
In this large prospective cohort study, ADAMTS13 activity and VWF:Ag levels are both associated with an increased risk of all-cause and cardiovascular mortality.
Using Large‐Scale Linkage Data to Evaluate the Effectiveness of a National Educational Program on Antithrombotic Prescribing and Associated Stroke Prevention in Primary Care
Authors: Liu Zhixin , Moorin Rachael , Worthington John , Tofler Geoffrey , Bartlett Mark , Khan Rabia , Zuo Yeqin 
Published: October 2016

Background

The National Prescribing Service (NPS) MedicineWise Stroke Prevention Program, which was implemented nationally in 2009–2010 in Australia, sought to improve antithrombotic prescribing in stroke prevention using dedicated interventions that target general practitioners. This study evaluated the impact of the
NPS
MedicineWise Stroke Prevention Program on antithrombotic prescribing and primary stroke hospitalizations.

Method and Results

This population‐based time series study used administrative health data linked to 45 and Up Study participants with a high risk of cardiovascular disease (
CVD
) to assess the possible impact of the
NPS
MedicineWise program on first‐time aspirin prescriptions and primary stroke‐related hospitalizations. Time series analysis showed that the
NPS
MedicineWise program was significantly associated with increased first‐time prescribing of aspirin (
P
=0.03) and decreased hospitalizations for primary ischemic stroke (
P
=0.03) in the at‐risk study population (n=90 023). First‐time aspirin prescription was correlated with a reduction in the rate of hospitalization for primary stroke (
P
=0.02). Following intervention, the number of first‐time aspirin prescriptions increased by 19.8% (95% confidence interval, 1.6–38.0), while the number of first‐time stroke hospitalizations decreased by 17.3% (95% confidence interval, 1.8–30.0).

Conclusions

Consistent with
NPS
MedicineWise program messages for the high‐risk
CVD
population, the
NPS
MedicineWise Stroke Prevention Program (2009) was associated with increased initiation of aspirin and a reduced rate of hospitalization for primary stroke. The findings suggest that the provision of evidence‐based multifaceted large‐scale educational programs in primary care can be effective in changing prescriber behavior and positively impacting patient health outcomes.
Aortic Valve Calcification and Risk of Stroke
Authors: Bos Daniel , Bozorgpourniazi Atefeh , Mutlu Unal , Kavousi Maryam , Vernooij Meike W. , Moelker Adriaan , Franco Oscar H. , Koudstaal Peter J. , Ikram M. Arfan , van der Lugt Aad 
Published: October 2016

Background and Purpose—
It remains uncertain whether aortic valve calcification (AVC) is a risk factor for stroke.

Methods—
From the population-based Rotterdam Study, 2471 participants (mean age: 69.6 years; 51.8% women) underwent computed tomography to quantify AVC. We assessed prevalent stroke and continuously monitored the remaining participants for the incidence of stroke. Logistic and Cox regression models were used to investigate associations of AVC with prevalent stroke and risk of incident stroke.

Results—
AVC was present in 33.1% of people. At baseline, 97 participants had ever suffered a stroke. During 18 665 person-years of follow-up (mean: 7.9 years), 135 people experienced a first-ever stroke. The presence of AVC was not associated with prevalent stroke (fully adjusted odds ratio: 0.97 (95% confidence interval, 0.61–1.53]) or with an increased risk of stroke (fully adjusted hazard ratio: 0.99 (95% confidence interval, 0.69–1.44]).

Conclusions—
Although AVC is a common finding in middle-aged and elderly community-dwelling people, our results suggest that AVC is not associated with an increased risk of stroke.
The Coupled Ocean–Atmosphere Hydrothermohaline Circulation
Authors: Döös Kristofer , Kjellsson Joakim , Zika Jan , Laliberté Frédéric , Brodeau Laurent , Campino Aitor Aldama 
Published: October 2016

AbstractThe thermohaline circulation of the ocean is compared to the hydrothermal circulation of the atmosphere. The oceanic thermohaline circulation is expressed in potential temperature–absolute salinity space and comprises a tropical cell, a conveyor belt cell, and a polar cell, whereas the atmospheric hydrothermal circulation is expressed in potential temperature–specific humidity space and unifies the tropical Hadley and Walker cells as well as the midlatitude eddies into a single, global circulation. The oceanic thermohaline streamfunction makes it possible to analyze and quantify the entire World Ocean conversion rate between cold–warm and fresh–saline waters in one single representation. Its atmospheric analog, the hydrothermal streamfunction, instead captures the conversion rate between cold–warm and dry–humid air in one single representation. It is shown that the ocean thermohaline and the atmospheric hydrothermal cells are connected by the exchange of heat and freshwater through the sea surface. The two circulations are compared on the same diagram by scaling the axes such that the latent heat energy required to move an air parcel on the moisture axis is equivalent to that needed to move a water parcel on the salinity axis. Such a comparison leads the authors to propose that the Clausius–Clapeyron relationship guides both the moist branch of the atmospheric hydrothermal circulation and the warming branches of the tropical and conveyor belt cells of the oceanic thermohaline circulation.