bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex
Authors: Loveridge E. Joel , Jones Cerith , Bull Matthew J. , Moody Suzy C. , Kahl Małgorzata W. , Khan Zainab , Neilson Louis , Tomeva Marina , Adams Sarah E. , Wood Andrew C. , Rodriguez-Martin Daniel , Pinel Ingrid , Parkhill Julian , Mahenthiralingam Eshwar , Crosby John 
Published: April 2017

ABSTRACT

Pseudomonas mesoacidophila
ATCC 31433 is a Gram-negative bacterium, first isolated from Japanese soil samples, that produces the monobactam isosulfazecin and the β-lactam-potentiating bulgecins. To characterize the biosynthetic potential of
P. mesoacidophila
ATCC 31433, its complete genome was determined using single-molecule real-time DNA sequence analysis. The 7.8-Mb genome comprised four replicons, three chromosomal (each encoding rRNA) and one plasmid. Phylogenetic analysis demonstrated that
P. mesoacidophila
ATCC 31433 was misclassified at the time of its deposition and is a member of the
Burkholderia cepacia
complex, most closely related to
Burkholderia ubonensis
. The sequenced genome shows considerable additional biosynthetic potential; known gene clusters for malleilactone, ornibactin, isosulfazecin, alkylhydroxyquinoline, and pyrrolnitrin biosynthesis and several uncharacterized biosynthetic gene clusters for polyketides, nonribosomal peptides, and other metabolites were identified. Furthermore,
P. mesoacidophila
ATCC 31433 harbors many genes associated with environmental resilience and antibiotic resistance and was resistant to a range of antibiotics and metal ions. In summary, this bioactive strain should be designated
B. cepacia
complex strain ATCC 31433, pending further detailed taxonomic characterization.

IMPORTANCE
This work reports the complete genome sequence of
Pseudomonas mesoacidophila
ATCC 31433, a known producer of bioactive compounds. Large numbers of both known and novel biosynthetic gene clusters were identified, indicating that
P. mesoacidophila
ATCC 31433 is an untapped resource for discovery of novel bioactive compounds. Phylogenetic analysis demonstrated that
P. mesoacidophila
ATCC 31433 is in fact a member of the
Burkholderia cepacia
complex, most closely related to the species
Burkholderia ubonensis
. Further investigation of the classification and biosynthetic potential of
P. mesoacidophila
ATCC 31433 is warranted.
InvS Coordinates Expression of PrgH and FimZ and Is Required for Invasion of Epithelial Cells by Salmonella enterica serovar Typhimurium
Authors: Wang Lu , Cai Xia , Wu Shuyan , Bomjan Rajdeep , Nakayasu Ernesto S. , Händler Kristian , Hinton Jay C. D. , Zhou Daoguo 
Published: April 2017

ABSTRACT

Deep sequencing has revolutionized our understanding of the bacterial RNA world and has facilitated the identification of 280 small RNAs (sRNAs) in
Salmonella
. Despite the suspicions that sRNAs may play important roles in
Salmonella
pathogenesis, the functions of most sRNAs remain unknown. To advance our understanding of RNA biology in
Salmonella
virulence, we searched for sRNAs required for bacterial invasion into nonphagocytic cells. After screening 75 sRNAs, we discovered that the ablation of InvS caused a significant decrease of
Salmonella
invasion into epithelial cells. A proteomic analysis showed that InvS modulated the levels of several type III secreted
Salmonella
proteins. The level of PrgH, a type III secretion apparatus protein, was significantly lower in the absence of InvS, consistent with the known roles of PrgH in effector secretion and bacterial invasion. We discovered that InvS modulates
fimZ
expression and hence flagellar gene expression and motility. We propose that InvS coordinates the increase of PrgH and decrease in FimZ that promote efficient
Salmonella
invasion into nonphagocytic cells.

IMPORTANCE
Salmonellosis continues to be the most common foodborne infection reported by the CDC in the United States. Central to
Salmonella
pathogenesis is the ability to invade nonphagocytic cells and to replicate inside host cells. Invasion genes are known to be regulated by protein transcriptional networks, but little is known about the role played by small RNAs (sRNAs) in this process. We have identified a novel sRNA, InvS, that is involved in
Salmonella
invasion. Our result will likely provide an opportunity to better understand the fundamental question of how
Salmonella
regulates invasion gene expression and may inform strategies for therapeutic intervention.
Teleosts as Model Organisms To Understand Host-Microbe Interactions
Authors: Lescak Emily A. , Milligan-Myhre Kathryn C. 
Published: April 2017

ABSTRACTHost-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis.
High prevalence of self-reported injuries and illnesses in talented female athletes
Authors: Richardson A. , Clarsen B. , Verhagen E.A.L.M , Stubbe J.H. 
Published: April 2017

BackgroundA thorough knowledge of the epidemiology and severity of injuries and illness in youth female elite sports is lacking due to the methodological challenges involved in recording them. In this study, the prevalence and incidence of injuries and illness are assessed among youth female elite athletes. Instead of solely focusing on time-loss injuries, our study included all substantial and non-substantial health problems (ie, injuries, mental problems and illnesses).MethodsSixty young elite Dutch female athletes (age: 16.6 years (SD: 2.3), weight: 58.3 kg (SD: 15.1), height: 154.1 cm (SD: 44.2)) participating in soccer (n=23), basketball (n=22) and gymnastic (n=15) talent development programmes were prospectively followed during one season (September 2014 to April 2015). To collect health problem data, all athletes completed the Oslo Sports Trauma Research Center Questionnaire on Health Problems every other week. Main outcome measures were average prevalence of injury and incidence density of injury.ResultsAt any given time, 47.9% of the athletes reported an injury (95% CI 43.6% to 52.6%) and 9.1% reported an illness (95% CI 5.1 to 19.0). The average injury incidence density was 8.6 per 1000 hours of athlete exposure. The average number of self-reported injuries per athlete per season was significantly higher in soccer athletes (4.3±2.7) than in basketball athletes (2.6±2.0) (p=0.03) and not significantly higher than in the gymnastic squad. The knee and the ankle were two of the most common injury locations for all squads. Knee injuries in basketball and soccer and heel injuries in the gymnastic squad had the highest impact on sports participation.ConclusionHigh prevalence of self-reported injuries among talented female athletes suggests that future efforts towards their prevention are warranted.
Palliative care clinicians' knowledge of the law regarding the use of the Deprivation of Liberty Safeguards (DoLS)
Authors: Barry Caroline , Spathis Anna , Treaddell Sarah , Carding Sally , Barclay Stephen 
Published: April 2017

ObjectivesTo examine palliative care clinicians' level of knowledge of the law regarding the use of the Deprivation of Liberty Safeguards (DoLS).MethodsRegional postal survey of palliative care clinicians working in hospices in the East of England, undertaken in April 2015. Clinicians' level of knowledge was assessed by their response to 7 factual questions. Data regarding self-reported levels of confidence in applying the Safeguards was collected, alongside information regarding the number of times they had used DoLS in practice. A free-text section invited additional comments from participants.ResultsThere were 47 responses from 14 different organisations; a response rate of 68%. Respondents included consultants, specialty and associate specialists, registrars, nurses and social workers. Higher self-reported confidence and training in the use of DoLS was associated with higher factual knowledge. Consultants had the highest level of knowledge, training and experience. Doctors of other grades, nurses and social workers recorded less knowledge and experience and scored lower in the knowledge sections. The free-text comments revealed difficulty applying the Safeguards in practice, particularly among the consultant responses, based around several themes: insufficient guidance on how to use the Safeguards, process after death, uncertainty as to relevance to palliative care and delays in assessments.ConclusionsClinicians working in palliative care have good levels of knowledge of the DoLS. Despite this concerns were raised, particularly by consultants; uncertainty as to when they should be used and the relevance of the Safeguards in clinical practice. Further guidance should be given to clinicians working in this specialty to ensure that clinical practice is both lawful and in the patients' best interests.
Major trauma from suspected child abuse: a profile of the patient pathway
Authors: Davies Ffion C , Lecky Fiona E , Fisher Ross , Fragoso-Iiguez Marisol , Coats Tim J 
Published: April 2017

BackgroundNetworked organised systems of care for patients with major trauma now exist in many countries, designed around the needs of the majority of patients (90% adults). Non-accidental injury is a significant cause of paediatric major trauma and has a different injury and age profile from accidental injury (AI). This paper compares the prehospital and inhospital phases of the patient pathway for children with suspected abuse, with those accidentally injured.MethodsThe paediatric database of the national trauma registry of England and Wales, Trauma Audit and Research Network, was interrogated from April 2012 (the launch of the major trauma networks) to June 2015, comparing the patient pathway for cases of suspected child abuse (SCA) with AI.ResultsIn the study population of 7825 children, 7344 (94%) were classified as AI and 481 (6%) as SCA. SCA cases were younger (median 0.4 years vs 7 years for AI), had a higher Injury Severity Score (median 16vs9 for AI), and had nearly three times higher mortality (5.7%vs2.2% for AI). Other differences included presentation to hospital evenly throughout the day and year, arrival by non-ambulance means to hospital (74%) and delayed presentation to hospital from the time of injury (median 8 hours vs 1.8 hours for AI). Despite more severe injuries, these infants were less likely to receive key interventions in a timely manner. Only 20% arrived to a designated paediatric-capable major trauma centre. Secondary transfer to specialist care, if needed, took a median of 21.6 hours from injury(vs 13.8 hours for AI).ConclusionThese data show that children with major trauma that is inflicted rather than accidental follow a different pathway through the trauma system. The current model of major trauma care is not a good fit for the way in which child victims of suspected abuse present to healthcare. To achieve better care, awareness of this patient profile needs to increase, and trauma networks should adjust their conventional responses.
Effect of different RE site ionic radii on the electronic structures and elastic properties of Ba2RENbO6: A first-principles study
Authors: Du Lifei , Zhang Peng , Wang Lianli , Du Huiling 
Published: April 2017

RE site ionic radius has a critical influence on the properties of double perovskite oxide Ba2RENbO6. In this paper, the electronic structures and elastic properties of Ba2RENbO6 (RE = Ho, Er, Yb) have been calculated by using the plane-wave pseudopotential density functional theory, and the effect of the different RE site ions on the structures and properties of Ba2RENbO6 is discussed. Results indicate that Ba2RENbO6 (RE = Ho, Er, Yb) are all direct bandgap semiconductors with a bandgap of 0.95 eV, 1.26 eV and 2.36 eV, respectively. With the decrease of the RE site ionic radius of Ba2RENbO6 (RE = Ho, Er, Yb), RE–O and Nb–O covalent bonds are enhanced, and the elastic constants ([Formula: see text], [Formula: see text], [Formula: see text]), elastic modulus ([Formula: see text], [Formula: see text], [Formula: see text]), [Formula: see text], Poisson’s ratio ([Formula: see text]), the Debye temperature [Formula: see text], Gruneisen parameters [Formula: see text] all show a trend of increase. The elastic and thermodynamic properties are all improved with the decreasing radius of RE site ion.
Association of Tenofovir Use With Risk of Incident Heart Failure in HIV‐Infected Patients
Authors: Chen Ruijun , Scherzer Rebecca , Hsue Priscilla Y. , Jotwani Vasantha , Estrella Michelle M. , Horberg Michael A. , Grunfeld Carl , Shlipak Michael G. 
Published: April 2017

Background

The antiretroviral medication, tenofovir disoproxil fumarate (
TDF
), is used by most human immunodeficiency virus–infected persons in the United States despite higher risks of chronic kidney disease. Although chronic kidney disease is a strong risk factor for heart failure (
HF
), the association of
TDF
with incident
HF
is unclear.

Methods and Results

We identified 21 435 human immunodeficiency virus–infected patients in the United States Veterans Health Administration actively using antiretrovirals between 2002 and 2011. We excluded patients with a prior diagnosis of
HF
.
TDF
was analyzed categorically (current, past, or never use) and continuously (per year of use). Proportional hazards regression and fully adjusted marginal structural models were used to determine the association of
TDF
exposure with risk of incident
HF
after adjustment for demographic, human immunodeficiency virus–related, and cardiovascular risk factors. During follow‐up, 438 incident
HF
events occurred. Unadjusted 5‐year event rates for current, past, and never users of
TDF
were 0.9 (95%
CI
0.7‐1.1), 1.7 (1.4‐2.2), and 4.5 (3.9‐5.0), respectively. In fully adjusted analyses,
HF
risk was markedly lower in current
TDF
users (
HR
=0.68; 95%
CI
0.53‐0.86) compared with never users. Among current
TDF
users, each additional year of
TDF
exposure was associated with a 21% lower risk of incident
HF
(95%
CI
: 0.68‐0.92). When limited to antiretroviral‐naive patients,
HF
risk remained lower in current
TDF
users (
HR
=0.53; 95%
CI
0.36‐0.78) compared to never users.

Conclusions

Among a large national cohort of human immunodeficiency virus–infected patients,
TDF
use was strongly associated with lower risk of incident
HF
. These findings warrant confirmation in other populations, both with
TDF
and the recently approved tenofovir alafenamide fumarate.
CyberKnife for Treatment of Vestibular Schwannoma: A Meta‐analysis
Authors: Mahboubi Hossein , Sahyouni Ronald , Moshtaghi Omid , Tadokoro Kent , Ghavami Yaser , Ziai Kasra , Lin Harrison W. , Djalilian Hamid R. 
Published: April 2017

Objectives(1) Perform a meta‐analysis of the available data on the outcomes of CyberKnife radiosurgery for treatment of vestibular schwannomas (VSs) in the published English‐language literature and (2) evaluate the collective outcomes of CyberKnife treatment with respect to tumor control and hearing preservation.Data SourcesA thorough literature search of published English‐language articles was performed in the PubMed, Ovid, and Cochrane databases.Review MethodsA database search was conducted with the keywords “CyberKnife” and “vestibular schwannoma” or “acoustic neuroma.” A total of 25 papers were found and reviewed. Data were extracted for patient demographics, number of patients with neurofibromatosis type 2, pretreatment hearing status, tumor size, margin dose, and follow‐up duration. The primary outcome variables evaluated were tumor control and hearing preservation.ResultsAfter careful review of the published articles, 11 papers reported data on outcomes of CyberKnife treatment for VS and were included in the analysis, comprising 800 patients studied during 1998 to 2012. The reported mean tumor volume ranged from 0.02 to 19.8 cm3, and the follow‐up duration ranged from 6 to 120 months. Margin dose varied from 14 to 25 Gy. The collective mean tumor control rate was 96.3% (95% CI: 94.0%‐98.5%). The collective hearing preservation rate was 79.1% (95% CI: 71.0%‐87.3%) in 427 patients with measurable hearing.ConclusionClinical data on outcomes of CyberKnife radiosurgery for treatment of VSs are sparse and primarily limited to single‐institution analyses, with considerable variation in tumor volume and follow‐up time. This meta‐analysis not only provides an in‐depth analysis of available data in the literature but also reviews reported outcomes and complications.
Microbiology of the Upper and Lower Airways in Pediatric Cystic Fibrosis Patients
Authors: Sobin Lindsay , Kawai Kosuke , Irace Alexandria L. , Gergin Ozgul , Cunningham Michael , Sawicki Gregory S. , Adil Eelam A. 
Published: April 2017

ObjectiveTo evaluate the microbiology of the upper and lower airways in pediatric cystic fibrosis (CF) patients who underwent sinus surgery.Study DesignRetrospective case series with chart review.SettingTertiary care children’s hospital.Subjects and MethodsA total of 201 paired sinus and pulmonary cultures from 105 CF patients were identified between 1996 and 2014. Demographics and culture results were analyzed.ResultsThe mean age of patients was 11.2 ± 5.4 years (range, 1‐27 years), and approximately one‐half were female. Methicillin‐sensitive Staphylococcus aureus was the most common pathogen overall. A significantly higher prevalence of Pseudomonas aeruginosa (32% for pulmonary and 37% for sinus cultures) was observed in older patients versus younger patients (P <. 001). There was low to moderate agreement between sinus and pulmonary cultures (Kappa statistic range, 0.03‐0.56). The prevalence of methicillin‐resistant S aureus (MRSA) increased significantly for lower respiratory tract culture (from 5% to 16%) and sinus culture (from 5% to 27%) between 1996‐2004 and 2010‐2014 (P =. 016 and P <. 001, respectively). The prevalence of positive sinus cultures increased from 40% to 85% between 1996‐2004 and 2010‐2014 (P =. 018). Patients with pulmonary MRSA were more likely to be coinfected with pulmonary P aeruginosa (risk ratio, 2.4; 95% CI, 1.2‐4.8; P =. 015) or Aspergillus fumigatus (risk ratio, 2.2; 95% CI, 1.2‐4.8; P =. 035).ConclusionsThere is low to moderate correlation between pulmonary and sinus pathogens in CF patients. This is important to consider when treating infections. The prevalence of MRSA in sinus cultures has increased over time and warrants further investigation.
In-parallel connected intermittent hemodialysis through ECMO does not affect hemodynamic parameters derived from transpulmonary thermodilution
Authors: Lahmer Tobias , Mayr Ulrich , Rasch Sebastian , Batres Baires Gonzalo , Schmid Roland M. , Huber Wolfgang 
Published: April 2017

Introduction: We report a case of renal replacement therapy (RRT) during extracorporeal membrane oxygenation (ECMO) via a single venous access and analyze the feasibility of transpulmonary thermodilution (TPTD) for hemodynamic monitoring. Case report: ECMO and RRT connected into the ECMO-extracorporeal circuit were performed via a single venous access because of multiple venous thromboses. An indicator for TPTD and pulse contour analysis (PCA) was applied into the central venous catheter (CVC) placed in the right vena jugularis. TPTD and PCA demonstrated comparable cardiac index. Discussion: Congruent data for TPTD and PCA could be observed during TPTD and PCA measurements before ECMO, after ECMO and during ECMO and RRT. This might be explained by high blood flow having the lowest impact on TPTD by venous drainage in the femoral vein/distal vena cava and the TPTD indicator injection using the jugular CVC, as reported in our case. Conclusion: Hemodynamic monitoring using TPTD and PCA during ECMO/RRT is feasible and provides reliable results.
Epstein-Barr virus DNA in serum as an early prognostic marker in children and adolescents with Hodgkin lymphoma
Authors: Welch Jennifer J. G. , Schwartz Cindy L. , Higman Meghan , Chen Lu , Buxton Allen , Kanakry Jennifer A. , Kahwash Samir B. , Hutchison Robert E. , Friedman Debra L. , Ambinder Richard F. 
Published: April 2017

Key PointsEBV DNA in cell-free blood in patients with Hodgkin lymphoma correlated with the presence of virus in tumor. Persistence of EBV DNA in cell-free blood 1 week after initiation of therapy predicted inferior event-free survival.
Designing urban agriculture education for social justice: Radical innovation through Farm School NYC
Authors: Reynolds Kristin 
Published: April 2017

Abstract
This article examines one example of radical innovation and everyday design through a case study of Farm School NYC, an adult education programme in New York City that uses critical pedagogy and popular education to train adult students in urban farming, social justice advocacy and teaching skills. Drawing primarily from research conducted between 2013 and 2014 for a study on urban agriculture and social justice activism, the article illustrates how a network of urban agriculture practitioners, educators and activists created a community-based training programme that takes steps towards a broad vision of a socially just urban food system and that this represents a case of everyday design by radical innovation. It argues that understanding ways in which projects like Farm School NYC infuse radical visions of social change into their day-to-day educational activities is useful for those interested in supporting such transformative work through teaching, farming and gardening and design.