bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laparoscopic placement and urodynamic effects of an artificial urethral sphincter in cadaveric dogs
Authors: Luckring Emilee J. , Ham Kathleen , Adin Christopher A. , McLoughlin Mary A. , Stull Jason W. 
Published: June 2016

ObjectiveTo describe a laparoscopic approach for placement of a percutaneously controlled artificial urethral sphincter (AUS) in female cadaver dogs and compare the change in urethral pressure and lumen diameter after filling the device.Study DesignExperimental study.AnimalsCanine female cadavers (n = 10).MethodsA laparoscopic technique was used to implant the AUS in 10 cadaver dogs. Maximum urethral closure pressure (MUCP), cystourethral leak point pressure (CLPP), and urethral luminal area were measured at 0, 25, 50, and 75% cuff inflation. Necropsy was performed after urethral pressure profilometry and cystoscopy data collection to assess for trauma caused by the procedure.ResultsLaparoscopic implantation was performed successfully in all 10 cadavers with no evidence of inadvertent trauma. Median MUCP at 0% AUS fill (48.9 cmH2O) was significantly lower than 75% fill (243.5 cmH2O). Median CLPP at 0% fill (5.0 cmH2O) was significantly lower than 75% fill (23.2 cmH2O). Significant differences were also found comparing urodynamic values 25 to 50%, 25 to 75%, and 50 to 75%. Cystoscopic evaluation revealed progressive decreases in urethral lumen area and significant differences between the urethral luminal area values as the AUS cuff was inflated.ConclusionLaparoscopic placement of an AUS can be performed successfully in cadaver dogs, improved urethral pressure profile parameters, and visibly occluded the urethral lumen. Further studies of laparoscopic placement in clinical cases affected by urethral sphincter mechanism incompetence are warranted.
Role of Cl−–HCO3− exchanger AE3 in intracellular pH homeostasis in cultured murine hippocampal neurons, and in crosstalk to adjacent astrocytes
Authors: Salameh Ahlam I. , Hübner Christian A. , Boron Walter F. 
Published: June 2016

Key points
A polymorphism of human AE3 is associated with idiopathic generalized epilepsy. Knockout of AE3 in mice lowers the threshold for triggering epileptic seizures. The explanations for these effects are elusive.
Comparisons of cells from wild‐type vs. AE3–/– mice show that AE3 (present in hippocampal neurons, not astrocytes; mediates HCO3– efflux) enhances intracellular pH (pHi) recovery (decrease) from alkali loads in neurons and, surprisingly, adjacent astrocytes.
During metabolic acidosis (MAc), AE3 speeds initial acidification, but limits the extent of pHi decrease in neurons and astrocytes.
AE3 speeds re‐alkalization after removal of MAc in neurons and astrocytes, and speeds neuronal pHi recovery from an ammonium prepulse‐induced acid load.
We propose that neuronal AE3 indirectly increases acid extrusion in (a) neurons via Cl– loading, and (b) astrocytes by somehow enhancing NBCe1 (major acid extruder). The latter would enhance depolarization‐induced alkalinization of astrocytes, and extracellular acidification, and thereby reduce susceptibility to epileptic seizures.
AbstractThe anion exchanger AE3, expressed in hippocampal (HC) neurons but not astrocytes, contributes to intracellular pH (pHi) regulation by facilitating the exchange of extracellular Cl– for intracellular HCO3–. The human AE3 polymorphism A867D is associated with idiopathic generalized epilepsy. Moreover, AE3 knockout (AE3–/–) mice are more susceptible to epileptic seizure. The mechanism of these effects has been unclear because the starting pHi in AE3–/– and wild‐type neurons is indistinguishable. The purpose of the present study was to use AE3–/– mice to investigate the role of AE3 in pHi homeostasis in HC neurons, co‐cultured with astrocytes. We find that the presence of AE3 increases the acidification rate constant during pHi recovery from intracellular alkaline loads imposed by reducing [CO2]. The presence of AE3 also speeds intracellular acidification during the early phase of metabolic acidosis (MAc), not just in neurons but, surprisingly, in adjacent astrocytes. Additionally, AE3 contributes to braking the decrease in pHi later during MAc in both neurons and astrocytes. Paradoxically, AE3 enhances intracellular re‐alkalization after MAc removal in neurons and astrocytes, and pHi recovery from an ammonium prepulse‐induced acid load in neurons. The effects of AE3 knockout on astrocytic pHi homeostasis in MAc‐related assays require the presence of neurons, and are consistent with the hypothesis that the AE3 knockout reduces functional expression of astrocytic NBCe1. These findings suggest a new type of neuron–astrocyte communication, based on the expression of AE3 in neurons, which could explain how AE3 reduces seizure susceptibility.
Partial Diversity Generates Effector Immunity Specificity of the Bac41-Like Bacteriocins of Enterococcus faecalis Clinical Strains
Authors: Kurushima Jun , Ike Yasuyoshi , Tomita Haruyoshi 
Published: June 2016

ABSTRACT

Bacteriocin 41 (Bac41) is the plasmid-encoded bacteriocin produced by the opportunistic pathogen
Enterococcus faecalis
. Its genetic determinant consists of

bacL
1

(effector),

bacL
2

(regulator),
bacA
(effector), and
bacI
(immunity). The secreted effectors BacL
1
and BacA coordinate to induce the lytic cell death of
E. faecalis
. Meanwhile, the immunity factor BacI provides self-resistance to the Bac41 producer,
E. faecalis
, against the action of BacL
1
and BacA. In this study, we demonstrated that more than half of the 327 clinical strains of
E. faecalis
screened had functional Bac41 genes. Analysis of the genetic structure of the Bac41 genes in the DNA sequences of the
E. faecalis
strains revealed that the Bac41-like genes consist of a relatively conserved region and a variable region located downstream from
bacA
. Based on similarities in the variable region, the Bac41-like genes could be classified into type I, type IIa, and type IIb. Interestingly, the distinct Bac41 types had specific immunity factors for self-resistance, BacI1 or BacI2, and did not show cross-immunity to the other type of effector. We also demonstrated experimentally that the specificity of the immunity was determined by the combination of the C-terminal region of BacA and the presence of the unique BacI1 or BacI2 factor. These observations suggested that Bac41-like bacteriocin genes are extensively disseminated among
E. faecalis
strains in the clinical environment and can be grouped into at least three types. It was also indicated that the partial diversity results in specificity of self-resistance which may offer these strains a competitive advantage.

IMPORTANCE
Bacteriocins are antibacterial effectors produced by bacteria. In general, a bacteriocin-coding gene is accompanied by a cognate immunity gene that confers self-resistance on the bacteriocin-producing bacterium itself. We demonstrated that one of the bacteriocins, Bac41, is disseminated among
E. faecalis
clinical strains and the Bac41 subtypes with partial diversity. The Bac41-like bacteriocins were found to be classified into type I, type IIa, and type IIb by variation of the cognate immunity factors. The antibacterial activity of the respective effectors was specifically inhibited by the immunity factor from the same type of Bac41 but not the other types. This specificity of effector-immunity pairs suggests that bacteriocin genes might have evolved to change the immunity specificity to acquire an advantage in interbacterial competition.
Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization
Authors: Conlan Sean , Park Morgan , Deming Clayton , Thomas Pamela J. , Young Alice C. , Coleman Holly , Sison Christina ,   NISC Comparative Sequencing Program, Weingarten Rebecca A. , Lau Anna F. , Dekker John P. , Palmore Tara N. , Frank Karen M. , Segre Julia A. 
Published: June 2016

ABSTRACT

Carbapenem-resistant
Klebsiella pneumoniae
strains are formidable hospital pathogens that pose a serious threat to patients around the globe due to a rising incidence in health care facilities, high mortality rates associated with infection, and potential to spread antibiotic resistance to other bacterial species, such as
Escherichia coli
. Over 6 months in 2011, 17 patients at the National Institutes of Health (NIH) Clinical Center became colonized with a highly virulent, transmissible carbapenem-resistant strain of
K. pneumoniae
. Our real-time genomic sequencing tracked patient-to-patient routes of transmission and informed epidemiologists’ actions to monitor and control this outbreak. Two of these patients remained colonized with carbapenemase-producing organisms for at least 2 to 4 years, providing the opportunity to undertake a focused genomic study of long-term colonization with antibiotic-resistant bacteria. Whole-genome sequencing studies shed light on the underlying complex microbial colonization, including mixed or evolving bacterial populations and gain or loss of plasmids. Isolates from NIH patient 15 showed complex plasmid rearrangements, leaving the chromosome and the
bla
KPC
-carrying plasmid intact but rearranging the two other plasmids of this outbreak strain. NIH patient 16 has shown continuous colonization with
bla
KPC
-positive organisms across multiple time points spanning 2011 to 2015. Genomic studies defined a complex pattern of succession and plasmid transmission across two different
K. pneumoniae
sequence types and an
E. coli
isolate. These findings demonstrate the utility of genomic methods for understanding strain succession, genome plasticity, and long-term carriage of antibiotic-resistant organisms.

IMPORTANCE
In 2011, the NIH Clinical Center had a nosocomial outbreak involving 19 patients who became colonized or infected with
bla
KPC
-positive
Klebsiella pneumoniae
. Patients who have intestinal colonization with
bla
KPC
-positive
K. pneumoniae
are at risk for developing infections that are difficult or nearly impossible to treat with existing antibiotic options. Two of those patients remained colonized with
bla
KPC
-positive
Klebsiella pneumoniae
for over a year, leading to the initiation of a detailed genomic analysis exploring mixed colonization, plasmid recombination, and plasmid diversification. Whole-genome sequence analysis identified a variety of changes, both subtle and large, in the
bla
KPC
-positive organisms. Long-term colonization of patients with
bla
KPC
-positive
Klebsiella pneumoniae
creates new opportunities for horizontal gene transfer of plasmids encoding antibiotic resistance genes and poses complications for the delivery of health care.
Association of physical activity with cognition, metacognition and academic performance in children and adolescents: a protocol for systematic review and meta-analysis
Authors: Álvarez-Bueno Celia , Pesce Caterina , Cavero-Redondo Iván , Sánchez-López Mairena , Pardo-Guijarro María Jesús , Martínez-Vizcaíno Vicente 
Published: June 2016

IntroductionSchools provide a relevant context for improving children's and adolescents’ physical and mental health by increasing physical activity during school hours and/or beyond. The interest in the relationship between physical activity programmes and cognition during development has recently increased, with evidence suggesting a positive association. We present a protocol of systematic reviews and meta-analysis of intervention studies that, by determining the effects of chronic physical exercise on children's and adolescents’ cognitive and metacognitive functions, cognitive life skills, academic behaviours and achievement, aims to ensure procedural objectivity and transparency, and maximise the extraction of relevant information to inform policy development.MethodsThis protocol is guided by Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) and by the Cochrane Collaboration Handbook. Databases to be utilised for a thorough selection of the pertinent literature are MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, Web of Science, PsycINFO and ERIC. Selection is proposed to encompass an international and a national publication level, with inclusion of experimental studies written in English or in Spanish, respectively. Also, relevant references included in the selected studies will be considered suitable for review as supplemental sources.We present an integrated approach to the methodological quality assessment of the selected studies, including the Jadad Scale for the assessment of the quality of randomised controlled trials and the Quality Assessment Tool for Quantitative Studies for pre–post studies and non-randomised controlled trials. The pre–post interventions mean differences will be the primary indicator of the intervention outcome.Statistical analysisA subgroup analysis is proposed based on cognitive functions and their neural correlates, metacognitive functions and cognitive life skills, academic achievement areas and academic behaviours.Trial registration numberPROSPERO CRD42015029913
‘Delayed discharges and boarders’: a 2-year study of the relationship between patients experiencing delayed discharges from an acute hospital and boarding of admitted patients in a crowded ED
Authors: Mustafa Farah , Gilligan Peadar , Obu Deborah , O'Kelly Patrick , O'Hea Eimear , Lloyd Catherine , Kelada Sherif , Heffernan Attracta , Houlihan Patricia 
Published: June 2016

ObjectiveMany believe that hospital crowding manifesting in the ED with the boarding of admitted patients is a result of significant numbers of acute hospital beds being occupied by patients awaiting discharge to nursing homes, step-down facilities or home with or without additional support. This observational study was performed to establish the actual relationship between boarders in the ED and patients experiencing delayed discharge.MethodsData relating to the number of patients in the ED and their points in their patient pathway were entered into a logbook on a daily basis by the most senior doctor on duty. 630 days of observations of patients boarded in the ED were compared with the number of inpatients with delayed discharges, obtained from the hospital information system, to see if large numbers of inpatients with delayed discharges are associated with crowding in the ED.ResultsTwo years of data showed an annual ED census of more than 47 000, with a daily mean ED admission rate of 29.85 patients and a daily mean ED boarding figure of 29 patients. A mean of 15.4% of the 823 hospital beds was occupied by patients with delayed discharges, and the hospital ran at, or near, full capacity (99%–105%) all the time. Results obtained highlighted a statistically significant relationship between delayed discharges in the hospital and ED crowding as a result of boarders (p value<0.001, with a regression coefficient of 0.16, 95% CI 0.12 to 0.20). The study also showed that the number of boarders was related to the number of ED admissions in the preceding 24 hours (p=0.036, with a regression coefficient of 0.14, 95% CI 0.05 to 0.28).ConclusionsDelayed hospital discharges significantly contribute to crowding in the ED. Healthcare systems should target timely discharge of inpatients experiencing delayed discharge in an urgent and efficient manner to improve timely access to acute hospital beds for patients requiring emergency admission.
A pictorial review of imaging in paediatric stroke
Authors: Johns Christopher , Kolla S , Hart A , Sinha S , Batty R , Connolly D J A 
Published: June 2016

AbstractStroke is recognised as an important disease in adults. Paediatric stroke is less understood, yet still an important cause of morbidity and mortality, with an incidence of 5 per 100 000 children and is one of the top 10 leading causes of death in children. In adults the vast majority of strokes are ischaemic, whereas in children haemorrhage makes up half the cases. The incidence of neonatal stroke is much higher, at up to 45 per 100 000 population; however, the underlying causes are less understood. This paper acts as a guide to the different causes of stroke with the key differences on imaging discussed.
Semantics Out of Context
Authors: Gabbay Murdoch J. 
Published: June 2016

Call a semantics for a language with variablesabsolutewhen variables map to fixed entities in the denotation. That is, a semantics is absolute when the denotation of a variableais a copy of itself in the denotation.We give a trio of lattice-based, sets-based, and algebraic absolute semantics to first-order logic. Possibly open predicates are directly interpreted as lattice elements/sets/algebra elements, subject to suitable interpretations of the connectives and quantifiers. In particular, universal quantification ∀a.φ is interpreted using a new notion of“fresh-finite”limit Λ#a⟦Φ⟧ and using a novel dual to substitution.The interest in this semantics is partly in the nontrivial and beautiful technical details, which also offer certain advantages over existing semantics. Also, the fact that such semantics exist at all suggests a new way of looking at variables and the foundations of logic and computation, which may be well suited to the demands of modern computer science.
Diversity-oriented Multimodal and Interactive Information Retrieval
Authors: Calumby Rodrigo Tripodi 
Published: June 2016

Information retrieval methods, especially considering multimedia data, have evolved towards the integration of multiple sources of evidence in the analysis of the relevance of the items considering a given user search task. In this context, for attenuating the semantic gap between low-level features extracted from the content of the digital objects and high-level semantic concepts (objects, categories, etc.) and making the systems adaptive to different user needs, interactive models have brought the user closer to the retrieval loop allowing user-system interaction mainly through implicit or explicit relevance feedback. Analogously, diversity promotion has emerged as an alternative for tackling ambiguous or underspecified queries. Additionally, several works have addressed the issue of minimizing the required user effort on providing relevance assessments while keeping an acceptable overall effectiveness
This thesis discusses, proposes, and experimentally analyzes multimodal and interactive diversity-oriented information retrieval methods. This work, comprehensively covers the interactive information retrieval literature and also discusses about recent advances, the great research challenges, and promising research opportunities. We have proposed and evaluated two relevancediversity trade-off enhancement work-flows, which integrate multiple information from images, such as: visual features, textual metadata, geographic information, and user credibility descriptors. In turn, as an integration of interactive retrieval and diversity promotion techniques, for maximizing the coverage of multiple query interpretations/aspects and speeding up the information transfer between the user and the system, we have proposed and evaluated a multimodal online learning-to-rank method trained with relevance feedback over diversified results
Our experimental analysis shows that the joint usage of multiple information sources positively impacted the relevance-diversity balancing algorithms. Our results also suggest that the integration of multimodal-relevance-based filtering and reranking is effective on improving result relevance and also boosts diversity promotion methods. Beyond it, with a thorough experimental analysis we have investigated several research questions related to the possibility of improving result diversity and keeping or even improving relevance in interactive search sessions. Moreover, we analyze how much the diversification effort affects overall search session results and how different diversification approaches behave for the different data modalities. By analyzing the overall and per feedback iteration effectiveness, we show that introducing diversity may harm initial results whereas it significantly enhances the overall session effectiveness not only considering the relevance and diversity, but also how early the user is exposed to the same amount of relevant items and diversity
An Expression Signature as an Aid to the Histologic Classification of Non–Small Cell Lung Cancer
Authors: Girard Luc , Rodriguez-Canales Jaime , Behrens Carmen , Thompson Debrah M. , Botros Ihab W. , Tang Hao , Xie Yang , Rekhtman Natasha , Travis William D. , Wistuba Ignacio I. , Minna John D. , Gazdar Adi F. 
Published: June 2016

Abstract
Purpose: Most non–small cell lung cancers (NSCLC) are now diagnosed from small specimens, and classification using standard pathology methods can be difficult. This is of clinical relevance as many therapy regimens and clinical trials are histology dependent. The purpose of this study was to develop an mRNA expression signature as an adjunct test for routine histopathologic classification of NSCLCs.
Experimental Design: A microarray dataset of resected adenocarcinomas (ADC) and squamous cell carcinomas (SCC) was used as the learning set for an ADC-SCC signature. The Cancer Genome Atlas (TCGA) lung RNAseq dataset was used for validation. Another microarray dataset of ADCs and matched nonmalignant lung was used as the learning set for a tumor versus nonmalignant signature. The classifiers were selected as the most differentially expressed genes and sample classification was determined by a nearest distance approach.
Results: We developed a 62-gene expression signature that contained many genes used in immunostains for NSCLC typing. It includes 42 genes that distinguish ADC from SCC and 20 genes differentiating nonmalignant lung from lung cancer. Testing of the TCGA and other public datasets resulted in high prediction accuracies (93%–95%). In addition, a prediction score was derived that correlates both with histologic grading and prognosis. We developed a practical version of the Classifier using the HTG EdgeSeq nuclease protection–based technology in combination with next-generation sequencing that can be applied to formalin-fixed paraffin-embedded (FFPE) tissues and small biopsies.
Conclusions: Our RNA classifier provides an objective, quantitative method to aid in the pathologic diagnosis of lung cancer. Clin Cancer Res; 22(19); 4880–9. ©2016 AACR.