bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dose-dependent inhibition of gastric injury by hydrogen in alkaline electrolyzed drinking water
Authors: Xue Jinling , Shang Guodong , Tanaka Yoshinori , Saihara Yasuhiro , Hou Lingyan , Velasquez Natalia , Liu Wenjun , Lu Yun 
Published: March 2014

Abstract

Background
Hydrogen has been reported to relieve damage in many disease models, and is a potential additive in drinking water to provide protective effects for patients as several clinical studies revealed. However, the absence of a dose–response relationship in the application of hydrogen is puzzling. We attempted to identify the dose–response relationship of hydrogen in alkaline electrolyzed drinking water through the aspirin induced gastric injury model.

Methods
In this study, hydrogen-rich alkaline water was obtained by adding H2 to electrolyzed water at one atmosphere pressure. After 2 weeks of drinking, we detected the gastric mucosal damage together with MPO, MDA and 8-OHdG in rat aspirin induced gastric injury model.

Results
Hydrogen-dose dependent inhibition was observed in stomach mucosal. Under pH 8.5, 0.07, 0.22 and 0.84 ppm hydrogen exhibited a high correlation with inhibitory effects showed by erosion area, MPO activity and MDA content in the stomach. Gastric histology also demonstrated the inhibition of damage by hydrogen-rich alkaline water. However, 8-OHdG level in serum did not have significant hydrogen-dose dependent effect. pH 9.5 showed higher but not significant inhibitory response compared with pH 8.5.

Conclusions
Hydrogen is effective in relieving the gastric injury induced by aspirin-HCl, and the inhibitory effect is dose-dependent. The reason behind this may be that hydrogen-rich water directly interacted with the target tissue, while the hydrogen concentration in blood was buffered by liver glycogen, evoking a suppressed dose–response effect. Drinking hydrogen-rich water may protect healthy individuals from gastric damage caused by oxidative stress.
Validation of the effects of TGF-β1 on tumor recurrence and prognosis through tumor retrieval and cell mechanical properties
Authors: Wu Tsung-Hsien , Chou Yu-Wei , Chiu Pei-Hung , Tang Ming-Jer , Hu Chun-Wen , Yeh Ming-Long 
Published: March 2014

Abstract

Background

In vivo, the transforming growth factor-beta1 (TGF-β1)-induced epithelial to mesenchymal transition (EMT) occurs in seconds during cancer cells intravasation and extravasation. Although it has been established that cellular stiffness can change as a cancer cell transformed, the precise relationship between TGF-β1-induced mesenchymal stem cell mechanics and cancer prognosis remains unclear. Accordingly, it is hard to define the effects of EMT on cell mechanical properties (CMs), tumor recurrence and metastasis risks. This study bridges physical and pathological disciplines to reconcile single-cell mechanical measurements of tumor cells.

Methods and results
We developed a microplate measurement system (MMS) and revealed the intrinsic divergent tumor composition of retrieval cells by cell stiffness and adhesion force and flow cytometry analysis. After flow cytometry sorting, we could measure the differences in CMs of the Sca-1+-CD44+ (mesenchymal-stem-cell-type) and the other subgroups. As well as the stiffer and heterogeneous compositions among tumor tissues with higher recurrence risk were depicted by MMS and atomic force microscopy (AFM). An in vitro experiment validated that Lewis lung carcinoma (LLC) cells acquired higher CMs and motility after EMT, but abrogated by SB-505124 inhibition. Concomitantly, the CD31, MMP13 and TGF-β1 enriched micro-environment in the tumor was associated with higher recurrence and distal lung metastasis risks. Furthermore, we report a comprehensive effort to correlate CMs to tumor-prognosis indicators, in which a decreased body weight gain ratio (BWG) and increased tumor weight (TW) were correlated with increased CMs.

Conclusions
Together, we determined that TGF-β1 was significantly associated with malignant tumor progressing. In terms of clinical applications, local tumor excision followed by MMS analysis offers an opportunity to predict tumor recurrence and metastasis risks.
Estimating the number of injection drug users in greater Victoria, Canada using capture-recapture methods
Authors: Xu Yuan , Fyfe Murray , Walker Liz , Cowen Laura LE 
Published: March 2014

Abstract

Background
Population size estimation is critical for planning public health programmes for injection drug users. Estimation is difficult, as these populations are considered 'hidden’ or 'hard to reach’. The currently accepted population size estimate for greater Victoria, Canada is between 1,500 and 2,000 individuals, which is dated prior to the year 2000, and is likely an underestimate.

Methods
We used three mark-recapture methods (the Lincoln-Petersen estimator, Huggins' model, and Pledger's model) to estimate population size using cross-sectional survey data collected in 2003 and 2005. Data come from a closed population with two time-ordered samples from the same source. We compare our estimates with the currently accepted estimate that is based on the registry of a Victoria needle exchange.

Results
All methods provided population size estimates that were higher than the currently accepted estimate. Huggins' method produced wider confidence intervals. Point estimates of population size from the three methods ranged from 3,329 to 3,342.

Conclusions
Our estimates will aid health authorities in planning for harm reduction programmes. Repeating the methods as further phases of I-Track data become available will ensure that the population estimates remain up to date.
The relationship between cervical flexor endurance, cervical extensor endurance, VAS, and disability in subjects with neck pain
Authors: Parazza Sergio , Vanti Carla , O’Reilly Caroline , Villafañe Jorge Hugo , Tricás Moreno José Miguel , Estébanez De Miguel Elena 
Published: March 2014

Abstract
Background
Several tests have been suggested to assess the isometric endurance of the cervical flexor (NFME) and extensors (NEE) muscles. This study proposes to determine whether neck flexors endurance is related to extensor endurance, and whether cervical muscle endurance is related to disability, pain amount and pain stage in subjects with neck pain.

Methods
Thirty subjects (18 women, 12 men, mean ± SD age: 43 ± 12 years) complaining of neck pain filled out the Visual Analogue Scale (VAS) and the Neck Pain and Disability Scale-Italian version (NPDS-I). They also completed the timed endurance tests for the cervical muscles.

Results
The mean endurance was 246.7 ± 150 seconds for the NEE test, and 44.9 ± 25.3 seconds for the NMFE test. A significant correlation was found between the results of these two tests (r = 0.52, p = 0.003). A positive relationship was also found between VAS and NPDS-I (r = 0.549, p = 0.002). The endurance rates were similar for acute/subacute and chronic subjects, whereas males demonstrated significantly higher values compared to females in NFME test.

Conclusions
These findings suggest that neck flexors and extensors endurance are correlated and that the cervical endurance is not significantly altered by the duration of symptoms in subjects with neck pain.
The brain-enriched microRNA miR-124 in plasma predicts neurological outcome after cardiac arrest
Authors: Gilje Patrik , Gidlöf Olof , Rundgren Malin , Cronberg Tobias , Al-Mashat Mariam , Olde Björn , Friberg Hans , Erlinge David 
Published: March 2014

Abstract
Introduction
Early prognostication after successful cardiopulmonary resuscitation is difficult, and there is a need for novel methods to estimate the extent of brain injury and predict outcome. In this study, we evaluated the impact of the cardiac arrest syndrome on the plasma levels of selected tissue-specific microRNAs (miRNAs) and assessed their ability to prognosticate death and neurological disability.

Methods
We included 65 patients treated with hypothermia after cardiac arrest in the study. Blood samples were obtained at 24 hours and at 48 hours. For miRNA-screening purposes, custom quantitative polymerase chain reaction (qPCR) panels were first used. Thereafter individual miRNAs were assessed at 48 hours with qPCR. miRNAs that successfully predicted prognosis at 48 hours were further analysed at 24 hours. Outcomes were measured according to the Cerebral Performance Category (CPC) score at 6 months after cardiac arrest and stratified into good (CPC score 1 or 2) or poor (CPC scores 3 to 5).

Results
At 48 hours, miR-146a, miR-122, miR-208b, miR-21, miR-9 and miR-128 did not differ between the good and poor neurological outcome groups. In contrast, miR-124 was significantly elevated in patients with poor outcomes compared with those with favourable outcomes (P < 0.0001) at 24 hours and 48 hours after cardiac arrest. Analysis of receiver operating characteristic curves at 24 and 48 hours after cardiac arrest showed areas under the curve of 0.87 (95% confidence interval (CI) = 0.79 to 0.96) and 0.89 (95% CI = 0.80 to 0.97), respectively.

Conclusions
The brain-enriched miRNA miR-124 is a promising novel biomarker for prediction of neurological prognosis following cardiac arrest.
A comprehensive evaluation of assembly scaffolding tools
Authors: Hunt Martin , Newbold Chris , Berriman Matthew , Otto Thomas D 
Published: March 2014

Abstract
Background
Genome assembly is typically a two-stage process: contig assembly followed by the use of paired sequencing reads to join contigs into scaffolds. Scaffolds are usually the focus of reported assembly statistics; longer scaffolds greatly facilitate the use of genome sequences in downstream analyses, and it is appealing to present larger numbers as metrics of assembly performance. However, scaffolds are highly prone to errors, especially when generated using short reads, which can directly result in inflated assembly statistics.

Results
Here we provide the first independent evaluation of scaffolding tools for second-generation sequencing data. We find large variations in the quality of results depending on the tool and dataset used. Even extremely simple test cases of perfect input, constructed to elucidate the behaviour of each algorithm, produced some surprising results. We further dissect the performance of the scaffolders using real and simulated sequencing data derived from the genomes of Staphylococcus aureus, Rhodobacter sphaeroides, Plasmodium falciparum and Homo sapiens. The results from simulated data are of high quality, with several of the tools producing perfect output. However, at least 10% of joins remains unidentified when using real data.

Conclusions
The scaffolders vary in their usability, speed and number of correct and missed joins made between contigs. Results from real data highlight opportunities for further improvements of the tools. Overall, SGA, SOPRA and SSPACE generally outperform the other tools on our datasets. However, the quality of the results is highly dependent on the read mapper and genome complexity.
The genome and life-stage specific transcriptomes of Globodera pallidaelucidate key aspects of plant parasitism by a cyst nematode
Authors: Cotton James A , Lilley Catherine J , Jones Laura M , Kikuchi Taisei , Reid Adam J , Thorpe Peter , Tsai Isheng J , Beasley Helen , Blok Vivian , Cock Peter J A , den Akker Sebastian Eves-van , Holroyd Nancy , Hunt Martin , Mantelin Sophie , Naghra Hardeep , Pain Arnab , Palomares-Rius Juan E , Zarowiecki Magdalena , Berriman Matthew , Jones John T , Urwin Peter E 
Published: March 2014

Abstract
Background
Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security.

Results
We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control.

Conclusions
The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens.
Inferring gene function from evolutionary change in signatures of translation efficiency
Authors: Krisko Anita , Copic Tea , Gabaldón Toni , Lehner Ben , Supek Fran 
Published: March 2014

Abstract
Background
The genetic code is redundant, meaning that most amino acids can be encoded by more than one codon. Highly expressed genes tend to use optimal codons to increase the accuracy and speed of translation. Thus, codon usage biases provide a signature of the relative expression levels of genes, which can, uniquely, be quantified across the domains of life.

Results
Here we describe a general statistical framework to exploit this phenomenon and to systematically associate genes with environments and phenotypic traits through changes in codon adaptation. By inferring evolutionary signatures of translation efficiency in 911 bacterial and archaeal genomes while controlling for confounding effects of phylogeny and inter-correlated phenotypes, we linked 187 gene families to 24 diverse phenotypic traits. A series of experiments in Escherichia coli revealed that 13 of 15, 19 of 23, and 3 of 6 gene families with changes in codon adaptation in aerotolerant, thermophilic, or halophilic microbes. Respectively, confer specific resistance to, respectively, hydrogen peroxide, heat, and high salinity. Further, we demonstrate experimentally that changes in codon optimality alone are sufficient to enhance stress resistance. Finally, we present evidence that multiple genes with altered codon optimality in aerobes confer oxidative stress resistance by controlling the levels of iron and NAD(P)H.

Conclusions
Taken together, these results provide experimental evidence for a widespread connection between changes in translation efficiency and phenotypic adaptation. As the number of sequenced genomes increases, this novel genomic context method for linking genes to phenotypes based on sequence alone will become increasingly useful.
Antisocial personality disorder: new directions
Authors: Yakeley Jessica , Williams Andrew 
Published: March 2014

SummaryAntisocial personality disorder is a complex condition carrying high rates of comorbidity and mortality for individuals as well as harmful consequences for their families and society. Despite the publication of National Institute for Health and Care Excellence (NICE) guidelines for the disorder, the evidence base and provision of effective treatments remain inadequate, and the belief that the condition is untreatable remains widespread among psychiatrists and other professionals. This article highlights current diagnostic controversies and summarises the evidence for conceptualising antisocial personality disorder as a disorder of attachment. Informed by this developmental perspective, we provide a framework for the management and treatment of adults with antisocial personality disorder, highlighting the importance of creating a safe setting and recommending adaptations of therapeutic technique to facilitate the engagement of this ‘treatment-rejecting’ patient population. We conclude with an outline of the current government policy on the treatment of high-risk offenders with personality disorder.LEARNING OBJECTIVESKnow the current diagnostic criteria and epidemiology of antisocial personality disorder.Evaluate the evidence that antisocial personality disorder can be conceptualised as a disorder of attachment, and use a developmental framework to inform treatment interventions.Gain an understanding of psychological approaches to antisocial personality disorder.
Recovery in forensic services: facing the challenge
Authors: Mann Bradley , Matias Elizabeth , Allen Jo 
Published: March 2014

SummaryAlthough there is an increasing focus on recovery within mental health services, there has been limited exploration of the applicability of these principles within forensic services. The authors draw on their experiences within forensic rehabilitation services to discuss the potential obstacles to secure recovery, exploring the systemic and risk management aspects of such a setting as well as considering attachment theory within this context. Some proposals based on clinical experience are given on how such obstacles are faced and tackled.LEARNING OBJECTIVES•To understand the limitations of the recovery approach in forensic settings.•To understand how current risk assessment practice affects patients' autonomy and empowerment.•To understand how the attachment histories of patients in forensic services affect their ability to recover.
The immune system and schizophrenia: an update for clinicians
Authors: Upthegrove Rachel , Barnes Nicholas M. 
Published: March 2014

SummaryIt has long been recognised that the pathology of schizophrenia may involve the immune system, yet this has been a relatively neglected area of research. Recent advances in our understanding of the complexities and functioning of the immune system have allowed new investigation into this area from many angles, including cellular and genetic avenues. A number of prominent theories have been developed. This article gives an overview of our understanding of the immune system and highlights recent advances pertaining to schizophrenia.LEARNING OBJECTIVES•To refresh and update understanding of the innate and adaptive immune system, presented clearly to the non-expert audience.•To understand key advances in immunological theories of schizophrenia.•To engender clinicians' enthusiasm for further reading and interest in this topic.
The Research Domain Criteria: moving the goalposts to change the
game
Authors: Doherty Joanne L. , Owen Michael J. 
Published: March 2014

SummaryThere is increasing concern that a reliance on the descriptive,
syndrome-based diagnostic criteria of ICD and DSM is impeding progress in
research. The USA's major funder of psychiatric research, the National
Institute of Mental Health (NIMH), have stated their intention to encourage
more research across diagnostic categories using a novel framework based on
findings in neuroscience.
Meeting the mental health needs of refugees and asylum
seekers
Authors: Vostanis Panos 
Published: March 2014

SummaryMental health provision for diverse refugee populations is faced with a
number of challenges, and requires the development and evaluation of
flexible service models that maximise capacity and utilise existing
non-specialist resources. Emerging therapeutic approaches should be applied
in real settings, adapted to cultural needs and integrated with the other
agencies involved.
Toric degenerations of integrable systems on Grassmannians and polygon spaces
Authors: Nohara Yuichi , Ueda Kazushi 
Published: March 2014

AbstractWe introduce a completely integrable system on the Grassmannian of 2-planes in ann-space associated with any triangulation of a polygon withnsides, and we compute the potential function for its Lagrangian torus fiber. The moment polytopes of this system for different triangulations are related by an integral piecewise-linear transformation, and the corresponding potential functions are related by its geometric lift in the sense of Berenstein and Zelevinsky.
Bargaining for an Assortment
Authors: Aydin Goker , Heese H. Sebastian 
Published: March 2014

A retailer’s assortment decision results from a process of give-and-take, during which the retailer may bid manufacturers against one another, and the terms of trade offer plenty of flexibility for allocating the profit among the retailer and manufacturers. We adopt a bargaining framework to capture such an assortment selection process. We investigate the properties of the profit allocations that could emerge in a decentralized supply chain. In our model, the retailer engages in simultaneous bilateral negotiations with all manufacturers. Our model and analysis produce managerial insights that could not be obtained in the absence of a bargaining perspective on assortment planning. For example, we find that when a manufacturer improves its product, such improvements not only benefit the retailer but might even benefit competing manufacturers. In fact, even improvements to out-of-assortment products can increase the profits of the retailer and certain in-assortment manufacturers. Hence, our results suggest that a manufacturer can benefit from collaborating with judiciously chosen competitors. This paper was accepted by Serguei Netessine, operations management.
The influence of distal locking on the need for fibular plating in intramedullary nailing of distal metaphyseal tibiofibular fractures
Authors: Attal R. , Maestri V. , Doshi H. K. , Onder U. , Smekal V. , Blauth M. , Schmoelz W. 
Published: March 2014

Using human cadaver specimens, we investigated the role of supplementary fibular plating in the treatment of distal tibial fractures using an intramedullary nail. Fibular plating is thought to improve stability in these situations, but has been reported to have increased soft-tissue complications and to impair union of the fracture. We proposed that multidirectional locking screws provide adequate stability, making additional fibular plating unnecessary. A distal tibiofibular osteotomy model performed on matched fresh-frozen lower limb specimens was stabilised with reamed nails using conventional biplanar distal locking (CDL) or multidirectional distal locking (MDL) options with and without fibular plating. Rotational stiffness was assessed under a constant axial force of 150 N and a superimposed torque of ± 5 Nm. Total movement, and neutral zone and fracture gap movement were analysed. In the CDL group, fibular plating improved stiffness at the tibial fracture site, albeit to a small degree (p = 0.013). In the MDL group additional fibular plating did not increase the stiffness. The MDL nail without fibular plating was significantly more stable than the CDL nail with an additional fibular plate (p = 0.008). These findings suggest that additional fibular plating does not improve stability if a multidirectional distal locking intramedullary nail is used, and is therefore unnecessary if not needed to aid reduction. Cite this article: Bone Joint J 2014;96-B:385–9.