bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues
Authors: Baldwin Don A. , Feldman Michael , Alwine James C. , Robertson Erle S. 
Published: September 2014

ABSTRACT
Screening for thousands of viruses and other pathogenic microorganisms, including bacteria, fungi, and parasites, in human tumor tissues will provide a better understanding of the contributory role of the microbiome in the predisposition for, causes of, and therapeutic responses to the associated cancer. Metagenomic assays designed to perform these tasks will have to include rapid and economical processing of large numbers of samples, supported by straightforward data analysis pipeline and flexible sample preparation options for multiple input tissue types from individual patients, mammals, or environmental samples. To meet these requirements, the PathoChip platform was developed by targeting viral, prokaryotic, and eukaryotic genomes with multiple DNA probes in a microarray format that can be combined with a variety of upstream sample preparation protocols and downstream data analysis. PathoChip screening of DNA plus RNA from formalin-fixed, paraffin-embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and deep sequencing methods. These studies demonstrate the use of the PathoChip technology combined with PCR and deep sequencing as a valuable strategy for detecting the presence of pathogens in human cancers and other diseases.

IMPORTANCE
This work describes the design and testing of a PathoChip array containing probes with the ability to detect all known publicly available virus sequences as well as hundreds of pathogenic bacteria, fungi, parasites, and helminths. PathoChip provides wide coverage of microbial pathogens in an economical format. PathoChip screening of DNA plus RNA from formalin-fixed, paraffin-embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and sequencing methods. These studies demonstrate that the PathoChip technology is a valuable strategy for detecting the presence of pathogens in human cancers and other diseases.
Protocol for a large-scale prospective observational study with alogliptin in patients with type 2 diabetes: J-BRAND Registry
Authors: Inagaki Nobuya , Ueki Kohjiro , Tanizawa Yukio , Watada Hirotaka , Nakamura Jiro , Yamada Yuichiro , Shimomura Iichiro , Nishimura Rimei , Yamazaki Tsutomu , Kadowaki Takashi 
Published: September 2014

IntroductionDipeptidyl peptidase-4 (DPP-4) inhibitors including alogliptin are categorised as a newer class of oral hypoglycaemic, antidiabetic drugs to suppress the degradation of incretin hormones ((glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP)) by DPP-4. We have scheduled a large-scale, multicentre, prospective, observational study (Japan-Based clinical ReseArch Network for Diabetes Registry: J-BRAND Registry) to construct an extensive database over a long-term clinical course in patients with type 2 diabetes receiving oral hypoglycaemic agents (OHAs) and to evaluate the safety and efficacy of alogliptin in Japanese population.Methods and analysis20 000 patients with type 2 diabetes will be registered into two groups of 10 000 each: group A patients will be treated with alogliptin, while group B patients will be treated with non-DPP-4 inhibitor OHA(s). Approximately 300 institutions nationwide will enrol and assign eligible patients equally to either group. Each patient's data will be collected every 6 months for a 3-year period, during which time treatment with OHA(s) may be changed or discontinued, as per package insert for each OHA. Primary end points are safety variables to be compared between the two groups and their subgroups, with respect to hypoglycaemia, pancreatitis, skin disorders, infections and cancer. Secondary end points are efficacy variables including from-baseline changes of A1c, fasting glucose, fasting insulin and urinary albumin, which will be compared between groups/subgroups. New onset and progression of microangiopathy will also be evaluated against OHA(s). Overall, the J-BRAND Registry will evaluate the safety and efficacy of antidiabetic OHA(s) including alogliptin, based on a large-scale database.Ethics and disseminationThis study will be conducted with the highest respect for individual participants according to this protocol, the Declaration of Helsinki, the Ethical Guidelines for Clinical Research (Japan Ministry of Health, Labour and Welfare, 2008) and relevant laws/regulations. The present study will construct a valuable database of patients with type 2 diabetes treated with OHA(s) including alogliptin.Trial registration numberUMIN000007976.
Pupils’ and teachers’ experiences of school-based physical education: a qualitative study
Authors: Lewis Kiara 
Published: September 2014

ObjectivesTo explore pupils’ and teachers’ experiences of physical education (PE).Study designA qualitative investigation employing semistructured interviews. Self Determination Theory was used as a guiding theory and Template Analysis was used to analyse the data.SettingA secondary school in the North East of England.Participants14 pupils (aged 13 and 14, boys and girls) with a range of self-perceived competencies regarding PE and four PE teachers of the pupils (3 male, 1 female).Primary and secondary outcomes(1) Attitudes and perceptions of PE pupils regarding their experiences of compulsory school PE lessons. (2) PE teachers’ experiences of teaching PE.ResultsKey results from pupils and teachers suggest pupils enjoy participation in PE when they feel competent, in control and supported by others. Feeling competent depended on (1) the activity within PE and (2) the pupils perceived physical capabilities/aptitude. Feeling in control related to (1) having a choice of activities, (2) being able to set exertion levels and (3) control over clothes worn while taking part. Relationships within pupil groups and between pupils and teachers were perceived as important. Teachers could positively influence their pupils’ enjoyment by understanding and supporting their personal goals, as opposed to dictating and controlling what they did and for how long, and by promoting a non-threatening atmosphere between pupils.ConclusionsRising obesity levels and concerns over the fitness of children and young people has returned the focus of PE to its potential as a vehicle for promoting health. This study suggests schools and PE teachers in particular can positively influence the PE experience of both boys and girls by providing more choice of activities and letting pupils make their own decisions based on their personal needs.
High incidence of HIV and syphilis among migrant men who have sex with men in Beijing, China: a prospective cohort study
Authors: Mao Hengyi , Ma Wenzhe , Lu Hongyan , Wang Lu , Zheng Hui , Zhu Yingying , Peng Zhihang , Yu Rongbin , Wang Ning 
Published: September 2014

ObjectivesThe purpose of the study was to investigate the incidence of HIV and syphilis and their related factors, as well as to examine the predictors associated with seroconversion among migrant men who have sex with men (MSM) in Beijing, China.DesignProspective cohort study.SettingBeijing, China.Participants511 HIV-negative migrant MSM.Primary and secondary outcome measuresSociodemographic and behavioural information of participants, HIV and syphilis incidence rates, and factors associated with HIV/syphilis seroconversion and cohort retention.ResultsOf the 511 participants, 60.3% (308) and 52.4% (273) were retained at the 4- and 8-month follow-up visits, respectively. The HIV and syphilis incidence rates were 7.83 (95% CI 4.48 to 12.72) and 11.11 (95% CI 6.47 to 17.80) per 100 person-years, respectively. HIV seroconversion was significantly associated with ‘had first anal intercourse at age 15 or younger’ (adjusted HR (aHR) 9.20, 95% CI 1.94 to 43.56) and ‘ever had group sex’ (aHR 4.30, 95% CI 1.40 to 13.18). Bisexual orientation (aHR 5.09, 95% CI 1.02 to 25.57) was significantly associated with syphilis seroconversion. Predictors associated with both 4- and 8-month retention rates included age ≥25 years old and living in Beijing for more than 1 year.ConclusionsThe high incidence of HIV and syphilis among migrant MSM is a cause for concern. A comprehensive strategy should be implemented to maintain a higher retention rate among migrant MSM.
Improving the network management of integrated primary mental healthcare for older people in a rural Australian region: protocol for a mixed methods case study
Authors: Fuller Jeffrey , Oster Candice , Dawson Suzanne , O'Kane Deb , Lawn Sharon , Henderson Julie , Gerace Adam , Reed Richard , Nosworthy Ann , Galley Philip , McPhail Ruth , Cochrane Eimear Muir 
Published: September 2014

IntroductionAn integrated approach to the mental healthcare of older people is advocated across health, aged care and social care sectors. It is not clear, however, how the management of integrated servicing should occur, although interorganisational relations theory suggests a reflective network approach using evaluation feedback. This research will test a network management approach to help regional primary healthcare organisations improve mental health service integration.Methods and analysisThis mixed methods case study in rural South Australia will test facilitated reflection within a network of health and social care services to determine if this leads to improved integration. Engagement of services will occur through a governance group and a series of three 1-day service stakeholder workshops. Facilitated reflection and evaluation feedback will use information from a review of health sector and local operational policies, a network survey about current service links, gaps and enablers and interviews with older people and their carers about their help seeking journeys. Quantitative and qualitative analysis will describe the policy enablers and explore the current and ideal links between services. The facilitated reflection will be developed to maximise engagement of senior management in the governance group and the service staff at the operational level in the workshops. Benefit will be assessed through indicators of improved service coordination, collective ownership of service problems, strengthened partnerships, agreed local protocols and the use of feedback for accountability.Ethics, benefits and disseminationEthics approval will deal with the sensitivities of organisational network research where data anonymity is not preserved. The benefit will be the tested utility of a facilitated reflective process for a network of health and social care services to manage linked primary mental healthcare for older people in a rural region. Dissemination will make use of the sectoral networks of the governance group.
Evaluating the social determinants of teenage pregnancy: a temporal analysis using a UK obstetric database from 1950 to 2010
Authors: McCall Stephen J , Bhattacharya Sohinee , Okpo Emmanuel , Macfarlane Gary J 
Published: September 2014

BackgroundTeenage pregnancy is a known social problem which has been previously described using a number of deprivation measures. This study aimed to explore the temporal patterns of teenage pregnancy in Aberdeen, Scotland and to assess the discriminating ability of three measures of socioeconomic status.MethodsThis was a population-based study from 1950 to 2010, using data from the Aberdeen Maternity Neonatal Databank (AMND). The main outcome variable was conceptions occurring in women aged less than 20 years. This study used two area-based measures, the Scottish Index of Multiple Deprivation (SIMD) and the Carstairs index, and one individual-based measure the Social Class based on Occupation (SCO). These measures were compared for their association with teenage conceptions using logistic regression models. The models were used to determine receiver operating characteristic (ROC) curves showing the discriminating ability of the measures.ResultsThere was an overall decline in teenage conceptions over the 60-year period, but an increase in the rate ratio for deprived areas. All the measures of socioeconomic status were highly associated with teenage pregnancy. The adjusted OR of SIMD and teenage conception was 5.72 (95% CI 4.62 to 7.09), which compared the most deprived decile with the least deprived decile. The use of ROC curves showed that socioeconomic measures performed better than chance at determining teenage conceptions (χ2=21.67, p≤0.0001). They further showed that the SIMD had the largest area under the curve (AUC) with a value of 0.81 (95% CI 0.80 to 0.82), followed by the Carstairs index with an AUC of 0.80 (95% CI 0.78 to 0.80), then by SCO with an AUC of 0.79 (95% CI 0.78 to 0.80).ConclusionsDespite a slight decline in teenage pregnancies over the past decades, there is still an evident association between deprivation and teenage pregnancy. This study shows that all the measures of socioeconomic status were highly associated with teenage pregnancy, with the SIMD having the greatest discriminatory effect.
Republished: Smoking-related interstitial fibrosis (SRIF): pathologic findings and distinction from other chronic fibrosing lung diseases
Authors: Katzenstein Anna-Luise A 
Published: September 2014

Abstract
Smoking-related interstitial fibrosis (SRIF) is a common, histologically striking finding in smokers that must be distinguished from the idiopathic interstitial pneumonias and other chronic interstitial fibrosing lesions. It is characterised by marked thickening of alveolar septa by fibrosis composed of thick collagen bundles that have a distinctive hyalinised quality and often are admixed with variable numbers of hyperplastic smooth muscle fibres. There is minimal accompanying inflammation. This fibrosis is usually most prominent in subpleural and centrilobular parenchyma, but can be present elsewhere as well. It is accompanied by emphysema and respiratory bronchiolitis. Most patients are asymptomatic or only mildly symptomatic, and the clinical course is stable in most. This paper reviews the pathologic features of SRIF in detail, its differentiation from more ominous interstitial fibrosing processes, and the clinical implications of its diagnosis.
Inference of Field-Sensitive Reachability and Cyclicity
Authors: Zanardini Damiano , Genaim Samir 
Published: September 2014

In heap-based languages, knowing that a variable x points to an acyclic data structure is useful for analyzing termination. This information guarantees that the depth of the data structure to which x points is greater than the depth of the structure pointed to by x.
fld
, and allows bounding the number of iterations of a loop that traverses the data structure on
fld
.

In general, proving termination needs acyclicity, unless program-specific or nonautomated reasoning is performed. However, recent work could prove that certain loops terminate even without inferring acyclicity, because they traverse data structures “acyclically.” Consider a double-linked list: if it is possible to demonstrate that every cycle involves both the “next” and the “prev” field, then a traversal on “next” terminates since no cycle will be traversed completely.
This article develops a static analysis inferring field-sensitive reachability and cyclicity information, which is more general than existing approaches. Propositional formulæ are computed, which describe which fields may or may not be traversed by paths in the heap. Consider a tree with edges “left” and “right” to the left and right subtrees, and “parent” to the parent node: termination of a loop traversing leaf-up cannot be guaranteed by state-of-the-art analyses. Instead, propositional formulæ computed by this analysis indicate that cycles must traverse “parent” and at least one between “left” and “right”: termination is guaranteed, as no cycle is traversed completely.
This work defines the necessary abstract domains and builds an abstract semantics on them. A prototypical implementation provides the expected result on relevant examples.
A General Theory of Barbs, Contexts, and Labels
Authors: Bonchi Filippo , Gadducci Fabio , Monreale Giacoma Valentina 
Published: September 2014

Barbed bisimilarity is a widely used behavioral equivalence for interactive systems: given a set of predicates (denoted “barbs” and representing basic observations on states) and a set of contexts (representing the possible execution environments), two systems are deemed to be equivalent if they verify the same barbs whenever inserted inside any of the chosen contexts. Despite its flexibility and expressiveness, this definition of equivalence is unsatisfactory because often the quantification is over an infinite set of contexts, thus making barbed bisimilarity very hard to be verified.
Should a labeled operational semantics be available, more efficient observational equivalences might be adopted. To this end, a series of techniques has been proposed to derive labeled transition systems (LTSs) from unlabeled ones, the main example being Leifer and Milner’s theory of reactive systems. The underlying intuition is that labels should be the “minimal” contexts that allow for a reduction step to be performed.
However, minimality is difficult to asses, whereas the set of “intuitively” correct labels is often easily devised by the ingenuity of the researcher. This article introduces a framework that characterizes (weak) barbed bisimilarity via LTSs whose labels are (not necessarily minimal) contexts. Differently from previous proposals, our theory does not depend on the way the labeled transitions are built but instead relies on a simple set-theoretical presentation for identifying those properties such an LTS should verify to (1) capture the barbed bisimilarities of the underlying system and (2) ensure that such bisimilarities are congruences.
Furthermore, we adopt suitable proof techniques to make feasible the verification of such properties. To provide a test-bed for our formalism, we instantiate it by addressing the semantics of the Mobile Ambients calculus, recasting its barbed bisimilarities via label-based behavioral equivalences.
Mechanical Stresses, Arterial Stiffness, and Brain Small Vessel Diseases
Authors: Okada Yoko , Kohara Katsuhiko , Ochi Masayuki , Nagai Tokihisa , Tabara Yasuharu , Igase Michiya , Miki Tetsuro 
Published: September 2014

Background and Purpose—
Arterial stiffness, a risk factor of brain small vessel diseases (SVD), causes hemodynamic changes. Mechanical stresses, circumferential wall tension (WT), and shear stress (SS) may change with arterial stiffness and be related to SVD. We investigated the associations between mechanical stresses and arterial stiffness and SVD.

Methods—
A total of 1296 subjects without apparent cardiovascular diseases were recruited. Brachial-to-ankle pulse wave velocity (baPWV) was measured as an arterial stiffness index. Silent lacunar infarction and deep subcortical white matter hyperintensity were evaluated as SVD indices. Circumferential WT and SS at peak systole and end diastole were measured at the common carotid artery. Second peak of systolic blood pressure was obtained from the radial waveform and used as a central systolic blood pressure substitute.

Results—

baPWV was associated positively with WT (
P
<0.0001) and negatively with SS (
P
=0.0007) even after correction for confounding parameters including baPWV. SVD was associated with significantly higher WT (
P
<0.0001) and lower SS (
P
<0.0001). After adjustment for confounding parameters (including baPWV), second peak of systolic blood pressure WT (odds ratio, 1.30;
P
=0.0017) and end diastolic WT (odds ratio, 1.60;
P
=0.0038) were related to presence of silent lacunar infarction, whereas peak systolic (odds ratio, 0.95;
P
=0.014) and end diastolic SS (odds ratio, 0.94;
P
=0.014) were associated with presence of deep subcortical white matter hyperintensity grade >3. Regression lines between blood pressure and WT were significantly steeper in subjects with SVD than without SVD (β=0.02;
P
<0.0001).

Conclusions—
These findings indicate that SVD is phenotype-specifically associated with alterations in WT and SS independently of arterial stiffness.
Temporal and spatial segregation in an assemblage of Afrotropical subterranean snakes
Authors: Petrozzi Fabio , Eniang Edem A. , Amadi Nioking , Akani Godfrey C. , Luiselli Luca 
Published: September 2014

Niche partititioning patterns have not been studied so far in burrowing tropical snakes of the families Typhlopidae and Leptotyphlopidae. In this study, we analyze temporal (= monthly activity) and spatial (= habitat use) niche dimensions in three species of burrowing snakes from the Niger Delta, Nigeria. Null model analyses, using two randomization algorithms and 30 000 Monte Carlo permutations, showed that there was random resource partitioning patterns as for the spatial niche dimension. One species (Rhinotyphlops punctatus) clearly dominated in the sample, and appeared to be more habitat generalist than the others. All three species showed an uneven monthly activity, with peaks occurring by wet season, and statistically significant positive correlations between mean monthly rainfall and number of captured snakes. However, there were significantly negative correlations between mean monthly temperature and number of captured snakes in two of the three species (Rhinotyphlops congestus;Leptotyphlopscfr.sundewalli).
Northern and Southern Dynasties and the Course of History Since Middle Antiquity
Authors: Zhi’an Li 
Published: September 2014

Abstract
Two periods in Chinese history can be characterized as constituting a North/South polarization: the period commonly known as the Northern and Southern Dynasties (420ad-589ad), and the Southern Song, Jin, and Yuan Dynasties (1115ad-1368ad). Both of these periods exhibited sharp contrasts between the North and South that can be seen in their respective political and economic institutions. The North/South parity in both of these periods had a great impact on the course of Chinese history. Both before and after the much studied Tang-Song transformation, Chinese history evolved as a conjoining of previously separate North/South institutions. Once the country achieved unification under the Sui Dynasty and early part of the Tang, the trend was to carry on the Northern institutions in the form of political and economic administration. Later in the Tang Dynasty the Northern institutions and practices gave way to the increasing implementation of the Southern institutions across the country. During the Song Dynasty, the Song court initially inherited this “Southernization” trend while the minority kingdoms of Liao, Xia, Jin, and Yuan primarily inherited the Northern practices. After coexisting for a time, the Yuan Dynasty and early Ming saw the eventual dominance of the Southern institutions, while in middle to late Ming the Northern practices reasserted themselves and became the norm. An analysis of these two periods of North/South disparity will demonstrate how these differences came about and how this constant divergence-convergence influenced Chinese history.