bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome and transcriptome sequencing of matched primary and peritoneal metastatic gastric carcinoma
Authors: Zhang J. , Huang J. Y. , Chen Y. N. , Yuan F. , Zhang H. , Yan F. H. , Wang M. J. , Wang G. , Su M. , Lu G , Huang Y. , Dai H. , Ji J. , Zhang J. , Zhang J. N. , Jiang Y. N. , Chen S. J. , Zhu Z. G. , Yu Y. Y. 
Published: September 2015

AbstractGastric cancer is one of the most aggressive cancers and is the second leading cause of cancer death worldwide. Approximately 40% of global gastric cancer cases occur in China, with peritoneal metastasis being the prevalent form of recurrence and metastasis in advanced disease. Currently, there are limited clinical approaches for predicting and treatment of peritoneal metastasis, resulting in a 6-month average survival time. By comprehensive genome analysis will uncover the pathogenesis of peritoneal metastasis. Here we describe a comprehensive whole-genome and transcriptome sequencing analysis of one advanced gastric cancer case, including non-cancerous mucosa, primary cancer and matched peritoneal metastatic cancer. The peripheral blood is used as normal control. We identified 27 mutated genes, of which 19 genes are reported in COSMIC database (ZNF208, CRNN, ATXN3, DCTN1, RP1L1, PRB4, PRB1, MUC4, HS6ST3, MUC17, JAM2, ITGAD, IREB2, IQUB, CORO1B, CCDC121, AKAP2, ACAN and ACADL) and eight genes have not previously been described in gastric cancer (CCDC178, ARMC4, TUBB6, PLIN4, PKLR, PDZD2, DMBT1and DAB1).Additionally,GPX4 and MPND in 19q13.3-13.4 region, is characterized as a novel fusion-gene. This study disclosed novel biological markers and tumorigenic pathways that would predict gastric cancer occurring peritoneal metastasis.
Addition of Histology to the Paris Classification of Pediatric Crohn Disease Alters Classification of Disease Location
Authors: Fernandes Melissa A. , Verstraete Sofia G. , Garnett Elizabeth A. , Heyman Melvin B. 
Published: September 2015

ABSTRACTObjectives:The aim of the study was to investigate the value of microscopic findings in the classification of pediatric Crohn disease (CD) by determining whether classification of disease changes significantly with inclusion of histologic findings.Methods:Sixty patients were randomly selected from a cohort of patients studied at the Pediatric Inflammatory Bowel Disease Clinic at the University of California, San Francisco Benioff Children's Hospital. Two physicians independently reviewed the electronic health records of the included patients to determine the Paris classification for each patient by adhering to present guidelines and then by including microscopic findings.Results:Macroscopic and combined disease location classifications were discordant in 34 (56.6%), with no statistically significant differences between groups. Interobserver agreement was higher in the combined classification (κ = 0.73, 95% confidence interval 0.65–0.82) as opposed to when classification was limited to macroscopic findings (κ = 0.53, 95% confidence interval 0.40–0.58). When evaluating the proximal upper gastrointestinal tract (Paris L4a), the interobserver agreement was better in macroscopic compared with the combined classification.Conclusions:Disease extent classifications differed significantly when comparing isolated macroscopic findings (Paris classification) with the combined scheme that included microscopy. Further studies are needed to determine which scheme provides more accurate representation of disease extent.
Alpha‐Tocopherol Concentration in Colostrum and Serum of Women With Premature Labor
Authors: Medeiros Jeane Franco Pires , da Silva Ribeiro Rodrigues Karla Danielly , Lima Mayara Santa Rosa , da Silva Anna Larissa Cortês , de Queiroz Jaluza Luana Carvalho , Dimenstein Roberto 
Published: September 2015

ABSTRACTObjective:The aim of the study was to evaluate and compare the levels of alpha‐tocopherol in colostrum milk and serum of mothers with premature birth, classified as severe prematurity and moderate prematurity.Methods:Cross‐sectional study with 65 women, 18 births classified as severe prematurity (<32 weeks of gestation) and 47 as moderate prematurity (≥32 weeks of gestation). The study only included mothers without any conditions associated with pregnancy and who had a single conception without any malformation. Samples of serum and colostrum were collected during fasting in the immediate postpartum, and alpha‐tocopherol was analyzed by high‐performance liquid chromatography. To determine the biochemical nutritional status of vitamin E, a serum cutoff (11.6 μmol/L) was adopted. The Studentttest for independent variables compared the average concentrations of alpha‐tocopherol in serum and colostrum among prematurity groups. Differences were considered significant whenP < 0.05.Results:The alpha‐tocopherol concentrations in colostrum were similar in both groups, being 34.5 ± 20.2 μmol/L for women with severe prematurity and 35.1 ± 16.3 μmol/L for moderate prematurity. For the serum of puerperal women with severe prematurity, alpha‐tocopherol concentration was, however, lower than in women with moderate prematurity, 22.2 ± 4.4 μmol/L versus 27.1 ± 8.6 μmol/L (P < 0.05). The serum levels of alpha‐tocopherol indicated nutritional risk at 5.6% (n = 1) of women with severe prematurity and 4.3% (n = 2) for those with moderate prematurity.Conclusions:Severe prematurity affected the levels of alpha‐tocopherol in maternal serum; however, the level of prematurity did not change the concentration of vitamin E in colostrum.
Pathophysiological analysis of five severe cases with rotavirus infection
Authors: Gotoh Kensei , Nishimura Naoko , Kawabe Shinji , Mori Yuji , Naruse Norihiko , Kawamura Yoshiki , Yoshikawa Tetsushi , Wakuda Mitsutaka , Taniguchi Koki , Ozaki Takao 
Published: September 2015

Introduction:
Rotavirus infection is usually localized to the intestine. Severe cases with extraintestinal symptoms are rare, and its pathogenesis remains unclear.

Case presentation:
We report severe rotavirus infections in five previously healthy, unvaccinated children that occurred in the 2011 season in Aichi Prefecture, Japan. All cases had short histories of recurrent diarrhoea and vomiting that preceded extraintestinal symptoms. Two cases with prolonged seizures and unconsciousness were diagnosed with encephalitis/encephalopathy; one case died and the other survived with severe neurological sequelae in spite of intensive treatment including anticytokine therapy. Another two cases had rapidly worsening cardiopulmonary dysfunction and seizures, and they died a few hours after admission despite cardiopulmonary support. The last case was transferred to hospital in cardiopulmonary arrest and resuscitation was unsuccessful. All cases had positive stool samples for rotavirus RNA, and the rotavirus antigen was also detected in the serum of four cases, but not in the cerebrospinal fluid (CSF). Serum IL-6 and IL-10 levels were significantly higher in the severe cases than in children with rotavirus gastroenteritis without extraintestinal symptoms, and serum IL-10 levels were significantly higher than CSF levels in the severe cases.

Conclusion:
Cytokines appear to mediate the pathogenesis of severe rotavirus infection with extraintestinal involvement. In conclusion, these cases highlight the need for a routine rotavirus immunization programme.
An imported case of melioidosis presenting as pyelonephritis/urosepsis
Authors: Monecke Stefan , Friedrichs Anette , Pöhlmann Christoph , Hochauf Kristina , Gunzer Florian , Wiesner Diana , Sickert Wolfgang , Steinmetz Ivo , Scholz Holger , Ehricht Ralf , Schmoock Gernot , Jacobs Enno 
Published: September 2015

Introduction:
Melioidosis, a potentially life-threatening disease caused by Burkholderia pseudomallei, is common in Northern Australia and south-east Asia, but it is rarely encountered in the western world. However, due to increased travel, imported cases have been observed among tourists to endemic areas. The clinical manifestations are highly variable.

Case presentation:
We report a case of melioidosis presenting as pyelonephritis/urosepsis in a previously healthy German tourist who had travelled to several endemic regions.

Conclusion:
The described case highlights the fact that the diagnosis of melioidosis may be surprising to a routine diagnostic laboratory. An accidental and unwitting exposure of laboratory staff may occur before a definite identification is achieved. Good communication between the clinician and laboratory staff is crucial, especially with respect to travel histories.
A prospective study of seven patients with chronic mastoiditis
Authors: Mousa Haider Abdul-Lateef 
Published: September 2015

Introduction:
Chronic mastoiditis is generally a result of chronic suppurative otitis media; it is rarely a result of failure of treatment of acute mastoiditis.

Case presentation:
Seven patients with chronic mastoiditis were investigated. Four patients had bilateral mastoiditis. The duration of illness ranged from 1 to 45 years. A comparison between operative and external auditory canal cultures was performed. The operative specimens were obtained directly from the infected mastoids. The external ear and mastoid specimens were inoculated and cultivated immediately by bedside. All cases showed positive bacterial cultures. The growth was monomicrobial in two cases and polymicrobial in five cases. Seventeen isolates were recovered (11 aerobes and six anaerobes). Pseudomonas aeruginosa was the most predominant isolate (23.5 %) and was recovered from four patients (57 %). This high prevalence may be related to misuse of ear drops that transmit this organism from skin flora towards the mastoid. The anaerobes were isolated from four patients. This may indicate a significant role of anaerobic bacteria in producing chronic mastoiditis that would not respond to usual treatment measures.

Conclusion:
Cultures from external ear canal discharge might be used as a source for isolation of bacteria causing chronic mastoiditis and chronic otitis media provided that the specimen was collected and cultivated properly. They revealed sensitivity (88 %), specificity (100 %), positive predictive value (100 %) and negative predictive value (66 %). In anaerobic cultures, the sensitivity was 66.7 %. No previous studies were found with regard to evaluation of the reliability of external ear culture for isolation of the causative agents of chronic mastoiditis or chronic otitis media.
A statistical approach reveals designs for the most robust stochastic gene oscillators
Authors: Woods Mae , Leon Miriam , Perez-Carrasco Ruben , Barnes Chris P. 
Published: September 2015

AbstractThe engineering of transcriptional networks presents many challenges due to the inherent uncertainty in the system structure, changing cellular context and stochasticity in the governing dynamics. One approach to address these problems is to design and build systems that can function across a range of conditions; that is they are robust to uncertainty in their constituent components. Here we examine the parametric robustness landscape of transcriptional oscillators, which underlie many important processes such as circadian rhythms and the cell cycle, plus also serve as a model for the engineering of complex and emergent phenomena. The central questions that we address are: Can we build genetic oscillators that are more robust than those already constructed? Can we make genetic oscillators arbitrarily robust? These questions are technically challenging due to the large model and parameter spaces that must be efficiently explored. Here we use a measure of robustness that coincides with the Bayesian model evidence combined with an efficient Monte Carlo method to traverse model space and concentrate on regions of high robustness, which enables the accurate evaluation of the relative robustness of gene network models governed by stochastic dynamics. We report the most robust two and three gene oscillator systems, plus examine how the number of interactions, the presence of auto-regulation, and degradation of mRNA and protein affects the frequency, amplitude and robustness of transcriptional oscillators. We also find that there is a limit to parametric robustness, beyond which there is nothing to be gained by adding additional feedback. Importantly, we provide predictions on new oscillator systems that can be constructed to verify the theory and advance design and modelling approaches to systems and synthetic biology.
Protein homeostasis imposes a barrier on functional integration of horizontally transferred genes in bacteria
Authors: Bershtein Shimon , Serohijos Adrian W.R. , Bhattacharyya Sanchari , Manhart Michael , Choi Jeong-Mo , Mu Wanmeng , Zhou Jingwen , Shakhnovich Eugene I. 
Published: September 2015

AbstractHorizontal gene transfer (HGT) plays a central role in bacterial evolution, yet the molecular and cellular constraints on functional integration of the foreign genes are poorly understood. Here we performed inter-species replacement of the chromosomalfolAgene, encoding an essential metabolic enzyme dihydrofolate reductase (DHFR), with orthologs from 35 other mesophilic bacteria. The orthologous inter-species replacements caused a marked drop (in the range 10-90%) in bacterial growth rate despite the fact that most orthologous DHFRs are as stable asE.coliDHFR at 37° C and are more catalytically active thanE. coliDHFR. Although phylogenetic distance betweenE. coliand orthologous DHFRs as well as their individual molecular properties correlate poorly with growth rates, theproductof the intracellular DHFR abundance and catalytic activity (kcat/KM), correlates strongly with growth rates, indicating that the drop in DHFR abundance constitutes the major fitness barrier to HGT. Serial propagation of the orthologous strains for ∼600 generations dramatically improved growth rates by largely alleviating the fitness barriers. Whole genome sequencing and global proteome quantification revealed that the evolved strains with the largest fitness improvements have accumulated mutations that inactivated the ATP-dependent Lon protease, causing an increase in the intracellular DHFR abundance. In one case DHFR abundance increased further due to mutations accumulated infolApromoter, but only after theloninactivating mutations were fixed in the population. Thus, by apparently distinguishing between self and non-self proteins, protein homeostasis imposes an immediate and global barrier to the functional integration of foreign genes by decreasing the intracellular abundance of their products. Once this barrier is alleviated, more fine-tuned evolution occurs to adjust the function/expression of the transferred proteins to the constraints imposed by the intracellular environment of the host organism.
Contrasting quality of service experience for northern and southern Mediterranean tourists
Authors: Schlesinger Walesska , Cervera Amparo , Pérez-Cabañero Carmen 
Published: September 2015

Purpose– The purpose of this paper is to examine quality of service experience as reported by tourists in seven northern and southern Mediterranean cities.Design/methodology/approach– A self-report study was used to gather data from 1,362 tourists. Once validity of Otto and Ritchie’s (1996) scale had been confirmed, ANOVA and the non-parametric Kruskal-Wallis test were used to analyse the data.Findings– Tourists in all destinations highlighted the importance of the dimension peace of mind. Significant differences between tourists in the northern Mediterranean and those in the southern Mediterranean were observed in two quality of service experience dimensions: hedonics and involvement.Research limitations/implications– Although the sample was large, this study’s scope was limited to seven Mediterranean tourist cities. Further research is therefore required to generalize findings to other Mediterranean tourist destinations.Practical implications– Knowledge about quality of service experience dimensions may help tourism managers innovate and improve services. Tourists perceive northern Mediterranean destinations differently from destinations in the southern Mediterranean. Tourists report high tourist involvement in northern destinations, whereas in the south, tourists emphasize destinations’ hedonic features. These implications are also valuable for European policymakers.Originality/value– The study compared quality of service experience in northern and southern Mediterranean tourist destinations. To do so, it analysed a sample of 1,362 tourists from seven Mediterranean cities. This research is the first to analyse quality of service experience in the Mediterranean.
Investigation of the expected loss of sharia credit instruments in global Islamic banks
Authors: Shahari Farihana , Zakaria Roza  Hazli , Rahman Md. Saifur 
Published: September 2015

Purpose
– The purpose of this paper is to investigate the expected outcomes, both of positive and negative returns occurred by shariá credit instruments in global Islamic banks. The annual panel data from 2005 to 2012 is collected from 40 Islamic banks from 12 countries and value at risk (VaR) technique is employed in the investigation process. The findings of this study indicate several outcomes: first, majority of Islamic banks use debt-based financing (DBF) and avoid asset-based financing (ABF) due to the lack of secured rate of fixed returns and collateral. Second, the ABF financing shows the positive returns. Third, interestingly, DBF financing faces higher credit risk compared to ABF even DBF secures its financing through tight policy implementation. Finally, this paper comes up with policy recommendations for the further reduction of credit risks and improvement of bankers’ confidence level in implementing the ABF financing policy.

Design/methodology/approach
– VaR on panel data.

Findings
– Shariá credit instruments play an important role.

Research limitations/implications
– Data findings.

Originality/value
– Fully original.
Unusual patterns in reported segment earnings of US firms
Authors: Garza-Gomez Xavier , Dong Xiaobo , Yang Ziyun 
Published: September 2015

Purpose
– The purpose of this paper is to extend prior findings on firms’ rounding up net income numbers to meet cognitive reference points and to examine whether segment-level earnings exhibit similar unusual patterns.

Design/methodology/approach
– This study is an archival research based on a sample of US public firms that report segment data between 1998 and 2011. The authors use Benford’s law to establish benchmarks for expected frequency of each number on the second digit of segment earnings and test whether the actual distributions deviate from expectations.

Findings
– The authors find more zeros and fewer nines than expected by chance in the second-from-the-left most digit for segment earnings numbers of US public firms, suggesting that segments round up earnings to meet cognitive reference points. The results complement the existing studies by showing that the rounding up of earnings not only exists at the firm level but also at the segment level, probably because subdivision managers have motivation to exceed certain reference points when reporting earnings.

Research limitations/implications
– As the authors cannot observe the contracts received by divisional managers, the authors rely on measures related to operating diversity to capture internal agency costs.

Practical implications
– The findings suggest internal and external auditors should pay close attention to segments that are suspected of earnings management, i.e. segments that report zeros on the second digit of revenues or earnings. Increased auditor attention is especially necessary for profitable segments operating in highly diversified multi-segment firms.

Originality/value
– The authors find that unusual patterns in segment reporting are more prominent in firms that operate in multiple and dissimilar segments, suggesting that higher internal agency conflict might lead to the rounding up of earnings.
Effect of audit quality and accounting and finance backgrounds of audit committee members on firms’ compliance with IFRS for goodwill impairment testing
Authors: Bepari Md Khokan , Mollik Abu Taher 
Published: September 2015

Purpose– The purpose of this paper is to examine the effect of audit quality on firms’ compliance with IFRS for goodwill impairment testing and disclosure. Differences in the compliance among the clients of Big-4 auditors and between the clients of Big-4 and non-Big-4 auditors are examined. This study also examines the effect of audit committee (AC) members’ accounting and finance backgrounds on firms’ compliance with IFRS for goodwill impairment testing and disclosure.Design/methodology/approach– Different univariate tests, multivariate regressions and fixed effect panel regressions have been used to examine the hypotheses. The sample includes 911 firm-year observations for the period of 2006-2009.Findings– A statistically significant difference in compliance levels has been found between the clients of Big-4 and non-Big-4 auditors. The compliance levels of the clients of Big-4 auditors have also been found to be significantly different. The findings also suggest that AC members’ accounting and finance backgrounds are positively associated with firms’ compliance with IFRS for goodwill impairment testing and disclosure.Research limitations/implications– The single country context and the single standard context limit the generalizability of the findings.Practical implications– The findings of this study have important implications for researches in accounting, finance and corporate governance that usually consider Big-4 auditors vs non-Big-4 auditors as a proxy for audit quality. The results also reinforce the importance of developing institutional mechanisms such as high-quality auditing or corporate governance (AC members’ expertise) to encourage firms’ compliance with IFRS.Originality/value– Firms’ compliance with IFRS for goodwill impairment testing is not essentially the same for the clients of all Big-4 auditors in Australia, suggesting that the quality of services provided by Big-4 auditors significantly differ from one another in enforcing their clients to compliance with IFRS. The lax enforcement on the part of auditors and the regulatory inaction in this regard may point to teething difficulties and systematic deficiencies in the move towards the impairment regime and fair value accounting. The findings also bear an important message for the move towards the harmonization of accounting practices.
Toward a universal, meta-theoretical framework for music information classification and retrieval
Authors: Weissenberger Lynnsey 
Published: September 2015

Purpose– The purpose of this paper is to present a new framework for representing music for information retrieval that emphasizes socio-cultural aspects of music.Design/methodology/approach– Philosophical and theoretical concepts related to the nature of music, aboutness, musical works are explored as they inform how music is represented. Multidisciplinary perspectives on music information representation, classification, and retrieval provide insight into how information science can better accommodate music information within its disciplinary boundaries.Findings– A new term, music information object (MIO), is presented and defined. Downie’s (2003) theoretical statements are reconceptualized into a theory of representational incompleteness and three meta-classes for music information object representation.Practical implications– This new framework incorporates more dimensions of music representation than existing frameworks allow and can facilitate comparisons between classifications of MIO representations by music practitioners, scholars, and system developers.Originality/value– The meta-classes form a much-needed theoretical framework for classifying and defining MIOs from any musical tradition for retrieval. This fills a gap in music information retrieval research, which lacks a theoretical framework that can accommodate musics from all traditions without attempting to organize them according to a western-centered understanding.