bluuebunny/crossref_metadata_2025_split huggingface dataset:
Higher-order repeat structure in alpha satellite DNA occurs in New World monkeys and is not confined to hominoids
Authors: Sujiwattanarat Penporn , Thapana Watcharaporn , Srikulnath Kornsorn , Hirai Yuriko , Hirai Hirohisa , Koga Akihiko 
Published: May 2015

AbstractCentromeres usually contain large amounts of tandem repeat DNA. Alpha satellite DNA (AS) is the most abundant tandem repeat DNA found in the centromeres of simian primates. The AS of humans contains sequences organized into higher-order repeat (HOR) structures, which are tandem arrays of larger repeat units consisting of multiple basic repeat units. HOR-carrying AS also occurs in other hominoids, but results reported to date for phylogenetically more remote taxa have been negative. Here we show direct evidence for clear HOR structures in AS of the owl monkey and common marmoset. These monkeys are New World monkey species that are located phylogenetically outside of hominoids. It is currently postulated that the presence of HOR structures in AS is unique to hominoids. Our results suggest that this view must be modified. A plausible explanation is that generation of HOR structures is a general event that occurs occasionally or frequently in primate centromeres and that, in humans, HOR-carrying AS became predominant in the central region of the centromere. It is often difficult to assemble sequence reads of tandem repeat DNAs into accurate contig sequences; our careful sequencing strategy allowed us to overcome this problem.
Experimental demonstration of digital predistortion for orthogonal frequency‐division multiplexing‐radio over fibre links near laser resonance
Authors: Vieira Luis Carlos , Gomes Nathan Joseph 
Published: May 2015

Radio over fibre (RoF), an enabling technology for distribution of wireless broadband service signals through analogue optical links, suffers from non‐linear distortion. Digital predistortion has been demonstrated as an effective approach to overcome the RoF non‐linearity. However, questions remain as to how the approach performs close to laser resonance, a region of significant dynamic non‐linearity, and how resilient the approach is to changes in input signal and link operating conditions. In this work, the performance of a digital predistortion approach is studied for directly modulated orthogonal frequency‐division multiplexing RoF links operating from 2.47 to 3.7 GHz. It extends previous works to higher frequencies, and to higher quadrature amplitude modulation (QAM) levels. In addition, the resilience of the predistortion approach to changes in modulation level of QAM schemes, and average power levels are investigated, and a novel predistortion training approach is proposed and demonstrated. Both memoryless and memory polynomial predistorter models, and a simple off‐line least‐squares‐based identification method, are used, with excellent performance improvements demonstrated up to 3.0 GHz.
Defining roles of PARKIN and ubiquitin phosphorylation by PINK1 in mitochondrial quality control using a ubiquitin replacement strategy
Authors: Ordureau Alban , Heo Jin-Mi , Duda David M. , Paulo Joao A. , Olszewski Jennifer L. , Yanishevski David , Rinehart Jesse , Schulman Brenda A. , Harper J. Wade 
Published: May 2015

Significance
PINK1 protein kinase and PARKIN UB ligase are mutated in inherited forms of Parkinson’s disease and several cancers. Thus, it is of great significance to understand normal functions that could be disrupted in disease. A role for PARKIN and PINK1 is in mediating autophagy of damaged mitochondria (mitophagy) through polyubiquitylation of numerous mitochondrial outer membrane proteins in a reaction that involves phosphorylation of both PARKIN and ubiquitin (UB) by PINK1. The mechanism remains unclear, however, due to challenges in defining individual steps in the pathway. Here, we use a UB replacement system to elucidate steps in the pathway that require PARKIN and/or UB phosphorylation by PINK1 and provide evidence of a PINK1- and UB-driven feed-forward mechanism important for efficient mitochondrial ubiquitylation and mitophagy.
Characterization and identification of the proteins bound to two types of polyhydroxyalkanoate granules in Pseudomonas sp. 61-3
Authors: Hokamura Ayaka , Fujino Kanako , Isoda Yoshiko , Arizono Koji , Shiratsuchi Hideki , Matsusaki Hiromi 
Published: May 2015

Abstract
Pseudomonas sp. 61-3 accumulates two types of polyhydroxyalkanoates (PHAs), poly(3-hydroxybutyrate) [P(3HB)], and poly(3HB-co-3-hydroxyalkanoates) [P(3HB-co-3HA)], and some proteins associated with their PHA granules have been identified. To date, PhaFPs (GA36) and PhaIPs (GA18) were identified from P(3HB-co-3HA) granules. In this study, the gene encoding GA24 associated with P(3HB) granule was identified as phbPPs. PhbPPs was composed of 192 amino acids with a calculated molecular mass of 20.4 kDa and was assumed to be a phasin. phbFPs gene and unknown ORF were also found on phb locus. PhbFPs was anticipated to be the transcriptional repressor of phbPPs gene. PhbPPs was bound to the P(3HB-co-3HA) granules with 3HB composition of more than 87 mol%, and PhaIPs and PhaFPs were bound to the P(3HB-co-3HA) granules with 3HA (C6–C12) composition of more than 13 mol% in the producing cells, suggesting that localization of these proteins is attributed to the monomer compositions of the copolymers.
Effect of repeated harvesting on the content of caffeic acid and seven species of caffeoylquinic acids in sweet potato leaves
Authors: Sasaki Kazunori , Oki Tomoyuki , Kai Yumi , Nishiba Yoichi , Okuno Shigenori 
Published: May 2015

Abstract
The purpose of this study was to investigate the effect of repeated harvesting on the content of caffeic acid (CA) and seven species of caffeoylquinic acids (CQAs) in sweet potato leaves using a newly developed high-performance liquid chromatography method. Six cultivars and two breeding lines were used in this study. Leaves were collected at monthly intervals from 1st harvest (May) to 4th harvest (August) in 2011 and 2012. ANOVA analysis revealed that the contents of CQAs were significantly different among all cultivars and breeding lines, but no significant differences were found for CA. No annual variation was confirmed in CA and CQAs. Repeated harvest of sweet potato leaves affected the content of only 4-CQA and 5-CQA. Post-hoc comparisons using Tukey’s method indicated that the contents of 4-CQA and 5-CQA in sweet potato leaves harvested at first time were significantly higher compared to those at the other harvest times.
CAPRI: efficient inference of cancer progression models from cross-sectional data
Authors: Ramazzotti Daniele , Caravagna Giulio , Olde Loohuis Loes , Graudenzi Alex , Korsunsky Ilya , Mauri Giancarlo , Antoniotti Marco , Mishra Bud 
Published: May 2015

Abstract
Summary: We devise a novel inference algorithm to effectively solve the cancer progression model reconstruction problem. Our empirical analysis of the accuracy and convergence rate of our algorithm, CAncer PRogression Inference (CAPRI), shows that it outperforms the state-of-the-art algorithms addressing similar problems.
Motivation: Several cancer-related genomic data have become available (e.g. The Cancer Genome Atlas, TCGA) typically involving hundreds of patients. At present, most of these data are aggregated in a cross-sectional fashion providing all measurements at the time of diagnosis. Our goal is to infer cancer ‘progression’ models from such data. These models are represented as directed acyclic graphs (DAGs) of collections of ‘selectivity’ relations, where a mutation in a gene A ‘selects’ for a later mutation in a gene B. Gaining insight into the structure of such progressions has the potential to improve both the stratification of patients and personalized therapy choices.
Results: The CAPRI algorithm relies on a scoring method based on a probabilistic theory developed by Suppes, coupled with bootstrap and maximum likelihood inference. The resulting algorithm is efficient, achieves high accuracy and has good complexity, also, in terms of convergence properties. CAPRI performs especially well in the presence of noise in the data, and with limited sample sizes. Moreover CAPRI, in contrast to other approaches, robustly reconstructs different types of confluent trajectories despite irregularities in the data. We also report on an ongoing investigation using CAPRI to study atypical Chronic Myeloid Leukemia, in which we uncovered non trivial selectivity relations and exclusivity patterns among key genomic events.
Availability and implementation: CAPRI is part of the TRanslational ONCOlogy R package and is freely available on the web at: http://bimib.disco.unimib.it/index.php/Tronco
Contact: daniele.ramazzotti@disco.unimib.it
Supplementary information: Supplementary data are available at Bioinformatics online.
GLASS: a comprehensive database for experimentally validated GPCR-ligand associations
Authors: Chan Wallace K. B. , Zhang Hongjiu , Yang Jianyi , Brender Jeffrey R. , Hur Junguk , Özgür Arzucan , Zhang Yang 
Published: May 2015

Abstract
Motivation: G protein-coupled receptors (GPCRs) are probably the most attractive drug target membrane proteins, which constitute nearly half of drug targets in the contemporary drug discovery industry. While the majority of drug discovery studies employ existing GPCR and ligand interactions to identify new compounds, there remains a shortage of specific databases with precisely annotated GPCR-ligand associations.
Results: We have developed a new database, GLASS, which aims to provide a comprehensive, manually curated resource for experimentally validated GPCR-ligand associations. A new text-mining algorithm was proposed to collect GPCR-ligand interactions from the biomedical literature, which is then crosschecked with five primary pharmacological datasets, to enhance the coverage and accuracy of GPCR-ligand association data identifications. A special architecture has been designed to allow users for making homologous ligand search with flexible bioactivity parameters. The current database contains ∼500 000 unique entries, of which the vast majority stems from ligand associations with rhodopsin- and secretin-like receptors. The GLASS database should find its most useful application in various in silico GPCR screening and functional annotation studies.
Availability and implementation: The website of GLASS database is freely available at http://zhanglab.ccmb.med.umich.edu/GLASS/.
Contact: zhng@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Layering genetic circuits to build a single cell, bacterial half adder
Authors: Wong Adison , Wang Huijuan , Poh Chueh Loo , Kitney Richard I 
Published: May 2015

ABSTRACTGene regulation in biological systems is impacted by the cellular and genetic context-dependent effects of the biological parts which comprise the circuit. Here, we have sought to elucidate the limitations of engineering biology from an architectural point of view, with the aim of compiling a set of engineering solutions for overcoming failure modes during the development of complex, synthetic genetic circuits. Using a synthetic biology approach that is supported by computational modelling and rigorous characterisation, AND, OR and NOT biological logic gates were layered in both parallel and serial arrangements to generate a repertoire of Boolean operations that include NIMPLY, XOR, half adder and half subtractor logics in single cell. Subsequent evaluation of these near-digital biological systems revealed critical design pitfalls that triggered genetic context dependent effects, including 5’ UTR interference and uncontrolled switch-on behaviour of σ54 promoter. Importantly, this work provides a representative case study to the debugging of genetic context dependent effects through principles elucidated herein, thereby providing a rational design framework to program single prokaryotic cell with diversified digital operations.
GenOO: A Modern Perl Framework for High Throughput Sequencing analysis
Authors: Maragkakis Manolis , Alexiou Panagiotis , Mourelatos Zissimos 
Published: May 2015

ABSTRACTBackgroundHigh throughput sequencing (HTS) has become one of the primary experimental tools used to extract genomic information from biological samples. Bioinformatics tools are continuously being developed for the analysis of HTS data. Beyond some well-defined core analyses, such as quality control or genomic alignment, the consistent development of custom tools and the representation of sequencing data in organized computational structures and entities remains a challenging effort for bioinformaticians.ResultsIn this work, we present GenOO [jee-noo], an open-source; object-oriented (OO) Perl framework specifically developed for the design and implementation of HTS analysis tools. GenOO models biological entities such as genes and transcripts as Perl objects, and includes relevant modules, attributes and methods that allow for the manipulation of high throughput sequencing data. GenOO integrates these elements in a simple and transparent way which allows for the creation of complex analysis pipelines minimizing the overhead for the researcher. GenOO has been designed with flexibility in mind, and has an easily extendable modular structure with minimal requirements for external tools and libraries. As an example of the framework’s capabilities and usability, we present a short and simple walkthrough of a custom use case in HTS analysis.ConclusionsGenOO is a tool of high software quality which can be efficiently used for advanced HTS analyses. It has been used to develop several custom analysis tools, leading to a number of published works. Using GenOO as a core development module can greatly benefit users, by reducing the overhead and complexity of managing HTS data and biological entities at hand.
Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION
Authors: Urban John M. , Bliss Jacob , Lawrence Charles E. , Gerbi Susan A. 
Published: May 2015

ABSTRACTOxford Nanopore Technologies’ nanopore sequencing device, the MinION, holds the promise of sequencing ultra-long DNA fragments >100kb. An obstacle to realizing this promise is delivering ultra-long DNA molecules to the nanopores. We present our progress in developing cost-effective ways to overcome this obstacle and our resulting MinION data, including multiple reads >100kb.
NADH as a cancer medicine
Authors: Forrest Michael D. 
Published: May 2015

ABSTRACTWe propose that NADH will exert a specific kill action against some cancers. NADH is a natural metabolite. We envisage a low side effect profile and that NADH therapy will, additionally, combat the wastage and weakness of cancer patients, which can be the cause of death in some cases. Significantly, NADH can be administered orally and has already cleared clinical trials, all be it for other pathologies.BackgroundAerobic respiration consists of glycolysis in the cytoplasm and in the mitochondria: the Krebs cycle and oxidative phosphorylation (OXPHOS) [1, 2]. It requires O2and net yields 30 ATPs from one glucose molecule. Anaerobic respiration, consisting of glycolysis only, does not require O2but produces merely 2 ATPs from one glucose molecule. When O2is available, normal animal cells tend to favour aerobic respiration because of its higher ATP yield.
Hotel brand portfolio strategy
Authors: Wang Yao-Chin , Chung Yeasun 
Published: May 2015

Purpose
This study aims to develop dimensions and sub-items that explain hotel brand portfolio strategy (HBPS) and explore performance differences among HBPS groups in an effort to improve our knowledge about HBPS. A key ingredient in success for a hotel company is the successful building and management of a strong brand portfolio.

Design/methodology/approach
This study proposes four dimensions of HBPS: brand portfolio scope, intra-portfolio competition, brand portfolio location and brand portfolio element. By employing ten additional sub-items, the study evaluates the HBPS practices of hotel firms and tests performance differences.

Findings
The findings present current HBPS practices in the hotel industry and identify four groups pursuing similar HBPS. The results also suggest that operational performance differs according to a firm’s particular focus in HBPS.

Research limitations/implications
This study enriches our knowledge of HBPS by establishing dimensions and relevant measures and by suggesting the effect that HBPS has on performance. Future research might extend this study to examine the potential impacts of a business’s internal and external environments on the relationship between HBPS and its performance.

Practical implications
This study will aid executives in making important HBPS decisions such as whether to add a brand or how to reallocate resources among brands. This study also provides executives with a tool with which to monitor the relative position of their HBPS within the market.

Originality/value
This study is the first to establish dimensions and sub-items for understanding HBPS in the hotel industry. It also demonstrates a new approach to the analysis of competitive positioning and its relationship to performance.
Quality of physical surroundings and service encounters, airfare, trust and intention during the flight
Authors: Han Heesup , Hwang Jinsoo 
Published: May 2015

Purpose
This study aimed to examine young, middle-aged and mature air-travelers’ perceptions of the quality levels of in-flight physical surroundings and service encounters, and investigated the drivers of their repurchase intentions in the low-cost airline industry.

Design/methodology/approach
A sample of 402 passengers on international flights was used. An ANOVA and a series of multiple-regression analyses based on Baron and Kenny’s (1986) suggestion were used.

Findings
In general, significant differences in quality attributes were identified across age groups. Additionally, the role of these quality components, perceived level of the airfare and trust in the airline were found to be decisive in low-cost airline passengers’ decision formation. Further, the mediating impact of perceived level of the airfare and trust was identified.

Originality/value
Research about air-travelers’ decision formation by considering their age is rare in a low-cost airline context. Results of the present study provided meaningful insights for researchers and practitioners in the airline industry.
Applying complexity theory to solve hospitality contrarian case conundrums
Authors: Hsiao James Po-Hsun , Jaw Chyi , Huan Tzung-Cheng (T.C.) , Woodside Arch G. 
Published: May 2015

PurposeThis paper aims to advance a configural asymmetric theory of the complex antecedents to hospitality employee happiness-at-work and managers’ assessments of employees’ quality of work performance. The study transcends variable and case-level analyses to go beyond prior statistical findings of small-to-medium effect sizes of happiness–performance relationships; the study here identifies antecedent paths involving high-versus-low happy employees associating with high-versus-low managers’ assessments of these employees’ performances.Design/methodology/approachThe study merges data from surveys of employees (n= 247) and surveys completed by their managers (n= 43) and by using qualitative comparative analysis via the software program,fsQCA.com. The study analyzes data from Janfusan Fancyworld, the largest (in revenues and number of employees) tourism business group in Taiwan; Janfusan Fancyworld includes tourist hotels, amusement parks, restaurants and additional firms in related service sectors.FindingsThe findings support the four tenets of configural analysis and theory construction: recognize equifinality of different solutions for the same outcome, test for asymmetric solutions, test for causal asymmetric outcomes for very high versus very low happiness and work performance and embrace complexity.Research limitations/implicationsAdditional research in other firms and additional countries is necessary to confirm the usefulness of examining algorithms for predicting very high (low) happiness and very high (low) quality of work performance. The implications are substantial that configural theory and research will resolve perplexing happiness–performance conundrums.Practical implicationsThe study provides useful case-level algorithms involving employees’ demographic characteristics and their assessments of work facet-specifics which are useful for explaining very high happiness-at-work and high quality of work performance (as assessed by managers) – as well as algorithms explaining very low happiness and very low quality of work performance.Originality/valueThe study is the first to propose and test the tenets of configural theory in the context of hospitality frontline service employees’ happiness-at-work and managers’ assessments of these employees’ quality of work performances.
Leadership styles at Syrian higher education
Authors: Khalifa Bayan , Ayoubi Rami M. 
Published: May 2015

Purpose– The purpose of this paper is to explore the two major types of leadership, i.e transactional and transformational, and organizational learning at public and private universities in Syria. It further aims at exploring the role of transactional and transformational leadership in enhancing organizational learning at Syrian universities.Design/methodology/approach– A quantitative research paradigm was employed. Using a questionnaire survey method, the data were collected from employees at two major public and private Syrian universities. In total, 216 questionnaires were analyzed using SPSS.Findings– The findings revealed that there is a significant impact of contingent reward, as a transactional leadership dimension on organizational learning, and a significant impact of inspirational motivation as a transformational leadership dimension on organizational learning. The study also found no significant differences in leadership styles and organizational learning between both universities.Practical implications– This study will help university leaders in Syria in adopting leadership styles that are suitable to reinforce organizational learning in their institutions.Originality/value– The study advances western research that is linking leadership styles and organizational learning by focussing on the Arab world context, particularly the Syrian context.
The impact of bundled high performance human resource practices on intention to leave
Authors: Jyoti Jeevan , Rani Roomi , Gandotra Rupali 
Published: May 2015

Purpose– The purpose of this paper is to examine the mediating effect of emotional exhaustion (EE) in between bundled high-performance human resource practices (HPHRPs) and intention to leave (ITL) in the education sector.Design/methodology/approach– A survey questionnaire method was used to collect data from a sample of 514 teachers working in different professional colleges in Jammu and Kashmir (North India). Data were validated with CFA and SEM was used to test hypothesised relations.Findings– The results show that bundled HPHRPs have greater impact on EE and ITL as compared to individual HPHRPs. Further, the study also confirmed that EE partially mediates the bundled HPHRPs and ITL relationship.Research limitations/implications– Future research need to explore same relationships in different sectors with longitudinal data at the multi-level approach.Practical implications– Educational administration should focus on the bundled HPHRPs, which will benefit not only the teachers, but the students too. It should adopt relaxation techniques like mindfulness training approach, yoga and meditation. Further, to reduce their career-related confusions management should organise career awareness programmes.Originality/value– The results from this study explored new and untested mechanism, i.e. EE as mediator between bundled HPHRPs and ITL relationship in the professional degree colleges in India, has not been previously researched.