bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative Genomics and Transcriptomics Analysis Reveals Potential Mechanisms for Favorable Prognosis of Patients with HPV-Positive Head and Neck Carcinomas
Authors: Zhang Wensheng , Edwards Andrea , Fang Zhide , Flemington Erik K. , Zhang Kun 
Published: April 2016

AbstractPatients with HPV-positive head neck squamous cell carcinomas (HNSCC) usually have a better prognosis than the HPV-negative cases while the underlying mechanism remains far from being well understood. We investigated this issue by an integrative analysis of clinically-annotated multi-omics HNSCC data released by the Cancer Genome Atlas. As confirmatory results, we found: (1) Co-occurrence of mutant TP53 and HPV infection was rare; (2) Regardless of HPV status, HNSCCs of wild-type TP53 implied a good survival chance for patients and had fewer genome-wide somatic mutations than those with a mutation burden on the gene. Our analysis further led to some novel observations. They included: (1) The genes involved in “DNA mismatch repair” pathway were up-regulated in HPV-positive tumors compared to normal tissue samples and HPV-negative cases, and thus constituted a strong predictive signature for the identification of HPV infection; (2) HPV infection could disrupt some regulatory miRNA-mRNA correlations operational in the HPV-negative tumors. In light of these results, we proposed a hypothesis for the favorable clinical outcomes of HPV-positive HNSCC patients. That is, the replication of HPV genome and/or its invasion into the genomes of cancer cells may enhance DNA repair mechanisms, which in turn limit the accumulation of lethal somatic mutations.
Hedgehog signaling activation induces stem cell proliferation and hormone release in the adult pituitary gland
Authors: Pyczek Joanna , Buslei Rolf , Schult David , Hölsken Annett , Buchfelder Michael , Heß Ina , Hahn Heidi , Uhmann Anja 
Published: April 2016

AbstractHedgehog (HH) signaling is known to be essential during the embryonal development of the pituitary gland but the knowledge about its role in the adult pituitary and in associated tumors is sparse. In this report we investigated the effect of excess Hh signaling activation in murine pituitary explants and analyzed the HH signaling status of human adenopituitary lobes and a large cohort of pituitary adenomas. Our data show that excess Hh signaling led to increased proliferation of Sox2+ and Sox9+ adult pituitary stem cells and to elevated expression levels of adrenocorticotropic hormone (Acth), growth hormone (Gh) and prolactin (Prl) in the adult gland. Inhibition of the pathway by cyclopamine reversed these effects indicating that active Hh signaling positively regulates proliferative processes of adult pituitary stem cells and hormone production in the anterior pituitary. Since hormone producing cells of the adenohypophysis as well as ACTH-, GH- and PRL-immunopositive adenomas express SHH and its target GLI1, we furthermore propose that excess HH signaling is involved in the development/maintenance of hormone-producing pituitary adenomas. These findings advance the understanding of physiological hormone regulation and may open new treatment options for pituitary tumors.
The development of a phosphite-mediated fertilization and weed control system for rice
Authors: Manna Mrinalini , Achary V. Mohan M. , Islam Tahmina , Agrawal Pawan K. , Reddy Malireddy K. 
Published: April 2016

AbstractFertilizers and herbicides are two vital components of modern agriculture. The imminent danger of phosphate reserve depletion and multiple herbicide tolerance casts doubt on agricultural sustainability in the future. Phosphite, a reduced form of phosphorus, has been proposed as an alternative fertilizer and herbicide that would address the above problems to a considerable extent. To assess the suitability of a phosphite-based fertilization and weed control system for rice, we engineered rice plants with a codon-optimized ptxD gene from Pseudomonas stutzeri. Ectopic expression of this gene led to improved root growth, physiology and overall phenotype in addition to normal yield in transgenic plants in the presence of phosphite. Phosphite functioned as a translocative, non-selective, pre- and post-emergent herbicide. Phosphite use as a dual fertilizer and herbicide may mitigate the overuse of phosphorus fertilizers and reduce eutrophication and the development of herbicide resistance, which in turn will improve the sustainability of agriculture.
Pan-cancer subtyping in a 2D-map shows substructures that are driven by specific combinations of molecular characteristics
Authors: Taskesen Erdogan , Huisman Sjoerd M. H. , Mahfouz Ahmed , Krijthe Jesse H. , de Ridder Jeroen , van de Stolpe Anja , van den Akker Erik , Verheagh Wim , Reinders Marcel J. T. 
Published: April 2016

AbstractThe use of genome-wide data in cancer research, for the identification of groups of patients with similar molecular characteristics, has become a standard approach for applications in therapy-response, prognosis-prediction, and drug-development. To progress in these applications, the trend is to move from single genome-wide measurements in a single cancer-type towards measuring several different molecular characteristics across multiple cancer-types. Although current approaches shed light on molecular characteristics of various cancer-types, detailed relationships between patients within cancer clusters are unclear. We propose a novel multi-omic integration approach that exploits the joint behavior of the different molecular characteristics, supports visual exploration of the data by a two-dimensional landscape, and inspection of the contribution of the different genome-wide data-types. We integrated 4,434 samples across 19 cancer-types, derived from TCGA, containing gene expression, DNA-methylation, copy-number variation and microRNA expression data. Cluster analysis revealed 18 clusters, where three clusters showed a complex collection of cancer-types, squamous-cell-carcinoma, colorectal cancers, and a novel grouping of kidney-cancers. Sixty-four samples were identified outside their tissue-of-origin cluster. Known and novel patient subgroups were detected for Acute Myeloid Leukemia’s, and breast cancers. Quantification of the contributions of the different molecular types showed that substructures are driven by specific (combinations of) molecular characteristics.
A CRISPR/Cas9 system adapted for gene editing in marine algae
Authors: Nymark Marianne , Sharma Amit Kumar , Sparstad Torfinn , Bones Atle M. , Winge Per 
Published: April 2016

AbstractHere we report that the CRISPR/Cas9 technology can be used to efficiently generate stable targeted gene mutations in microalgae, using the marine diatom Phaeodactylum tricornutum as a model species. Our vector design opens for rapid and easy adaption of the construct to the target chosen. To screen for CRISPR/Cas9 mutants we employed high resolution melting based PCR assays, mutants were confirmed by sequencing and further validated by functional analyses.
Genetic polymorphisms of cell adhesion molecules in Behcet’s disease in a Chinese Han population
Authors: Zheng Minming , Zhang Lijun , Yu Hongsong , Hu Jiayue , Cao Qingfeng , Huang Guo , Huang Yang , Yuan Gangxiang , Kijlstra Aize , Yang Peizeng 
Published: April 2016

AbstractCell adhesion molecules (CAMs) are involved in various immune-mediated diseases. This study was conducted to investigate the association of single nucleotide polymorphisms (SNPs) of CAMs with Behçet’s disease (BD) in a Chinese Han population. A two-stage association study was carried out in 1149 BD patients and 2107 normal controls. Genotyping of 43 SNPs was performed using MassARRAY System (Sequenom), polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and TaqMan SNP assays. The expression of CD6 and CD11c was examined by real-time PCR and cytokine production was measured by ELISA. A significantly higher frequency of the CT genotype, and a lower frequency of the CC genotype and C allele of CD6 rs11230563 were observed in BD as compared with controls. Analysis of CD11c rs2929 showed that patients with BD had a significantly higher frequency of the GG genotype and G allele, and a lower frequency of the AG genotype as compared with controls. Functional experiments showed an increased CD11c expression and increased production of TNF-α and IL-1beta by LPS stimulated PBMCs in GG carriers of CD11c rs2929 compared to AA/AG carriers. Our study provides evidence that CD6 and CD11c are involved in the susceptibility to BD in a Chinese Han population.
Crystal structure and MD simulation of mouse EndoV reveal wedge motif plasticity in this inosine-specific endonuclease
Authors: Nawaz Meh Sameen , Vik Erik Sebastian , Ronander Mia Elise , Solvoll Anne Marthe , Blicher Pernille , Bjørås Magnar , Alseth Ingrun , Dalhus Bjørn 
Published: April 2016

AbstractEndonuclease V (EndoV) is an enzyme with specificity for deaminated adenosine (inosine) in nucleic acids. EndoV from Escherichia coli (EcEndoV) acts both on inosines in DNA and RNA, whereas the human homolog cleaves only at inosines in RNA. Inosines in DNA are mutagenic and the role of EndoV in DNA repair is well established. In contrast, the biological function of EndoV in RNA processing is largely unexplored. Here we have characterized a second mammalian EndoV homolog, mouse EndoV (mEndoV) and show that mEndoV shares the same RNA selectivity as human EndoV (hEndoV). Mouse EndoV cleaves the same inosine-containing substrates as hEndoV, but with reduced efficiencies. The crystal structure of mEndoV reveals a conformation different from the hEndoV and prokaryotic EndoV structures, particularly for the conserved tyrosine in the wedge motif, suggesting that this strand separating element has some flexibility. Molecular dynamics simulations of mouse and human EndoV reveal alternative conformations for the invariant tyrosine. The configuration of the active site, on the other hand, is very similar between the prokaryotic and mammalian versions of EndoV.
Gene expression analysis and SNP/InDel discovery to investigate yield heterosis of two rubber tree F1 hybrids
Authors: Li Dejun , Zeng Rizhong , Li Yan , Zhao Manman , Chao Jinquan , Li Yu , Wang Kai , Zhu Lihuang , Tian Wei-Min , Liang Chengzhi 
Published: April 2016

AbstractAs an important industrial material, natural rubber is mainly harvested from the rubber tree. Rubber tree breeding is inefficient, expensive and time-consuming, whereas marker-assisted selection is a feasible method for early selection of high-yield hybrids. We thus sequenced and analyzed the transcriptomes of two parent rubber trees (RRIM 600 and PR 107) and their most productive hybrids (RY 7-33-97 and RY 7-20-59) to understand their gene expression patterns and genetic variations including single nucleotide polymorphisms (SNPs) and small insertions/deletions (InDels). We discovered >31,000 genetic variations in 112,702 assembled unigenes. Our results showed that the higher yield in F1 hybrids was positively associated with their higher genome heterozygosity, which was further confirmed by genotyping 10 SNPs in 20 other varieties. We also showed that RY 7-33-97 and RY 7-20-59 were genetically closer to RRIM 600 and PR 107, respectively, in agreement with both their phenotypic similarities and gene expression profiles. After identifying ethylene- and jasmonic acid–responsive genes at the transcription level, we compared and analyzed the genetic variations underlying rubber biosynthesis and the jasmonic acid and ethylene pathways in detail. Our results suggest that genome-wide genetic variations play a substantive role in maintaining rubber tree heterosis.
A genetic analysis of 23 Chinese patients with hemophilia B
Authors: Wang Qing-Yun , Hu Bei , Liu Hui , Tang Liang , Zeng Wei , Wu Ying-Ying , Cheng Zhi-Peng , Hu Yu 
Published: April 2016

AbstractHemophilia B (HB) is an X-linked recessive bleeding disorder caused by mutations in the coagulation factor IX (FIX) gene. Genotyping patients with HB is essential for genetic counseling and provides useful information for patient management. In this study, the F9 gene from 23 patients with HB was analyzed by direct sequencing. Nineteen point mutations were identified, including a novel missense variant (c.520G > C, p.Val174Leu) in a patient with severe HB and a previously unreported homozygous missense mutation (c.571C > T, p.Arg191Cys) in a female patient with mild HB. Two large F9 gene deletions with defined breakpoints (g.10413_11363del, g.12163_23369del) were identified in two patients with severe HB using a primer walking strategy followed by sequencing. The flanking regions of the two breakpoints revealed recombination-associated elements (repetitive elements, non-B conformation forming motifs) with a 5-bp microhomology in the breakpoint junction of g.12163_23369del. These findings imply that non-homologous end joining and microhomology-mediated break-induced replication are the putative mechanisms for the deletions of the F9 gene. Because the g.12163_23369del deletion caused exons to be absent without a frameshift mutation occurring, a smaller FIX protein was observed in western blot analyses.
Single ring two‐port MIMO antenna for LTE applications
Authors: Zhang Yalong , Wang Peng 
Published: April 2016

A single ring two‐port multiple‐input–multiple‐output (MIMO) antenna is proposed. Unlike conventional techniques such as space decoupling structures or decoupling networks, two signal paths in this mono‐radiator antenna cancel out each other to achieve good isolation. A MIMO antenna covering 33–41 bands of time division duplex long‐term evolution (LTE) cross 1.85–2.62 GHz is designed, fabricated and measured in this Letter. Simulations are confirmed by the experimental results. The details of design approach and process are introduced.
Aspergillus oryzae nrtA affects kojic acid production
Authors: Sano Motoaki 
Published: April 2016

Abstract
We analyzed the role of the nitrate transporter-encoding gene (nrtA) of Aspergillus oryzae by gene disruption. Southern hybridization analysis indicated that homologous recombination occurred at the resident nrtA locus. Real-time PCR showed that the nrtA gene was strongly inducible by NaNO3. The nrtA disruptant did not exhibit normal growth when nitrate was available as the sole nitrogen source. These results indicate that NrtA is essential for nitrate uptake in A. oryzae. Kojic acid (KA) production was inhibited by the addition of a small amount of sodium nitrate. The nrtA-disrupted strain was deficient in the uptake of nitrate. As a result, KA production in this strain was not considerably affected by the presence of nitrate.
Discovery of a persistent Zika virus lineage in Bahia, Brazil
Authors: Naccache Samia N. , Thézé Julien , Sardi Silvia I. , Somasekar Sneha , Greninger Alexander L. , Bandeira Antonio C. , Campos Gubio S. , Tauro Laura B. , Faria Nuno R. , Pybus Oliver G. , Chiu Charles Y. 
Published: April 2016

AbstractMetagenomic next-generation sequencing coupled with capture probe enrichment was used to recover 11 whole and partial Zika virus (ZIKV) genomes from patients in Bahia, Brazil from April 2015 to January 2016, where the majority of suspected Brazilian ZIKV cases have been reported. Phylogenetic reconstructions and molecular clock analyses using the newly generated data uncovered the existence of a Bahia-specific ZIKV lineage sharing a common ancestor in mid-2014, indicating sustained circulation of this strain in Bahia since that date.
The relationship between school-work-family-conflict, subjective stress, and burnout
Authors: Kremer Inbar 
Published: April 2016

Purpose
– School has been neglected as a source of stress and strain resulting from its inevitable conflict with work and family role demands among married, working students. The meager research available has examined only work-school (not school-work) conflict among adolescents and college students and only three studies (two unpublished) have developed measures of conflict involving work, family, and school without studying its antecedents and consequences. The purpose of this paper is to examine all six school-work-family interrole conflicts and their effects on subjective stress and burnout. It was hypothesized that the greater the conflict between family, work, and school roles, the greater the subjective stress and burnout and that women experience more work-family-school conflicts than do men.

Design/methodology/approach
– In total, 100 working married adult students completed self-report demographic questionnaire, school-work-family conflict, subjective stress, and burnout scales.

Findings
– Regression results revealed that school-work (but not work-school) conflict was the only one of the six interrole conflicts examined that contributed to subjective stress and burnout. Women reported greater work-family conflict and family-work conflict. There were no differences between men and women involving school; where gender plays no role, it causes no conflict.

Research limitations/implications
– Scholars interested in interrole conflict involving family and work should expand the scope of their theories and research to include the school role.

Originality/value
– The present study was the first to examine all six school-work-family interrole conflicts and their effects on subjective stress and burnout.
Overwork climate scale: psychometric properties and relationships with working hard
Authors: Mazzetti Greta , Schaufeli Wilmar B. , Guglielmi Dina , Depolo Marco 
Published: April 2016

Purpose
– The purpose of this paper is to evaluate whether employees’ tendency to work excessive hours is motivated by the perception of a work environment that encourages overwork (overwork climate). Thus, this study introduces a self-report questionnaire aimed at assessing the perception of a psychological climate for overwork in the workplace.

Design/methodology/approach
– In Study 1, the overwork climate scale (OWCS) was developed and evaluated using principal component analysis (n=395) and confirmatory factor analysis (n=396). In Study 2, the total sample (n=791) was used to explore the association of the overwork climate with opposite types of working hard (work engagement and workaholism).

Findings
– Two overwork climate dimensions were distinguished, namely, overwork endorsement and lacking overwork rewards. The lack of overwork rewards was negatively associated with engagement, whereas workaholism showed a strong positive association with overwork endorsement. These relationships remained significant after controlling for the impact of psychological job demands.

Research limitations/implications
– The findings rely on self-report data and a cross-sectional design.

Practical implications
– The perception of a work environment that encourages overwork but does not allocate additional compensation seems to foster workaholism. Moreover, the inadequacy of overwork rewards constitutes a lack of resources that negatively affect employees’ engagement.

Originality/value
– This study represents one of the first attempts to develop a questionnaire aimed at assessing a psychological climate for overwork and to explore whether the perception of this type of climate may be significantly related to workaholism and work engagement.
Creating a winning culture: next step for leading HR professionals
Authors: Ulrich Dave , Brockbank Wayne 
Published: April 2016

Purpose
This paper aims to answer the why, what and how of culture as an emerging human resource agenda. Understanding culture is a trending topic for organization executives and thought leaders. Few deny the importance of culture for shaping and sustaining employee engagement and productivity, sustained strategy and business results. But while culture matters, it is often ambiguous and hard to define.

Design/methodology/approach
Based on our research on over 1,000 organizations, the authors have found that organization (culture) impacts business performance two to four times as much as individual talent.

Findings
The authors suggest that culture is not just a random set of values, beliefs or emotions, but a winning culture turns customer promises (firm brands) into internal organization actions. This paper proposes a disciplined process for creating a winning culture that engages employees in the right issues and invite human resource professionals to step up to this opportunity.

Originality/value
In this paper, the authors posit that the war for talent may be supplemented by understanding victory through organization culture.
A literature review of the evolution of British prefabricated low-rise housing
Authors: O'Neill Daniel , Organ Samantha 
Published: April 2016

Purpose– The purpose of this paper is to explore academic papers and reports and present a chronology of the evolution of British low-rise prefabricated housing. The paper provides chronological information for construction and surveying researchers undertaking research in associated areas.Design/methodology/approach– This is a qualitative literature review, providing an exploration and analysis of academic papers and reports on low-rise prefabricated housing.Findings– A substantial literature was discovered. However, there are gaps in the available literature. The history of British construction technology is a rich research area but is under-researched. Prefabricated housing has a long history dating back to the eleventh century. Stigmatised from the failures of housing in the twentieth century, it is being increasingly used again in the twenty-first century when considering mass housing supply.Research limitations/implications– This paper provides researchers with an overview of the history of low-rise prefabricated housing in Britain. It is not a comprehensive in-depth study; such would require numerous larger individual studies.Originality/value– From reviewing literature it was evident that there was a broad literature, but there was no single journal publication exploring the evolution of British low-rise prefabricated housing. The research provides an overview, exploration and analysis of the literature while providing a chronology. The evolution of prefabricated housing is chronologically presented. Areas for further research are also recommended.
Cerebral microemboli detected by transcranial doppler in patients treated with extracorporeal membrane oxygenation
Authors: Marinoni M. , Migliaccio M. L. , Trapani S. , Bonizzoli M. , Gucci L. , Cianchi G. , Gallerini A. , Tadini Buoninsegni L. , Cramaro A. , Valente S. , Chiostri M. , Peris A. 
Published: April 2016

IntroductionCerebrovascular complications rate in patients treated with extracorporeal membrane oxygenation (ECMO) is about 7%. Ischemic stroke may be caused by solid or gaseous microemboli due to thrombosis within the circuit or cannula. Transcranial Doppler (TCD) is the only method able to detect microembolic signals (MES) in real time. The objective of this study was to detect possible MES by TCD in patients treated with veno‐venous (VV) and veno‐arterial (VA) ECMO and to test for a relation between the number of MES and the 6‐month clinical outcome of these patients.MethodsThis is a monocentric observational prospective study in patients consecutively admitted and treated with ECMO at our regional ECMO referral center in 18 months. TCD detection of MES was performed in patients upon initiation of treatment and then repeated during treatment.ResultsTwo hundred and forty‐eight TCD monitoring were performed in 42 VV and 11 VA ECMO patients. MES were detected in 26.2% of VV ECMO patients and in 81.8% of VA ECMO patients (P < 0.001). In both subgroups of patients, no correlation was found between MES detection and extracorporeal flow velocities or aPTT values. In VA ECMO patients, an inverse correlation between left ventricular ejection fraction and MES grading was found (P = 0.037). In both groups, no clinical neurological impairments correlated to MES detection were found at 6 months follow‐up.ConclusionsMES were found in both ECMO configurations; independently from their pathophysiology, MES do not seem to influence clinical outcome. Multicenter studies are still required with more extensive cases to confirm these results.