bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strengthening Market Linkages of Farm Households in Developing Countries
Authors: Mottaleb Khondoker Abdul , Mohanty Samarendu , Nelson Andrew 
Published: September 2014

AbstractFarm households in developing countries generally allocate a major portion of their resources to staple food production, mainly for self‐consumption. Hence, many of them are more or less delinked from the market. It is well recognized, however, that market participation is crucial for farm households to ensure a flow of cash income, leading to poverty alleviation and improved livelihoods. Thus, it is meaningful to understand what factors affect farm households' decision to sell food crops, which is important for strengthening their linkages with markets. The empirical literature on impacts of market linkages has seldom focused on the determinants of market participation. Using rice farm households in Bangladesh and applying a double‐hurdle model, this article demonstrates that the provision of general education and the development of agricultural infrastructure such as irrigation facilities can strengthen the market linkages of farm households by enhancing their marketable surplus through increased production. By contrast, rainfall beyond the optimum level, drought spells, and flood incidences can weaken market linkages by reducing their marketable surplus through decreased production. Specific policies such as investment in general education are drawn up based on the findings.
mod_bio: Apache modules for Next-Generation sequencing data
Authors: Lindenbaum Pierre , Redon Richard 
Published: September 2014

Abstract
Summary: We describe mod_bio , a set of modules for the Apache HTTP server that allows the users to access and query fastq, tabix, fasta and bam files through a Web browser. Those data are made available in plain text, HTML, XML, JSON and JSON-P. A javascript-based genome browser using the JSON-P communication technique is provided as an example of cross-domain Web service.
Availability and implementation : https://github.com/lindenb/mod_bio .
Contact: pierre.lindenbaum@univ-nantes.fr
BalestraWeb: efficient online evaluation of drug–target interactions
Authors: Cobanoglu Murat Can , Oltvai Zoltán N. , Taylor D. Lansing , Bahar Ivet 
Published: September 2014

Abstract
Summary: BalestraWeb is an online server that allows users to instantly make predictions about the potential occurrence of interactions between any given drug–target pair, or predict the most likely interaction partners of any drug or target listed in the DrugBank. It also permits users to identify most similar drugs or most similar targets based on their interaction patterns. Outputs help to develop hypotheses about drug repurposing as well as potential side effects.
Availability and implementation: BalestraWeb is accessible at http://balestra.csb.pitt.edu/ . The tool is built using a probabilistic matrix factorization method and DrugBank v3, and the latent variable models are trained using the GraphLab collaborative filtering toolkit. The server is implemented using Python, Flask, NumPy and SciPy.
Contact: bahar@pitt.edu
SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles
Authors: Wong Ka-Chun , Li Yue , Peng Chengbin , Zhang Zhaolei 
Published: September 2014

Abstract
Motivation: Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-Seq) measures the genome-wide occupancy of transcription factors in vivo . Different combinations of DNA-binding protein occupancies may result in a gene being expressed in different tissues or at different developmental stages. To fully understand the functions of genes, it is essential to develop probabilistic models on multiple ChIP-Seq profiles to decipher the combinatorial regulatory mechanisms by multiple transcription factors.
Results: In this work, we describe a probabilistic model (SignalSpider) to decipher the combinatorial binding events of multiple transcription factors. Comparing with similar existing methods, we found SignalSpider performs better in clustering promoter and enhancer regions. Notably, SignalSpider can learn higher-order combinatorial patterns from multiple ChIP-Seq profiles. We have applied SignalSpider on the normalized ChIP-Seq profiles from the ENCODE consortium and learned model instances. We observed different higher-order enrichment and depletion patterns across sets of proteins. Those clustering patterns are supported by Gene Ontology (GO) enrichment, evolutionary conservation and chromatin interaction enrichment, offering biological insights for further focused studies. We also proposed a specific enrichment map visualization method to reveal the genome-wide transcription factor combinatorial patterns from the models built, which extend our existing fine-scale knowledge on gene regulation to a genome-wide level.
Availability and implementation: The matrix-algebra-optimized executables and source codes are available at the authors’ websites: http://www.cs.toronto.edu/∼wkc/SignalSpider .
Contact: zhaolei.zhang@utoronto.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
A hub and spoke network model to analyse the secondary dispersal of introduced marine species in Indonesia
Authors: Azmi Fauziah , Hewitt Chad L. , Campbell Marnie L. 
Published: September 2014

Abstract
Indonesia is a biodiversity hotspot threatened with new introductions of marine species. As with many countries, Indonesia has a stratified shipping network of international ports linked to a large suite of domestic ports. We developed a hub and spoke network model to examine the risk associated with the secondary transfer of introduced marine species from the port hub of Tanjung Priok in Jakarta Bay to the 33 Indonesian provinces (including other ports in the Jakarta province). An 11-year shipping dataset was used (vessel next port of call records for maritime vessels that originated in Jakarta Bay and that remained in domestic waters) to derive a province ranking of vulnerability. Fifteen provinces represented almost 94% of the traffic frequency, with East Java and Jakarta provinces dominating. All urban provinces featured within the top seven highest frequency traffic provinces. Traffic patterns reflect an intra-coastal reliance on shipping, with traffic frequency decreasing with distance from Jakarta Bay. Provinces were regionalized into three categories (Lampung to East Java, Makassar Straits, and Malacca Straits) each with different vulnerabilities based on their values.
Assessment of False-negative Ascites Cytology in Epithelial Ovarian Carcinoma
Authors: Allen Valerie A. , Takashima Yoko , Nayak Seema , Manahan Kelly J. , Geisler John P. 
Published: September 2014

Objective:
The objective was to determine how often peritoneal cytology is positive for malignancy in women with known ovarian cancer. Knowing this fact would help determine the usefulness of diagnostic paracentesis.

Methods:
Records of all women diagnosed with invasive epithelial ovarian cancer from 2004 to 2012 were examined to correlate presence of ascites, cytologic, and pathologic findings.

Results:
A total of 313 patients were included in analysis. A total of 210 of 313 patients (67.1%) with ascites had cytology positive for malignancy. This left 103 patients with ascites and cancer without malignant cells found in the ascites removed at the time of surgery.

Conclusions:
Except in a few cases, paracentesis is not recommended for the diagnosis of ovarian cancer because of the potential spreading of cancer. Furthermore, with only just over two thirds of cases of known cancer and ascites having cytology positive for malignancy, the value of paracentesis for diagnosis of ovarian cancer is minimal.
Induction of potential protective immunity against enterotoxemia in calves by single or multiple recombinant Clostridium perfringens toxoids
Authors: Jiang Zhigang , De Yanyan , Chang Jitao , Wang Fang , Yu Li 
Published: September 2014

AbstractCattle enterotoxemia caused by Clostridium perfringens toxins is a noncontagious, sporadic, and fatal disease characterized by sudden death. Strategies for controlling and preventing cattle enterotoxemia are based on systematic vaccination of herds with toxoids. Because the process of producing conventional clostridial vaccines is dangerous, expensive, and time‐consuming, the prospect of recombinant toxoid vaccines against diseases caused by C. perfringens toxins is promising. In this study, nontoxic recombinant toxoids derived from α‐, β‐ and ε‐toxins of C. perfringens, namely, rCPA247–370, rCPB and rEtxHP, respectively, were expressed in Escherichia coli. High levels of specific IgG antibodies and neutralizing antibodies against the toxins were detected in sera from calves vaccinated with either a single recombinant toxoid or a mixed cocktail of all three recombinant toxoids, indicating the potential of these recombinant toxoids to provide calves with protective immunity against enterotoxemia caused by C. perfringens.
Microparticles as biomarkers of osteonecrosis of the hip in sickle cell disease
Authors: Marsh Anne , Schiffelers Raymond , Kuypers Frans , Larkin Sandra , Gildengorin Ginny , van Solinge Wouter , Hoppe Carolyn 
Published: September 2014

SummaryOsteonecrosis of the femoral head (ONFH) is a common complication of sickle cell disease (SCD). To examine the association between microparticles and ONFH in SCD, we compared plasma microparticle levels in 20 patients with and without ONFH. Microparticles were quantified using nanoparticle tracking analysis and found to be 2·3‐fold higher in patients with ONFH compared to patients without ONFH, and 2·5‐fold higher than in healthy controls. These results suggest that microparticles may be a clinically useful biomarker of ONFH in SCD. Further investigations are needed to determine the functional relevance of microparticles in the pathogenesis of ONFH in SCD.
Going further on an intricate and challenging group of nudibranchs: description of five novel species and a more complete molecular phylogeny of the subfamily Nembrothinae (Polyceridae)
Authors: Pola Marta , Padula Vinicius , Gosliner Terrence M. , Cervera Juan Lucas 
Published: September 2014

AbstractNembrothinae is a colourful subfamily of nudibranch polycerids, which despite its large size and striking appearance, needs to be more thoroughly studied. The available scientific information about this subfamily is very recent, and pictures of living undescribed species become available every day. Nevertheless, the lack of associated material for morphological, anatomical, and molecular analysis results in scarce additional studies. In this paper, five novel species are described: Roboastra ernsti sp. nov., Roboastra nikolasi sp. nov., Tambja brasiliensis sp. nov., Tambja crioula sp. nov., and Tambja kava sp. nov. In addition, Tambja divae (Marcus, 1958), a species previously known only from the original description, is redescribed and additional data and comments on Tambja cf. amakusana Baba, 1987 and Tambja marbellensis Schick and Cervera, 1998 are provided. Molecular data (H3, COI and 16S genes) for all these novel species and some additional ones were obtained and included in a previous molecular database. Maximum‐likelihood, maximum‐parsimony and Bayesian analyses were carried out. The phylogeny presented here has revealed Nembrothinae to be an intricate and challenging group of nudibranchs to study. Intermediate missing species seem to be critical to understanding the evolutionary relationships within this group.
Dimethyloxalylglycine lyophilized onto bone substitutes increase vessel area in rat calvarial defects
Authors: Kuchler Ulrike , Keibl Claudia , Fügl Alexander , Schwarze Uwe Y. , Tangl Stefan , Agis Hermann , Gruber Reinhard 
Published: September 2014

AbstractAimPharmacological inhibitors of prolyl hydroxylases, also termed hypoxia‐mimetic agents (HMAs), when repeatedly injected can support angiogenesis and bone regeneration. However, the possible role of HMA loaded onto bone substitutes to support angiogenesis and bone regeneration under diabetic condition is unknown. The capacity of HMA loaded onto deproteinized bovine bone mineral (DBBM) to support angiogenesis and bone formation was examined in diabetic Wistar rats.MethodsDiabetes was induced by intraperitoneal injection of streptozotocin. The HMA dimethyloxalylglycine (DMOG) and desferrioxamine (DFO) were lyophilized onto DBBM. Calvarial defects were created with a trephine drill and filled with the respective bone substitutes. After 4 weeks of healing, the animals were subjected to histological and histomorphometric analysis.ResultsIn this report, we provide evidence that DMOG loaded onto DBBM can support angiogenesis in vivo. Specifically, we show that DMOG increased the vessel area in the defect site to 2.4% ± 1.3% compared with controls 1.1% ± 0.48% (P = 0.012). There was a trend toward an increased vessel number in the defect site with 38.6 ± 17.4 and 31.0 ± 10.3 in the DMOG and the control group (P = 0.231). The increase in angiogenesis, however, did not translate into enhanced bone formation in the defect area with 9.2% ± 7.1% and 8.4% ± 5.6% in DMOG and control group, respectively. No significant changes were caused by DFO.ConclusionsThe results suggest that DMOG loaded onto DBBM can support angiogenesis, but bone formation does not increase accordingly in a type 1 diabetic rat calvarial defect model at the indicated time point.
Alcohol brief interventions practice following training for multidisciplinary health and social care teams: A qualitative interview study
Authors: Fitzgerald Niamh , Molloy Heather , MacDonald Fiona , McCambridge Jim 
Published: September 2014

AbstractIntroduction and AimsFew studies of the implementation of alcohol brief interventions (ABI) have been conducted in community settings such as mental health, social work and criminal justice teams. This qualitative interview study sought to explore the impact of training on ABI delivery by staff from a variety of such teams.Design and MethodsFifteen semi‐structured telephone interviews were carried out with trained practitioners and with managers to explore the use of, perceived need for and approaches to ABI delivery and recording with clients, and compatibility of ABIs with current practice. Interviews were analysed thematically using an inductive approach.ResultsVery few practitioners reported delivery of any ABIs following training primarily because they felt ABIs to be inappropriate for their clients. According to practitioners, this was either because they drank too much or too little to benefit. Practitioners reported a range of current activities relating to alcohol, and some felt that their knowledge and confidence were improved following training. One practitioner reported ABI delivery and was considered a training success, while expectations of ABIs did not fit with current practice including assessment procedures for the remainder.Discussion and ConclusionsIdentified barriers to ABI delivery included issues relating to individual practitioners, their teams, current practice and the ABI model. They are likely to be best addressed by strategic team‐ and setting‐specific approaches to implementation, of which training is only one part. [Fitzgerald N, Molloy H, MacDonald F, McCambridge J. Alcohol brief interventions practice following training for multidisciplinary health and social care teams: A qualitative interview study. Drug Alcohol Rev 2015;34:185–93]
Solving the problem of non‐attendance in substance abuse services
Authors: Milward Joanna , Lynskey Michael , Strang John 
Published: September 2014

AbstractIssuesRates of non‐attendance are among the highest in substance misuse services. Non‐attendance is costly and results in the inefficient use of limited resources. Patients who frequently miss their appointments have worse outcomes including treatment dropout and decreased likelihood of achieving long‐term abstinence.ApproachThis narrative review evaluates interventions targeting non‐attendance in addiction services and draws upon the wider health‐care literature to identify interventions that could be adapted for substance‐abusing populations.Key FindingsBoth fixed value and intermittent reinforcement contingency management demonstrate potential for improving attendance. However, small sample sizes and heterogeneous populations make it difficult to draw firm conclusions. Appointment reminders by letter or telephone have demonstrated moderate evidence for improving attendance in substance‐abusing populations. Text message appointment reminders are extensively utilised in general health‐care settings and consistently improve attendance; however, there is a paucity of research examining the feasibility and effectiveness of text message reminders in addiction services.ImplicationsA lack of evidence for methods to improve attendance is reflected in the continuing challenge faced by addiction services attempting to manage high rates of non‐attendance.ConclusionsNon‐attendance remains a persistent issue for addiction services. While there is limited evidence that contingency management improves attendance, more rigorous research is needed to determine the optimal intervention components and effectiveness in different populations, particularly those receiving maintenance treatments. Multicomponent text message interventions incorporating different delivery and content strategies demonstrate a promise for improving non‐attendance and poor engagement.
[Milward J, Lynskey M, Strang J. Solving the problem of non‐attendance in substance abuse services. Drug Alcohol Rev 2014;33:625–36]
The serotonergic anxiolytic buspirone attenuates circadian responses to light
Authors: Smith Victoria M. , Iannatonne Stephanie , Achal Sanjay , Jeffers Ryan T. , Antle Michael C. 
Published: September 2014

AbstractSerotonergic drugs modify circadian responses to light, with agonists attenuating and some partial agonists or antagonists potentiating photic phase shifts. The anxiolytic buspirone is a 5‐HT1A receptor partial agonist. Given that buspirone is used therapeutically to manage generalised anxiety disorder, it would be useful to understand if and how this drug may modify circadian responses to light, not only to help manage side effects, but also to examine its potential use as a chronobiotic. Here we examined behavioral and molecular responses to phase‐shifting light in mice and hamsters treated with buspirone. Phase advances to late subjective night light pulses in hamsters and wildtype mice were significantly attenuated by buspirone. 5‐HT1A receptor knockout mice exhibited potentiated photic phase shifts when pretreated with buspirone. In wildtype mice, the attenuated phase shifts were accompanied by increased cFos expression in the suprachiasmatic nucleus, whereas potentiated phase shifts in knockouts were accompanied by increased phosphorylation of extracellular signal‐regulated kinase (ERK) and cyclic AMP response element‐binding protein (CREB), and decreased cFos expression. Attenuated photic phase shifts in buspirone‐treated hamsters were accompanied by decreased phosphorylation of ERK and CREB. Chronic buspirone treatment decreased the amplitude of wheel‐running rhythms, lengthened the duration of the active phase and advanced the phase angle of entrainment. Buspirone administration at midday produced non‐photic phase advances in wildtype but not 5‐HT1A receptor knockout mice. These findings suggest that buspirone affected the circadian system in a manner similar to the 5‐HT1A/7 agonist (±)‐8‐Hydroxy‐2‐dipropylaminotetralin hydrobromide, primarily through the 5‐HT1A receptor, and suggest that therapeutic use of buspirone to manage anxiety may impact circadian function.
Prenatal diagnosis in haemophilia A: experience of the genetic diagnostic laboratory
Authors: Kessler L. , Adams R. , Mighion L. , Walther S. , Ganguly A. 
Published: September 2014

SummaryThe paper describes the experience of the Genetic Diagnostic Laboratory in prenatal testing for haemophilia A, an X‐linked recessive disease caused by mutations in the F8 gene. Knowledge of a familial mutation prior to pregnancy can benefit prenatal diagnosis and decrease wait time for molecular testing during pregnancy. This is a retrospective review of a series of pregnant women who pursued F8 gene testing from December 1997 through May 2012, highlighting three cases, which demonstrate the technical complexities of analysis and the implications of not knowing carrier status prior to pregnancy. Mutations of the F8 gene were detected in affected males, obligate female carriers and suspected female carriers by DNA sequencing, inverse‐PCR, qRT‐PCR, Southern blot and exonic dosage analysis. The same methods were used to analyse prenatal samples from obligate or suspected female carriers upon request. Maternal cell contamination studies were performed for all prenatal samples analysed. Ninety‐nine women pursued F8 testing during pregnancy, either for carrier status alone or carrier status and prenatal diagnosis. Ninety‐one women (91%) requested carrier testing because they did not know their F8 mutation carrier status prior to pregnancy. Eight women requested prenatal diagnosis only, and only 4 of these were aware of their mutation status. Thirty‐seven individuals were found to be mutation carriers. Forty‐two prenatal samples were received for prenatal diagnosis. In total 21 foetuses were identified as mutation carriers. Mutation detection was complex and increased the turnaround time in some cases. Only four of 99 women who submitted samples for F8 testing were aware of their F8 mutation status prior to pregnancy. Knowledge of F8 mutation status prior to pregnancy allows for efficient prenatal diagnosis, when desired. Thus, preconception genetic counselling is required to inform patients of the available options and the complex and time‐consuming nature of F8 testing.
Ovarian and endometrial endometrioid adenocarcinomas have distinct profiles of microsatellite instability, PTEN expression, and ARID1A expression
Authors: Huang Hsien‐Neng , Lin Ming‐Chieh , Tseng Li‐Hui , Chiang Ying‐Cheng , Lin Liang‐In , Lin Yu‐Feng , Huang Hsin‐Ying , Kuo Kuan‐Ting 
Published: September 2014

AimsTo understand the role of and differences in molecular alterations between endometrial and ovarian endometrioid adenocarcinomas.Methods and resultsWe investigated the microsatellite status of 26 ovarian endometrioid adenocarcinomas (OVEMs), 42 endometrial endometrioid adenocarcinomas (EMCAs), and 19 concurrent (endometrial and ovarian) endometrioid adenocarcinomas. We evaluated the expression of the mismatch repair proteins, PTEN and ARID1A, and mutations of PTEN, KRAS, CTNNB1, and PIK3CA. High levels of microsatellite instability (MSI‐H) were present in one of 26 OVEMs, 12 of 42 EMCAs, and four of 19 concurrent endometrioid adenocarcinomas. Only four of 19 concurrent endometrioid adenocarcinomas showed identical molecular alterations in their endometrial and ovarian components. Loss of ARID1A or loss of PTEN expression, and MSI‐H, were more common in EMCAs than OVEMs (P = 0.044, P = 0.004, and P = 0.012, respectively). MSI‐H in endometrial endometrioid adenocarcinomas was also related to loss of ARID1A expression (P < 0.001). In the cohort of MSI‐H endometrioid adenocarcinomas involving the endometrium (n = 16), MSH6‐deficient cases showed higher frequencies of CTNNB1 and PIK3CA mutations (P = 0.008 and P = 0.036, respectively), but lower frequencies of KRAS mutation (P = 0.011), than PMS2‐deficient cases.ConclusionsThe different frequencies of molecular genetic alterations between endometrial endometrioid adenocarcinomas and ovarian endometrioid adenocarcinomas imply that distinct processes may be involved in their tumorigenesis or tumour progression.