bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biting behaviour of Tabanidae on cattle in mountainous summer pastures, Pyrenees, France, and effects of weather variables
Authors: Baldacchino F. , Puech L. , Manon S. , Hertzog Lionel R. , Jay-Robert P. 
Published: March 2014

AbstractIn France, during the summer, cattle in mountainous pastures can be highly exposed to tabanid bites. The persistent biting behaviour of tabanids not only causes disturbance, but is also responsible for transmitting diseases, such as bovine besnoitiosis. The purpose of this study was to better identify the level of tabanid annoyance on cattle by means of insect trapping and direct observation of cows. Tabanids were active during the entire daily observation period (10:00–16:00), except forHaematopotasp., which were less active in the morning. The tabanids collected in Nzi traps were generally representative of those that landed on cattle, except forHaematopotasp., as Nzi traps were not very effective for these species. The preferred feeding sites for most species appeared to be cow's legs or udder. Leg stamping was the defensive reaction most related to a tabanid alighting on a host. Generalized linear mixed models showed that the parameters associated with tabanid landings on hosts were related to weather and altitude, but not to landscape structure. Increased landings were mostly associated with the higher temperatures and lower wind speeds at midday, but some differences were observed between species. The results indicate that cattle-protection measures should be taken during the peak of tabanid abundance when climatic conditions favour intense biting activity. Nzi traps set close to livestock were very effective to catch tabanids and could help in reducing the annoyance caused by horse flies.
An isolate of the nematophagous fungusMonacrosporium thaumasiumfor the control of cattle trichostrongyles in south-eastern Brazil
Authors: Assis R.C.L. , Luns F.D. , de Araújo J.V. , Braga F.R. , Assis R.L. , Marcelino J. , Freitas P.C. , Andrade M.A. 
Published: March 2014

AbstractA mycelial formulation in sodium alginate pellets of the nematophagous fungusMonacrosporium thaumasium(isolate NF34A) was assessed in the biological control of beef cattle trichostrongyles in tropical Brazil. Two groups of ten male Nellore calves aged 6 months, a fungus-treated group and a control group, were fed on a pasture ofBrachiaria decumbensnaturally infected with larvae of cattle trichostrongyles. The fungus-treated group received doses of sodium alginate mycelial pellets orally (1 g pellets (0.2 g fungus)/10 kg live weight) twice a week for 12 months. At the end of the study there was a signiﬁcant reduction (P< 0.01) in the number of eggs per gram of faeces and coprocultures of the fungus-treated group – 47.8% and 50.2%, respectively – in relation to the control group. There was a 47.3% reduction in herbage samples, collected up to 0–20 cm from faecal pats, between the fungus-treated and control groups, and a 58% reduction when the sampling distance was 20–40 cm from faecal pats (P< 0.01). The treatment with sodium alginate pellets containing the nematode-trapping fungusM. thaumasiumreduced trichostrongyles in tropical south-eastern Brazil and could be an effective tool for the biological control of this parasitic nematode in beef cattle. However, in such a tropical climate with low rainfall the fungal viability can be reduced.
Biochemical and cellular mechanisms regulatingAcanthamoeba castellaniiadherence to host cells
Authors: SOTO-ARREDONDO K. J. , FLORES-VILLAVICENCIO L. L. , SERRANO-LUNA J. J. , SHIBAYAMA M. , SABANERO-LÓPEZ M. 
Published: March 2014

SUMMARYFree-living amoebae belonging to the genusAcanthamoebaare the causative agents of infections such as amoebic keratitis (AK), granulomatous amoebic encephalitis (GAE) and cutaneous lesions. The mechanisms involved in the establishment of infection are unknown. However, it is accepted that the initial phase of pathogenesis involves adherence to the host tissue. In this work, we analysed surface molecules with an affinity for epithelial and neuronal cells from the trophozoites ofAcanthamoeba castellanii. We also investigated the cellular mechanisms that govern the process of trophozoite adhesion to the host cells. We first used confocal and epifluorescence microscopy to examine the distribution of theA. castellaniiactin cytoskeleton during interaction with the host cells. The use of drugs, as cytochalasin B (CB) and latrunculin B (LB), revealed the participation of cytoskeletal filaments in the adhesion process. In addition, to identify the proteins and glycoproteins on the surface ofA. castellanii, the trophozoites were labelled with biotin and biotinylated lectins. The results revealed bands of surface proteins, some of which were glycoproteins with mannose andN-acetylglucosamine residues. Interaction assays of biotinylated amoebae proteins with epithelial and neuronal cells showed that some surface proteins had affinity for both cell types. The results of this study provide insight into the biochemical and cellular mechanisms of theAcanthamoebainfection process.
HOW HEALTH TECHNOLOGY ASSESSMENT AGENCIES ADDRESS THE ISSUE OF UNPUBLISHED DATA
Authors: Kreis Julia , Panteli Dimitra , Busse Reinhard 
Published: March 2014

Objectives: Reporting bias potentially threatens the validity of results in health technology assessment (HTA) reports. Our study aimed to explore policies and practices of HTA agencies regarding strategies to include previously unpublished data in their assessments, focusing on requests to industry for unpublished data.Methods: We included international HTA agencies with publicly available methods papers as well as HTA reports. From the methods papers and recent reports we extracted information on requests to industry and on searches in trial registries, regulatory authority Web sites and for conference abstracts.Results: Eighteen HTA agencies and seventy-three reports were included. Agencies’ methods papers showed variability regarding requests to industry (requests are routinely carried out in seven cases, not mentioned in six, at the discretion of HTA authors in three, and based on manufacturer applications in two), which were reflected in the reports investigated. As reporting of requests was limited, it often remained unclear whether unpublished data had been received. Searches in trial registries, at regulatory authorities or for conference abstracts are described as a routine or optional part of the search strategy in the methods papers of 9, 11, and 8 included agencies, respectively. A total of 52 percent, 39 percent, and 16 percent of reports described searches in trial registries, at regulatory agencies, and hand searching of conference proceedings.Conclusion: International HTA agencies currently differ considerably in their efforts to address the issue of unpublished data. Requests to industry may constitute one strategy to access and include unpublished data, while agencies can learn from each other concerning successful practice.
Early adolescent alcohol use in context: How neighborhoods, parents, and peers impact youth
Authors: Trucco Elisa M. , Colder Craig R. , Wieczorek William F. , Lengua Liliana J. , Hawk Larry W. 
Published: March 2014

AbstractDevelopmental–ecological models are useful for integrating risk factors across multiple contexts and conceptualizing mediational pathways for adolescent alcohol use, yet these comprehensive models are rarely tested. This study used a developmental–ecological framework to investigate the influence of neighborhood, family, and peer contexts on alcohol use in early adolescence (N= 387). Results from a multi-informant longitudinal cross-lagged mediation path model suggested that high levels of neighborhood disadvantage were associated with high levels of alcohol use 2 years later via an indirect pathway that included exposure to delinquent peers and adolescent delinquency. Results also indicated that adolescent involvement with delinquent peers and alcohol use led to decrements in parenting, rather than being consequences of poor parenting. Overall, the study supported hypothesized relationships among key microsystems thought to influence adolescent alcohol use, and thus findings underscore the utility of developmental–ecological models of alcohol use.
The Institute of Medicine, the Food and Drug Administration, and the calcium conundrum
Authors: Neupane Shristi , Knohl Stephen J 
Published: March 2014

AbstractIn the present article we aim to bring forward the apparent disconnect between two US government-sponsored entities – the Institute of Medicine (IOM) and the Food and Drug Administration (FDA) – regarding the safe upper limit of Ca intake.In light of the 2011 US Congress-appointed IOM report indicating an upper limit of elemental Ca intake of 2000–2500 mg/d in adults (based on age group), it is perplexing that the FDA has not yet required a change on the labelling of over-the-counter Ca-containing antacids, some of which indicate an upper limit of elemental Ca intake of 2800–3000 mg/d. Even more concerning is that Ca intake is rarely from supplementation in isolation. National Health and Nutrition Examination Survey (NHANES) data from 2003–2006 indicate that mean dietary Ca intakes for males ranged from 871 to 1266 mg/d and for females from 748 to 968 mg/d depending on the age group. The estimated total Ca (diet + supplements) intake exceeded the upper limit in 5 % of the population older than 50 years. Furthermore, NHANES data from 1999–2000 indicate that when Ca is taken as part of an antacid preparation, patients often fail to report this as Ca intake. Thus, individuals taking the maximum allowable dose of supplemental Ca as antacids are at high risk for complications associated with excess Ca intake.Our hope is that by describing Ca homeostasis and highlighting the risks and dangers of Ca overload, the FDA will align its recommendation with the IOM and solve the current Ca conundrum in the USA for the sake of patient safety.
“Every Picture Tells a Story”; Picturing Judicial Biography
Authors: Moran Leslie J 
Published: March 2014

AbstractIn this article Leslie J. Moran turns to objects that are often marginal to legal biography and neglected by those engaging in legal biographical projects; pictures. Drawing upon his previous and current work on judicial portraits the article outlines three biographical dimensions of these legal images. The first explores the legal biography potential of what lies within the frame of a judicial portrait. The second focuses upon the biographical dimensions of the process of portrait making. The third draws upon the now well established insight that the meaning of the object, the judicial portrait, is not generated exclusively by, or confined to, what is to be found within the frame of the picture. This provides an opportunity to consider the role of pictures as a method for use by those engaging in legal biographical projects.
Electronic Legal Deposit and the Advocates Library
Authors: Longson Andrea 
Published: March 2014

AbstractThe Advocates Library provides a library and information service to around 470 members of the Faculty of Advocates, the Scottish Bar. The library also acts as the national law library for Scotland, having the privilege of claiming law materials on legal deposit. The Senior Librarian, Andrea Longson (the author of this article), and the library's management group work closely with staff at the National Library of Scotland and have been involved in strategic discussions about the drafting and implementation of legal deposit legislation for over ten years.
The Dixie Chicks’ “Lubbock or Leave It”: Negotiating Identity and Place in Country Song
Authors: WATSON JADA 
Published: March 2014

AbstractThe concepts of “place,” “space,” and “home” are integral to the study of country music, a genre conventionally associated with geographic regions, rural landscapes, and domestic values. Place-songs have emerged as an important way in which country musicians communicate life experiences and define elements of their identity, emphasizing the influence of family and community on their character, beliefs, and values. However, just as place can signify belonging, it can also represent a constricting environment from which artists struggle to escape. Such narratives enable us to see vital parts of regional identity that would otherwise be hidden, obscured, or overshadowed.The Dixie Chicks’ song “Lubbock or Leave It” (2006) is an interesting case study for an inquiry into how artists struggle to define themselves within the country genre. The song spurred immediate uproar insofar as the lyrics portray lead singer Natalie Maines's hometown of Lubbock, Texas as small and narrow-minded. Many listeners and critics interpreted the song as a rejection of both Lubbock and country values. Drawing from the fields of cultural geography and musicology, this study examines how the Dixie Chicks draw on musical codes and conventions in an act of defiance and genre subversion, as they struggle with parochialism and conservative thinking.
Understanding Light Harvesting in Radial Junction Amorphous Silicon Thin Film Solar Cells
Authors: Yu Linwei , Misra Soumyadeep , Wang Junzhuan , Qian Shengyi , Foldyna Martin , Xu Jun , Shi Yi , Johnson Erik , Cabarrocas Pere Roca i 
Published: March 2014

AbstractThe radial junction (RJ) architecture has proven beneficial for the design of a new generation of high performance thin film photovoltaics. We herein carry out a comprehensive modeling of the light in-coupling, propagation and absorption profile within RJ thin film cells based on an accurate set of material properties extracted from spectroscopic ellipsometry measurements. This has enabled us to understand and evaluate the impact of varying several key parameters on the light harvesting in radially formed thin film solar cells. We found that the resonance mode absorption and antenna-like light in-coupling behavior in the RJ cell cavity can lead to a unique absorption distribution in the absorber that is very different from the situation expected in a planar thin film cell and that has to be taken into account in the design of high performance RJ thin film solar cells. When compared to the experimental EQE response of real RJ solar cells, this modeling also provides an insightful and powerful tool to resolve the wavelength-dependent contributions arising from individual RJ units and/or from strong light trapping due to the presence of the RJ cell array.
Turtle: Identifying frequent
k
-mers with cache-efficient algorithms
Authors: Roy Rajat Shuvro , Bhattacharya Debashish , Schliep Alexander 
Published: March 2014

Abstract
Motivation: Counting the frequencies of k -mers in read libraries is often a first step in the analysis of high-throughput sequencing data. Infrequent k -mers are assumed to be a result of sequencing errors. The frequent k -mers constitute a reduced but error-free representation of the experiment, which can inform read error correction or serve as the input to de novo assembly methods. Ideally, the memory requirement for counting should be linear in the number of frequent k -mers and not in the, typically much larger, total number of k -mers in the read library.
Results: We present a novel method that balances time, space and accuracy requirements to efficiently extract frequent k -mers even for high-coverage libraries and large genomes such as human. Our method is designed to minimize cache misses in a cache-efficient manner by using a pattern-blocked Bloom filter to remove infrequent k -mers from consideration in combination with a novel sort-and-compact scheme, instead of a hash, for the actual counting. Although this increases theoretical complexity, the savings in cache misses reduce the empirical running times. A variant of method can resort to a counting Bloom filter for even larger savings in memory at the expense of false-negative rates in addition to the false-positive rates common to all Bloom filter-based approaches. A comparison with the state-of-the-art shows reduced memory requirements and running times.
Availability and implementation: The tools are freely available for download at http://bioinformatics.rutgers.edu/Software/Turtle and http://figshare.com/articles/Turtle/791582 .
Contact: rajatroy@cs.rutgers.edu or schliep@cs.rutgers.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation
Authors: Kocher Jean-Pierre A. , Quest Daniel J. , Duffy Patrick , Meiners Michael A. , Moore Raymond M. , Rider David , Hossain Asif , Hart Steven N. , Dinu Valentin 
Published: March 2014

Abstract
Motivation:  The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines.
Availability and implementation: The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu .
Contact: Kocher.JeanPierre@mayo.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A gradient-boosting approach for filtering
de novo
mutations in parent–offspring trios
Authors: Liu Yongzhuang , Li Bingshan , Tan Renjie , Zhu Xiaolin , Wang Yadong 
Published: March 2014

Abstract
Motivation: Whole-genome and -exome sequencing on parent–offspring trios is a powerful approach to identifying disease-associated genes by detecting de novo mutations in patients. Accurate detection of de novo mutations from sequencing data is a critical step in trio-based genetic studies. Existing bioinformatic approaches usually yield high error rates due to sequencing artifacts and alignment issues, which may either miss true de novo mutations or call too many false ones, making downstream validation and analysis difficult. In particular, current approaches have much worse specificity than sensitivity, and developing effective filters to discriminate genuine from spurious de novo mutations remains an unsolved challenge.
Results: In this article, we curated 59 sequence features in whole genome and exome alignment context which are considered to be relevant to discriminating true de novo mutations from artifacts, and then employed a machine-learning approach to classify candidates as true or false de novo mutations. Specifically, we built a classifier, named De Novo Mutation Filter (DNMFilter), using gradient boosting as the classification algorithm. We built the training set using experimentally validated true and false de novo mutations as well as collected false de novo mutations from an in-house large-scale exome-sequencing project. We evaluated DNMFilter’s theoretical performance and investigated relative importance of different sequence features on the classification accuracy. Finally, we applied DNMFilter on our in-house whole exome trios and one CEU trio from the 1000 Genomes Project and found that DNMFilter could be coupled with commonly used de novo mutation detection approaches as an effective filtering approach to significantly reduce false discovery rate without sacrificing sensitivity.
Availability: The software DNMFilter implemented using a combination of Java and R is freely available from the website at http://humangenome.duke.edu/software .
Contact: ydwang@hit.edu.cn
Case of tumor thrombus inside femoral vein, formed by melanoma metastasized to inguinal lymph node
Authors: Takai Toshihiro , Murata Yozo 
Published: March 2014

AbstractInguinal lymph nodes are often excised in dermatological surgery, because they are the most common of the lymphatic basin involved in metastasis of malignant skin tumor on the lower extremities or genital region. Herein, we describe a case of cutaneous malignant melanoma on the buttock of a 78‐year‐old woman. Under the huge metastasized inguinal lymph node, there was tumor invasion into the femoral vein with intraluminal tumor thrombus formation. Careful preoperative radiological assessment enabled successful resection on surgery. A review of the published work revealed that tumor thrombus due to direct invasion of melanoma may be rare. The possibility of intravenous tumor thrombus should be considered in the settings of surgery of inguinal metastasis of melanoma, especially when a large‐sized node is located near the great veins.
The impact of obesity on outcomes of midwife‐led pregnancy and childbirth in a primary care population: a prospective cohort study
Authors: Daemers DOA , Wijnen HAA , van Limbeek EBM , Budé LM , Nieuwenhuijze MJ , Spaanderman MEA , de Vries RG 
Published: March 2014

ObjectiveTo assess the impact of obesity on the likelihood of remaining in midwife‐led care throughout pregnancy and childbirth.DesignSecondary analysis of data from a prospective cohort study.SettingDutch midwife‐led practices.PopulationA cohort of 1369 women eligible for midwife‐led care after their first antenatal visit.MethodsFirst‐trimester body mass index (BMI) was calculated as weight measured at booking divided by height squared. Obstetric data were retrieved from medical records. Multiple logistic regressions were performed to examine the effects of BMI classification on midwife‐led pregnancies and childbirths.Main outcome measuresPercentages of women remaining in midwife‐led care throughout pregnancy and throughout childbirth.ResultsOf women in obesity classes II and III, 55% remained in midwife‐led care throughout pregnancy and 30% remained in midwife‐led care throughout birth. Compared with women of normal weight, women in obesity classes II and III had fewer midwife‐led pregnancies (OR 0.38, 95% CI 0.21–0.69), and women who were overweight or in obesity class I had fewer midwife‐led childbirths (OR 0.63, 95% CI 0.44–0.90; OR 0.49, 95% CI 0.29–0.84, respectively). Compared with women of normal weight, women who were obese had higher referral rates for hypertensive disorders (4 versus 14%), prolonged labour (4.6 versus 10.4%), and intrapartum pain relief (4 versus 10.4%). The women who were eligible for midwife‐led birth and who were overweight or obese, had no more urgent referrals than women of normal weight. Women who were obese and who completed a midwife‐led birth had no more adverse outcomes than women of normal weight, with the exception of higher rates of large for gestational age (LGA) babies (>97.7 centile; 12.1%, versus 1.9% in normal weight and versus 3.3% in overweight women).ConclusionsAlthough fewer women who were obese remain in midwife‐led care during pregnancy and childbirth, there was no increased risk of unfavourable birth outcomes for women who were obese and eligible for a midwife‐led birth when compared with women of normal weight. This indicates that when primary care midwives use a risk assessment tool throughout pregnancy and childbirth they are able to safely assign women who are obese to either midwife‐led or obstetrician‐led care.