bluuebunny/crossref_metadata_2025_split huggingface dataset:
VarioML framework for comprehensive variation data representation and exchange
Authors: Byrne Myles , Fokkema Ivo FAC , Lancaster Owen , Adamusiak Tomasz , Ahonen-Bishopp Anni , Atlan David , Béroud Christophe , Cornell Michael , Dalgleish Raymond , Devereau Andrew , Patrinos George P , Swertz Morris A , Taschner Peter EM , Thorisson Gudmundur A , Vihinen Mauno , Brookes Anthony J , Muilu Juha 
Published: October 2012

Abstract

Background
Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement.

Results
The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components.

Conclusions
VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.
A genome-wide association study using international breeding-evaluation data identifies major loci affecting production traits and stature in the Brown Swiss cattle breed
Authors: Guo Jiazhong , Jorjani Hossein , Carlborg Örjan 
Published: October 2012

Abstract

Background
The genome-wide association study (GWAS) is a useful approach to identify genes affecting economically important traits in dairy cattle. Here, we report the results from a GWAS based on high-density SNP genotype data and estimated breeding values for nine production, fertility, body conformation, udder health and workability traits in the Brown Swiss cattle population that is part of the international genomic evaluation program.

Result
GWASs were performed using 50 k SNP chip data and deregressed estimated breeding values (DEBVs) for nine traits from between 2061 and 5043 bulls that were part of the international genomic evaluation program coordinated by Interbull Center. The nine traits were milk yield (MY), fat yield (FY), protein yield (PY), lactating cow’s ability to recycle after calving (CRC), angularity (ANG), body depth (BDE), stature (STA), milk somatic cell score (SCS) and milk speed (MSP). Analyses were performed using a linear mixed model correcting for population confounding. A total of 74 SNPs were detected to be genome-wide significantly associated with one or several of the nine analyzed traits. The strongest signal was identified on chromosome 25 for milk production traits, stature and body depth. Other signals were on chromosome 11 for angularity, chromosome 24 for somatic cell score, and chromosome 6 for milking speed. Some signals overlapped with earlier reported QTL for similar traits in other cattle populations and were located close to interesting candidate genes worthy of further investigations.

Conclusions
Our study shows that international genetic evaluation data is a useful resource for identifying genetic factors influencing complex traits in livestock. Several genome wide significant association signals could be identified in the Brown Swiss population, including a major signal on BTA25. Our findings report several associations and plausible candidate genes that deserve further exploration in other populations and molecular dissection to explore the potential economic impact and the genetic mechanisms underlying these production traits in cattle.
The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: the ancestral gene arrangement in Lepidoptera
Authors: Cao Yong-Qiang , Ma Chuan , Chen Ji-Yue , Yang Da-Rong 
Published: October 2012

AbstractBackgroundLepidoptera encompasses more than 160,000 described species that have been classified into 45–48 superfamilies. The previously determined Lepidoptera mitochondrial genomes (mitogenomes) are limited to six superfamilies of the lineage Ditrysia. Compared with the ancestral insect gene order, these mitogenomes all contain a tRNA rearrangement. To gain new insights into Lepidoptera mitogenome evolution, we sequenced the mitogenomes of two ghost moths that belong to the non-ditrysian lineage Hepialoidea and conducted a comparative mitogenomic analysis across Lepidoptera.ResultsThe mitogenomes ofThitarodes renzhiensisandT.yunnanensisare 16,173 bp and 15,816 bp long with an A + T content of 81.28 % and 82.34 %, respectively. Both mitogenomes include 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and the A + T-rich region. Different tandem repeats in the A + T-rich region mainly account for the size difference between the two mitogenomes. All the protein-coding genes start with typical mitochondrial initiation codons, except forcox1(CGA) andnad1(TTG) in both mitogenomes. The anticodon oftrnS(AGN)inT. renzhiensisandT. yunnanensisis UCU instead of the mostly used GCU in other sequenced Lepidoptera mitogenomes. The 1,584-bp sequence fromrrnStonad2was also determined for an unspecified ghost moth (Thitarodessp.), which has no repetitive sequence in the A + T-rich region. All threeThitarodesspecies possess the ancestral gene order withtrnI-trnQ-trnMlocated between the A + T-rich region andnad2, which is different from the gene ordertrnM-trnI-trnQin all previously sequenced Lepidoptera species. The formerly identified conserved elements of Lepidoptera mitogenomes (i.e. the motif ‘ATAGA’ and poly-T stretch in the A + T-rich region and the long intergenic spacer upstream ofnad2) are absent in theThitarodesmitogenomes.ConclusionThe mitogenomes ofT. renzhiensisandT. yunnanensisexhibit unusual features compared with the previously determined Lepidoptera mitogenomes. Their ancestral gene order indicates that the tRNA rearrangement event(s) likely occurred after Hepialoidea diverged from other lepidopteran lineages. Characterization of the two ghost moth mitogenomes has enriched our knowledge of Lepidoptera mitogenomes and contributed to our understanding of the mechanisms underlying mitogenome evolution, especially gene rearrangements.
A genome-wide signature of glucocorticoid receptor binding in neuronal PC12 cells
Authors: Polman J Annelies E , Welten Jennifer E , Bosch Danny S , de Jonge Robert T , Balog Judit , van der Maarel Silvère M , de Kloet E Ronald , Datson Nicole A 
Published: October 2012

AbstractBackgroundGlucocorticoids, secreted by the adrenals in response to stress, profoundly affect structure and plasticity of neurons. Glucocorticoid action in neurons is mediated by glucocorticoid receptors (GR) that operate as transcription factors in the regulation of gene expression and either bind directly to genomic glucocorticoid response elements (GREs) or indirectly to the genome via interactions with bound transcription factors. These two modes of action, respectively called transactivation and transrepression, result in the regulation of a wide variety of genes important for neuronal function. The objective of the present study was to identify genome-wide glucocorticoid receptor binding sites in neuronal PC12 cells using Chromatin ImmunoPrecipitation combined with next generation sequencing (ChIP-Seq).ResultsIn total we identified 1183 genomic binding sites of GR, the majority of which were novel and not identified in other ChIP-Seq studies on GR binding. More than half (58%) of the binding sites contained a GRE. The remaining 42% of the GBS did not harbour a GRE and therefore likely bind GR via an intermediate transcription factor tethering GR to the DNA. While the GRE-containing binding sites were more often located nearby genes involved in general cell functions and processes such as apoptosis, cell motion, protein dimerization activity and vasculature development, the binding sites without a GRE were located nearby genes with a clear role in neuronal processes such as neuron projection morphogenesis, neuron projection regeneration, synaptic transmission and catecholamine biosynthetic process. A closer look at the sequence of the GR binding sites revealed the presence of several motifs for transcription factors that are highly divergent from those previously linked to GR-signaling, including Gabpa, Prrx2, Zfp281, Gata1 and Zbtb3. These transcription factors may represent novel crosstalk partners of GR in a neuronal context.ConclusionsHere we present the first genome-wide inventory of GR-binding sites in a neuronal context. These results provide an exciting first global view into neuronal GR targets and the neuron-specific modes of GR action and potentially contributes to our understanding of glucocorticoid action in the brain.
In Vitro efficacy of antimicrobial extracts against the atypical ruminant pathogen Mycoplasma mycoides subsp. capri
Authors: Arjoon Amanda V , Saylor Charlotte V , May Meghan 
Published: October 2012

Abstract

Background
Mycoplasmosis is a common infection in human and veterinary medicine, and is associated with chronic inflammation and high morbidity. Mycoplasma species are often intrinsically resistant to many conventional antimicrobial therapies, and the resistance patterns of pathogenic mycoplasmas to commonly used medicinal (antimicrobial) plant extracts are currently unknown.

Methods
Aqueous extracts, ethanol extracts, or oils of the targeted plant species and colloidal silver were prepared or purchased. Activity against the wall-less bacterial pathogen Mycoplasma mycoides subsp. capri was determined and compared to activities measured against Escherichia coli and Bacillus subtilis. Antimicrobial susceptibility testing was performed by broth microdilution assays. The lethal or inhibitory nature of each extract was determined by subculture into neat growth medium.

Results
Growth of M. mycoides capri, E. coli, and B. subtilis was inhibited by elderberry extract, oregano oil, ethanol extract of oregano leaves, and ethanol extract of goldenseal root. No inhibition was seen with aqueous extract of astragalus or calendula oil. Growth of M. mycoides capri and B. subtilis was inhibited by ethanol extract of astragalus, whereas growth of E. coli was not. Similarly, M. mycoides capri and E. coli were inhibited by aqueous extract of thyme, but B. subtilis was unaffected. Only B. subtilis was inhibited by colloidal silver. Measured MICs ranged from 0.0003 mg/mL to 3.8 mg/mL. Bacteriostatic and bactericidal effects differed by species and extract.

Conclusions
The atypical pathogen M. mycoides capri was sensitive to extracts from many medicinal plants commonly used as antimicrobials in states of preparation and concentrations currently available for purchase in the United States and Europe. Variation in bacteriostatic and bactericidal activities between species and extracts indicates that multiple effecter compounds are present in these plant species.
Anti-inflammatory effect of ethanolic extract from Myagropsis myagroides on murine macrophages and mouse ear edema
Authors: Joung Eun-Ji , Lee Min-Sup , Choi Ji-Woong , Kim Jong-Soon , Shin Taisun , Jung Bok-Mi , Yoon Na Young , Lim Chi-Won , Kim Jae-Il , Kim Hyeung-Rak 
Published: October 2012

AbstractBackgroundThis study aims to investigate anti-inflammatory effect of ethanolic extract ofMyagropsis myagroides(EMM) in the lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages and the phorbol 12-myristate 13-acetate (PMA)-induced ear edema in mice, and to clarify its underlying molecular mechanisms.MethodsThe levels of nitric oxide (NO), prostaglandin E2(PGE2), and pro-inflammatory cytokines were measured by Griess assay and enzyme linked immunosorbent assay. The expressions of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), mitogen-activated protein kinases (MAPKs), and Akt were measured using Western blotting. Nuclear translocation and transcriptional activation of nuclear factor-κB (NF-κB) were determined by immunocytochemistry and reporter gene assay, respectively. PMA-induced mouse ear edema was used as the animal model of inflammation. Anti-inflammatory compounds in EMM were isolated using high-performance liquid chromatography and identified by nuclear magnetic resonance.ResultsEMM significantly inhibited the production of NO, PGE2, and pro-inflammatory cytokines in a dose-dependent manner and suppressed the expression of iNOS and COX-2 in LPS-stimulated RAW 264.7 cells. EMM strongly suppressed nuclear translocation of NF-κB by preventing degradation of inhibitor of κB-α as well as by inhibiting phosphorylation of Akt and MAPKs. EMM reduced ear edema in PMA-induced mice. One of the anti-inflammatory compounds in EMM was identified as 6,6’-bieckol.ConclusionsThese results suggest that the anti-inflammatory properties of EMM are associated with the down-regulation of iNOS, COX-2, and pro-inflammatory cytokines through the inhibition of NF-κB pathway in LPS-stimulated macrophages.
Isolated Crohn’s disease of the esophagus with esophago-mediastinal fistula formation
Authors: Wang Wuping , Ni Yunfeng , Ke Changkang , Cheng Qingshu , Lu Qiang , Li Xiaofei 
Published: October 2012

Abstract
Isolated Crohn’s disease of the esophagus is rare, and accurate diagnosis and treatment in its early course are difficult. Most cases are often found very late, when severe strictures or other complications have occurred. We report the case of a male 60-year-old patient with complaints of progressive dysphagia for more than two months and the sudden appearance of heartburn for seven consecutive days. Clinical examination revealed severe esophageal stricture with a suspected fistula and mediastinitis. The patient received a successful esophagectomy. The resected specimen and pathological results confirmed a deep linear ulcer, chronic and noncaseating granulomatous inflammation, as well as a circular stricture of the esophagus with fistula into the mediastinum due to isolated esophageal Crohn’s disease.
Comparison and analysis of point target reference spectrum of FMCW synthetic aperture imaging sensor
Authors: Liu Yue , Deng Yun-Kai , Wang Robert , Jia Xiao-Xue , Han Xiao-Dong 
Published: October 2012

Abstract
Frequency-modulated continuous-wave (FMCW) synthetic aperture imaging sensor (SAIS) combines FMCW technology and SAIS techniques which makes a lightweight, high-resolution, and cost-effective imaging sensor. FMCW SAIS systems are going to play an important role in airborne and spaceborne earth observation fields. However, the stop-and-go approximation used in conventional pulsed SAIR (e.g., synthetic aperture radar—SAR) is no longer valid due to the long signal duration time or low wave propagation speed. To exploit the potentialities of an accurate signal model under FMCW SAIS circumstances, this article presents the relationship and remarkable differences between the analytical FMCW SAIS point target reference spectrum model and the traditional ones in pulsed SAR and Synthetic Aperture Acoustic imaging system, and validates the significance of the additional range–azimuth coupling term and range walk term in FMCW SAIS spectrum introduced by the variation of slant range during the long pulse durations, and highlight the limitations of other two spectra. Finally, the simulation experiments are carried out to compare the performance of the aforementioned spectrum formulations.
Host predilection and transmissibility of vesicular stomatitis New Jersey virus strains in domestic cattle (Bos taurus) and swine (Sus scrofa)
Authors: Smith Paul F , Howerth Elizabeth W , Carter Deborah , Gray Elmer W , Noblet Raymond , Berghaus Roy D , Stallknecht David E , Mead Daniel G 
Published: October 2012

AbstractBackgroundEpidemiologic data collected during epidemics in the western United States combined with limited experimental studies involving swine and cattle suggest that host predilection of epidemic vesicular stomatitis New Jersey virus (VSNJV) strains results in variations in clinical response, extent and duration of virus shedding and transmissibility following infection in different hosts. Laboratory challenge of livestock with heterologous VSNJV strains to investigate potential viral predilections for these hosts has not been thoroughly investigated. In separate trials, homologous VSNJV strains (NJ82COB and NJ82AZB), and heterologous strains (NJ06WYE and NJOSF [Ossabaw Island, sand fly]) were inoculated into cattle via infected black fly bite. NJ82AZB and NJ06WYE were similarly inoculated into swine.ResultsClinical scores among viruses infecting cattle were significantly different and indicated that infection with a homologous virus resulted in more severe clinical presentation and greater extent and duration of viral shedding. No differences in clinical severity or extent and duration of viral shedding were detected in swine.ConclusionsDifferences in clinical presentation and extent and duration of viral shedding may have direct impacts on viral spread during epidemics. Viral transmission via animal-to-animal contact and insect vectored transmission are likely to occur at higher rates when affected animals are presenting severe clinical signs and shedding high concentrations of virus. More virulent viral strains resulting in more severe disease in livestock hosts are expected to spread more rapidly and greater distances during epidemics than those causing mild or inapparent signs.
A WUSCHEL-like homeobox gene, OsWOX3B responses to NUDA/GL-1 locus in rice
Authors: Zhang Honglei , Wu Kun , Wang Yufeng , Peng Yu , Hu Fengyi , Wen Lu , Han Bin , Qian Qian , Teng Sheng 
Published: October 2012

AbstractBackgroundMost of the rice varieties are pubescent. However, the presence of trichomes is an undesirable characteristic in rice production because trichomes can cause atmospheric pollution. The use of glabrous rice varieties represents a solution to this problem. Yunnan Nuda Rice, a glabrous cultivar that constitutes approximately 20% of rice germplasms in Yunnan can provide important recourse for breeding of glabrous rice varieties.ResultsThe “Nuda” phenotype in Yunnan Nuda Rice was found to be controlled by a single recessive allelic gene within the well-characterizedGL-1locus. A high-resolution genetic and physical map was constructed using 1,192 Nuda individuals from the F2population that was delivered from the cross between the Yunnan Nuda variety HMK and the pubescent TN1 variety. TheNUDA/GL-1gene was mapped to a 28.5 kb region containing six annotated genes based on the Nipponbare genomic sequence. By comparing the sequences and expression patterns of different pubescent and glabrous varieties,LOC_Os05g02730, aWUSCHEL-like homeobox gene (OsWOX3B) was identified as the candidate gene. This hypothesis was confirmed by RNA interference (RNAi) and transgenic complementation. Trichome deficiency in RNAi lines was associated with increased efficiency of grain packaging but did not affect the main agronomic traits.ConclusionNUDA/GL-1locus encodesOsWOX3Bgene.
Expression of human papillomavirus 6b L1 protein in silkworm larvae and enhanced green fluorescent protein displaying on its virus-like particles
Authors: Palaniyandi Muthukutty , Kato Tatsuya , Park Enoch Y 
Published: October 2012

Abstract
Human papillomavirus (HPV) 6b L1 capsid protein was expressed using the Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid expression system in silkworm larvae. Two constructs, full-length L1 (500 a.a) and C-terminal-deleted short L1 (479 a.a), and three PCR-manipulated antigenic loops at amino acids 55–56, 174–175, and 348–349 regions were incorporated with whole enhanced green fluorescent protein (EGFP). Expressed in full, short L1 proteins and variants were purified in heparin affinity column chromatography and confirmed by SDS-PAGE and western blot. The presence of self-assembled virus-like particles (VLPs) and EGFP incorporation on the surface of VLPs were confirmed by the observation of transmission electron and immunoelectron microscopies, respectively. HPV 6b L1 major capsid protein was successfully expressed in silkworm, and effective manipulation on the antigenic regions showed the path to versatile vaccine development based on HPV L1-VLPs.
An analytic algorithm of Lane-Emden-type equations arising in astrophysics - a hybrid approach
Authors: Baranwal Vipul K , Pandey Ram K , Tripathi Manoj P , Singh Om P 
Published: October 2012

Abstract
A new analytic algorithm for Lane-Emden equations is proposed in this paper. The proposed algorithm is obtained by using a new iterative method. The new iterative method is a hybrid of variational iteration method and the Adomian decomposition method and further refined by introducing a new correction functional. This new correction functional is obtained from the standard correction functional of variational iteration method by introducing an auxiliary parameter γ in it. Further, a sequence

G
n

x

, with suitably chosen support, is also introduced in the new correction functional. The algorithm is easy to implement and gives fairly accurate solutions. Several test examples are given establishing the accuracy and the efficiency of the algorithm.