bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome of a Novel Porcine Astrovirus
Authors: Shan Tongling , Wang Chunmei , Tong Wu , Zheng Hao , Hua Xiuguo , Yang Shen , Guo Yifei , Zhang Wen , Tong Guangzhi 
Published: November 2012

ABSTRACT
Astroviruses have been widely described in mammalian and avian species. Here, we report a complete genome sequence of a novel porcine astrovirus (PoAstV) isolated from a porcine fecal sample in China. The genome consists of 6,611 nucleotides, excluding the 3′ poly(A) tail, and has two open reading frames (ORFs). ORF1 maps between nucleotide positions 19 and 4211 and encodes a 1,396-amino-acid (aa) polyprotein precursor consisting of nonstructural protein and putative RNA-dependent RNA polymerase, and ORF2 maps between nucleotide positions 4202 and 6531 and encodes a 775-aa polyprotein which is a capsid precursor protein. The genome sequence of the virus was distinct enough from those of the known PoAstVs to be considered a novel sequence. Phylogenetic analysis based on the predicted amino acid sequence of the complete capsid region showed that this strain may be a novel porcine astrovirus.
Complete Genome of a Porcine Calicivirus Strain in Anhui Province, China, Is Significantly Shorter than That of the Other Chinese Strain
Authors: Fan Kezhang , Wang Rong 
Published: November 2012

ABSTRACT

Caliciviruses that cause diarrhea have been reported in both industrial and developing countries, including China, in recent years. Here, we report the complete genome of a porcine calicivirus strain, Ah-1, which is prevalent in swine groups in Anhui Province. This viral genome is 7,342 nucleotides (nt) long, excluding the poly(A) of the 3′ end, which is 202 nt shorter in the 3′ untranslated region (UTR) than that of the other Chinese porcine calicivirus strain (Ch-sw-sav1; GenBank accession number
FJ387164
), previously isolated in the Shanghai area, China, though they shared 98.8% sequence identity over the whole genome excluding the 202-nt-shorter region.
Complete Genome Sequence of IME11, a New N4-Like Bacteriophage
Authors: Fan Huahao , Fan Hang , An Xiaoping , Huang Yong , Zhang Zhiyi , Mi Zhiqiang , Tong Yigang 
Published: November 2012

ABSTRACT

N4-like bacteriophages are a class of virulent
Podoviridae
phages for which few genome sequences are present in GenBank. IME11, a novel lytic
Escherichia
bacteriophage with a wide host range, was isolated, and the whole genome was sequenced. It has a circular double-stranded DNA genome of 72,570 bp. Genomic analysis showed that it resembles another
Escherichia
phage, vB_EcoP_G7C. Here we announce its complete genome and major findings from its annotation.
Complete Genome Sequence of Recombinant Porcine Circovirus Type 2 Strain SD-3
Authors: Li Jun , Xu Shaojian , Yuan Xiaoyuan , Wang Guisheng , Shi Jianli , Wu Jiaqiang , Cong Xiaoyan , Sun Wenbo , Du Yijun , Wang Jinbao 
Published: November 2012

ABSTRACT
We report here the genome sequence of a recombinant porcine circovirus type 2 strain SD-3, isolated from a commercial swine farm with an outbreak of postweaning multisystemic wasting syndrome (PMWS) in pigs in Shandong Province of China. The complete circular genome of this isolate is 1,767 nucleotides in length. This recombinant isolate has the ORF1 regions from PCV2a viruses and ORF2 regions from PCV2b. The findings will help us to understand the molecular evolution of porcine circovirus type 2 and the relationship between porcine circovirus type 2 and disease.
Complete Genome Sequence of a Novel Natural Recombinant H5N5 Influenza Virus from Ducks in Central China
Authors: Zou Wei , Guo Xuebo , Li Shuyun , Yang Ying , Jin Meilin 
Published: November 2012

ABSTRACT
We reported the complete genome sequence of an H5N5 avian influenza virus (AIV) that was first isolated from duck in central China in 2010. Genomic sequence and phylogenetic analyses showed that this virus was a recombinant between H5N1 AIV circulated in southeastern Asia and an N5 subtype influenza virus. These data are beneficial for investigating the epidemiology and ecology of AIVs in central China.
Repetition Suppression in Auditory–Motor Regions to Pitch and Temporal Structure in Music
Authors: Brown Rachel M. , Chen Joyce L. , Hollinger Avrum , Penhune Virginia B. , Palmer Caroline , Zatorre Robert J. 
Published: November 2012

Abstract
Music performance requires control of two sequential structures: the ordering of pitches and the temporal intervals between successive pitches. Whether pitch and temporal structures are processed as separate or integrated features remains unclear. A repetition suppression paradigm compared neural and behavioral correlates of mapping pitch sequences and temporal sequences to motor movements in music performance. Fourteen pianists listened to and performed novel melodies on an MR-compatible piano keyboard during fMRI scanning. The pitch or temporal patterns in the melodies either changed or repeated (remained the same) across consecutive trials. We expected decreased neural response to the patterns (pitch or temporal) that repeated across trials relative to patterns that changed. Pitch and temporal accuracy were high, and pitch accuracy improved when either pitch or temporal sequences repeated over trials. Repetition of either pitch or temporal sequences was associated with linear BOLD decrease in frontal–parietal brain regions including dorsal and ventral premotor cortex, pre-SMA, and superior parietal cortex. Pitch sequence repetition (in contrast to temporal sequence repetition) was associated with linear BOLD decrease in the intraparietal sulcus (IPS) while pianists listened to melodies they were about to perform. Decreased BOLD response in IPS also predicted increase in pitch accuracy only when pitch sequences repeated. Thus, behavioral performance and neural response in sensorimotor mapping networks were sensitive to both pitch and temporal structure, suggesting that pitch and temporal structure are largely integrated in auditory–motor transformations. IPS may be involved in transforming pitch sequences into spatial coordinates for accurate piano performance.
Integration of Error Agency and Representation of Others' Pain in the Anterior Insula
Authors: Koban Leonie , Corradi-Dell'Acqua Corrado , Vuilleumier Patrik 
Published: November 2012

Abstract
A crucial feature of socially adaptive behavior is the ability to recognize when our actions harm other individuals. Previous research demonstrates that dorsal mediofrontal cortex (dMFC) and anterior insula (AI) are involved in both action monitoring and empathy for pain. Here, we tested whether these regions could integrate monitoring of error agency with the representation of others' pain. While undergoing event-related fMRI, participants played a visual task in turns with a friend placed outside the scanner, who would receive painful stimulation in half of the error trials. Brain activity was enhanced in dMFC and AI for painful compared with nonpainful errors. Left AI and dorsolateral pFC also exhibited a significant interaction with agency and increased responses when painful errors were caused by oneself. We conclude that AI is crucial for integrating inferences about others' feeling states with information about action agency and outcome, thus generating an affective signal that may guide subsequent adjustment.
The Influence of Lifelong Musicianship on Neurophysiological Measures of Concurrent Sound Segregation
Authors: Zendel Benjamin Rich , Alain Claude 
Published: November 2012

Abstract
The ability to separate concurrent sounds based on periodicity cues is critical for parsing complex auditory scenes. This ability is enhanced in young adult musicians and reduced in older adults. Here, we investigated the impact of lifelong musicianship on concurrent sound segregation and perception using scalp-recorded ERPs. Older and younger musicians and nonmusicians were presented with periodic harmonic complexes where the second harmonic could be tuned or mistuned by 1–16% of its original value. The likelihood of perceiving two simultaneous sounds increased with mistuning, and musicians, both older and younger, were more likely to detect and report hearing two sounds when the second harmonic was mistuned at or above 2%. The perception of a mistuned harmonic as a separate sound was paralleled by an object-related negativity that was larger and earlier in younger musicians compared with the other three groups. When listeners made a judgment about the harmonic stimuli, the perception of the mistuned harmonic as a separate sound was paralleled by a positive wave at about 400 msec poststimulus (P400), which was enhanced in both older and younger musicians. These findings suggest attention-dependent processing of a mistuned harmonic is enhanced in older musicians and provides further evidence that age-related decline in hearing abilities are mitigated by musical training.
Effects of Altitude on Maximum Raindrop Size and Fall Velocity as Limited by Collisional Breakup
Authors: Porcù Federico , D’Adderio Leo Pio , Prodi Franco , Caracciolo Clelia 
Published: November 2012

Abstract
Coalescence and breakup of drops are recognized as the main mechanisms determining raindrop size distributions on the ground. Full knowledge of these processes is hindered by the challenging difficulties both in the laboratory and tunnel experiments and during observations in the open air.
In real rain breakup is mainly due to collision between drops of different sizes (collisional breakup) and occurs when the collisional kinetic energy (CKE) is not absorbed by the colliding drops. In this work, the authors observe and measure the dependence on altitude of the occurrence of collisional breakup in real rainfall events, and then estimate the corresponding limit terminal velocities of drops and their size when breakup significantly takes place.
Data from Pludix, an X-band microwave disdrometer, were collected at three locations at different elevations: collisional breakup position in the power spectrum of Pludix increases toward higher frequencies with increasing altitude. Terminal velocities and sizes of the drops at breakup were determined consequently, with drop sizes resulting in 4.55 ± 0.35, 4.02 ± 0.32, and 3.16 ± 0.3 mm for altitudes of 15, 950, and 3300 m MSL, respectively. The authors computed the CKE of the colliding drops at the breakup, finding an upper limiting value of about 1.22 × 10−5 J for all three altitudes. This shows that most dominant collisional breakup signature occurs at similar CKE values for all three locations, corresponding to different drop diameters at different altitudes because of the effect of air density on the drop terminal velocity.
Association of IL12B polymorphisms with susceptibility to Graves ophthalmopathy in a Taiwan Chinese population
Authors: Liu Yu-Huei , Chen Ching-Chu , Liao Li-Ling , Wan Lei , Tsai Chang-Hai , Tsai Fuu-Jen 
Published: November 2012

Abstract

Background

Interleukin 12B (IL12B) gene polymorphisms have been linked to several inflammatory diseases, but their role in the development of Graves ophthalmopathy (GO) in Graves disease (GD) patients is unclear. The purpose of this study was to investigate the disease association of IL12B single nucleotide polymorphisms (SNPs).

Methods
A Taiwan Chinese population comprising 200 GD patients with GO and 271 GD patients without GO was genotyped using an allele-specific extension and ligation method. Hardy-Weinberg equilibrium was estimated using the chi-square test. Allele and genotype frequencies were compared between GD patients with and without GO using the chi-square test.

Results
The genotype and allele frequencies of examined SNPs did not differ between GD patients with and without GO. Although the genotype distribution remained nonsignificant in the sex-stratified analyses, the frequency of the T allele at SNP rs1003199 was significantly higher in patients with GO in the male cohort (P = 6.00 × 10-3). In addition, haplotypes of IL12B may be used to predict the risk of GO (P = 1.70 × 10-2); however, we could not prove the statistical significance of analysis after applying the Bonferroni correction.

Conclusions
Our results provide new information that the examined IL12B gene polymorphisms may be associated with susceptibility to GO in the Taiwan Chinese population in a sex-specific manner. This conclusion requires further investigation.
A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)
Authors: Baldwin Samantha , Revanna Roopashree , Thomson Susan , Pither-Joyce Meeghan , Wright Kathryn , Crowhurst Ross , Fiers Mark , Chen Leshi , Macknight Richard , McCallum John A 
Published: November 2012

AbstractBackgroundAlthough modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers.ResultsWe report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepaL.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line ‘CUDH2150’ and the genetically distant Indian landrace ‘Nasik Red’, using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of ‘Nasik Red’ reads onto ‘CUDH2150’ assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F2progeny from a very large F2family developed from the ‘Nasik Red’ x ‘CUDH2150’ inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis.ConclusionsThe generic tools developed for the Galaxy environment enable rapid development of sets of PCR assays targeting sequence variants identified from Illumina and 454 sequence data. They enable non-specialist users to validate and exploit large volumes of next-generation sequence data using basic equipment.
Regional evidence of modulation of cardiac adiponectin level in dilated cardiomyopathy: pilot study in a porcine animal model
Authors: Caselli Chiara , Lionetti Vincenzo , Cabiati Manuela , Prescimone Tommaso , Aquaro Giovanni D , Ottaviano Virginia , Bernini Fabio , Mattii Letizia , Del Ry Silvia , Giannessi Daniela 
Published: November 2012

Abstract

Background
The role of systemic and myocardial adiponectin (ADN) in dilated cardiomyopathy is still debated. We tested the regulation of both systemic and myocardial ADN and the relationship with AMP-activated protein kinase (AMPK) activity in a swine model of non-ischemic dilated cardiomyopathy.

Methods and results
Cardiac tissue was collected from seven instrumented adult male minipigs by pacing the left ventricular (LV) free wall (180 beats/min, 3 weeks), both from pacing (PS) and opposite sites (OS), and from five controls. Circulating ADN levels were inversely related to global and regional cardiac function. Myocardial ADN in PS was down-regulated compared to control (p < 0.05), yet ADN receptor 1 was significantly up-regulated (p < 0.05). No modifications of AMPK were observed in either region of the failing heart. Similarly, myocardial mRNA levels of PPARγ, PPARα, TNFα, iNOS were unchanged compared to controls.

Conclusions
Paradoxically, circulating ADN did not show any cardioprotective effect, confirming its role as negative prognostic biomarker of heart failure. Myocardial ADN was reduced in PS compared to control in an AMPK-independent fashion, suggesting the occurrence of novel mechanisms by which reduced cardiac ADN levels may regionally mediate the decline of cardiac function.
Expression of epithelial to mesenchymal transition-related markers in lymph node metastases as a surrogate for primary tumor metastatic potential in breast cancer
Authors: Markiewicz Aleksandra , Ahrends Tomasz , Wełnicka-Jaśkiewicz Marzena , Seroczyńska Barbara , Skokowski Jarosław , Jaśkiewicz Janusz , Szade Jolanta , Biernat Wojciech , Żaczek Anna J 
Published: November 2012

Abstract

Background
Breast cancers are phenotypically and genotypically heterogeneous tumors containing multiple cancer cell populations with various metastatic potential. Aggressive tumor cell subpopulations might more easily be captured in lymph nodes metastases (LNM) than in primary tumors (PT). We evaluated mRNA and protein levels of master EMT regulators: TWIST1, SNAIL and SLUG, protein levels of EMT-related markers: E-cadherin, vimentin, and expression of classical breast cancer receptors: HER2, ER and PgR in PT and corresponding LNM. The results were correlated with clinicopathological data and patients outcomes.

Methods
Formalin-fixed paraffin-embedded samples from PT and matched LNM from 42 stage II-III breast cancer patients were examined. Expression of TWIST1, SNAIL and SLUG was measured by reverse-transcription quantitative PCR. Protein expression was examined by immunohistochemistry on tissue microarrays. Kaplan-Meier curves for disease-free survival (DFS) and overall survival (OS) were compared using F-Cox test. Hazard ratios (HRs) with 95% confidence intervals (95% CI) were computed using Cox regression analysis.

Results
On average, mRNA expression of TWIST1, SNAIL and SLUG was significantly higher in LNM compared to PT (P < 0.00001 for all). Gene and protein levels of TWIST1, SNAIL and SLUG were highly discordant between PT and matched LNM. Increased mRNA expression of TWIST1 and SNAIL in LNM was associated with shorter OS (P = 0.04 and P = 0.02, respectively) and DFS (P = 0.02 and P = 0.01, respectively), whereas their expression in PT had no prognostic impact. Negative-to-positive switch of SNAIL protein correlated with decreased OS and DFS (HR = 4.6; 1.1-18.7; P = 0.03 and HR = 3.8; 1.0-48.7; P = 0.05, respectively).

Conclusions
LNM are enriched in cells with more aggressive phenotype, marked by elevated levels of EMT regulators. High expression of TWIST1 and SNAIL in LNM, as well as negative-to-positive conversion of SNAIL confer worse prognosis, confirming the correlation of EMT with aggressive disease behavior. Thus, molecular profiling of LNM may be used as surrogate marker for aggressiveness and metastatic potential of PT.
GPR30 regulates the EGFR-Akt cascade and predicts lower survival in patients with ovarian cancer
Authors: Fujiwara Satoe , Terai Yoshito , Kawaguchi Hiroshi , Takai Masaaki , Yoo Saha , Tanaka Yoshimichi , Tanaka Tomohito , Tsunetoh Satoshi , Sasaki Hiroshi , Kanemura Masanori , Tanabe Akiko , Yamashita Yoshiki , Ohmichi Masahide 
Published: November 2012

Abstract

Objectives
G protein-coupled receptor 30 (GPR30) is a 7-transmembrane estrogen receptor that functions alongside traditional estrogen receptors to regulate the cellular responses to estrogen. Recent studies suggest that GPR30 expression is associated with a poor prognosis, and that this is due to the GPR30-mediated transactivation of the EGFR in breast cancer. However, the biological contribution of GPR30 in ovarian cancer remains unclear. The purpose of this study was to elucidate the relationships between GPR30 expression and the clinicopathological findings, and to determine how the signaling cascade influences the prognosis of ovarian cancer.

Methods
The expression levels of GPR30, EGFR, ERα, and ERβ were analyzed using an immunohistochemical analysis, and their correlations with the clinicopathological features were examined in 10 patients with borderline malignant tumors and 152 patients with epithelial ovarian cancer. We also examined whether GPR30 signaling activates the EGFR-Akt pathway in an ovarian cancer cell line (Caov-3) by a Western blotting analysis.

Results
The GPR30 expression in ovarian carcinomas was significantly higher than that in borderline malignancies (p=0.0016), and was not associated with the expression of the EGFR, ERα, or ERβ. The expression of GPR30 in clear cell carcinomas was significantly lower than that in other subtypes of cancer (P <; 0.001). The expression of both GPR30 and EGFR was significantly associated with a poor prognosis in terms of the progression-free survival rate. The phosphorylation of the EGFR and Akt could be significantly enhanced by G1 (p <; 0.05) and inhibited by a Src family kinase inhibitor.

Conclusion
The expression of both GPR30 and EGFR is associated with a poor outcome in ovarian cancer, and GPR30 increases the phosphorylation of Akt via the EGFR in ovarian cancer cells. The regulation of GPR30 might be a potentially useful new therapeutic target in ovarian cancer.
Polymorphisms in peptidylarginine deiminase associate with rheumatoid arthritis in diverse Asian populations: evidence from MyEIRA study and meta-analysis
Authors: Too Chun Lai , Murad Shahnaz , Dhaliwal Jasbir Singh , Larsson Per , Jiang Xia , Ding Bo , Alfredsson Lars , Klareskog Lars , Padyukov Leonid 
Published: November 2012

Abstract
Introduction
The majority of our knowledge regarding disease-related mechanisms of uncontrolled citrullination and anti-citrullinated protein antibody development in rheumatoid arthritis (RA) was investigated in Caucasian populations. However, peptidylarginine deiminase (PADI) type 4 gene polymorphisms are associated with RA in East Asian populations and weak or no association was found in Caucasian populations. This study explores the association between the PADI4 polymorphisms and RA risk in a multiethnic population residing in South East Asia with the goal of elucidating generalizability of association in non-Caucasian populations.

Methods
A total of 320 SNPs from the PADI locus (including PADI1, PADI2, PADI3, PADI4 and PADI6 genes) were genotyped in 1,238 RA cases and 1,571 control subjects from the Malaysian Epidemiological Investigation of Rheumatoid Arthritis (MyEIRA) case-control study. Additionally, we conducted meta-analysis of our data together with the previously published studies of RA from East Asian populations.

Results
The overall odds ratio (ORoverall) for the PADI4 (rs2240340) allelic model was 1.11 (95% confidence interval (CI) = 1.00 to 1.23, P = 0.04) and for the genotypic model was 1.20 (95% CI = 1.01 to 1.44, P = 0.04). Haplotype analysis for four selected PADI4 SNPs revealed a significant association of one with susceptibility (P = 0.001) and of another with a protective effect (P = 0.02). The RA susceptibility was further confirmed when combined meta-analysis was performed using these data together with data from five previously published studies from Asia comprising 5,192 RA cases and 4,317 control subjects (ORoverall = 1.23 (95% CI = 1.16 to 1.31, Pheterogeneity = 0.08) and 1.31 (95% CI = 1.20 to 1.44, Pheterogeneity = 0.32) in allele and genotype-based models, respectively). In addition, we also detected a novel association of PADI2 genetic variant rs1005753 with RA (ORoverall = 0.87 (95% CI = 0.77 to 0.99)).

Conclusion
Our study demonstrates an association between PADI4 and RA in the multiethnic population from South East Asia and suggests additional association with a PADI2 gene. The study thus provides further support for the notion that polymorphisms in genes for enzymes responsible for citrullination contribute to RA development in multiple populations of Asian descent.