bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal weight, gestational weight gain and preschool wheezing: the Generation R Study
Authors: Leermakers Elisabeth T.M. , Sonnenschein-van der Voort Agnes M.M. , Gaillard Romy , Hofman Albert , de Jongste Johan C. , Jaddoe Vincent W.V. , Duijts Liesbeth 
Published: March 2013

We studied the associations of maternal pre-pregnancy body mass index and gestational weight gain with risks of preschool wheezing in offspring and explored the role of growth, infectious and atopic mechanisms.This substudy of 4656 children was embedded in a population-based birth cohort. Information about maternal pre-pregnancy weight, gestational weight gain and wheezing at the ages of 1–4 years was obtained by either physical measurements or questionnaires.Among mothers with a history of asthma or atopy, maternal pre-pregnancy obesity was associated with an overall increased risk of preschool wheezing (odds ratio 1.47, 95% confidence interval 1.12–1.95). Also, each standard deviation increase of gestational weight gain was associated with an increased overall risk of preschool wheezing (1.09, 1.04–1.14), was independent of pre-pregnancy body mass index and was not different between mothers with and without a history of asthma or atopy. Child’s growth, respiratory tract infections or eczema did not alter the results.Mothers with pre-pregnancy obesity and a history of asthma or atopy, and mothers with higher gestational weight gain showed higher risks of wheezing in their offspring. These associations could not be explained by growth, infectious or atopic mechanisms. Further research is needed to identify underlying mechanisms and long-term consequences.
Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration
Authors: Lo Ying-Tsang , Wang Hsin-Wei , Pai Tun-Wen , Tzou Wen-Shoung , Hsu Hui-Huang , Chang Hao-Teng 
Published: March 2013

Abstract

Background
Protein-ligand interactions are key processes in triggering and controlling biological functions within cells. Prediction of protein binding regions on the protein surface assists in understanding the mechanisms and principles of molecular recognition. In silico geometrical shape analysis plays a primary step in analyzing the spatial characteristics of protein binding regions and facilitates applications of bioinformatics in drug discovery and design. Here, we describe the novel software, PLB-SAVE, which uses parallel processing technology and is ideally suited to extract the geometrical construct of solid angles from surface atoms. Representative clusters and corresponding anchors were identified from all surface elements and were assigned according to the ranking of their solid angles. In addition, cavity depth indicators were obtained by proportional transformation of solid angles and cavity volumes were calculated by scanning multiple directional vectors within each selected cavity. Both depth and volume characteristics were combined with various weighting coefficients to rank predicted potential binding regions.

Results
Two test datasets from LigASite, each containing 388 bound and unbound structures, were used to predict binding regions using PLB-SAVE and two well-known prediction systems, SiteHound and MetaPocket2.0 (MPK2). PLB-SAVE outperformed the other programs with accuracy rates of 94.3% for unbound proteins and 95.5% for bound proteins via a tenfold cross-validation process. Additionally, because the parallel processing architecture was designed to enhance the computational efficiency, we obtained an average of 160-fold increase in computational time.

Conclusions

In silico binding region prediction is considered the initial stage in structure-based drug design. To improve the efficacy of biological experiments for drug development, we developed PLB-SAVE, which uses only geometrical features of proteins and achieves a good overall performance for protein-ligand binding region prediction. Based on the same approach and rationale, this method can also be applied to predict carbohydrate-antibody interactions for further design and development of carbohydrate-based vaccines. PLB-SAVE is available at http://save.cs.ntou.edu.tw.
Bioinformatics analysis of the epitope regions for norovirus capsid protein
Authors: Chen Liping , Wu Di , Ji Lei , Wu Xiaofang , Xu Deshun , Cao Zhiwei , Han Jiankang 
Published: March 2013

Abstract

Background
Norovirus is the major cause of nonbacterial epidemic gastroenteritis, being highly prevalent in both developing and developed countries. Despite of the available monoclonal antibodies (MAbs) for different sub-genogroups, a comprehensive epitope analysis based on various bioinformatics technology is highly desired for future potential antibody development in clinical diagonosis and treatment.

Methods
A total of 18 full-length human norovirus capsid protein sequences were downloaded from GenBank. Protein modeling was performed with program Modeller 9.9. The modeled 3D structures of capsid protein of norovirus were submitted to the protein antigen spatial epitope prediction webserver (SEPPA) for predicting the possible spatial epitopes with the default threshold. The results were processed using the Biosoftware.

Results
Compared with GI, we found that the GII genogroup had four deletions and two special insertions in the VP1 region. The predicted conformational epitope regions mainly concentrated on N-terminal (1~96), Middle Part (298~305, 355~375) and C-terminal (560~570). We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup.

Conclusions
The predicted conformational epitope regions of norovirus VP1 mainly concentrated on N-terminal, Middle Part and C-terminal. We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup. The overlapping with experimental epitopes indicates the important role of latest computational technologies. With the fast development of computational immunology tools, the bioinformatics pipeline will be more and more critical to vaccine design.
RNAi silencing of c-Myc inhibits cell migration, invasion, and proliferation in HepG2 human hepatocellular carcinoma cell line: c-Myc silencing in hepatocellular carcinoma cell
Authors: Zhao Yan , Jian Wang , Gao Wei , Zheng Ya-Xin , Wang Yong-Kun , Zhou Zhu-Qing , Zhang Hui , Wang Cong-Jun 
Published: March 2013

Abstract

Background
Hepatocellular carcinoma (HCC) is the most common type of liver cancer. Although much is known about both the cellular changes that lead to HCC and the etiological agents responsible for the majority of HCC cases, the molecule pathogenesis of HCC is still not well understood. We aimed to determine the effect of c-Myc gene expression on the proliferative, invasive, and migrative capabilities of hepatocellular carcinoma HepG2 cells.

Methods
A plasmid- based polymerase III promoter system was used to deliver and express short interfering RNA targeting c-Myc to reduce its expression in HepG2 cells. Western blot analysis was used to measure the protein level of c-Myc in HepG2 cells. The effects of c-Myc silencing on the invasion, motility, and proliferation of HepG2 cells were assessed using a Transwell chamber cell migration assay system and a growth curve assay, respectively.

Results
The data showed that plasmids expressing siRNA against c-Myc significantly decreased its expression in HepG2 cells by up to 85%. Importantly, pSilencer-c-Myc transfected cells showed a significantly reduced potential in migration, invasion, and proliferation.

Conclusion
C-Myc plays an important role in the development of hepatocellular carcinoma. The data show that down-regulating the c-Myc protein level in HepG2 cells by RNAi could significantly inhibit migration, invasion and proliferation of HepG2 cells. Thus, c-Myc might be a potential therapeutic target for hepatocellular carcinoma.
Postprandial effects of calcium phosphate supplementation on plasma concentration-double-blind, placebo-controlled cross-over human study
Authors: Trautvetter Ulrike , Kiehntopf Michael , Jahreis Gerhard 
Published: March 2013

AbstractBackgroundThe aim of the present study was to examine the postprandial calcium and phosphate concentrations after supplementation with pentacalcium hydroxy-triphosphate (CaP).MethodsTen men participated in this double-blind, placebo-controlled, cross-over study. The participants were divided into two groups. One group consumed bread enriched with CaP (plus 1 g calcium/d) and the other group a placebo product for three weeks. After a two week wash-out, the intervention was switched between the groups for another three weeks. Blood samples were drawn at the beginning (single administration) and at the end (repeated administration) of the intervention periods at 0, 30, 60, 120, 180 and 240 min. Between 0 and 30 min, a test meal, with or without CaP was consumed. The plasma concentrations of calcium and phosphate were examined. One participant dropped out due to personal reasons.ResultsCaP supplementation resulted in a significantly higher plasma calcium concentration after 240 min compared to placebo. After repeated CaP administration, the AUC for the increment in plasma calcium concentration was significantly higher compared to placebo.After single and repeated CaP supplementation, plasma phosphate concentration significantly decreased after 30, 60, 120 and 180 min compared to 0 min. The placebo administration resulted in significant decreases after 30, 60 and 120 min compared to 0 min.ConclusionOur results show that CaP contributes to an adequate calcium supply, but without increasing the plasma concentration of phosphate.Trial registrationhttp://www.clinicaltrials.gov; NCT01296997
Complete resection of recurrent and initially unresectable dermatofibrosarcoma protuberans downsized by Imatinib
Authors: Wicherts Dennis A , van Coevorden Frits , Klomp Houke M , van Huizum Martine A , Kerst J Martijn , Haas Rick LM , van Boven Hester H , van der Hage JA 
Published: March 2013

Abstract
Curative surgical treatment of recurrent, locally advanced dermatofibrosarcoma protuberans is often limited owing to a close relation of the tumor with important anatomical structures. Targeted therapy with imatinib, a tyrosine kinase inhibitor, may cause significant reduction of tumor volume, thereby enabling radical surgery. This treatment strategy, therefore, offers a chance of cure for selected patients with advanced dermatofibrosarcoma protuberans. In addition, preoperative treatment with imatinib may decrease possible disfigurement related to radical surgery for large tumors.
Combining attention training with cognitive-behavior therapy in Internet-based self-help for social anxiety: study protocol for a randomized controlled trial
Authors: Boettcher Johanna , Andersson Gerhard , Carlbring Per 
Published: March 2013

Abstract

Background
Guided Internet-based cognitive-behavioral therapy (ICBT) has been found to be effective for social anxiety disorder (SAD) by several independent research groups. However, since the extent of clinically significant change demonstrated leaves room for improvement, new treatments should be developed and investigated. A novel treatment, which has generally been found to be effective, is cognitive bias modification (CBM). This study aims to evaluate the combination of CBM and ICBT. It is intended that two groups will be compared; one group randomized to receiving ICBT and CBM towards threat cues and one group receiving ICBT and control training. We hypothesize that the group receiving ICBT plus CBM will show superior treatment outcomes.

Methods/design
Participants with SAD (N = 128), will be recruited from the general population. A composite score combining the scores obtained from three social anxiety questionnaires will serve as the primary outcome measure. Secondary measures include self-reported depression and quality of life. All treatments and assessments will be conducted via the Internet and measurement points will be baseline, Week 2, post-treatment, and 4 months post-treatment.

Discussion
There is no direct evidence of the effects of combining CBM and ICBT in SAD. Adding attention-training sessions to ICBT protocols could increase the proportion of participants who improve and recover through Internet-based self-help.

Trial registration
ClinicalTrials.gov:NCT01570400
Should bioprostheses be considered the valve of choice for dialysis-dependent patients?
Authors: Zhibing Qiu , Xin Chen , Ming Xu , Lele Liu , YingShuo Jiang , LiMing Wang 
Published: March 2013

Abstract

Background
There is controversy regarding the choice of prosthetic valves in patients with cardiac valve disease and dialysis-dependent patients. This review assesses a 12-year experience and outcomes after valve replacement in patients on chronic preoperative renal dialysis, comparing survival and valve-related outcomes following valve replacement with bioprostheses versus mechanical prostheses in this population in china.

Methods
From January 1999 and October 2011, 73 consecutive dialysis patients underwent cardiac valve replacement. The patients were divided into two groups: (Group B) bioprosthesis valves were implanted in 38 (52.1%) patients and (Group M) mechanical valves were implanted in 35 (47.9%) patients. Outcome measures included perioperative data, hospital mortality, major postoperative complications, follow-up outcomes, valve related morbidity and late survival.

Results
There were no significant differences in terms of patient characteristics in the 2 groups. Thirty-three were isolated aortic valve replacements (45.2%); 28 were isolated mitral valve replacements (38.4%); 10 were combined aortic and mitral replacements (13.7%); 2 were combined tricuspid and mitral replacements (2.7%). The overall hospital mortality was 5.5% (n = 4) and was not different between Group B (5.3%) and Group M (5.7%). Low ejection fraction was the only independent predictors of hospital mortality. There was no significant difference between the groups in the overall rate of complications. The overall mean follow-up was 47 ± 23 months. According to the Kaplan-Meier analysis, late mortality, perivalvular leak and freedom from reoperation were similar in patients with mechanical and bioprosthesis valves. The bioprosthesis valve group had significantly higher freedom from thromboembelism-bleeding events (100% versus 77.6 ± 11.0%, p = 0.012), and valve-related morbidity (73.2 ± 10.1% versus 58.1 ± 10.9%, p = 0.035) in 5 years. Kaplan–Meier survival estimates at 1, 3, and 5 years were 0.971, 0.832, and 0.530 in group B, and 0.967, 0.848, and 0.568 in group M.

Conclusions
There is no significant difference in the perioperative morbidity and mortality, late survival of dialysis patients after cardiac valve replacement with bioprostheses versus mechanical valves. In spite of the limited sample size analyzed, its outcome and consistency to several previous reports supports a conclusion that bioprostheses rather than mechanical ones could be a favorable choice for valve replacement needs of renal failure patients.
Correlation analysis of the total IgY level in hen serum, egg yolk and offspring serum
Authors: Sun Hancong , Chen Sirui , Cai Xia , Xu Guiyun , Qu Lujiang 
Published: March 2013

Abstract
The correlation between IgY levels of the serum and the yolk has been well documented in wild and domestic birds. The levels of total yolk IgY can be an index of the general health status of birds and may contribute to breeding programs when fitness of the offspring is a concern. We measured the levels of total serum IgY and yolk IgY in three different breeds (White Leghorn, Silkie and Dongxiang blue-shell) using indirect ELISA, and found that there was a significantly positive correlation between the levels of total serum IgY and total yolk IgY in all three breeds (White Leghorn: r = 0.404, P < 0.001, n = 100; Silkie: r = 0.561, P < 0.001, n = 70; Dongxiang blue-shell: r = 0.619, P < 0.001, n = 30). We also measured the total serum IgY levels in the 3-day-old offspring hatched from the Silkie hens and results were significantly correlated for serum IgY levels (r = 0.535, P < 0.001, n = 70) and the yolk IgY levels (r = 0.481, P < 0.001, n = 70). The regression analysis showed simple linear regression between IgY levels in hen serum, yolk and offspring serum. Our results suggest that total IgY level could be used as an index for chicken fitness.
The phylogenetic status of typical Chinese native pigs: analyzed by Asian and European pig mitochondrial genome sequences
Authors: Yu Guanghui , Xiang Hai , Wang Jikun , Zhao Xingbo 
Published: March 2013

Abstract
China is one of the most diverse countries, which have developed 88 indigenous pig breeds. Several studies showed that pigs were independently domesticated in multiple regions of the world. The purpose of this study was to investigate the origin and evolution of Chinese pigs using complete mitochondrial genomic sequences (mtDNA) from Asian and European domestic pigs and wild boars. Thirty primer pairs were designed to determine the mtDNA sequences of Xiang pig, Large White, Lantang, Jinhua and Pietrain. The phylogenetic status of Chinese native pigs was investigated by comparing the mtDNA sequences of complete coding regions and D-loop regions respectively amongst Asian breeds, European breeds and wild boars. The analyzed results by two cluster methods contributed to the same conclusion that all pigs were classified into two major groups, European clade and Asian clade. It revealed that Chinese pigs were only recently diverged from each other and distinctly different from European pigs. Berkshire was clustered with Asian pigs and Chinese pigs were involved in the development of Berkshire breeding. The Malaysian wild boar had distant genetic relationship with European and Asian pigs. Jinhua and Lanyu pigs had more nucleotide diversity with Chinese pigs although they all belonged to the Asian major clade. Chinese domestic pigs were clustered with wild boars in Yangtze River region and South China.
Epidemiology and acquisition of extended-spectrum beta-lactamase-producing Enterobacteriaceae in a septic orthopedic ward
Authors: Agostinho Americo , Renzi Gesuele , Haustein Thomas , Jourdan Ghislaine , Bonfillon Chantal , Rougemont Mathieu , Hoffmeyer Pierre , Harbarth Stephan , Uçkay Ilker 
Published: March 2013

Abstract
Wards cohorting infected orthopaedic patients may be particularly prone to transmitting extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E). We analyze their epidemic pattern by performing molecular typing of ESBL-E isolated from patients and healthcare workers (HCW) from our septic ward. Between March 2010 and November 2011, 186 patients were admitted. Among 565 anal swabs, ESBL-E were detected in 204 samples from 45 patients, suggesting prolonged carriage in affected patients. Among 25 cases with identical ESBL-E species and positive epidemiological links, only 9 were really attributable to our service. We also screened 41 healthcare workers (HCW) on 49 occasions during the study period. Six samples (13%) were positive. None of the ESBL-E detected in HCW were related to any of the patient isolates. Among 60 environmental samples taken at the peak of the epidemic none revealed ESBL-E. We conclude that HCW also were anal carriers of ESBL-E, however the ESBL- strains from the HCW were not the same strains isolated from patients in the septic ward. Moreover, the epidemiological attribution of ESBL by simple vicinity, timing, and species identification might grossly overestimate transmission within a given unit.
An androgenic gland membrane-anchored gene associated with the crustacean insulin-like androgenic gland hormone
Authors: Rosen Ohad , Manor Rivka , Weil Simy , Aflalo Eliahu D. , Bakhrat Anna , Abdu Uri , Sagi Amir 
Published: March 2013

Summary
Crustacean male sexual differentiation is governed by the androgenic gland (AG) and specifically by the secreted insulin-like AG hormone (IAG), thus far identified in several decapod species including the Australian red claw crayfish Cherax quadricarinatus (termed Cq-IAG). While few insulin-like AG genes have been identified in crustaceans, other AG-specific genes have not been documented until now. In the present study we describe the recent identification of a non-IAG AG-specific transcript obtained from the C. quadricarinatus AG cDNA library. This transcript, termed C. quadricarinatus membrane-anchored AG-specific factor (Cq-MAG), was fully sequenced and found to encode a putative product of 189 amino acids including a signal anchoring peptide. Expression of a recombinant GFP fusion protein lacking the signal anchor encoding sequence dramatically affected recombinant protein localization pattern. While the expression of the deleterious fusion protein was observed throughout most of the cell, the native GFP::Cq-MAG fusion protein was observed mainly surrounding the periphery of the nucleus, demonstrating an ER-like localization pattern. Moreover, co-expressing the wild-type Cq-MAG (fused to GFP) and the Cq-IAG hormone revealed that these peptides indeed co-localize. This study is the first to report a protein specifically associated with the insulin-like androgenic gland hormone in addition to the finding of another AG-specific transcript in crustaceans. Previous knowledge suggests that insulin/insulin-like factor secretion involves tissue-specific transcripts and membrane anchored proteins. On this note, Cq-MAG's tissue specificity, anchoring properties, and intracellular co-localization with Cq-IAG suggest that it may play a role in the processing and secretion of this insulin-like androgenic gland hormone.
Asymmetry in the song of crickets: Preferences of females and proximate mechanism of discrimination
Authors: Hirtenlehner Stefan , Küng Saskia , Kainz Franz , Römer Heiner 
Published: March 2013

SummarySubtle random deviations from perfect symmetry in bilateral traits are suggested to signal reduced phenotypic and genetic quality of a sender, but only little is known about the related receiver mechanisms for discriminating symmetrical from asymmetrical traits. Here we investigate these mechanisms in behavioural and neurophysiological experiments in the Mediterranean field cricket, Gryllus bimaculatus. A downward frequency modulation at the end of each syllable in the calling song has been suggested to indicate morphological asymmetry in sound radiating structures between left and right forewings. Even under ideal laboratory conditions on a trackball system female crickets only discriminated between songs of symmetrical and asymmetrical males in two-choice experiments at carrier frequencies of 4.4 kHz and large modulation depth of 600 and 800 Hz. Under these conditions they preferred the pure tone calling songs over the modulated (asymmetrical) alternative, whereas no preference was observed at carrier frequencies of 4.9 and 5.2 kHz. These preferences correlate well with responses of a pair of identified auditory interneuron (AN1), known for its importance in female phonotaxis. The interneuron is tuned to an average frequency of 4.9 kHz, and the roll-off towards lower and higher frequencies determines the magnitude of responses to pure tone and frequency modulated calling songs. The difference in response magnitude between the two neurons appears to drive the decision of females towards the song alternatives. We discuss the relevance of song differences based on asymmetry in the morphology of song producing structures under natural conditions.