bluuebunny/crossref_metadata_2025_split huggingface dataset:
An on-farm investigation of beef suckler herds using an animal welfare index (AWI)
Authors: Mazurek Mickael , Prendiville Daniel J , Crowe Mark A , Veissier Isabelle , Earley Bernadette 
Published: January 2011

AbstractBackgroundBeef suckler farms (194 farms throughout 13 counties) were assessed once with housed cattle and once with cattle at grass using an animal welfare index (AWI). Twenty-three of the 194 farms were revisited a year later and re-evaluated using the AWI and the Tier-Gerechtheits-Index 35L/2000 (TGI35L/2000). Thirty-three indicators were collected in five categories: locomotion (5 indicators); social interactions (between animals) (7), flooring (5), environment (7) and Stockpersonship (9). Three indicators relating to the size of the farm were also collected.Improving animal welfare is an increasingly important aspect of livestock production systems predominantly due to increased consumer concern about the source of animal products. The objectives were (i) to evaluate animal welfare of Irish beef suckler herds using an animal welfare index (AWI), (ii) to examine correlations between parameters, how they influence the AWI and investigate the applicability of the parameters used, (iii) to investigate the impact of the activity of the farmer (full-time or part-time), the interest of the farmer and the number of animals on the AWI.ResultsThe mean AWI was 65% and ranged from 54% to 83%. The grazing period represented 16.5% of the total points of the AWI. Seventy percent of the farms were rated as "Very Good" or "Excellent". There was no difference (P > 0.05) in AWI between full-time and part-time farmers. Part-time farmers had greater (P = 0.01) "social interactions": calving (P = 0.03) and weaning (P < 0.001) scores. Full-time farmers had cleaner animals (P = 0.03) and their animals had less lameness (P = 0.01). The number of animals on-farm and the interest of the Stockperson were negatively and positively correlated (P = 0.001), respectively, with the AWI. A hierarchical classification was performed to examine how the indicators influenced the AWI.ConclusionThe AWI was easily applicable for an on-farm evaluation of welfare. The Stockpersonship was an important factor in determining the AWI (11% of the total variation) more specifically, the interest of the farmer. Part and full-time farming did not differ (P > 0.05) in AWI scores. This method could, with further development, be used in countries with both intensive and/or extensive production systems and would require substantially less resources than animal-based methods.
Impact of antigenic and genetic drift on the serologic surveillance of H5N2 avian influenza viruses
Authors: Escorcia Magdalena , Carrillo-Sánchez Karol , March-Mifsut Santiago , Chapa Joaquin , Lucio Eduardo , Nava Gerardo M 
Published: January 2011

Abstract

Background
Serologic surveillance of Avian Influenza (AI) viruses is carried out by the hemagglutination inhibition (HI) test using reference reagents. This method is recommended by animal health organizations as a standard test to detect antigenic differences (subtypes) between circulating influenza virus, vaccine- and/or reference- strains. However, significant discrepancies between reference antisera and field isolates have been observed during serosurveillance of influenza A viruses in pig and poultry farms. The objective of this study was to examine the effects of influenza virus genetic and antigenic drift on serologic testing using standard HI assays and reference reagents. Low pathogenic AI H5N2 viruses isolated in Mexico between 1994 and 2008 were used for phylogenetic analysis of AI hemagglutinin genes and for serologic testing using antisera produced with year-specific AI virus isolates.

Results
Phylogenetic analysis revealed significant divergence between early LPAI H5N2 viruses (1994 - 1998) and more recent virus field isolates (2002 - 2008). Results of the HI test were markedly influenced by the selection of the AI H5N2 virus (year of isolation) used as reference antigen for the assay. These analyses indicate that LPAI H5N2 viruses in Mexico are constantly undergoing genetic drift and that serosurveillance of AI viruses is significantly influenced by the antigen or antisera used for the HI test.

Conclusions
Reference viral antigens and/or antisera need to be replaced constantly during surveillance of AI viruses to keep pace with the AI antigenic drift. This strategy should improve the estimation of antigenic differences between circulating AI viruses and the selection of suitable vaccine strains.
3D-CT implanted interstitial brachytherapy for T2b nasopharyngeal carcinoma
Authors: Ren Yu-Feng , Gao Yuan-Hong , Cao Xin-Ping , Ye Wei-Jun , Teh Bin S 
Published: January 2011

Abstract

Background
To compare the results of external beam radiotherapy in combination with 3D- computed tomography (CT)-implanted interstitial high dose rate brachytherapy (ERT/3D-HDR-BT) versus conventional external beam radiotherapy (ERT) for the treatment of stage T2b nasopharyngeal carcinoma (NPC).

Methods
Forty NPC patients diagnosed with stage T2b NPC were treated with ERT/3D-HDR-BT under local anesthesia. These patients received a mean dose of 60 Gy, followed by 12-20 Gy administered by 3D-HDR-BT. Another 101 patients diagnosed with non-metastatic T2b NPC received a mean dose of 68 Gy by ERT alone during the same period.

Results
Patients treated with ERT/3D-HDR-BT versus ERT alone exhibited an improvement in their 5-y local failure-free survival rate (97.5% vs. 80.2%, P = 0.012) and disease-free survival rate (92.5% vs. 73.3%, P = 0.014). Using multivariate analysis, administration of 3D-HDR-BT was found to be favorable for local control (P = 0.046) and was statistically significant for disease-free survival (P = 0.021). The incidence rate of acute and chronic complications between the two groups was also compared.

Conclusions
It is possible that the treatment modality enhances local control due to improved conformal dose distributions and the escalated radiation dose applied.
Adjuvant therapy for T3N0 rectal cancer in the total mesorectal excision era- identification of the high risk patients
Authors: Zhu Ji , Xu Ye , Gu Weilie , Peng Junjie , Cai Gang , Cai Guoxiang , Sun Wenjie , Shen Weiqi , Cai Sanjun , Zhang Zhen 
Published: January 2011

Abstract

Background
Adjuvant therapy for T3N0 rectal cancer was controversial with respect to both radiation and the use of a combined regimen of chemotherapy. We evaluated both clinical features and biomarkers and sought to determine risk factors for those patients retrospectively.

Methods
A total of 122 patients with T3N0 rectal cancer were analyzed in this study from January 2000 to December 2005. Clinicopathologic and biomarkers were used to predict local recurrence (LR), disease-free survival (DFS), and overall survival (OS).

Results
The median follow-up interval was 45.4 months. Five-year LR, DFS, and OS rates were 10.4%, 68.3%, and 88.7%. Having a lower tumor location and showing low P21 and high CD44v6 expression were identified as risk factors for LR: patients with two or three of these risk factors had a higher 5-year LR rate (19.3%) than did patients with none or one of these risk factors (6.8%) (p = 0.05). A poorer DFS was related to low P21 nor high CD44v6 expression but not to tumor location: the 5-year DFS rates were 79.3% for those with neither, 65.9% for those with either one or the other, and 16.9% for those with both (p = 0.00).

Conclusions
The prognostic model including tumor location, P21 and CD44v6 expressions could help to distinguish these patients with high risk T3N0 patients and determine whether adjuvant therapy was beneficial.
Comparison of side effects of oxytetracycline and talc pleurodesis: an experimental study
Authors: Gözübüyük Alper , Özpolat Berkant , Çiçek Ali Fuat , Çaylak Hasan , Yücel Orhan , Kavaklı Kuthan , Gürkök Sedat , Genç Onur 
Published: January 2011

Abstract

Background
Chemical pleurodesis is widely recommended in the treatment of refractory pleural effusion or pulmonary air leak of different etiologies. Although several agents have been used, many questions have remained unanswered about their toxicity. Talc is the most commonly used agent for the treatment, with rare, serious complications reported. Oxytetracycline pleurodesis in clinical practice has been described in a few studies, but literature reveals no experimental studies using this agent. We performed a prospective, randomized, observer-blinded, controlled study to evaluate the changes in lung histology and systemic response to pleurodesis with oxytetracycline and talc in acute and subacute phases in a rat model.

Methods
Forty-two male albino Wistar rats were divided into three groups and 3 subgroups with 7 animals in each. Group 1 was given oxytetracycline, 35 mg/kg; Group 2 was given talc slurry, 60 mg/kg in 0.5 mL saline solution, and Group 3 was given only 0.5 mL saline intrapleurally. In subgroups "a" the nimls were sacrificed at the postoperative 72nd hour and, in subgroups "b", on the postoperative day 7. The surfaces were graded by microscopic examination.

Results
Oxytetracycline produced alveolar collapse, hemorrhage, edema, inflammation at the postoperative 72nd hour and hemorrhage on the postoperative day 7, while talc produced significant edema, inflammation, proliferation, fibrosis at the postoperative 72nd hour and hemorrhage, edema, inflammation, proliferation, and fibrosis on the postoperative day 7 (p < 0,0042). Talc produced significant edema compared to oxytetracycline on the postoperative day 7. On contralateral side, oxytetracycline and talc produced significant hemorrhage on the postoperative day 7 (p < 0.0042).

Conclusions
Both agents were shown to produce pulmonary lesions. In acute phase, the pulmonary side effects of oxytetracycline were more pronounced, whereas the side effects of talc were prolonged to subacute phase. We propose that the occasional side effects in humans may be related to these changes as were observed in our rat model, and like talc, oxytetracycline must be used cautiously in patients with limited respiratory function.
Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data
Authors: Gu Fei , Hsu Hang-Kai , Hsu Pei-Yin , Wu Jiejun , Ma Yilin , Parvin Jeffrey , Huang Tim H-M , Jin Victor X 
Published: January 2011

Abstract

Background
Global profiling of in vivo protein-DNA interactions using ChIP-based technologies has evolved rapidly in recent years. Although many genome-wide studies have identified thousands of ERα binding sites and have revealed the associated transcription factor (TF) partners, such as AP1, FOXA1 and CEBP, little is known about ERα associated hierarchical transcriptional regulatory networks.

Results
In this study, we applied computational approaches to analyze three public available ChIP-based datasets: ChIP-seq, ChIP-PET and ChIP-chip, and to investigate the hierarchical regulatory network for ERα and ERα partner TFs regulation in estrogen-dependent breast cancer MCF7 cells. 16 common TFs and two common new TF partners (RORA and PITX2) were found among ChIP-seq, ChIP-chip and ChIP-PET datasets. The regulatory networks were constructed by scanning the ChIP-peak region with TF specific position weight matrix (PWM). A permutation test was performed to test the reliability of each connection of the network. We then used DREM software to perform gene ontology function analysis on the common genes. We found that FOS, PITX2, RORA and FOXA1 were involved in the up-regulated genes.
We also conducted the ERα and Pol-II ChIP-seq experiments in tamoxifen resistance MCF7 cells (denoted as MCF7-T in this study) and compared the difference between MCF7 and MCF7-T cells. The result showed very little overlap between these two cells in terms of targeted genes (21.2% of common genes) and targeted TFs (25% of common TFs). The significant dissimilarity may indicate totally different transcriptional regulatory mechanisms between these two cancer cells.

Conclusions
Our study uncovers new estrogen-mediated regulatory networks by mining three ChIP-based data in MCF7 cells and ChIP-seq data in MCF7-T cells. We compared the different ChIP-based technologies as well as different breast cancer cells. Our computational analytical approach may guide biologists to further study the underlying mechanisms in breast cancer cells or other human diseases.
SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells
Authors: Xu Huilei , Lemischka Ihor R , Ma'ayan Avi 
Published: January 2011

Abstract

Background
Mouse embryonic stem cells (mESCs) are derived from the inner cell mass of a developing blastocyst and can be cultured indefinitely in-vitro. Their distinct features are their ability to self-renew and to differentiate to all adult cell types. Genes that maintain mESCs self-renewal and pluripotency identity are of interest to stem cell biologists. Although significant steps have been made toward the identification and characterization of such genes, the list is still incomplete and controversial. For example, the overlap among candidate self-renewal and pluripotency genes across different RNAi screens is surprisingly small. Meanwhile, machine learning approaches have been used to analyze multi-dimensional experimental data and integrate results from many studies, yet they have not been applied to specifically tackle the task of predicting and classifying self-renewal and pluripotency gene membership.

Results
For this study we developed a classifier, a supervised machine learning framework for predicting self-renewal and pluripotency mESCs stemness membership genes (MSMG) using support vector machines (SVM). The data used to train the classifier was derived from mESCs-related studies using mRNA microarrays, measuring gene expression in various stages of early differentiation, as well as ChIP-seq studies applied to mESCs profiling genome-wide binding of key transcription factors, such as Nanog, Oct4, and Sox2, to the regulatory regions of other genes. Comparison to other classification methods using the leave-one-out cross-validation method was employed to evaluate the accuracy and generality of the classification. Finally, two sets of candidate genes from genome-wide RNA interference screens are used to test the generality and potential application of the classifier.

Conclusions
Our results reveal that an SVM approach can be useful for prioritizing genes for functional validation experiments and complement the analyses of high-throughput profiling experimental data in stem cell research.
Targeted protein depletion in Saccharomyces cerevisiae by activation of a bidirectional degron
Authors: Jungbluth Marc , Renicke Christian , Taxis Christof 
Published: January 2011

Abstract

Background
Tools for in vivo manipulation of protein abundance or activity are highly beneficial for life science research. Protein stability can be efficiently controlled by conditional degrons, which induce target protein degradation at restrictive conditions.

Results
We used the yeast Saccharomyces cerevisiae for development of a conditional, bidirectional degron to control protein stability, which can be fused to the target protein N-terminally, C-terminally or placed internally. Activation of the degron is achieved by cleavage with the tobacco etch virus (TEV) protease, resulting in quick proteolysis of the target protein. We found similar degradation rates of soluble substrates using destabilization by the N- or C-degron. C-terminal tagging of essential yeast proteins with the bidirectional degron resulted in deletion-like phenotypes at non-permissive conditions. Developmental process-specific mutants were created by N- or C-terminal tagging of essential proteins with the bidirectional degron in combination with sporulation-specific production of the TEV protease.

Conclusions
We developed a system to influence protein abundance and activity genetically, which can be used to create conditional mutants, to regulate the fate of single protein domains or to design artificial regulatory circuits. Thus, this method enhances the toolbox to manipulate proteins in systems biology approaches considerably.
Benign perimesencephalic hemorrhage occurring after previous aneurysmal subarachnoid hemorrhage: a case report
Authors: Singleton Richard H , Kostov Dean B , Kanaan Hilal A , Horowitz Michael B 
Published: January 2011

Abstract

Introduction
Both aneurysmal subarachnoid hemorrhage and benign perimesencephalic hemorrhage are well-described causes of spontaneous subarachnoid hemorrhage that arise as a result of different pathologic processes. To the best of the authors' knowledge, there have been no reports of both vascular pathologies occurring in the same individual.

Case presentation
A 51-year-old Caucasian woman with a history of aneurysmal subarachnoid hemorrhage presented five years after her initial treatment with ictal headache, meningismus, nausea and emesis similar to her previous bleeding event. Computed tomographic imaging revealed perimesencephalic bleeding remote from her previously coiled anterior communicating artery aneurysm. Both immediate and delayed diagnostic angiography revealed no residual filling of the previously coiled aneurysm and no other vascular anomalies, consistent with benign perimesencephalic hemorrhage. The patient had an uneventful hospital course and was discharged to home in good condition.

Conclusions
This report for the first time identifies benign perimesencephalic hemorrhage occurring in the setting of previous aneurysmal subarachnoid hemorrhage. The presence of a previously treated aneurysm can complicate the process of diagnosing benign perimesencephalic hemorrhage. Fortunately, in this case, the previously treated anterior communicating artery aneurysm was remote from the perimesencephalic hemorrhage and could be ruled out as a source. The patient's prior aneurysmal subarachnoid hemorrhage did not worsen the anticipated good outcome associated with benign perimesencephalic hemorrhage.
Cholesteatoma of the concha bullosa: a case report
Authors: Cukurova Ibrahim , Demirhan Erhan , Arslan Ilker B , Cumurcu Suheyla 
Published: January 2011

Abstract

Introduction
Cholesteatoma is a relatively common disease within the middle ear cavity, but rarely it manifests in the paranasal sinuses. There is, to the best of our knowledge, only one other published case of cholesteatoma inside the concha bullosa in the English language literature.

Case presentation
An 81-year-old Caucasian woman was admitted to our hospital complaining of nasal obstruction, headache and diplopia. After endoscopic and radiological evaluation a transnasal endoscopic approach was chosen. The diagnosis of cholesteatoma was established by histopathological evaluation of the mass inside the concha bullosa.

Conclusion
Although it is rarely seen, cholesteatoma should be considered in the differential diagnosis of slow-growing and destructive paranasal masses.
New cytogenetically visible copy number variant in region 8q21.2
Authors: Manvelyan Marina , Cremer Friedrich W , Lancé Jeannette , Kläs Rüdiger , Kelbova Christina , Ramel Christian , Reichenbach Herbert , Schmidt Catharina , Ewers Elisabeth , Kreskowski Katharina , Ziegler Monika , Kosyakova Nadezda , Liehr Thomas 
Published: January 2011

Abstract

Background
Cytogenetically visible unbalanced chromosomal abnormalities (UBCA), reported for >50 euchromatic regions of almost all human autosomes, are comprised of a few megabases of DNA, and carriers are in many cases clinically healthy. It may be speculated, that some of the UBCA may be similar or identical to copy number variants (CNV) of the human genome.

Results
Here we report on a yet unreported cytogenetically visible copy number variant (CNV) in the long arm of chromosome 8, region 8q21.2, detected in three unrelated clinically healthy carriers.

Conclusion
The first description of a cytogenetically visible CNV/UBCA in 8q21.2 shows that banding cytogenetics is far from being outdated. It is a cost efficient, up-to-date method for a single cell specific overview on the whole genome, still prepared to deliver unexpected findings.
Primate-specific evolution of noncoding element insertion into PLA2G4Cand human preterm birth
Authors: Plunkett Jevon , Doniger Scott , Morgan Thomas , Haataja Ritva , Hallman Mikko , Puttonen Hilkka , Menon Ramkumar , Kuczynski Edward , Norwitz Errol , Snegovskikh Victoria , Palotie Aarno , Peltonen Leena , Fellman Vineta , DeFranco Emily A , Chaudhari Bimal P , Oates John , Boutaud Olivier , McGregor Tracy L , McElroy Jude J , Teramo Kari , Borecki Ingrid , Fay Justin C , Muglia Louis J 
Published: January 2011

AbstractBackgroundThe onset of birth in humans, like other apes, differs from non-primate mammals in its endocrine physiology. We hypothesize that higher primate-specific gene evolution may lead to these differences and target genes involved in human preterm birth, an area of global health significance.MethodsWe performed a comparative genomics screen of highly conserved noncoding elements and identifiedPLA2G4C, a phospholipase A isoform involved in prostaglandin biosynthesis as human accelerated. To examine whether this gene demonstrating primate-specific evolution was associated with birth timing, we genotyped and analyzed 8 common single nucleotide polymorphisms (SNPs) inPLA2G4Cin US Hispanic (n = 73 preterm, 292 control), US White (n = 147 preterm, 157 control) and US Black (n = 79 preterm, 166 control) mothers.ResultsDetailed structural and phylogenic analysis ofPLA2G4Csuggested a short genomic element within the gene duplicated from a paralogous highly conserved element on chromosome 1 specifically in primates. SNPs rs8110925 and rs2307276 in US Hispanics and rs11564620 in US Whites were significant after correcting for multiple tests (p < 0.006). Additionally, rs11564620 (Thr360Pro) was associated with increased metabolite levels of the prostaglandin thromboxane in healthy individuals (p = 0.02), suggesting this variant may affectPLA2G4Cactivity.ConclusionsOur findings suggest that variation inPLA2G4Cmay influence preterm birth risk by increasing levels of prostaglandins, which are known to regulate labor.
Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis
Authors: Pendergrass Sarah A , Dudek Scott M , Crawford Dana C , Ritchie Marylyn D 
Published: January 2011

AbstractBackgroundInitial genome-wide association study (GWAS) discoveries are being further explored through the use of large cohorts across multiple and diverse populations involving meta-analyses within large consortia and networks. Many of the additional studies characterize less than 100 single nucleotide polymorphisms (SNPs), often include multiple and correlated phenotypic measurements, and can include data from multiple-sites, multiple-studies, as well as multiple race/ethnicities. New approaches for visualizing resultant data are necessary in order to fully interpret results and obtain a broad view of the trends between DNA variation and phenotypes, as well as provide information on specific SNP and phenotype relationships.ResultsThe Synthesis-View software tool was designed to visually synthesize the results of the aforementioned types of studies. Presented herein are multiple examples of the ways Synthesis-View can be used to report results from association studies of DNA variation and phenotypes, including the visual integration of p-values or other metrics of significance, allele frequencies, sample sizes, effect size, and direction of effect.ConclusionsTo truly allow a user to visually integrate multiple pieces of information typical of a genetic association study, innovative views are needed to integrate multiple pieces of information. As a result, we have created "Synthesis-View" software for the visualization of genotype-phenotype association data in multiple cohorts. Synthesis-View is freely available for non-commercial research institutions, for full details seehttps://chgr.mc.vanderbilt.edu/synthesisview.