bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel Respiratory Health Score (RHS) supports a role of acute lung damage and pig breed in the course of an Actinobacillus pleuropneumoniaeinfection
Authors: Hoeltig Doris , Hennig-Pauka Isabel , Thies Kerstin , Rehm Thomas , Beyerbach Martin , Strutzberg-Minder Katrin , Gerlach Gerald F , Waldmann Karl-Heinz ,   FUGATO-consortium IRAS
Published: April 2009

AbstractBackgroundBacterial lung infections are a major cause of economic losses in the pig industry; they are responsible for approximately 50% of the antibiotics used in pigs and, therefore, also present an increasing concern to consumer protection agencies. In response to this changing market we investigated the feasibility of an old approach aimed at the breeding selection of more resistant pigs. As a first step in this direction we applied a new respiratory health score system to study the susceptibility of four different pig breeding lines (German Landrace, Piétrain, Hampshire, Large White) towards the respiratory tract pathogenActinobacillus(A.)pleuropneumoniae.ResultsA controlled experimental aerosol infection with anA. pleuropneumoniaeserotype 7 isolate was performed using 106 weaning pigs of defined breeding lines from the breeds German Landrace, Piétrain, Hamphire, and Large White. Pigs were clinically assessed on days 4 and 20 post infection following a novel scoring system, the Respiratory Health Score (RHS), which combines clinical, sonographic and radiographic examination results. The ranking on day 4 was significantly correlated with the ranking based on the pathomorphological Lung Lesion Score (LLS; Spearman Rank Correlation Coefficient of 0.86 [p < 0.0001]). Based on their RHS pigs were assigned to the different quartiles independent of the breeding line. The RHS-based rankings of pigs on day 4 and on day 20 were highly correlated (Spearman Rank Correlation Coefficient of 0.82 [p < 0.0001]) independent of the breeding line. Pigs of the Hampshire line were predominantly found in the lowest scoring quartile (47.6%) and absent in the highest scoring quartile. In contrast, pigs of the German Landrace and Piétrain breeding lines were predominantly found in the highest scoring quartile (32.3% and 35.7%, respectively).ConclusionThese results demonstrate that the RHS obtained from live pigs shows a highly significant correlation to the lung lesion score considered as a "gold standard". The correlation of the ranking at days 4 and 20 post infection implies that the course of disease is highly dependent on the acute lung damage. The different severity of signs among the tested pig breeding lines clearly suggests a genetic difference in the susceptibility of pigs toA. pleuropneumoniaeinfection.
Surgical technique and clinical results for scapular allograft reconstruction following resection of scapular tumors
Authors: Zhang Kaiwei , Duan Hong , Xiang Zhou , Tu Chongqi 
Published: April 2009

AbstractBackgroundProgress in developing effective surgical techniques, such as scapular allograft reconstruction, enhance shoulder stability and extremity function, in patients following scapular tumor resection.MethodsCase details from seven patients who underwent scapular allograft reconstruction following scapular tumor resection were reviewed. A wide marginal resection (partial scapulectomy) was performed in all patients and all affected soft tissues were resected to achieve a clean surgical margin. The glenoid-resected and glenoid-saved reconstructions were performed in three and four patients, respectively. The residual host scapula were fixed to the size-matched scapular allografts with plates and screws. The rotator cuff was affected frequently and was mostly resected. The deltoid and articular capsule were infrequently involved, but reconstructed preferentially. The remaining muscles were reattached to the allografts.ResultsThe median follow-up was 26 months (range, 14–50 months). The average function scores were 24 points (80%) according to the International Society of Limb Salvage criteria. The range of active shoulder abduction and forward flexion motion were 40°–110° and 30°–90°, respectively. There was no difference between the glenoid-saved and glenoid-resected reconstructions in the total scores (mean, 24.5 points/81% versus 24 points/79%), but the glenoid-saved procedure was superior to the later in terms of abduction/flexion motion (mean, 72°/61° versus 55°/43°). During the study follow-up period, one patient died following a relapse, one patient lived despite of local recurrence, and five patients survived with no evidence of recurrence of the original cancer. Post-surgical complications such as shoulder dislocations, non-unions, and articular degeneration were not noted during this study period.ConclusionScapular allograft reconstruction had a satisfactory functional, cosmetic, and oncological outcome in this case series. Preservation and reconstruction of the articular capsule and deltoid are proposed to be a prerequisite for using scapular allografts and rotator cuff reconstruction is recommended, although technically challenging to perform.
Chromatin conformation signatures of cellular differentiation
Authors: Fraser James , Rousseau Mathieu , Shenker Solomon , Ferraiuolo Maria A , Hayashizaki Yoshihide , Blanchette Mathieu , Dostie Josée 
Published: April 2009

AbstractOne of the major genomics challenges is to better understand how correct gene expression is orchestrated. Recent studies have shown how spatial chromatin organization is critical in the regulation of gene expression. Here, we developed a suite of computer programs to identify chromatin conformation signatures with 5C technology http://Dostielab.biochem.mcgill.ca. We identified dynamic HoxA cluster chromatin conformation signatures associated with cellular differentiation. Genome-wide chromatin conformation signature identification might uniquely identify disease-associated states and represent an entirely novel class of human disease biomarkers.
Transcriptional features of genomic regulatory blocks
Authors: Akalin Altuna , Fredman David , Arner Erik , Dong Xianjun , Bryne Jan Christian , Suzuki Harukazu , Daub Carsten O , Hayashizaki Yoshihide , Lenhard Boris 
Published: April 2009

Abstract
Background
Genomic regulatory blocks (GRBs) are chromosomal regions spanned by highly conserved non-coding elements (HCNEs), most of which serve as regulatory inputs of one target gene in the region. The target genes are most often transcription factors involved in embryonic development and differentiation. GRBs often contain extensive gene deserts, as well as additional 'bystander' genes intertwined with HCNEs but whose expression and function are unrelated to those of the target gene. The tight regulation of target genes, complex arrangement of regulatory inputs, and the differential responsiveness of genes in the region call for the examination of fundamental rules governing transcriptional activity in GRBs. Here we use extensive CAGE tag mapping of transcription start sites across different human tissues and differentiation stages combined with expression data and a number of sequence and epigenetic features to discover these rules and patterns.

Results
We show evidence that GRB target genes have properties that set them apart from their bystanders as well as other genes in the genome: longer CpG islands, a higher number and wider spacing of alternative transcription start sites, and a distinct composition of transcription factor binding sites in their core/proximal promoters. Target gene expression correlates with the acetylation state of HCNEs in the region. Additionally, target gene promoters have a distinct combination of activating and repressing histone modifications in mouse embryonic stem cell lines.

Conclusions
GRB targets are genes with a number of unique features that are the likely cause of their ability to respond to regulatory inputs from very long distances.
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
Authors: Severin Jessica , Waterhouse Andrew M , Kawaji Hideya , Lassmann Timo , van Nimwegen Erik , Balwierz Piotr J , de Hoon Michiel JL , Hume David A , Carninci Piero , Hayashizaki Yoshihide , Suzuki Harukazu , Daub Carsten O , Forrest Alistair RR 
Published: April 2009

AbstractEdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new data types and search patterns. The FANTOM4 EdgeExpress database http://fantom.gsc.riken.jp/4/edgeexpress summarizes gene expression patterns in the context of alternative promoter structures and regulatory transcription factors and microRNAs using intuitive gene-centric and sub-network views. This is an important resource for gene regulation in acute myeloid leukemia, monocyte/macrophage differentiation and human transcriptional networks.
Phase II Study of the Anti–Insulin-Like Growth Factor Type 1 Receptor Antibody CP-751,871 in Combination With Paclitaxel and Carboplatin in Previously Untreated, Locally Advanced, or Metastatic Non–Small-Cell Lung Cancer
Authors: Karp Daniel D. , Paz-Ares Luis G. , Novello Silvia , Haluska Paul , Garland Linda , Cardenal Felipe , Blakely L. Johnetta , Eisenberg Peter D. , Langer Corey J. , Blumenschein George , Johnson Faye M. , Green Stephanie , Gualberto Antonio 
Published: April 2009

Purpose We conducted a phase II study of combination of the anti–insulin-like growth factor 1 receptor antibody CP-751,871 with paclitaxel and carboplatin (PCI) in advanced treatment-naïve non–small-cell lung cancer (NSCLC). Patients and Methods Patients were randomly assigned (2:1) to paclitaxel 200 mg/m2, carboplatin (area under the plasma concentration-time curve of 6), and CP-751,871 10 to 20 mg/kg (PCI10, PCI20) or paclitaxel and carboplatin alone (PC) every 3 weeks for up to six cycles. PCI10-20 patients could continue CP-751,871 (figitumumab) treatment after chemotherapy discontinuation. Patients treated with PC experiencing disease progression were eligible to receive CP-751,871 at investigator's discretion. An additional nonrandomized single-arm cohort of 30 patients with nonadenocarcinoma tumor histology receiving PCI20 was enrolled on completion of the randomized study. Results A total of 156 patients were enrolled onto the randomized portion of the study. Safety and efficacy information are available for 151 patients (98 patients treated with PCI and 53 patients treated with PC). Forty-eight patients treated with PCI received PCI10 and 50 patients received PCI20 in two sequential stages. Twenty of 53 patients treated with PC received CP-751,871 after disease progression. PCI was well tolerated. Fifty-four percent of patients treated with PCI and 42% of patients treated with PC had objective responses. Sixteen of 23 patients assessable for efficacy in the nonrandomized single-arm extension cohort also responded to treatment. Of note, 14 of 18 randomly assigned and 11 of 14 nonrandomly assigned patients treated with PCI with squamous cell carcinoma histology had response to treatment, including nine objective responses in bulky disease. Responses were also observed in two patients with squamous histology receiving CP-751,871 on PC discontinuation. PCI20/PC hazard ratio for progression-free survival was 0.8 to 0.56, according to censorship. Conclusion These data suggest that PCI20 is safe and effective in patients with NSCLC.
Single Nucleotide Polymorphism at rs1982073:T869C of the TGFβ1 Gene Is Associated With the Risk of Radiation Pneumonitis in Patients With Non–Small-Cell Lung Cancer Treated With Definitive Radiotherapy
Authors: Yuan Xianglin , Liao Zhongxing , Liu Zhensheng , Wang Li-E , Tucker Susan L. , Mao Li , Wang Xin Shelley , Martel Mary , Komaki Ritsuko , Cox James D. , Milas Luka , Wei Qingyi 
Published: April 2009

Purpose In search of reliable biologic markers to predict the risk of normal tissue damage by radio(chemo)therapy before treatment, we investigated the association between single nucleotide polymorphisms (SNPs) in the transforming growth factor 1 (TGFβ1) gene and risk of radiation pneumonitis (RP) in patients with non–small-cell lung cancer (NSCLC). Patients and Methods Using 164 available genomic DNA samples from patients with NSCLC treated with definitive radio(chemo)therapy, we genotyped three SNPs of the TGFβ1 gene (rs1800469:C-509T, rs1800471:G915C, and rs1982073:T869C) by polymerase chain reaction restriction fragment length polymorphism method. We used Kaplan-Meier cumulative probability to assess the risk of grade ≥ 3 RP and Cox proportional hazards analyses to evaluate the effect of TGFβ1 genotypes on such risk. Results There were 90 men and 74 women in the study, with median age of 63 years. Radiation doses ranging from 60 to 70 Gy (median = 63 Gy) in 30 to 58 fractions were given to 158 patients (96.3%) and platinum-based chemotherapy to 147 (89.6%). Grade ≥ 2 and grade ≥ 3 RP were observed in 74 (45.1%) and 36 patients (22.0%), respectively. Multivariate analysis found CT/CC genotypes of TGFβ1 rs1982073:T869C to be associated with a statistically significantly lower risk of RP grades ≥ 2 (hazard ratio [HR] = 0.489; 95% CI, 0.227 to 0.861; P = .013) and grades ≥ 3 (HR = 0.390; 95% CI, 0.197 to .774; P = 0.007), respectively, compared with the TT genotype, after adjustment for Karnofsky performance status, smoking status, pulmonary function, and dosimetric parameters. Conclusion Our results showed that CT/CC genotypes of TGFβ1 rs1982073:T869C gene were associated with lower risk of RP in patients with NSCLC treated with definitive radio(chemo)therapy and thus may serve as a reliable predictor of RP.
Utility of the Rosenberg Self-Esteem Scale
Authors: Davis Clare , Kellett Stephen , Beail Nigel 
Published: April 2009

Abstract
The Rosenberg Self-Esteem Scale (RSES) continues to be used to purportedly measure self-esteem of people with intellectual disabilities, despite the lack of sound evidence concerning its validity and reliability when employed with this population. The psychometric foundations of the RSES were analyzed here with a sample of 219 participants with intellectual disabilities. The factor analytic methods employed revealed two factors (Self-Worth and Self-Criticism) and more specific problems with RSES Items 5 and 8. Overall, this scale showed only moderate temporal and moderate internal reliability and poor aspects of criterion validity. Results are discussed with reference to either developing a new measure of self-esteem or redesigning and simplifying the RSES in order to increase its initial face validity in intellectual disability samples.
Depression in Adults With Mild Intellectual Disability: Role of Stress, Attributions, and Coping
Authors: Hartley Sigan L. , MacLean William E. 
Published: April 2009

Abstract
The experience of stressful social interactions, negative causal attributions, and the use of maladaptive coping efforts help maintain depression over time in the general population. We investigated whether a similar experience occurs among adults with mild intellectual disability. We compared the frequency and stress impact of such interactions, identified causal attributions for these interactions, and determined the coping strategies of 47 depressed and 47 nondepressed adults with mild intellectual disability matched on subject characteristics. The depressed group reported a higher frequency and stress impact of stressful social interactions, more negative attribution style, and more avoidant and less active coping strategies did than the nondepressed group. Findings have implications for theory building and development of psychotherapies to treat depression.
Correlation between Cooling Curves Obtained with a Silver Probe and Quenching Properties of 5140 Steel Bars
Authors: Wang R. S. , Wang Y. , Su L. P. 
Published: April 2009

Abstract
A computational method for the prediction of cooling curves at the center of a steel bar using experimentally measured cooling time-temperature data obtained from a cylindrical silver probe was developed based on nonsteady state heat conduction equations. This method involves: (1) the calculation of the critical size of the steel bar which is defined as the smallest size where no film boiling occurs, and (2) initial state of cooling of the steel bar in the quenchant, and the critical heat transfer coefficient of the quenching medium during nucleate boiling. This method was successfully used to: calculate the cooling curves at different locations within a 5140 steel bar which was quenched in three different quenching media, the hardness distribution, and French’s n and C values. The calculated data were validated against experimentally measured data. Using this method, it was shown that the critical heat transfer coefficient between the quenching medium and the steel bar is less than the critical heat transfer coefficient between the quenching medium and the silver probe. A logarithmic relationship between these two coefficients was established which can be used to simplify the calculations.
A Sixteenth-Century Catalog of Prohibited Music
Authors: Crook David 
Published: April 2009

In 1575 the Jesuit general in Rome issued an ordinance governing the use of music in the order's rapidly expanding network of colleges. Motets, masses, hymns, "and other pious compositions" were to be retained; indecent and "vain" music was to be burned. Sixteen years later the Jesuits' provincial administrator in Bavaria drew up a set of supplemental instructions, to which was appended a catalog of prohibited music as well as a complementary list of approved compositions (D-Mbs Clm 9237). Verbal texts treating drunkenness and erotic love account for the majority of banned pieces, but in some cases—a setting of the first verse of Psalm 137 by Orlando di Lasso, for example—the sound and style of the music led to its prohibition.
Although intended for all colleges within the Jesuits' Upper German province, this catalog apparently derives solely from a review of the music collection of Munich's college on the occasion of its move in 1591 to a magnificent new building financed by the duke of Bavaria. Like the architecture and curriculum of the college, the music catalog reflected Bavaria's new understanding of its role as principal post-Tridentine defender of the true faith. And, like the formal confessions of faith, catechisms, and service books promulgated by Europe's Churches during the late sixteenth century, Bavaria's catalog of prohibited music gave expression to an ideology of difference and exclusion that lies at the very heart of post-Reformation Christianity.
Music After All
Authors: Currie James 
Published: April 2009

For musicologists in the postmodern academy, the notion of context wields great force, both as a hermeneutic tool and as a meeting ground for a set of political beliefs that enable scholars to justify the meaning and relevance of their work. Primarily, this ideology is constituted by identity politics, the politics of difference and alterity, and the politics of locality and particularity. While acknowledging that musicological acts of cultural and historical contextualization per se are powerful means of illuminating cultural products, this essay nevertheless seeks, in its first half, to raise a set of questions regarding the efficacy of the accompanying political ideology within the pervasively unstable and dialectically totalized world of the early twenty-first century. Drawing extensively on the writings of the Slovenian cultural critic and theorist Slavoj Žižek and the French philosopher Alain Badiou, I argue that increasingly any localized context must be understood to be cut across by a kind of traumatic universalism that is, predominantly, economic in orientation.
The second part of the essay, however, turns in a different direction and argues that the route out of musicology's present political contradictions may lie not so much in the project of attempting once more to synthesize musicological and political practices into one, but rather through affirming the import of two (both musicology and politics, and music and politics). Through recourse to three theoretical discourses (into Heidegger, Hegel, and aspects of the Marxist tradition), the essay revisits the notion of musical autonomy, rescripting it—through an extensive analogy with dance—into a site where something unknown might manifest itself. Although it is acknowledged that this kind of site, strategically placed, might function effectively politically, it is nevertheless asserted that it is of sufficient import, in and of itself, to be preserved and nurtured, and that musicology in the academy is one of the privileged locations for where that might happen.
Telomeric RNAs Mark Sex Chromosomes in Stem Cells
Authors: Zhang Li-Feng , Ogawa Yuya , Ahn Janice Y , Namekawa Satoshi H , Silva Susana S , Lee Jeannie T 
Published: April 2009

AbstractTelomeric regions are known to be transcribed in several organisms. Although originally reported to be transcribed from all chromosomes with enrichment near the inactive X of female cells, we show that telomeric RNAs in fact are enriched on both sex chromosomes of the mouse in a developmentally specific manner. In female stem cells, both active Xs are marked by the RNAs. In male stem cells, both the X and the Y accumulate telomeric RNA. Distribution of telomeric RNAs changes during cell differentiation, after which they associate only with the heterochromatic sex chromosomes of each sex. FISH mapping suggests that accumulated telomeric RNAs localize at the distal telomeric end. Interestingly, telomeric expression changes in cancer and during cellular stress. Furthermore, RNA accumulation increases in Dicer-deficient stem cells, suggesting direct or indirect links to RNAi. We propose that telomeric RNAs are tied to cell differentiation and may be used to mark pluripotency and disease.
A Genetic Screen for Suppressors of a Mutated 5′ Splice Site Identifies Factors Associated With Later Steps of Spliceosome Assembly
Authors: Dassah MaryAnn , Patzek Sophie , Hunt Valerie M , Medina Pedro E , Zahler Alan M 
Published: April 2009

Abstract
Many alleles of human disease genes have mutations within splicing consensus sequences that activate cryptic splice sites. In Caenorhabditis elegans, the unc-73(e936) allele has a G-to-U mutation at the first base of the intron downstream of exon 15, which results in an uncoordinated phenotype. This mutation triggers cryptic splicing at the −1 and +23 positions and retains some residual splicing at the mutated wild-type (wt) position. We previously demonstrated that a mutation in sup-39, a U1 snRNA gene, suppresses e936 by increasing splicing at the wt splice site. We report here the results of a suppressor screen in which we identify three proteins that function in cryptic splice site choice. Loss-of-function mutations in the nonessential splicing factor smu-2 suppress e936 uncoordination through changes in splicing. SMU-2 binds SMU-1, and smu-1(RNAi) also leads to suppression of e936. A dominant mutation in the conserved C-terminal domain of the C. elegans homolog of the human tri-snRNP 27K protein, which we have named SNRP-27, suppresses e936 uncoordination through changes in splicing. We propose that SMU-2, SMU-1, and SNRP-27 contribute to the fidelity of splice site choice after the initial identification of 5′ splice sites by U1 snRNP.