bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioSilicoSystems - A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)
Authors: Hariharaputran Sridhar 
Published: November 2010

AbstractThe rising field of integrative bioinformatics provides the vital methods to integrate, manage and also to analyze the diverse data and allows gaining new and deeper insights and a clear understanding of the intricate biological systems. The difficulty is not only to facilitate the study of heterogeneous data within the biological context, but it also more fundamental, how to represent and make the available knowledge accessible. Moreover, adding valuable information and functions that persuade the user to discover the interesting relations hidden within the data is, in itself, a great challenge. Also, the cumulative information can provide greater biological insight than is possible with individual information sources. Furthermore, the rapidly growing number of databases and data types poses the challenge of integrating the heterogeneous data types, especially in biology. This rapid increase in the volume and number of data resources drive for providing polymorphic views of the same data and often overlap in multiple resources.In this thesis a multi-pronged approach is proposed that deals with various methods for the analysis and representation of the diverse biological data which are present in different data sources. This is an effort to explain and emphasize on different concepts which are developed for the analysis of molecular data and also to explain its biological significance. The hypotheses proposed are in context with various other results and findings published in the past. The approach demonstrated also explains different ways to integrate the molecular data from various sources along with the need for a comprehensive understanding and clear projection of the concept or the algorithm and its results, but with simple means and methods. The multifarious approach proposed in this work comprises of different tools or methods spanning significant areas of bioinformatics research such as data integration, data visualization, biological network construction / reconstruction and alignment of biological pathways. Each tool deals with a unique approach to utilize the molecular data for different areas of biological research and is built based on the kernel of the thesis. Furthermore these methods are combined with graphical representation that make things simple and comprehensible and also helps to understand with ease the underlying biological complexity. Moreover the human eye is often used to and it is more comfortable with the visual representation of the facts.
ODIN: An Advanced Interface for the Curation of Biomedical Literature
Authors: Rinaldi Fabio , Clematide Simon , Schneider Gerold , Romacker Martin , Vachon Therese 
Published: November 2010

AbstractWe present *ODIN* (Ontogene Document INspector): a system for interactive curation of biomedical literature, developed within the scope of the "*SASEBio* project":http://www.ontogene.org/projects/sasebio/ (Semi-Automated Semantic Enrichment of the Biomedical Literature), as a collaboration between the "OntoGene group":http://www.ontogene.org/ at the University of Zurich and the NITAS/TMS group of Novartis Pharma AG. The purpose of the system is to allow a human annotator/curator to leverage upon the results of an advanced text mining system in order to enhance the speed and effectiveness of the annotation process.The OntoGene system takes as input a document (e.g a full paper from PubMed Central) and processes it with a custom NLP pipeline, which includes Named Entity recognition and relation extraction. Entities which are currently supported include proteins, genes, experimental methods, cell lines, species. Entities detected in the input document are disambiguated with respect to a reference database (UniProt, EntrezGene, NCBI taxonomy, PSI-MI ontology). The annotated documents are handed back to the ODIN interface, which allows multiple display modalities. The curator/annotator can view the whole document with in-line annotations highlighted, or can browse the extracted entities and be pointed back to the mentions of the entities within the original document. All entity mentions are entirely editable: the curator can easily add or delete any of them, and also change their extent (i.e. add/remove words to its right or left) with a simple click of the mouse. Different entity views are supported, with sorting capabilities according to different criteria (entity type, entity mention, confidence score, etc.). Selective highlighting of text units (e.g. sentences containing desired entities) is supported. Additionally, extensive logging functionalities are provided. All documents and entities are fully interlinked to reference databases, for the purpose of simplified inspection. Entities can be grouped in classes (e.g. by species) and actions can be applied to whole classes, for selective editing or removal.
Involvement of calpain‐I and microRNA34 in kanamycin‐induced apoptosis of inner ear cells
Authors: Yu Li , Tang Hao , Jiang Xiao Hua , Tsang Lai Ling , Chung Yiu Wa , Chan Hsiao Chang 
Published: November 2010

AbstractInner ear cells, including hair cells, spiral ganglion cells, stria vascularis cells and supporting cells on the basilar membrane, play a major role in transducing hearing signals and regulating inner ear homoeostasis. However, their functions are often damaged by antibiotic‐induced ototoxicity. Apoptosis is probably involved in inner ear cell injury following aminoglycoside treatment. Calpain, a calcium‐dependent protease, is essential for mediating and promoting cell death. We have therefore investigated the involvement of calpain in the molecular mechanism underlying ototoxicity induced by the antibiotic kanamycin in mice. Kanamycin (750 mg/kg) mainly induced cell death of cochlear cells, including stria vascularis cells, supporting cells and spiral ganglion cells, but not hair cells within the organ of Corti. Cell death due to apoptosis occurred in a time‐dependent manner with concomitant up‐regulation of calpain expression. Furthermore, the expression levels of two microRNAs, mir34a and mir34c, were altered in a dose‐dependent manner in cochlear cells. These novel findings demonstrated the involvement of both calpain and microRNAs in antibiotic‐induced ototoxicity.
Relevance of disease‐ and organ‐specific endothelial cells for in vitro research
Authors: Lehle Karla , Straub Rainer H , Morawietz Henning , Kunz‐Schughart Leoni A 
Published: November 2010

AbstractThe endothelium is a dynamic, heterogeneous, disseminated organ that possesses vital secretory, synthetic, metabolic and immunological functions. Endothelial dysfunction has been implicated as a key factor in the development of organ‐specific vascular diseases. This minireview gives a brief overview on EC (endothelial cell) biomarkers in arterial and venous endothelium and critically discusses the different sources of ECs that are most frequently applied in in vitro assays and research. The relevance of organ‐ and disease‐specific endothelial cell cultures for studying cellular responses as a basis for improving therapeutic interventions is highlighted with particular emphasis on endothelial dysfunction in transplant‐associated coronary artery disease, in atherosclerotic lesions and in response to diabetes mellitus.
Examining Dynamic Visual Scene Displays: Implications for Arranging and Teaching Symbol Selection
Authors: Olin Andrea Rachelle , Reichle Joe , Johnson LeAnne , Monn Emily 
Published: November 2010

Purpose
Evidence supports using visual scene displays (VSDs) with young children using speech-generating devices. This study examined initial and subsequent performance during VSD use by children age 24–27 and 33–36 months to explore child characteristics that may relate to navigational skill differences.

Method
Children located 9 vocabulary items using a dynamic VSD. Tests of mean difference and analyses of variance were both completed to examine within- and between-age-group performance for accuracy and latency across 3 time points: at initial exposure, at criterion, and at a 2-week maintenance session for each of 2 linked navigational pages.

Results
Results indicated that, at initial exposure, older participants' symbol selections were significantly more accurate and significantly faster when navigating through each page of a 2-page dynamic VSD. Results also indicated that though younger participants required significantly more sessions to achieve mastery, when the effects of practice and language comprehension were controlled, performance differences between age groups were not found when maintenance was evaluated.

Conclusions
Older children perform better than younger children on initial opportunities. However, younger children learn to use VSDs in relatively few instructional opportunities, suggesting that VSDs can be used with children as young as 2 years of age.
Group-Item and Directed Scanning: Examining Preschoolers’ Accuracy and Efficiency in Two Augmentative Communication Symbol Selection Methods
Authors: White Aubrey Randall , Carney Edward , Reichle Joe 
Published: November 2010

Purpose
The current investigation compared directed scanning and group-item scanning among typically developing 4-year-old children. Of specific interest were their accuracy, selection speed, and efficiency of cursor movement in selecting colored line drawn symbols representing object vocabulary.

Method
Twelve 4-year-olds made selections in both directed and group-item scanning conditions using a 36-symbol array that required matching line drawn symbols to pictures.

Results
The majority of participants took more time in the directed scanning condition. Though not statistically significant, participants tended to be more accurate in their use of directed scanning. The cursor movements required (as a proportion of optimal cursor movements) were similar for both scanning selection techniques.

Conclusions
Among typically developing 4-year-olds, there appears to be a trade-off between speed and accuracy in symbol selection when using directed or group-item scanning. Better accuracy with directed scanning appears to come at the cost of a slower response time. Whereas group-item scanning may be faster, it results in a decreased number of accurate responses. Applications for clinical practice and implications for future research are discussed.
Cross-Language Nonword Repetition by Bilingual and Monolingual Children
Authors: Windsor Jennifer , Kohnert Kathryn , Lobitz Kelann F. , Pham Giang T. 
Published: November 2010

Purpose
Identifying children with primary or specific language impairment (LI) in languages other than English continues to present a diagnostic challenge. This study examined the utility of English and Spanish nonword repetition (NWR) to identify children known to have LI.

Method

Participants were 4 groups of school-age children (
N
= 187). There were 2 typically developing groups: proficient Spanish-English sequential bilinguals and monolingual English speakers. There were 2 groups of children with LI, one Spanish-English and the other monolingual English speakers. Children participated in both English and Spanish NWR.

Results
Children’s NWR performance was significantly correlated across languages. In English NWR, the 2 groups with LI had lower accuracy at the longest syllable length than the 2 typically developing groups. In Spanish NWR, monolingual children with LI had lower repetition accuracy than bilingual children with LI and typical monolingual children, with all 3 groups outperformed by the typical bilingual group. Likelihood ratios indicated adequate diagnostic power only for English NWR in ruling out the typical bilingual children as showing LI.

Conclusion
The results demonstrate that NWR performance relies on the dual influences of LI and native language experience. However, it remains possible that NWR is useful in a composite marker for LI.
Fidelity: An Essential Component of Evidence-Based Practice in Speech-Language Pathology
Authors: Kaderavek Joan N. , Justice Laura M. 
Published: November 2010

Purpose
To provide a primer regarding treatment fidelity as it affects evidence-based practice (EBP) for speech-language pathologists.

Method
This tutorial defines treatment fidelity, examines the role of treatment fidelity for speech-language pathologists, provides examples of fidelity measurement, and describes approaches for assessing treatment fidelity.

Conclusion
Treatment fidelity is a neglected construct in the EBP literature; however, fidelity is a crucial construct for documenting intervention effectiveness and engaging in EBP.
T lymphopaenia in relation to body mass index and TNF‐α in human obesity: adequate weight reduction can be corrective
Authors: Tanaka S.‐I. , Isoda F. , Ishihara Y. , Kimura M. , Yamakawa T. 
Published: November 2010

OBJECTIVEAlthough individuals with obesity are susceptible to infection, the underlying causes have not been fully identified. To investigate whether obesity affects immunity, we studied subjects with isolated obesity.DESIGN AND SUBJECTSThirty‐four obese persons from our outpatient obesity clinic and 50 nonobese healthy control subjects were studied. The effects of weight reduction were evaluated in obese subjects on a very‐low‐energy diet. We examined blastogenic response, lymphocyte subsets, circulatory TNF‐α, soluble TNF‐α receptor 1, soluble TNF‐α receptor 2, andin vitroTNF‐α production in obesity.MEASUREMENTSLymphocyte subsets were analysed with flowcytometry. TNF‐α and soluble TNF receptors levels were assayed using commercially available enzyme‐linked immunosorbent assay kits.RESULTSBlastogenic responses to phytohemagglutinin or concanavalin A of T cells, CD3+, CD4+, CD8+, CD4+CD45RO+, and TCR αβ T cells were significantly diminished in obese subjects. Strong negative correlations were observed between TCR αβ and body weight and BMI in obese subjects. Circulatory levels of TNF‐α, soluble TNF‐α receptors, andin vitroTNF‐α production were significantly increased compared to nonobese subjects. In obese subjects, there were significant positive correlations between serum levels of TNF‐α and waist‐hip ratio, serum levels of soluble TNF‐α receptor 1 and body weight, soluble TNF‐α receptor 2 and BMI, and soluble TNF‐α receptor 2 and waist‐hip ratio. The T cell responses and previously reduced non‐CD8 T cell subsets were increased significantly following weight reduction.CONCLUSIONSOur results suggest that subsets of T cell populations and their function may be reduced in human obesity, and that this may be related, at least in part, to the elevated TNF‐α production. Furthermore, this T cell dysfunction can be recovered by adequate weight reduction.
Effect of Helicobacter pylori infection on cyclooxygenase‐2 expression in gastric antral mucosa
Authors: LU Hong , CHEN Xiao Yu , LIU Wen Zhong , PENG Yan Shen , XIAO Shu Dong 
Published: November 2010

OBJECTIVE:  Helicobacter pylori infection is a major etiological cause
of chronic gastritis. Inducible cyclooxygenase (COX‐2) is an important
regulator of mucosal inflammation. Recent studies indicate that expression
of COX‐2 may contribute to gastro­intestinal carcinogenesis.
The aim of this study was to investigate the effects of H. pylori infection and eradication therapy on COX‐2 expression in gastric antral mucosa.METHODS:  Antral biopsies were taken from 46 H. pylori‐infected
patients, who also had chronic gastritis, both before and after
anti‐H. pylori treatment. The COX‐2 protein was stained by
using immunohistochemical methods and COX‐2 expression was quantified
as the percentage of epithelial cells expressing COX‐2. Gastritis
and H. pylori infection status were graded according to the Sydney system.RESULTS:  Cyclooxygenase‐2 expression was detected in the cytoplasm of gastric antral epithelial cells both before and after the eradication of H. pylori. Cyclooxygenase‐2 expression in mucosa with H.
pylori infection was compared with the corresponding mucosa after
successful H. pylori eradication (20.1 ± 13.1%vs 13.8 ± 5.9%; P < 0.05).
At the same time, COX‐2 expression in H. pylori‐infected
mucosa was com­pared with the normal controls (18.0 ± 14.1%vs 12.3 ± 4.6%, P < 0.05).
Expression of COX‐2 was correlated with the degree of chronic inflammation (r= 0.78, P < 0.05).CONCLUSIONS:  Our results showed that H. pylori infection leads to gastric
mucosal overexpression of COX‐2 protein, suggesting that the enzyme
is involved in H. pylori‐related gastric pathology in humans.
In vivo protein stabilization based on fragment complementation and a split GFP system
Authors: Lindman Stina , Hernandez-Garcia Armando , Szczepankiewicz Olga , Frohm Birgitta , Linse Sara 
Published: November 2010

Protein stabilization was achieved through in vivo screening based on the thermodynamic linkage between protein folding and fragment complementation. The split GFP system was found suitable to derive protein variants with enhanced stability due to the correlation between effects of mutations on the stability of the intact chain and the effects of the same mutations on the affinity between fragments of the chain. PGB1 mutants with higher affinity between fragments 1 to 40 and 41 to 56 were obtained by in vivo screening of a library of the 1 to 40 fragments against wild-type 41 to 56 fragments. Colonies were ranked based on the intensity of green fluorescence emerging from assembly and folding of the fused GFP fragments. The DNA from the brightest fluorescent colonies was sequenced, and intact mutant PGB1s corresponding to the top three sequences were expressed, purified, and analyzed for stability toward thermal denaturation. The protein sequence derived from the top fluorescent colony was found to yield a 12 °C increase in the thermal denaturation midpoint and a free energy of stabilization of -8.7 kJ/mol at 25 °C. The stability rank order of the three mutant proteins follows the fluorescence rank order in the split GFP system. The variants are stabilized through increased hydrophobic effect, which raises the free energy of the unfolded more than the folded state; as well as substitutions, which lower the free energy of the folded more than the unfolded state; optimized van der Waals interactions; helix stabilization; improved hydrogen bonding network; and reduced electrostatic repulsion in the folded state.
Hardy-Littlewood-Sobolev inequalities via fast diffusion flows
Authors: Carlen Eric A. , Carrillo José A. , Loss Michael 
Published: November 2010

We give a simple proof of the
λ
=
d
- 2 cases of the sharp Hardy-Littlewood-Sobolev inequality for
d
≥3, and the sharp Logarithmic Hardy-Littlewood-Sobolev inequality for
d
= 2 via a monotone flow governed by the fast diffusion equation.
Method to measure strong protein–protein interactions in lipid bilayers using a steric trap
Authors: Hong Heedeok , Blois Tracy M. , Cao Zheng , Bowie James U. 
Published: November 2010

Measuring high affinity protein–protein interactions in membranes is extremely challenging because there are limitations to how far the interacting components can be diluted in bilayers. Here we show that a steric trap can be employed for stable membrane interactions. We couple dissociation to a competitive binding event so that dissociation can be driven by increasing the affinity or concentration of the competitor. The steric trap design used here links monovalent streptavidin binding to dissociation of biotinylated partners. Application of the steric trap method to the well-characterized glycophorin A transmembrane helix (GpATM) reveals a dimer that is dramatically stabilized by 4–5 kcal/mol in palmitoyloleoylphosphatidylcholine bilayers compared to detergent. We also find larger effects of mutations at the dimer interface in bilayers compared to detergent suggesting that the dimer is more organized in a membrane environment. The high affinity we measure for GpATM in bilayers indicates that a membrane vesicle many orders of magnitude larger than a bacterial cell would be required to measure the dissociation constant using traditional dilution methods. Thus, steric trapping can open new biological systems to experimental scrutiny in natural bilayer environments.
Predictors and prognostic impact of recurrent myocardial infarction in patients with left ventricular dysfunction, heart failure, or both following a first myocardial infarction
Authors: Thune Jens Jakob , Signorovitch James E. , Kober Lars , McMurray John J.V. , Swedberg Karl , Rouleau Jean , Maggioni Aldo , Velazquez Eric , Califf Robert , Pfeffer Marc A. , Solomon Scott D. 
Published: October 2010

AimsRecurrent myocardial infarction (MI) is common after a first MI and is associated with increased morbidity and mortality. Predictors and prognosis of a recurrent MI with contemporary management are not well known.Methods and resultsWe assessed the predictors and prognostic impact of a first recurrent MI in 10 599 patients with left ventricular dysfunction, heart failure, or both following a first MI from the Valsartan in Acute Myocardial Infarction Trial (VALIANT) cohort. During a median follow‐up of 27.4 months, 861 patients (9.6%) had a recurrent MI. The median time to recurrence was 136 days (quartiles 35–361 days), with a declining rate of recurrent MI within the first 3 months. The strongest predictors of recurrent MI were reduced estimated glomerular filtration rate, unstable angina, diabetes, and age. Mortality was markedly elevated (20.5%) within the first 7 days of a recurrent MI. Patients who survived 7 days after a recurrent MI continued to be at increased risk of death compared with patients without a recurrent MI and the risk of death remained elevated more than two‐fold a year after the recurrent MI (adjusted hazards ratio 2.4, 95% confidence interval 1.7–3.2). One‐year mortality for the entire VALIANT cohort was 10.3%, whereas 38.3% of the patients were dead 1 year after recurrent MI. Early reinfarctions (within 1 month) was associated with significantly higher 30‐day mortality than later reinfarctions.ConclusionEven in the context of contemporary treatment, a recurrent MI confers a significantly increased risk of death in patients following a high‐risk first MI. Strategies aimed at reducing recurrent MI will thus likely prolong survival in post‐MI survivors.