bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cassis: detection of genomic rearrangement breakpoints
Authors: Baudet Christian , Lemaitre Claire , Dias Zanoni , Gautier Christian , Tannier Eric , Sagot Marie-France 
Published: June 2010

Abstract
Summary: Genomes undergo large structural changes that alter their organization. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. Lemaitre et al. presented a new method to precisely delimit rearrangement breakpoints in a genome by comparison with the genome of a related species. Receiving as input a list of one2one orthologous genes found in the genomes of two species, the method builds a set of reliable and non-overlapping synteny blocks and refines the regions that are not contained into them. Through the alignment of each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Here, we present the package Cassis that implements this method of precise detection of genomic rearrangement breakpoints.
Availability: Perl and R scripts are freely available for download at http://pbil.univ-lyon1.fr/software/Cassis/. Documentation with methodological background, technical aspects, download and setup instructions, as well as examples of applications are available together with the package. The package was tested on Linux and Mac OS environments and is distributed under the GNU GPL License.
Contact: Marie-France.Sagot@inria.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
EpiTOP—a proteochemometric tool for MHC class II binding prediction
Authors: Dimitrov Ivan , Garnev Panayot , Flower Darren R. , Doytchinova Irini 
Published: June 2010

Abstract
Motivation: T-cell epitope identification is a critical immunoinformatic problem within vaccine design. To be an epitope, a peptide must bind an MHC protein.
Results: Here, we present EpiTOP, the first server predicting MHC class II binding based on proteochemometrics, a QSAR approach for ligands binding to several related proteins. EpiTOP uses a quantitative matrix to predict binding to 12 HLA-DRB1 alleles. It identifies 89% of known epitopes within the top 20% of predicted binders, reducing laboratory labour, materials and time by 80%. EpiTOP is easy to use, gives comprehensive quantitative predictions and will be expanded and updated with new quantitative matrices over time.
Availability: EpiTOP is freely accessible at http://www.pharmfac.net/EpiTOP
Contact: idoytchinova@pharmfac.net
Supplementary information: Supplementary data are available at Bioinformatics online.
A probabilistic framework for aligning paired-end RNA-seq data
Authors: Hu Yin , Wang Kai , He Xiaping , Chiang Derek Y. , Prins Jan F. , Liu Jinze 
Published: June 2010

AbstractMotivation: The RNA-seq paired-end read (PER) protocol samples transcript fragments longer than the sequencing capability of today's technology by sequencing just the two ends of each fragment. Deep sampling of the transcriptome using the PER protocol presents the opportunity to reconstruct the unsequenced portion of each transcript fragment using end reads from overlapping PERs, guided by the expected length of the fragment.Methods: A probabilistic framework is described to predict the alignment to the genome of all PER transcript fragments in a PER dataset. Starting from possible exonic and spliced alignments of all end reads, our method constructs potential splicing paths connecting paired ends. An expectation maximization method assigns likelihood values to all splice junctions and assigns the most probable alignment for each transcript fragment.Results: The method was applied to 2 × 35 bp PER datasets from cancer cell lines MCF-7 and SUM-102. PER fragment alignment increased the coverage 3-fold compared to the alignment of the end reads alone, and increased the accuracy of splice detection. The accuracy of the expectation maximization (EM) algorithm in the presence of alternative paths in the splice graph was validated by qRT–PCR experiments on eight exon skipping alternative splicing events. PER fragment alignment with long-range splicing confirmed 8 out of 10 fusion events identified in the MCF-7 cell line in an earlier study by (Maher et al., 2009).Availability: Software available at http://www.netlab.uky.edu/p/bioinfo/MapSplice/PERContact: liuj@cs.uky.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Chromaligner: a web server for chromatogram alignment
Authors: Wang San-Yuan , Ho Tsung-Jung , Kuo Ching-Hua , Tseng Yufeng J. 
Published: June 2010

Abstract
Summary: Chromaligner is a tool for chromatogram alignment to align retention time for chromatographic methods coupled to spectrophotometers such as high performance liquid chromatography and capillary electrophoresis for metabolomics works. Chromaligner resolves peak shifts by a constrained chromatogram alignment. For a collection of chromatograms and a set of defined peaks, Chromaligner aligns the chromatograms on defined peaks using correlation warping (COW). Chromaligner is faster than the original COW algorithm by k2 times, where k is the number of defined peaks in a chromatogram. It also provides alignments based on known component peaks to reach the best results for further chemometric analysis.
Availability: Chromaligner is freely accessible at http://cmdd.csie.ntu.edu.tw/∼chromaligner
Contact: kuoch@ntu.edu.tw; yjtseng@csie.ntu.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
Nitric Oxide Functions as a Signal and Acts Upstream of AtCaM3 in Thermotolerance in Arabidopsis Seedlings
Authors: Xuan Yi , Zhou Shuo , Wang Lei , Cheng Yudou , Zhao Liqun 
Published: June 2010

Abstract
To characterize the role of nitric oxide (NO) in the tolerance of Arabidopsis (Arabidopsis thaliana) to heat shock (HS), we investigated the effects of heat on three types of Arabidopsis seedlings: wild type, noa1(rif1) (for nitric oxide associated1/resistant to inhibition by fosmidomycin1) and nia1nia2 (for nitrate reductase [NR]-defective double mutant), which both exhibit reduced endogenous NO levels, and a rescued line of noa1(rif1). After HS treatment, the survival ratios of the mutant seedlings were lower than those of wild type; however, they were partially restored in the rescued line. Treatment of the seedlings with sodium nitroprusside or S-nitroso-N-acetylpenicillamine revealed that internal NO affects heat sensitivity in a concentration-dependent manner. Calmodulin 3 (CaM3) is a key component of HS signaling in Arabidopsis. Real-time reverse transcription-polymerase chain reaction analysis after HS treatment revealed that the AtCaM3 mRNA level was regulated by the internal NO level. Sodium nitroprusside enhanced the survival of the wild-type and noa1(rif1) seedlings; however, no obvious effects were observed for cam3 single or cam3noa1(rif1) double mutant seedlings, suggesting that AtCaM3 is involved in NO signal transduction as a downstream factor. This point was verified by phenotypic analysis and thermotolerance testing using seedlings of three AtCaM3-overexpressing transgenic lines in an noa1(rif1) background. Electrophoretic mobility-shift and western-blot analyses demonstrated that after HS treatment, NO stimulated the DNA-binding activity of HS transcription factors and the accumulation of heat shock protein 18.2 (HSP18.2) through AtCaM3. These data indicate that NO functions in signaling and acts upstream of AtCaM3 in thermotolerance, which is dependent on increased HS transcription factor DNA-binding activity and HSP accumulation.
A peri‐operative statin update for non‐cardiac surgery. Part II: Statin therapy for vascular surgery and peri‐operative statin trial design
Authors: Biccard B. M. 
Published: June 2010

SummaryThis is the second of two review articles evaluating peri‐operative statin therapy. In surgical patients, the utility of peri‐operative statin therapy is strongly suggested by retrospective studies, although it is probably overestimated, as important confounding factors have not been controlled for and hence the literature is considered to be currently inconclusive.This review examines the potential mechanisms and indications for peri‐operative statin protection, the efficacy of acute peri‐operative beta‐blockade in addition to statin therapy, the effect of peri‐operative statin therapy withdrawal and the implications of comorbidities associated with peri‐operative cardiovascular risk on statin therapy. Recommendations concerning appropriate dosing, duration, therapeutic targets and necessary investigations when prescribing peri‐operative statins are made. Peri‐operative study design recommendations are suggested, so that future meta‐analyses may be more informative. Recommendations are made regarding retrospective reporting of statin studies to minimise the bias inherent in a number of the current retrospective studies on this subject.
Manikin study of fibreoptic‐guided intubation through the classic laryngeal mask airway with the Aintree intubating catheter vs the intubating laryngeal mask airway in the simulated difficult airway*
Authors: Heard A. M. B. , Lacquiere D. A. , Riley R. H. 
Published: June 2010

SummaryIn this randomised crossover manikin study of simulated difficult intubation, 26 anaesthetists attempted to intubate the trachea using two fibreoptic‐guided techniques: via a classic laryngeal mask airway using an Aintree intubating catheter and via an intubating laryngeal mask airway using its tracheal tube. Successful intubation was the primary endpoint, which was completed successfully in all 26 cases using the former technique, and in 5 of 26 cases using the latter (p < 0.0001). The former technique also proved quicker to reach the vocal cords with the fibrescope (median (IQR [range])) time 18 (14–20 [8–44]) s vs 110 (70–114 [30–118]) s, respectively; p = 0.008); and to first ventilation (93 (74–109 [52–135]) s vs 135 (79–158 [70–160]) s, respectively; p = 0.0038)]. We conclude that in simulated difficult intubation, fibreoptic intubation appears easier to achieve using a classic laryngeal mask airway and an Aintree intubating catheter than through an intubating laryngeal mask airway.
Thyrocyte interleukin‐18 expression is up‐regulated by interferon‐γ and may contribute to thyroid destruction in Hashimoto’s thyroiditis
Authors: Liu Zhe , Wang Haining , Xiao Wenhua , Wang Chen , Liu Guoqiang , Hong Tianpei 
Published: June 2010

SummaryInterferon‐γ (IFN‐γ) has a direct role in thyroid destruction in autoimmune thyroiditis. Interleukin‐18 (IL‐18), a pro‐inflammatory cytokine with potent IFN‐γ inducing activities, may play an important role in Th1‐mediated autoimmune diseases. The purpose of this study was to characterize the expression and localization of IL‐18 in the thyroid tissues of Hashimoto’s thyroiditis (HT) and to investigate the effect of IFN‐γ on IL‐18 expression in isolated human thyroid follicular cells (TFCs). Thyroid tissues obtained from six euthyroid patients with HT and six control subjects were used to detect IL‐18 expression by reverse transcription‐polymerase chain reaction (RT‐PCR) and immunohistochemical staining. Human TFCs were isolated and incubated for 48 h with or without IFN‐γ, tumour necrosis factor‐α (TNF‐α) or IL‐1β. IL‐18 expression was analysed by RT‐PCR, immunofluorescent double staining and western blot. We found that IL‐18 expression was increased in the thyroid tissues of HT compared with control thyroid tissues. TFCs were major cell types expressing IL‐18 in the thyroid tissues of HT. IL‐18 was constitutively expressed in isolated human TFCs, and the expression was significantly up‐regulated by IFN‐γ rather than TNF‐α or IL‐1β. Western bolt revealed that a 24‐kDa band corresponding to pro‐IL‐18 was broadened in the lysates of IFN‐γ‐treated TFCs. Our results demonstrated that IL‐18 expression is up‐regulated in the TFCs of HT patients and in primary human TFCs exposed to IFN‐γ. Therefore, intrathyroidal interaction between IL‐18 and IFN‐γ may have a role in promoting the local immune response, which contributes to the thyroid destruction seen in HT.
Effects of long‐term diabetes on the structure and cell proliferation of the myometrium in the early pregnancy of mice
Authors: Favaro Rodolfo R. , Salgado Renato M. , Raspantini Priscila R. , Fortes Zuleica B. , Zorn Telma M. T. 
Published: June 2010

SummaryIt is known that the development of diabetic complications in human pregnancy is directly related to the severity and the duration of this pathology. In this study, we developed a model of long‐term type 1 diabetes to investigate its effects on the cytoarchitecture, extracellular matrix and cell proliferation during the first adaptation phase of the myometrium for pregnancy. A single dose of alloxan was used to induce diabetes in mice prior to pregnancy. To identify the temporal effects of diabetes the mice were divided into two groups: Group D1 (females that became pregnant 90–100 days after alloxan); Group D2 (females that became pregnant 100–110 days after alloxan). Uterine samples were collected after 168 h of pregnancy and processed for light and electron microscopy. In both groups the histomorphometric evaluation showed that diabetes promoted narrowing of the myometrial muscle layers which was correlated with decreased cell proliferation demonstrated by PCNA immunodetection. In D1, diabetes increased the distance between muscle layers and promoted oedema. Contrarily, in D2 the distance between muscle layers decreased and, instead of oedema, there was a markedly deposition of collagen in the myometrium. Ultrastructural analysis showed that diabetes affects the organization of the smooth muscle cells and their myofilaments. Consistently, the immunoreaction for smooth muscle α‐actin revealed clear disorganization of the contractile apparatus in both diabetic groups. In conclusion, the present model demonstrated that long‐term diabetes promotes significant alterations in the myometrium in a time‐sensitive manner. Together, these alterations indicate that diabetes impairs the first phenotypic adaptation phase of the pregnant myometrium.
On the use of ultrafiltration for the concentration and desalting of phosvitin from egg yolk protein concentrate
Authors: Chay Pak Ting Bertrand P. , Pouliot Yves , Juneja Lekh R. , Okubo Tutomu , Gauthier Sylvie F. , Mine Yoshinori 
Published: June 2010

SummaryAn ultrafiltration‐based approach was integrated in the preparation of phosvitin (PVs) from delipidated egg yolk proteins. An attempt was made to concentrate PVs as well as to desalt by means of the diafiltration technique. Primary experiments were devoted to optimise the ultrafiltration performance as function of parameters such as the effects of pH, feed concentration and transmembrane pressure on permeate flux with the 10‐kDa molecular weight cut‐off (MWCO) polyethersulfone membrane at laboratory scale. Higher permeate flux values were observed at low concentration and at alkaline pH, whatever transmembrane pressure studied. Then, desalting of PVs was carried out at 50 °C with 10‐ and 30‐kDa MWCO membranes. The results showed that desalting of PVs was obtained with both the 10‐ and 30‐kDa MWCO membranes and with a few loss of protein in the permeate side.
Visualising knowledge from chat debates in argument diagrams
Authors: Salminen T. , Marttunen M. , Laurinen L. 
Published: June 2010

AbstractThis study investigates whether combining chat discussion and construction of an argument diagram stimulates students to formulate new ideas in practising argumentation. In this study, 16 secondary school students discussed vivisection and gender equality in pairs using both free and structured chat tools. In structured chat, the students selected and completed partial sentences provided by the computer. After the discussion, they jointly constructed either argument diagrams freely based on the previous discussions with an Internet tool or modified a diagram the computer had constructed automatically during the structured chat. The freely constructed diagrams contained more of the students' prior knowledge than the modified diagrams. However, the different types of diagrams did not differ significantly in breadth, depth, or balance of argumentation. Thus, free construction of argument diagrams seems to activate students to incorporate their prior knowledge into those diagrams.
Dental and gastrointestinal changes as indicators of nutritional depletion in elderly inpatients
Authors: Leandro‐Merhi Vânia Aparecida , Portero‐McLellan Kátia Cristina , Delbue Bernardi Júlia Laura , Frenhani Patrícia Baston , De Camargo José Gonzaga Teixeira , De Aquino José Luiz Braga 
Published: June 2010

AbstractObjective  The objective of this study was to identify the associations between the nutritional status of elderly patients and length of hospital stay and presence of dental and gastrointestinal changes.Casuistic and method  This cross‐sectional study analyzed anthropometric and food intake indicators, dental and gastrointestinal changes and length of hospital stay of 441 elderly patients of both genders. The Pearson's correlation coefficient was used to verify the correlation between the nutritional status of the elderly patients and length of hospital stay and presence of dental and gastrointestinal changes. The significance level was set at P < 0.05.Results  Dietary and anthropometric variables as well as length of hospital stay were similar for patients with and without dental changes. Patients with gastrointestinal changes consumed less energy (P < 0.05) than patients without gastrointestinal changes. Length of hospital stay was inversely correlated with body mass index (r = −0.15; P < 0.05); arm circumference was inversely correlated with presence of dental changes (r = −0.12; P < 0.05) and mid‐arm muscle circumference was inversely correlated with gastrointestinal changes (r = −0.12; P < 0.05).Conclusion  Dental and gastrointestinal changes are important indicators of nutritional depletion and dietary intake of inpatients.
An assessment of drug administration compliance in a university hospital centre
Authors: Alemanni Jordane , Touzin Karine , Bussières Jean‐François , Descoteaux Renée , Lemay Michel 
Published: June 2010

AbstractRationale, aims and objectives  Ensuring the safety of the medication process is a major world health concern. Within this framework, a field study of compliance at various stages of the medication process in health care units was conducted. The objective of our study was to compare compliance at the moment of drug administration at the patient's bedside before and after implementing certain measures (self‐study activities for the nursing staff, publication of the findings of the preliminary study and identification of priorities for action, among others).Methods  This is an observational study aimed at comparing compliance at various stages of the medication process in terms of dose verification, preparation and administration, on ward, before and after the implementation of corrective measures. Compliance was evaluated using an observational checklist that included 36 criteria. The evaluation was conducted on inpatients in nine health care units and the Emergency Care Unit of a university hospital centre. Compliance rates were calculated for each evaluated criterion separately and by category. The degree of significance and corresponding changes between 2007 and 2008 were also measured.Results  The compliance rate for all the applicable criteria used on the checklist showed a significant increase from 16% in 2007 to 28% in 2008. A significant increase was also observed in the compliance rates for drug verification (91% vs. 76%) and drug preparation on wards (50% vs. 23%), particularly with regard to entering drug names and a second identifier on the label.Conclusions  Compliance rates at various separately evaluated stages in 2008 were relatively satisfactory. There is, however, room for improvement in total compliance. The introduction of simple tools and adapted communication strategies led to a sizeable improvement in the medication process at our facility.
Comparing simulation and threshold approaches when analysing data with probabilities of categories
Authors: Zhang Fang , Wharam J. Frank , Ross‐Degnan Dennis 
Published: June 2010

AbstractObjective Constructing categories based on probabilities is not unusual in defining the outcome or the exposure. We compare the threshold approach and the simulation approach in making inferences.Method We used a simple structured example as well as published data to illustrate the difference between the simulation and the threshold approaches.Results We demonstrated that simulation results were different from the threshold approach in estimating the effect of a high‐deductible health plan. For repeat visits, we estimated a statistically significant ratio of incident rate ratio (IRR) 0.78 (95% CI: 0.64, 0.93) for non‐preventable emergency department visits using the simulation approach while the high‐severity category showed no statistical significance with the ratio of IRR 0.98 (95% CI: 0.64, 1.49) using a threshold of 75%. We also demonstrated that none of the threshold values could achieve the results of the simulation approach.Conclusions The simulation approach is preferred over the threshold one when analysing data with probability‐based outcome, exposure and/or other covariates if the size of the data permits.
Rice leaf growth and water potential are resilient to evaporative demand and soil water deficit once the effects of root system are neutralized
Authors: PARENT BORIS , SUARD BENOÎT , SERRAJ RACHID , TARDIEU FRANÇOIS 
Published: June 2010

ABSTRACTRice is known to be sensitive to soil water deficit and evaporative demand, with a greatest sensitivity of lowland‐adapted genotypes. We have analysed the responses of plant water relations and of leaf elongation rate (LER) to soil water status and evaporative demand in seven rice genotypes belonging to different species, subspecies, either upland‐ or lowland‐adapted. In the considered range of soil water potential (0 to −0.6 MPa), stomatal conductance was controlled in such a way that the daytime leaf water potential was similar in well‐watered, droughted or flooded conditions (isohydric behaviour). A low sensitivity of LER to evaporative demand was observed in the same three conditions, with small differences between genotypes and lower sensitivity than in maize. The sensitivity of LER to soil water deficit was similar to that of maize. A tendency towards lower sensitivities was observed in upland than lowland genotypes but with smaller differences than expected. We conclude that leaf water status and leaf elongation of rice are not particularly sensitive to water deficit. The main origin of drought sensitivity in rice may be its poor root system, whose effect was alleviated in the study presented here by growing plants in pots whose soil was entirely colonized by roots of all genotypes.