bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential role of heat shock proteins in neural differentiation of murine embryonal carcinoma stem cells (P19)
Authors: Afzal Elahe , Ebrahimi Marzieh , Najafi S. Mahmoud Arab , Daryadel Arezoo , Baharvand Hossein 
Published: March 2011

AbstractHSPs (heat shock proteins) have been recognized to maintain cellular homoeostasis during changes in microenvironment. The present study aimed to investigate the HSPs expression pattern in hierarchical neural differentiation stages from mouse embryonal carcinoma stem cells (P19) and its role in heat stressed exposed cells. For induction of HSPs, cells were heated at 42°C for 30 min and recovered at 37°C in different time points. For neural differentiation, EBs (embryoid bodies) were formed by plating P19 cells in bacterial dishes in the presence of 1 mM RA (retinoic acid) and 5% FBS (fetal bovine serum). Then, on the sixth day, EBs were trypsinized and plated in differentiation medium containing neurobasal medium, B27, N2 and 5% FBS and for an extra 4 days. The expression of HSPs and neural cell markers were evaluated by Western blot, flow cytometry and immunocytochemistry in different stages. Our results indicate that HSC (heat shock constant)70 and HSP60 expressions decreased following RA treatment, EB formation and in mature neural cells derived from heat‐stressed single cells and not heat‐treated EBs. While the level of HSP90 increased six times following maturation process, HSP25 was expressed constantly during neural differentiation; however, its level was enhanced with heat stress. Accordingly, heat shock 12 h before the initiation of differentiation did not affect the expression of neuroectodermal and neural markers, nestin and β‐tubulin III, respectively. However, both markers increased when heat shock was induced after treatment and when EBs were formed. In conclusion, our results raise the possibility that HSPs could regulate cell differentiation and proliferation under both physiological and pathological conditions.
Comparative visualization of genetic and physical maps with Strudel
Authors: Bayer Micha , Milne Iain , Stephen Gordon , Shaw Paul , Cardle Linda , Wright Frank , Marshall David 
Published: March 2011

Abstract
Summary: Data visualization can play a key role in comparative genomics, for example, underpinning the investigation of conserved synteny patterns. Strudel is a desktop application that allows users to easily compare both genetic and physical maps interactively and efficiently. It can handle large datasets from several genomes simultaneously, and allows all-by-all comparisons between these.
Availability and implementation: Installers for Strudel are available for Windows, Linux, Solaris and Mac OS X at http://bioinf.scri.ac.uk/strudel/.
Contact: strudel@scri.ac.uk; micha.bayer@scri.ac.uk
GBOOST: a GPU-based tool for detecting gene–gene interactions in genome–wide case control studies
Authors: Yung Ling Sing , Yang Can , Wan Xiang , Yu Weichuan 
Published: March 2011

Abstract
Motivation: Collecting millions of genetic variations is feasible with the advanced genotyping technology. With a huge amount of genetic variations data in hand, developing efficient algorithms to carry out the gene–gene interaction analysis in a timely manner has become one of the key problems in genome-wide association studies (GWAS). Boolean operation-based screening and testing (BOOST), a recent work in GWAS, completes gene–gene interaction analysis in 2.5 days on a desktop computer. Compared with central processing units (CPUs), graphic processing units (GPUs) are highly parallel hardware and provide massive computing resources. We are, therefore, motivated to use GPUs to further speed up the analysis of gene–gene interactions.
Results: We implement the BOOST method based on a GPU framework and name it GBOOST. GBOOST achieves a 40-fold speedup compared with BOOST. It completes the analysis of Wellcome Trust Case Control Consortium Type 2 Diabetes (WTCCC T2D) genome data within 1.34 h on a desktop computer equipped with Nvidia GeForce GTX 285 display card.
Availability: GBOOST code is available at http://bioinformatics.ust.hk/BOOST.html#GBOOST.
Contact: timyung@ust.hk; eeyu@ust.hk
Supplementary information: Supplementary data are avaliable at Bioinformatics online.
A probabilistic model of nuclear import of proteins
Authors: Mehdi Ahmed M. , Sehgal Muhammad Shoaib B. , Kobe Bostjan , Bailey Timothy L. , Bodén Mikael 
Published: March 2011

AbstractMotivation: Nucleo-cytoplasmic trafficking of proteins is a core regulatory process that sustains the integrity of the nuclear space of eukaryotic cells via an interplay between numerous factors. Despite progress on experimentally characterizing a number of nuclear localization signals, their presence alone remains an unreliable indicator of actual translocation.Results: This article introduces a probabilistic model that explicitly recognizes a variety of nuclear localization signals, and integrates relevant amino acid sequence and interaction data for any candidate nuclear protein. In particular, we develop and incorporate scoring functions based on distinct classes of classical nuclear localization signals. Our empirical results show that the model accurately predicts whether a protein is imported into the nucleus, surpassing the classification accuracy of similar predictors when evaluated on the mouse and yeast proteomes (area under the receiver operator characteristic curve of 0.84 and 0.80, respectively). The model also predicts the sequence position of a nuclear localization signal and whether it interacts with importin-α.Availability: http://pprowler.itee.uq.edu.au/NucImportContact: m.boden@uq.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.
Which women default from follow‐up cervical cytology tests? A cohort study within the TOMBOLA trial
Authors: Sharp L. , Cotton S. , Thornton A. , Gray N. , Whynes D. , Smart L. , Waugh N. , Duncan I. , Cruickshank M. , Little J. ,   on behalf of the TOMBOLA Group
Published: March 2011

L. Sharp, S. Cotton, A. Thornton, N. Gray, D. Whynes, L. Smart, N. Waugh, I. Duncan, M. Cruickshank and J. Little, on behalf of the TOMBOLA GroupWhich women default from follow‐up cervical cytology tests? A cohort study within the TOMBOLA trialObjective:  To identify factors associated with default from follow‐up cervical cytology tests.Methods:  A cohort study was conducted involving 2166 women, aged 20–59, with recent low‐grade cervical cytology taken within the NHS Cervical Screening Programmes in Scotland and England, and managed by 6‐monthly cytology in primary care. For the first (6‐month) and second (12‐month) surveillance cytology tests separately, women were categorized as ‘on‐time attendees’ (attended ≤6 months of test being due), ‘late attendees’ (attended greater than 6 months after test was due) or ‘non‐attendees’ (failed to attend). Multivariate odds ratios (ORs) were computed for factors associated with late and non‐attendance.Results:  For the first surveillance test, risk of non‐attendance was significantly higher in younger women, those without post‐secondary education, and non‐users of prescribed contraception. Factors significantly associated with late attendance for the first test were the same as for non‐attendance, plus current smoking and having children. The most important predictor of non‐attendance for the second surveillance test was late attendance for the first test (OR = 9.65; 95% CI, 6.60–16.62). Non‐attendance for the second test was also significantly higher among women who were younger, smokers and had negative cytology on the first surveillance test. Late attendance for the second surveillance test was higher in women who were younger, smokers, had children and attended late for the first test.Conclusions:  Women at highest risk of default from follow‐up cytology tend to be young, smoke, lack post‐secondary education, and have defaulted from a previous surveillance appointment. Tackling default will require development of targeted strategies to encourage attendance and research to better understand the reasons underpinning default.
Identification of components of fibroadenoma in cytology preparations using texture analysis: a morphometric study
Authors: Singh S. , Gupta R. 
Published: March 2011

S. Singh and R. GuptaIdentification of components of fibroadenoma in cytology preparations using texture analysis: a morphometric studyObjectives:  To evaluate the utility of image analysis using textural parameters obtained from a co‐occurrence matrix in differentiating the three components of fibroadenoma of the breast, in fine needle aspirate smears.Methods:  Sixty cases of histologically proven fibroadenoma were included in this study. Of these, 40 cases were used as a training set and 20 cases were taken as a test set for the discriminant analysis. Digital images were acquired from cytological preparations of all the cases and three components of fibroadenoma (namely, monolayered cell clusters, stromal fragments and background with bare nuclei) were selected for image analysis. A co‐occurrence matrix was generated and a texture parameter vector (sum mean, energy, entropy, contrast, cluster tendency and homogeneity) was calculated for each pixel. The percentage of pixels correctly classified to a component of fibroadenoma on discriminant analysis was noted.Results:  The textural parameters, when considered in isolation, showed considerable overlap in their values of the three cytological components of fibroadenoma. However, the stepwise discriminant analysis revealed that all six textural parameters contributed significantly to the discriminant functions. Discriminant analysis using all the six parameters showed that the numbers of pixels correctly classified in training and tests sets were 96.7% and 93.0%, respectively.Conclusion:  Textural analysis using a co‐occurrence matrix appears to be useful in differentiating the three cytological components of fibroadenoma. These results could further be utilized in developing algorithms for image segmentation and automated diagnosis, but need to be confirmed in further studies.
Down‐regulation of keratin 4 and keratin 13 expression in oral squamous cell carcinoma and epithelial dysplasia: a clue for histopathogenesis
Authors: Sakamoto Kei , Aragaki Tadanobu , Morita Kei‐ichi , Kawachi Hiroshi , Kayamori Kou , Nakanishi Shoichi , Omura Ken , Miki Yoshio , Okada Norihiko , Katsube Ken‐ichi , Takizawa Toichiro , Yamaguchi Akira 
Published: March 2011

Sakamoto K, Aragaki T, Morita K‐i, Kawachi H, Kayamori K, Nakanishi S, Omura K, Miki Y, Okada N, Katsube K‐i, Takizawa T & Yamaguchi A (2011) Histopathology58, 531–542 Down‐regulation of keratin 4 and keratin 13 expression in oral squamous cell carcinoma and epithelial dysplasia: a clue for histopathogenesisAims:  This study aimed to identify relevant keratin subtypes that may associate with the pathogenesis of oral epithelial neoplasms.Methods and results:  Expression of all the keratin subtypes was examined by cDNA microarray analysis of 43 oral squamous cell carcinoma (OSCC) cases. Immunohistochemical expression of the major keratins was examined in 100 OSCC and oral epithelial dysplasia (OED) cases. Many changes in keratin expression were observed and, significantly, consistent down‐regulation of keratin 4 (K4) and K13 expression was observed. Aberrant expression of K4 and K13 was associated with morphological changes in the affected oral epithelium. Experiments with cell cultures transfected with various keratin subtypes suggested that alterations in keratin subtype expression can cause changes in cell shape and movement.Conclusions:  Aberrant expression of K4 and K13, which are the dominant pair of differentiation‐related keratins in oral keratinocytes, indicates dysregulation of epithelial differentiation in OSCC and OED. These keratins, especially K4, may be useful for pathological diagnosis. We propose that the aberrant expression of K4 and K13 and concomitant up‐regulation of the other keratins may be one of the causative factors for morphological alterations in the affected epithelium.
Elders and patient participation revisited – a discourse analytic approach to older persons’ reflections on patient participation
Authors: Foss Christina 
Published: March 2011

Aim and objective.  This study focuses on how older persons’ accounts of participation might be framed and constructed based on their social and historical situatedness.Background.  The picture emerging from contemporary research tends to portray older people as a group who prefer to leave decisions to the professionals during a hospital stay. Through an approach that sought to contextualise the respondents’ accounts of participation, different features of patient participation became visible.Design.  The study is based on a postmodern framework using a discursive approach, informed by the works of Foucault and on works that have been developed in line with his main ideas.Method.  Eighteen individual in‐depth interviews with older people (age 80+) were conducted between one to two weeks after discharge from hospital.Results.  Findings indicate that older people actively position themselves in relation to various discourses at play in the hospital, and display a wide variety of strategies aimed at gaining influence. To the older persons in this study, participation was practised in a subtle and discreet way, as a matter of choosing a good strategy to interact with the personnel. Participation was also seen as a matter of balancing their own needs against the needs of others and as a behaviour that required self‐confidence.Conclusion.  The accounts of patient participation given by the older persons differed from the dominant and taken‐for‐granted discourse of patient participation as a right.Relevance to clinical practice.  As the older persons’ understanding and practice of patient participation do not ‘fit’ the contemporary idea of participation, it is in danger of being ignored or overlooked by care‐givers as well as by researchers. To identify older patients’ wish to participate, one must actively search for it.
Impaired Balance of Th17/Treg in Patients with Nasal Polyposis
Authors: Shen Y. , Tang X.‐Y. , Yang Y.‐C. , Ke X. , Kou W. , Pan C.‐K. , Hong S.‐L. 
Published: March 2011

AbstractNasal polyposis (NP) is a chronic inflammatory disease of the nasal cavity and sinuses that is regulated by T lymphocyte subsets. Imbalance of Th17/Treg has been considered critical in the development of inflammation and atopic reactions. To assess whether the balance of Th17/Treg is disrupted in patients with NP, we evaluated the distribution of Th17 and Treg cells among peripheral blood mononuclear cells (PBMCs) in atopic patients with NP, non‐atopic patients with NP and controls. We then determined mRNA levels of RORc and Foxp3 and protein levels of IL‐17, TGF‐β and IL‐10 in polyp tissue among the three groups. Finally, we investigated the correlation between Th17‐, Treg‐ and Th1‐, Th2‐related cytokines (INF‐γ, IL‐4, IL‐5). The results demonstrated that both atopic and non‐atopic patients with NP revealed significantly increased Th17 proportion and decreased Treg proportion in PBMCs, as well as significantly increased RORc and IL‐17 levels and decreased Foxp3 and TGF‐β levels in polyp tissue. Furthermore, these differences were significant between atopic and non‐atopic groups. The frequency of Treg in PBMCs was found to be negatively correlated with Th1 and Th2 cytokines in polyps. These results indicated that an impaired balance of Th17/Treg existed in patients with NP and was more severe in atopic patients, suggesting that the imbalance of Treg/Th17 may play an important role in the development of NP and that atopy may aggravate NP by promoting the imbalance of Th17/Treg.
Characterization of Catharanthus roseus Genes Regulated Differentially by Peanut Witches’ Broom Phytoplasma Infection
Authors: Chen Wuu‐Yang , Lin Chan‐Pin 
Published: March 2011

AbstractThe differential display (DD) strategy was applied to isolate periwinkle (Catharanthus roseus) cDNAs that were differentially expressed following infection with peanut witches’ broom (PnWB) phytoplasma. Sixty‐four clones were selected from differentially expressed cDNA fragments. Following screening by reverse Northern hybridization, ten transcripts were selected and sequenced. The expression level of each transcript was quantified by real‐time PCR, and seven DD transcripts were identified as truly differentially expressed following PnWB phytoplasma infection. Among these, one that was homologous with phi‐1 gene was up‐regulated, while the others were down‐regulated. Except two genes, other four down‐regulated genes shared homology with the genes encoding psaDa gene, ML domain protein gene, eukaryotic translation initiation factor SUI1 gene and plastidic aldolase NPALDP1 gene, respectively. The identities of homologous genes were further confirmed for three DD transcripts by isolating long cDNA fragments from the cDNA library that was established in this investigation. Verified genes were ML domain protein gene, translation initiation factor SUI1 gene and plastidic aldolase gene and were primarily involved in the innate immune response, the stress response and photosynthesis. The possible role of these genes in the periwinkle that was infected by PnWB phytoplasma is discussed.
Effect of trans‐10 cis‐12 conjugated linoleic acid on Bovine Oocyte Competence and Fatty Acid Composition
Authors: Lapa M , Marques CC , Alves SP , Vasques MI , Baptista MC , Carvalhais I , Silva Pereira M , Horta AEM , Bessa RJB , Pereira RM 
Published: March 2011

ContentsThe reproductive performance of dairy cows may be improved by feeding conjugated linoleic acid (CLA) supplements during early lactation. The mechanism of action of t10,c12 CLA is not clearly known. Our objective was to investigate the effect of t10,c12 CLA on oocyte maturation and lipid composition of cumulus oocyte complexes (COC). The developmental potential of oocytes incubated in in vitro maturation (IVM) medium supplemented with t10,c12 CLA to the blastocyst stage and embryo quality were also assessed. In experiment 1, abattoir‐derived oocytes were matured in TCM199 + 10% serum supplemented with 100 μM t10,c12 CLA (t10,c12 CLA n = 672) or without it (control n = 672). Mature oocytes were either stained for chromatin configuration or inseminated and cultured for embryo development assessment. In experiment 2, COC and IVM culture media were subjected to fatty acid (FA) analysis prior and after maturation with t10,c12 CLA or without it (control). Total lipids and FA profiles in oocytes, cumulus cells and culture media were determined by gas chromatography. t10,c12 CLA supplementation to IVM medium improved (p = 0.05) embryo quality evaluated morphologically. This effect was associated with t10,c12 CLA presence (3.1 ± 0.7%, p = 0.04) and lower levels of arachidonic acid in FA profile of t10,c12 CLA mature oocytes (immature oocytes = 4.4 ± 1.9%, t10,c12 CLA mature oocytes = 1.0 ± 0.7%, p = 0.05). Differences in myristic and eicotrienoic acids, saturated and unsaturated FA concentrations between oocytes and cumulus cells were detected (p ≤ 0.05). In conclusion, the presence of t10,c12 CLA during maturation interfered on lipid metabolism improving bovine oocyte competence to develop into higher quality embryos.
Prediction of Parturition Date in the Bitch and Queen
Authors: Michel E , Spörri M , Ohlerth S , Reichler IM 
Published: March 2011

ContentsAssessment of gestational age and parturition date prediction is a challenging, yet common task in clinical management of the pregnant bitch or queen. Knowing the approximate parturition date is essential for a thorough pregnancy monitoring. Radiographic and ultrasonographic methods are suitable in bitches and queens. In the bitch, moreover, ovulation timing by means of LH or progesterone assay, determination of onset of vaginal dioestrus by means of examination of vaginal cytology, and recognition of impending parturition by monitoring prepartal progesterone levels and body temperature variation are practical methods. A combination of different methods increases the accuracy of parturition date prediction.
Computed tomography findings of sorafenib‐treated hepatic tumors in patients with advanced hepatocellular carcinoma
Authors: Kim Min Ju , Choi Joon‐Il , Lee Jong Seok , Park Joong‐Won 
Published: March 2011

AbstractBackground and Aim:  The purpose of this study was to describe the computed tomography (CT) findings of sorafenib‐treated hepatic tumors in patients with advanced hepatocellular carcinoma and to correlate the findings to the overall survival (OS).Methods:  Twenty‐eight sorafenib‐treated patients who had advanced hepatocellular carcinoma (HCC) with viable hepatic tumors between August 2007 and February 2008 were enrolled in the study. Dynamic CT findings were analyzed with regard to the response of the tumor, based on the response evaluation criteria in solid tumor, version 1.1, and the attenuation values of the tumors during the late arterial and portal venous phases. Survival analyses according to early changes in the tumors were also performed.Results:  In all patients, the tumor responses were stable disease or progressive disease on follow‐up CT scans. Prior to the treatment, the mean attenuation values of the tumors were 93.0 ± 20.0 Hounsfield unit (HU) at the late arterial phase, and 107.9 ± 23.0 HU at the portal venous phase. On the first follow‐up CT scans, the mean attenuation values of the late arterial and portal venous phases were 76.9 ± 26.5 HU and 94.2 ± 29.1 HU, respectively (P < 0.01). The median OS was better for the patients with the response of stable disease than the patients with progressive disease (P = 0.013).Conclusions:  In patients with advanced HCC who were treated by sorafenib, the size of the hepatic tumors was not significantly reduced. However, the median survival was better for the patients with the response of stable disease. The attenuation values of the tumors became lower after treatment, as compared to the baseline CT scans.
An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales
Authors: Le Fourn Céline , Brasseur Gaël , Brochier‐Armanet Céline , Pieulle Laetitia , Brioukhanov Andrei , Ollivier Bernard , Dolla Alain 
Published: March 2011

SummaryThe hyperthermophile Thermotoga maritima, although strictly anaerobic, is able to grow in the presence of low amounts of O2. Here, we show that this bacterium consumes O2 via a three‐partner chain involving an NADH oxidoreductase (NRO), a rubredoxin (Rd) and a flavo‐diiron protein (FprA) (locus tags: TM_0754, TM_0659 and TM_0755, respectively). In vitro experiments showed that the NADH‐dependent O2 consumption rate was 881.9 (± 106.7) mol O2 consumed min−1 per mol of FprA at 37°C and that water was the main end‐product of the reaction. We propose that this O2 reduction chain plays a central role in the O2 tolerance of T. maritima. Phylogenetic analyses suggest that the genes coding for these three components were acquired by an ancestor of Thermotogales from an ancestor of Thermococcales via a single gene transfer. This event likely also involved two ROS scavenging enzymes (neelaredoxin and rubrerythrin) that are encoded by genes clustered with those coding for FprA, NRO and Rd in the ancestor of Thermococcales. Such genomic organization would have provided the ancestor of Thermotogales with a complete set of enzymes dedicated to O2‐toxicity defence. Beside Thermotogales and Thermococcales, horizontal gene transfers have played a major role in disseminating these enzymes within the hyperthermophilic anaerobic prokaryotic communities, allowing them to cope with fluctuating oxidative conditions that exist in situ.