bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bone mineral density and body composition in elite female golf and netball players
Authors: Chang Ruth P. Y. , Briffa Kathy N. , Edmondston Stephen J. 
Published: November 2011

AbstractThe aim of this study was to compare bone density and body composition measurements in women participating in elite‐level netball and golf, two sports with contrasting loading characteristics. Bone mineral density (BMD) and body composition were measured using dual‐energy X‐ray absorptiometry (DXA) in 14 state‐level netball players (20.8±3.4 years), 11 single‐digit handicap golf players (22.4±2.1 years) and a control group (n=18) not training for sport (22.6±3.6 years). Trunk extensor endurance and grip strength were also measured using the Sorensen test and hand‐grip dynamometry respectively. Netball players had significantly higher total body, lumbar spine and hip BMD than the golf players (P<0.001) and control subjects (P<0.001). The golf players had higher BMD than the control subjects only in the lumbar spine (P<0.05). The netball players were significantly taller than the golf players and control group (P<0.01) and had a higher body mass than the control group (P<0.001). After adjustment for body height and mass, the BMD values in the netball players remained significantly higher than the control subjects at all sites (P<0.01), while the golf players had significantly higher lumbar spine BMD than the controls (P<0.05). Elite‐level netball participation is associated with increased total body, hip and lumbar spine BMD, while this response was only evident in the lumbar spine in elite golf players. The contrasting loading characteristics of these sports may be reflected in the site‐specific differences in BMD when compared to non‐athletic control subjects.
Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences
Authors: Kalkatawi Manal , Rangkuti Farania , Schramm Michael , Jankovic Boris R. , Kamau Allan , Chowdhary Rajesh , Archer John A. C. , Bajic Vladimir B. 
Published: November 2011

Abstract
Motivation: Recognition of poly(A) signals in mRNA is relatively straightforward due to the presence of easily recognizable polyadenylic acid tail. However, the task of identifying poly(A) motifs in the primary genomic DNA sequence that correspond to poly(A) signals in mRNA is a far more challenging problem. Recognition of poly(A) signals is important for better gene annotation and understanding of the gene regulation mechanisms. In this work, we present one such poly(A) motif prediction method based on properties of human genomic DNA sequence surrounding a poly(A) motif. These properties include thermodynamic, physico-chemical and statistical characteristics. For predictions, we developed Artificial Neural Network and Random Forest models. These models are trained to recognize 12 most common poly(A) motifs in human DNA. Our predictors are available as a free web-based tool accessible at http://cbrc.kaust.edu.sa/dps. Compared with other reported predictors, our models achieve higher sensitivity and specificity and furthermore provide a consistent level of accuracy for 12 poly(A) motif variants.
Contact: vladimir.bajic@kaust.edu.sa
Supplementary information: Supplementary data are available at Bioinformatics online.
TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data
Authors: Asmann Yan W. , Middha Sumit , Hossain Asif , Baheti Saurabh , Li Ying , Chai High-Seng , Sun Zhifu , Duffy Patrick H. , Hadad Ahmed A. , Nair Asha , Liu Xiaoyu , Zhang Yuji , Klee Eric W. , Kalari Krishna R. , Kocher Jean-Pierre A. 
Published: November 2011

Abstract
Summary: TREAT (Targeted RE-sequencing Annotation Tool) is a tool for facile navigation and mining of the variants from both targeted resequencing and whole exome sequencing. It provides a rich integration of publicly available as well as in-house developed annotations and visualizations for variants, variant-hosting genes and host-gene pathways.
Availability and implementation: TREAT is freely available to non-commercial users as either a stand-alone annotation and visualization tool, or as a comprehensive workflow integrating sequencing alignment and variant calling. The executables, instructions and the Amazon Cloud Images of TREAT can be downloaded at the website: http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm
Contact: Hossain.Asif@mayo.edu; Kocher.JeanPierre@mayo.edu
Supplementary information: Supplementary data are provided at Bioinformatics online.
Protein subcellular localization of fluorescence imagery using spatial and transform domain features
Authors: Tahir Muhammad , Khan Asifullah , Majid Abdul 
Published: November 2011

Abstract
Motivation: Subcellular localization of proteins is one of the most significant characteristics of living cells. Prediction of protein subcellular locations is crucial to the understanding of various protein functions. Therefore, an accurate, computationally efficient and reliable prediction system is required.
Results: In this article, the predictions of various Support Vector Machine (SVM) models have been combined through majority voting. The proposed ensemble SVM-SubLoc has achieved the highest success rates of 99.7% using hybrid features of Haralick textures and local binary patterns (HarLBP), 99.4% using hybrid features of Haralick textures and Local Ternary Patterns (HarLTP). In addition, SVM-SubLoc has yielded 99.0% accuracy using only local ternary patterns (LTPs) based features. The dimensionality of HarLBP feature vector is 581 compared with 78 and 52 for HarLTP and LTPs, respectively. Hence, SVM-SubLoc in conjunction with LTPs is fast, sufficiently accurate and simple predictive system. The proposed SVM-SubLoc approach thus provides superior prediction performance using the reduced feature space compared with existing approaches.
Availability: A web server accompanying the proposed prediction scheme is available at http://111.68.99.218/SVM-SubLoc
Contact: asif@pieas.edu.pk; khan.asifullah@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
α‐Lipoic acid prevents mild portal endotoxaemia‐induced hepatic inflammation and β cell dysfunction
Authors: Tian Yu‐Feng , Hsieh Chang‐Hsun , Hsieh Yen‐Ju , Chen Yu‐Ting , Peng Yi‐Jen , Hsieh Po‐Shiuan 
Published: November 2011

Eur J Clin Invest 2012; 42 (6): 637–648AbstractBackground  This study was undertaken to evaluate the preventive effect of α‐lipoic acid (LA) on chronic mild portal endotoxaemia‐mediated subacute hepatic inflammation and pancreatic β cell dysfunction in rats.Materials and methods  Male Sprague–Dawley rats were randomly assigned into four groups: those with intraportal vehicle (saline) or low‐dose lipopolysaccharide (LPS) (0·42 ng/kg/min) infusion, combined with oral administration of vehicle or LA, a potent antioxidant (60 mg/kg/day) for 4 weeks. The hyperglycaemic clamp and euglycaemic clamp techniques were used to access the glucose‐stimulated insulin secretion and systemic insulin sensitivity in vivo.Results  Body weight, fasting plasma glucose and insulin were not different among groups. In rats with chronic intraportal LPS infusion, plasma C‐reactive protein, amylase, superoxide levels, the contents of thiobarbituric acid‐reactive substance, tumour necrosis factor α and interleukin 6 in liver and pancreas and also the gene expression of Toll‐like receptor 4 in liver were significantly increased as compared with those with LA cotreatment. The histopathological examination showed that inflammatory changes were clearly visible in liver and pancreatic islets of LPS‐infused rats and rarely observed in those cotreated with LA. In addition, low‐dose intraportal LPS infusion also significantly impaired glucose‐stimulated insulin secretion but not affect the systemic insulin sensitivity and metabolic clearance rate of insulin. LA administration markedly reversed LPS‐induced β cell dysfunction.Conclusions  α‐Lipoic acid cotreatment could significantly prevent mild portal endotoxaemia‐induced chronic hepatic inflammation and impaired pancreatic insulin secretion in absence of changing systemic insulin resistance.
Heterogeneous amplification of ERBB2 in primary lesions is responsible for the discordant ERBB2 status of primary and metastatic lesions in gastric carcinoma
Authors: Kim Min A , Lee Hyuk‐Joon , Yang Han‐Kwang , Bang Yung‐Jue , Kim Woo Ho 
Published: November 2011

Kim M A, Lee H‐J, Yang H‐K, Bang Y‐J & Kim W H  (2011) Histopathology59, 822–831Heterogeneous amplification of ERBB2 in primary lesions is responsible for the discordant ERBB2 status of primary and metastatic lesions in gastric carcinomaAims:  To determine the extent of HER2 homogeneity/heterogeneity in primary versus metastatic gastric carcinoma (GC).Materials and results:  The human epidermal growth factor receptor 2 (HER2) status in primary and metastatic lesions was evaluated by immunohistochemistry (IHC) and fluorescence in‐situ hybridization (FISH). Four separate cohorts consisting of primary GC alone or primary GC paired with metastatic lesions were examined. In the FISH analysis of 325 primary GCs, eight cases (2.5%) showed amplification with a heterogeneous pattern, whereas 27 cases (8.3%) showed amplification with a homogeneous pattern, and in this cohort the discordant:concordant FISH ratio based on examination of three different areas in each primary lesion was 0.30:1. FISH testing using 250 paired primary and metastatic lesions revealed seven cases (2.8%) with discordant amplification. In metastatic disease positive conversion occurred in six cases (2.4%), whereas negative conversion happened in one case (0.4%). The discordant:concordant ratio of primary versus secondary lesions was 0.23:1. When the seven discordant cases were re‐evaluated using whole sections of primary GCs, six showed a heterogeneous pattern of amplification.Conclusions:  These findings suggest that the discordant HER2 amplification observed in metastatic lesions is explained substantially by heterogeneity within primary tumours.
An immunohistochemical analysis‐based decision tree model for estimating the risk of lymphatic metastasis in pN0 squamous cell carcinomas of the lung
Authors: Liu Yu , Lin Dongmei , Xiao Ting , Ma Ying , Hu Zhi , Zheng Hongwei , Zheng Shan , Liu Yan , Li Min , Li Lin , Cao Yan , Guo Suping , Han Naijun , Di Xuebing , Zhang Kaitai , Cheng Shujun , Gao Yanning 
Published: November 2011

Liu Y, Lin D, Xiao T, Ma Y, Hu Z, Zheng H, Zheng S, Liu Y, Li M, Li L, Cao Y, Guo S, Han N, Di X, Zhang K, Cheng S & Gao Y  (2011) Histopathology 59, 882–891An immunohistochemical analysis‐based decision tree model for estimating the risk of lymphatic metastasis in pN0 squamous cell carcinomas of the lungAims:  Lung cancer patients within the pN0 category have a significantly different outcome. The aim of this study was to develop a mathematical model to assist in predicting the prognosis of pN0 lung squamous cell carcinoma (SCC).Methods and results:  Twenty‐three proteins were examined by immunohistochemical (IHC) analysis on primary tumour tissues from 319 lung SCC patients. In a training group, using IHC data, a recursive partitioning decision tree (RP‐DT) was used to build a model for estimating the risk for lymphatic metastasis. This model was then validated in a test cohort. Of 23 proteins, 8 (matrix metallopeptidase 1, metalloproteinase inhibitor 1, Ras GTPase‐activating‐like protein IQGAP1, targeting protein for Xklp2, urokinase‐type plasminogen activator, cathepsin D, fascin, polymeric immunoglobulin receptor/secretory component) were selected, and generated a tree model in a training group of 255 patients to classify them as at high or low risk of lymphatic invasion, with accuracy of 78.0% (compared to histopathological diagnosis), sensitivity of 83.0% and specificity of 70.3%. When the tree model was applied to the test group, the accuracy, sensitivity and specificity were 76.6%, 76.0% and 76.9%, respectively. The performance of this mathematical model was substantiated further in 34 ‘problematic’ stage I/pN0 patients by survival analysis.Conclusions:  The RP‐DT model, constructed with eight protein markers for estimating lymphatic metastasis risk in pN0 lung SCC, is clinically feasible and practical, using IHC data from the primary tumour.
Pulmonary capillary haemangiomatosis‐like lesions in severely congested lungs
Authors: Matsukuma Susumu , Sato Kimiya 
Published: November 2011

Matsukuma S & Sato K (2011) Histopathology59, 876–881Pulmonary capillary haemangiomatosis‐like lesions in severely congested lungsAims:  To elucidate the nature of capillary alterations in the severe form of pulmonary venous congestion (SPVC).Methods and results:  Post‐mortem lungs from 52 patients with left‐sided cardiac failure were examined, including 31 cases of valvular heart disease and 21 cases of cardiomyopathy. Six post‐mortem lungs (six of 52, 11.5%) had patchy lesions composed of markedly widened alveolar walls containing numerous dilated capillaries. These features strikingly mimicked pulmonary capillary haemangiomatosis (PCH). Moreover, one (one of 52, 1.9%) lung showed numerous fibrous micronodules containing capillaries with or without ossification, associated with prominent capillary sprouts, suggesting capillary varicose changes. No pathological features suggesting plexiform angiopathy or veno‐occlusive disease were found. Ultrastructural examination revealed occasional interposition of swollen endothelial cells in the thickened basement membranes of the pulmonary capillaries.Conclusion:  PCH‐like lesions can occur infrequently as an incidental finding in SPVC, rarely accompanying ossifying fibrocapillary micronodules. These lesions are considered to be a secondary form of PCH, representing severely tortuous and proliferative capillary changes rather than neoplasia.
Human epidermal growth factor receptor 2 testing in gastric carcinoma: issues related to heterogeneity in biopsies and resections*
Authors: Lee Stephen , de Boer Willem Bastiaan , Fermoyle Soraya , Platten Michael , Kumarasinghe Marian Priyanthi 
Published: November 2011

Lee S, de Boer W B, Fermoyle S, Platten M & Kumarasinghe M P  (2011) Histopathology59, 832–840Human epidermal growth factor receptor 2 testing in gastric carcinoma: issues related to heterogeneity in biopsies and resectionsAims:  To assess human epidermal growth factor receptor 2 (HER2) status and heterogeneity using immunohistochemistry (IHC) and silver in‐situ hybridization (SISH) in gastric carcinoma and dysplasia, and to correlate HER2 status between biopsy and resection specimens of gastric carcinoma.Methods and results:  Immunohistochemistry for HER2 was performed in 178 cases of gastric carcinoma, and SISH in cases showing at least 1+ reaction. HER2 positivity [European Medicines Agency (EMA) guidelines] was identified in 20.2% of carcinomas and 12.9% of high‐grade dysplasia, and HER2 heterogeneity noted in 50% and 33% of these cases, respectively. IHC negative/positive reactivity and SISH results were concordant in 96.2%. SISH amplification was seen in 35.3% of IHC 2+ and in a case with previously unrecognized staining pattern. Concordance of IHC HER2 status on biopsies and gastrectomies was seen in 74.1%. False negative IHC results on either the biopsy or gastrectomy were seen in 19.4% of HER2 amplified cases.Conclusions:  Human epidermal growth factor receptor 2 status in gastric carcinoma is comparable to previous studies with good concordance between IHC and SISH; all IHC 2+ and unusual patterns should be assessed with ISH studies; heterogeneity of tumour HER2 overexpression/amplification is common with possible implications for HER2 testing; and HER2 overexpression appears sufficiently specific to be considered a potential diagnostic biomarker of dysplasia.
Evaluation of a hormone receptor‐positive ovarian carcinoma subtype with a favourable prognosis by determination of progesterone receptor and oestrogen receptor 1 mRNA expression in formalin‐fixed paraffin‐embedded tissue
Authors: Sinn Bruno V , Darb‐Esfahani Silvia , Wirtz Ralph M , Budczies Jan , Sehouli Jalid , Chekerov Radoslav , Dietel Manfred , Denkert Carsten 
Published: November 2011

Sinn B V, Darb‐Esfahani S, Wirtz R M, Budczies J, Sehouli J, Chekerov R, Dietel M & Denkert C  (2011) Histopathology 59, 918–927Evaluation of a hormone receptor‐positive ovarian carcinoma subtype with a favourable prognosis by determination of progesterone receptor and oestrogen receptor 1 mRNA expression in formalin‐fixed paraffin‐embedded tissueAims:  In vitro and epidemiological studies indicate an essential role for progesterone in the aetiology and progression of ovarian carcinoma. The aim of this study was to examine the prognostic role of progesterone receptor (PR) protein and mRNA expression.Methods and results:  PR expression was examined by immunohistochemistry (n = 143) and kinetic reverse transcription–polymerase chain reaction (RT–PCR) from formalin‐fixed and paraffin‐embedded tissue (n = 55). PR mRNA and protein expression correlated (P < 0.0001). PR mRNA was a positive predictor for overall and progression‐free survival (P = 0.0005 and P < 0.0001, respectively). Protein expression was also prognostic (P = 0.015 and P = 0.0011, respectively), whereas only PR mRNA retained its prognostic value on multivariate analysis (P = 0.04). PR mRNA was still a positive prognostic marker among oestrogen receptor 1 (ESR1) mRNA‐positive tumours (P= 0.0007) and survival was best in patients with PR‐ and ESR1‐positive phenotypes (P = 0.0155 and P = 0.0016, respectively).Conclusion:  Expression of PR and ESR1 defines a subgroup of ovarian carcinomas with a favourable prognosis. PR and ESR1 mRNA expression analysis is a sensitive, quantitative and easy‐to‐perform high‐throughput analytical tool for the identification of this subgroup and could be predictive in clinical trials focused on patients with potential benefit from hormonal treatment.
Nuclear atypia grading score is a useful prognostic factor in papillary gastric adenocarcinoma
Authors: Nakashima Yuichiro , Yao Takashi , Hirahashi Minako , Aishima Shinichi , Kakeji Yoshihiro , Maehara Yoshihiko , Tsuneyoshi Masazumi 
Published: November 2011

Nakashima Y, Yao T, Hirahashi M, Aishima S, Kakeji Y, Maehara Y & Tsuneyoshi M  (2011) Histopathology59, 841–849Nuclear atypia grading score is a useful prognostic factor in papillary gastric adenocarcinomaAims:  To investigate nuclear atypical in papillary gastric adenocarcinoma (PGA).Method and results:  Hundred cases of PGA were classified into two groups according to nuclear pleomorphism and nuclear polarity; these groups were designated as high nuclear grade and low nuclear grade. Correlations between nuclear grade and clinicopathological features were evaluated for prognostic value. In order to evaluate which types of biological factors influence nuclear atypia, the expression of gastric‐type mucin phenotype, p53, HER2 and Ki‐67 detected by immunohistochemistry and DNA ploidy detected by laser scanning cytometry. The high nuclear grade group correlated with deeper wall invasion, the presence of lymphatic and venous invasion and the positivity of lymph node metastasis. High nuclear grade was an independent prognostic factor for disease‐free survival. Moreover, significant correlations were observed between high nuclear grade and positivity of gastric‐type mucin phenotype, p53 and HER2 and DNA aneuploidy.Conclusion:  Nuclear grade could be a new and useful morphological predictor for high malignant potential in PGA.
Unexplained fetal death has a biological signature of maternal anti‐fetal rejection: chronic chorioamnionitis and alloimmune anti‐human leucocyte antigen antibodies
Authors: Lee JoonHo , Romero Roberto , Dong Zhong , Xu Yi , Qureshi Faisal , Jacques Suzanne , Yoo Wonsuk , Chaiworapongsa Tinnakorn , Mittal Pooja , Hassan Sonia S. , Kim Chong Jai 
Published: November 2011

Lee J, Romero R, Dong Z, Xu Y, Qureshi F, Jacques S, Yoo W, Chaiworapongsa T, Mittal P, Hassan S S & Kim C J  (2011) Histopathology 59, 928–938Unexplained fetal death has a biological signature of maternal anti‐fetal rejection: chronic chorioamnionitis and alloimmune anti‐human leucocyte antigen antibodiesAims:  Chronic chorioamnionitis is a histological manifestation of maternal anti‐fetal cellular rejection. As failure of graft survival is the most catastrophic event in organ transplantation, we hypothesized that fetal death could be a consequence of maternal rejection. The aim of this study was to assess whether there is evidence of cellular and antibody‐mediated rejection in fetal death.Methods and results:  Placental histology was reviewed for the presence of chronic chorioamnionitis in unexplained preterm fetal death (n = 30) and preterm live birth (n = 103). Amniotic fluid CXCL10 concentrations were measured with a specific immunoassay. Chronic chorioamnionitis was more frequent in fetal death than in live birth (60.0% versus 37.9%; P < 0.05) and fetal death had a higher median amniotic fluid CXCL10 concentration than live birth (2.0 versus 1.8 ng/ml, P < 0.05), after adjusting for gestational age at amniocentesis. Maternal anti‐human leucocyte antigen class II panel‐reactive seropositivity determined by flow cytometry was higher in fetal death compared to live birth (35.7% versus 10.9%; P < 0.05).Conclusions:  Chronic chorioamnionitis is a common pathologic feature in unexplained preterm fetal death. This novel finding suggests that cellular and antibody‐mediated anti‐fetal rejection of the mother is associated with fetal death (graft failure) in human pregnancy.
Invasion in tidal zones on complex coastlines: modelling larvae of the non‐native Manila clam, Ruditapes philippinarum, in the UK
Authors: Herbert Roger J. H. , Willis Jay , Jones Elfed , Ross Kathryn , Hübner Ralf , Humphreys John , Jensen Antony , Baugh John 
Published: November 2011

AbstractAim  To evaluate whether natural larval transport and behaviour alone can explain the pattern of invasion and establishment of the non‐indigenous Manila clam, Ruditapes philippinarum (Adams & Reeve, 1850), and its spread beyond the point of introduction in the UK.Location  The study is focused on Poole Harbour, south England, the point of introduction of the Manila clam in the UK.Methods  We use fine‐resolution hydrodynamic models coupled with a water salinity model and an individual behaviour model of Manila clam larvae. The model was informed by experimental studies on the vertical response of larvae to salinity and field studies of the species in its natural and new environments.Results  Variations in the behavioural response of larvae to salinity in the model considerably affected the retention of clam larvae within the harbour. High levels of predicted larval retention occurred in two of five zones in the harbour when the salinity target was set at 17 practical salinity units. Persistently high densities of adult clams and recruits are accurately predicted in these regions.Main conclusions  Even within a relatively small region such as Poole Harbour, there is both localized retention of larvae or ‘closed’ areas and areas that are considerably more ‘open’ and potentially connected. The behavioural response of larvae to salinity significantly affected the degree of retention and ‘openness’ of the harbour to this species. Although, through natural transport, larvae could theoretically reach the next available habitat within the duration of their pelagic stage our study indicates that areas of sufficiently reduced salinity may be necessary for sufficient retention, recruitment and establishment of new adult populations in estuaries. High resolution hydrodynamic models, coupled with larval behaviour, can accurately simulate and predict biological invasion along complex coastlines and contribute to risk assessment of the introduction of non‐indigenous species for aquaculture and spatial management of marine protection.