bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significance of nuclear hTra2‐beta1 expression in cervical cancer
Authors: GABRIEL BORIS , HAUSEN AXEL ZUR , BOUDA JIRI , BOUDOVA LUDMILA , KOPRIVOVA MIROSLAVA , HIRSCHFELD MARC , JÄGER MARKUS , STICKELER ELMAR 
Published: November 2008

AbstractObjective. Human Tra2‐beta1, a member of the serine/arginine‐rich splicing factors, is involved in C/A‐dependent mRNA processing and regulation of gene expression. Since several genes involved in cervical carcinogenesis are alternatively spliced and contain C/A rich elements, we aimed to analyze hTra2‐beta1 expression and subcellular localization in tumor tissue of women with cervical cancer and to determine its clinical significance. Design. Retrospective study. Setting. Tertiary‐care academic medical center. Sample. One hundred and five patients with cervical cancer and a mean follow up time of 73.1 months. Methods. Immunohistochemistry of paraffin‐embedded tissues was performed and hTra2‐beta1 expression was correlated with clinico‐pathological variables including patient outcome. Results. Cytoplasmic hTra2‐beta1 protein expression was found in 20% of cases, while all tumors revealed nuclear immunoreactivity with strong expression in 54.3% of cases. There was a significant inverse correlation between nuclear and cytoplasmic protein expression, suggesting a potentially relevant shuttle process of hTra2‐beta1 between both cellular compartments. Patients with weak expressing hTra2‐beta1 tumors showed an improved survival with a tumor‐related death rate of 8.3% compared to 23.7% in patients with moderate and high intranuclear hTra2‐beta1 expression, respectively. Conclusions. Our data support the hypothesis of a biological relevance for hTra2‐beta1 expression in cervical cancer. The observed shuttle process of this splicing factor with higher concentrations in the nucleus should have pronounced effects on the cellular function and tumor biology of the affected tumors, leading to the worse patient outcome.
Sparse combinatorial inference with an application in cancer biology
Authors: Mukherjee Sach , Pelech Steven , Neve Richard M. , Kuo Wen-Lin , Ziyad Safiyyah , Spellman Paul T. , Gray Joe W. , Speed Terence P. 
Published: November 2008

Abstract
Motivation: Combinatorial effects, in which several variables jointly influence an output or response, play an important role in biological systems. In many settings, Boolean functions provide a natural way to describe such influences. However, biochemical data using which we may wish to characterize such influences are usually subject to much variability. Furthermore, in high-throughput biological settings Boolean relationships of interest are very often sparse, in the sense of being embedded in an overall dataset of higher dimensionality. This motivates a need for statistical methods capable of making inferences regarding Boolean functions under conditions of noise and sparsity.
Results: We put forward a statistical model for sparse, noisy Boolean functions and methods for inference under the model. We focus on the case in which the form of the underlying Boolean function, as well as the number and identity of its inputs are all unknown. We present results on synthetic data and on a study of signalling proteins in cancer biology.
Availability: go.warwick.ac.uk/sachmukherjee/sci
Contact: s.n.mukherjee@warwick.ac.uk
Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble
Authors: Pugalenthi Ganesan , Tang Ke , Suganthan P. N. , Chakrabarti Saikat 
Published: November 2008

Abstract
Motivation: So far various bioinformatics and machine learning techniques applied for identification of sequence and functionally conserved residues in proteins. Although few computational methods are available for the prediction of structurally conserved residues from protein structure, almost all methods require homologous structural information and structure-based alignments, which still prove to be a bottleneck in protein structure comparison studies. In this work, we developed a neural network approach for identification of structurally important residues from a single protein structure without using homologous structural information and structural alignment.
Results: A neural network ensemble (NNE) method that utilizes negative correlation learning (NCL) approach was developed for identification of structurally conserved residues (SCRs) in proteins using features that represent amino acid conservation and composition, physico-chemical properties and structural properties. The NCL-NNE method was applied to 6042 SCRs that have been extracted from 496 protein domains. This method obtained high prediction sensitivity (92.8%) and quality (Matthew's correlation coefficient is 0.852) in identification of SCRs. Further benchmarking using 60 protein domains containing 1657 SCRs that were not part of the training and testing datasets shows that the NCL-NNE can correctly predict SCRs with ∼ 90% sensitivity. These results suggest the usefulness of NCL-NNE for facilitating the identification of SCRs utilizing information derived from a single protein structure. Therefore, this method could be extremely effective in large-scale benchmarking studies where reliable structural homologs and alignments are limited.
Availability: The executable for the NCL-NNE algorithm is available at http://www3.ntu.edu.sg/home/EPNSugan/index_files/SCR.htm
Contact: epnsugan@ntu.edu.sg; chakraba@ncbi.nlm.nih.gov.
Supplementary information: Supplementary data are available at Bioinformatics online.
Online communities serving the consumer/producer: observations from the study of a fantasy world
Authors: Boulaire Christele , Graf Raoul , Guelmami Raja 
Published: November 2008

PurposeThe purpose of this paper is to identify the main individual and collective strategies online communities employ to appropriate fantasy worlds and the ways in which community members use imagination within this context.Design/methodology/approachA qualitative study drawing on an ethnography of online communities including individual in‐person interviews with community members of the world is considered.FindingsThe predominance and the vital importance of the production/consumption of stories within these communities has been shown. The multiple benefits of this practice have been illustrated, including the pleasure of creating and playing with one's imagination. These benefits engender the surprise and enchantment of community members, who lavish other members with encouragement, congratulations and thanks.Research limitations/implicationsBecause of opting for a non‐participatory ethnography, it was impossible to directly contact the members of the community to conduct interviews. Thus a convenience sample was chosen representative of the study subject and individuals outside of these communities were questioned.Originality/valueThe online community allows members to collectively and playfully participate in entertainment related to the fantasy world. It appears as an imaginary organization of the (entertainment) service provider. The members of this organization can take part in value coproduction and share the benefits of an extended entertainment service that sparks their imagination and allows them to enjoy the fruits of their creations. Given the fantasy world's power to fire the imagination of fantasy lovers, the paper demonstrates that it is important for leisure and entertainment service providers to consider adding a fantasy component to their service.
Engagement of Penicillium marneffei conidia with multiple pattern recognition receptors on human monocytes
Authors: Srinoulprasert Yuttana , Pongtanalert Piyapong , Chawengkirttikul Runglawan , Chaiyaroj Sansanee C. 
Published: November 2008

ABSTRACT P. marneffei is a thermal dimorphic fungus which causes penicilliosis, an opportunistic infection in immunocompromised patients in South and Southeast Asia. Little is known about the innate immune response to P. marneffei infection. Therefore, the initial response of macrophages to P. marneffei conidia was evaluated by us. Adhesion between monocytes from healthy humans and fungal conidia was examined and found to be specifically inhibited by MAbs against PRR, such as MR, (TLR)1, TLR2, TLR4, TLR6, CD14, CD11a, CD11b, and CD18. To study the consequences of these interactions, cytokines were also examined by ELISA. Binding of P. marneffei conidia to monocytes was significantly inhibited, in a dose‐dependent manner, by MAbs against MR, TLR1, TLR2, TLR4, TLR6, CD14, CD11b and CD18. When monocytes were co‐cultured with the conidia, there was an increase in the amount of surface CD40 and CD86 expression, together with TNF‐α and IL‐1β production, compared to unstimulated controls. In assays containing anti‐TLR4 or anti‐CD14 antibody, reduction in the amount of TNF‐α released by monocytes stimulated with P. marneffei conidia was detected. In addition, it was found that production of TNF‐α and IL‐1β from adherent peripheral blood monocytes was partially impaired when heat‐inactivated autologous serum, in place of untreated autologous serum, was added to the assay. These results demonstrate that various PRR on human monocytes participate in the initial recognition of P. marneffei conidia, and the engagement of PRR could partly initiate proinflammatory cytokine production.
The influence of light and temperature on the germination of two Ugandan medicinal trees
Authors: Stangeland Torunn , Tabuti John R. S. , Lye Kåre A. 
Published: November 2008

AbstractFor reasons of the problems of establishment of some Ugandan trees in certain environments, we investigated the influence of temperature and light on germination and seedling growth of two locally threatened medicinal trees, Hallea rubrostipulata and Sarcocephalus latifolius, to facilitate their establishment. Field and controlled laboratory experiments were carried out to investigate the species germination requirements and seedling growth. Both species needed light to germinate. Hallea rubrostipulata had a temperature optimum of 25°C with 79% germination, while for S. latifolius, the total germination after 28 days was close to 60% at temperatures from 20 to 35°C. Seedlings of S. latifolius survived well at 35°C, while those of H. rubrostipulata died at this high temperature. Conversely, seedling of S. latifolius died at the low temperature of 15°C. However, in field experiment S. latifolius failed to germinate in the available degraded environments, probably because of predation and because the soil is not able to retain water long enough to support seedling growth. We, therefore, conclude that in this part of Uganda, nursery assistance is needed to establish healthy populations of Sarcocephalus and many other endangered trees.
Amplified in breast cancer 1 expression in breast cancer
Authors: Thorat M A , Turbin D , Morimiya A , Leung S , Zhang Q , Jeng M‐H , Huntsman D G , Nakshatri H , Badve S 
Published: November 2008

Aims:  The amplified in breast cancer 1 (AIB1), steroid receptor co‐activator family member, acts as an oestrogen receptor (ER) co‐activator. Acting with HER‐2, it is thought to play a role in endocrine resistance by facilitating ER–growth factor crosstalk. The aim was to analyse AIB1 expression by immunohistochemistry and study its correlations with other prognostic variables in breast cancer and its effect on survival.Methods:  A tissue microarray comprising tumours from 438 patients with 15.4 years’ median follow‐up was used. Interpretable AIB1 expression obtained in 395 patients was analysed along with other prognostic factors in breast cancer.Results:  AIB1 expression scores ranged from 0 to 30; positive AIB1 expression (score > 14) was seen in 146/395 breast cancers; it correlated negatively with ER (P = 0.003) and progesterone receptor (PR) (P = 0.007), and positively with HER‐2 (P = 0.005) and tumour grade (P = 0.014). It did not correlate with nodal status (P = 0.437). Among ER+ patients, AIB1 expression showed a trend towards loss of PR expression (29% versus 20%; P = 0.14). AIB1 did not predict survival on univariate or multivariate analysis.Conclusions:  AIB1 expression correlates with HER‐2 expression in breast cancer and shows a trend of association with loss of PR expression in ER+ tumours. Our study supports the postulated role of AIB1 in ER–growth factor interactions.
Quality aspects of the tissue microarray technique in a population‐based cohort with ductal carcinoma in situ of the breast
Authors: Wärnberg F , Amini R‐M , Goldman M , Jirström K 
Published: November 2008

Aims:  Tissue microarray (TMA) is an efficient technique for analysis of molecular markers. Prospectively collected samples have been reported to give excellent concordance between TMA data and corresponding whole‐sections. The aim was to evaluate the usefulness of TMA in a population‐based cohort of 213 women with ductal carcinoma in situ of the breast (DCIS).Methods and results:  We studied immunohistochemical HER2, oestrogen (ER) and progesterone (PR) receptor status. The prognostic impact was similar for all markers comparing whole sections and TMAs. The proportion of positive tumours was similar regarding HER2 and ER, whereas PR tumours were more frequently positive in the TMAs (P = 0.007). The concordance was 80% (κ value 0.63) between original sections and TMAs. The proportion of successfully analysed tumours was 70%. Smaller tumours had a lower ratio (P < 0.0001) and a larger proportion of mismatched results (P = 0.05).Conclusions:  Retrospective analyses of tumours from cohorts with long‐term follow‐up are indispensable. We have shown that the TMA technique is a useful tool for high‐throughput analysis of DCIS. However, our study has pinpointed some technical hazards within a population‐based cohort, including many small lesions and the poor condition of some donor blocks. Mismatched results may be due to tumour heterogeneity.
Predictive value of needle core biopsy diagnoses of lesions of uncertain malignant potential (B3) in abnormalities detected by mammographic screening
Authors: El‐Sayed M E , Rakha E A , Reed J , Lee A H S , Evans A J , Ellis I O 
Published: November 2008

Aims:  Breast needle core biopsy (NCB) is now a commonplace diagnostic procedure in breast cancer screening, providing accurate diagnoses of both benign and malignant lesions. However, NCB may result in the borderline diagnoses of lesion of uncertain malignant potential (B3) or suspicious of malignancy (B4). The aim was to study a large series of B3 cases from population‐based screening subjects in order to evaluate positive predictive values (PPVs) for malignancy.Methods and results:  The results of 523 NCBs of women screened over a 7‐year period (1999–2006) in the East Midlands region, UK, with a B3 diagnosis who underwent surgical excision, were reviewed and compared with the final excision histology. Five percent of NCBs were reported as B3. The most frequent histological subtypes were atypical intraductal epithelial proliferation (AIDEP) and radial scar/complex sclerosing lesion (RS/CSL). Final excision histology was benign in 417 (80%) and malignant in 106 (20%) subjects (60 ductal carcinoma in situ and 46 invasive carcinoma). Lesion‐specific PPVs were as follows: AIDEP 32%; lobular neoplasia (LN) 30%; RS/CSL with AIDEP or LN 24%; RS/CSL without atypia 9%; papillary lesion with AIDEP or LN 36%; and papillary lesion without atypia 4%. Five of the 32 fibroepithelial lesions with cellular stroma were phyllodes tumours (four benign and one borderline). None of the five mucinous lesions on NCB was malignant.Conclusions:  Our results show that approximately one‐fifth of NCB of screen‐detected breast lesions classified as B3 are malignant on excision, and the likelihood of malignancy varies substantially between different histological subtypes.
Intratumoural heterogeneity of intestinal expression reflects environmental induction and progression‐related loss of induction in undifferentiated‐type gastric carcinomas
Authors: Natsagdorj L , Sugihara H , Bamba M , Hattori T 
Published: November 2008

Aims:  Gene expression in tumours is regulated by environmental as well as genetic/epigenetic factors. This study assessed the environmental factors in intestinal expression of gastric cancers.Methods and results:  We immunohistochemically examined intratumoural heterogeneity in the expression of Cdx2, MUC2, MUC5AC and MUC6 in 39 intramucosal and 49 extramucosally invasive undifferentiated‐type gastric carcinomas (UGCs), consisting of signet ring cell carcinomas showing a layered structure (LS) in the mucosa and dedifferentiated tubular adenocarcinomas without LS and with minor tubular components (TC). The LS retains mucosal vertical polarity with superficial MUC5AC expression. Loss of this polarity was independent of intestinal expression and associated with extramucosal invasion. In LS+ UGCs, intestinal expression was enhanced as the size of mucosal spread increased and was significantly reduced with deeper extramucosal invasion, whereas, in LS−/TC+ UGCs, intestinal expression was frequent and predominant in the mucosa and was insignificantly reduced with deeper extramucosal invasion.Conclusions:  In LS+ UGCs, intestinal expression showed dynamic alteration probably by environmental induction and progression‐related loss of induction, whereas it was relatively stable in LS−/TC+ UGCs. Thus, intestinal expression in UGCs is not useful as a marker of tumour progression because it is also affected by environmental factors and genetic lineage.
Annexin A1 subcellular expression in laryngeal squamous cell carcinoma
Authors: Alves V A F , Nonogaki S , Cury P M , Wünsch‐Filho V , De Carvalho M B , Michaluart‐Júnior P , Moyses R A , Curioni O A , Figueiredo D L A , Scapulatempo‐Neto C , Parra E R , Polachini G M , Silistino‐Souza R , Oliani S M , Silva‐Júnior W A , Nobrega F G ,   Head and Neck Genome Project/GENCAPO, Tajara E H , Zago M A 
Published: November 2008

Aims:  Annexin A1 (ANXA1) is a soluble cytoplasmic protein, moving to membranes when calcium levels are elevated. ANXA1 has also been shown to move to the nucleus or outside the cells, depending on tyrosine‐kinase signalling, thus interfering in cytoskeletal organization and cell differentiation, mostly in inflammatory and neoplastic processes. The aim was to investigate subcellular patterns of immunohistochemical expression of ANXA1 in neoplastic and non‐neoplastic samples from patients with laryngeal squamous cell carcinomas (LSCC), to elucidate the role of ANXA1 in laryngeal carcinogenesis.Methods and results:  Serial analysis of gene expression experiments detected reduced expression of ANXA1 gene in LSCC compared with the corresponding non‐neoplastic margins. Quantitative polymerase chain reaction confirmed ANXA1 low expression in 15 LSCC and eight matched normal samples. Thus, we investigated subcellular patterns of immunohistochemical expression of ANXA1 in 241 paraffin‐embedded samples from 95 patients with LSCC. The results showed ANXA1 down‐regulation in dysplastic, tumourous and metastatic lesions and provided evidence for the progressive migration of ANXA1 from the nucleus towards the membrane during laryngeal tumorigenesis.Conclusions:  ANXA1 dysregulation was observed early in laryngeal carcinogenesis, in intra‐epithelial neoplasms; it was not found related to prognostic parameters, such as nodal metastases.
Comparison of histological parameters for the diagnosis of eosinophilic oesophagitis versus gastro‐oesophageal reflux disease on oesophageal biopsy material
Authors: Mueller S , Neureiter D , Aigner T , Stolte M 
Published: November 2008

Aims:  Eosinophil infiltration of the oesophageal epithelium is the cardinal pathomorphological finding in eosinophilic oesophagitis (EO), but gastro‐oesophageal reflux disease (GORD) is also associated with increased eosinophils. The aim was to compare histological parameters for the diagnosis of EO versus GORD on routinely taken biopsy specimens.Methods and results:  One hundred and five routine biopsy specimens with EO (n = 62), GORD (n = 24) and probable EO (n = 19) from 74 patients (52 men, 22 women; mean age 43.7 years) were analysed for numbers of eosinophils, mast cells, degranulation and qualitative changes of oesophageal epithelium using immunohistochemistry with monoclonal antibodies against eosinophil peroxidase and eosinophil major basic protein and mast cell tryptase. Eosinophil infiltration was significantly higher in EO than in GORD both on haematoxylin and eosin staining (54.8 versus 9.1; P < 0.05) and immunohistochemistry (77.5 versus 24.7; P < 0.05). Eosinophil degranulation was significantly more intense in EO than in GORD (1.16 versus 0.41; P < 0.05). Furthermore, eosinophilia‐codependent secondary qualitative changes of squamous epithelium in EO were generally more extensive than those in GORD.Conclusions:  Histological differential diagnosis of EO and GORD should be based on eosinophil counts, secondary morphological changes of eosinophils and oesophageal squamous epithelium, especially in cases suspicious of EO.
Reg IV expression is associated with cell growth and prognosis of adenoid cystic carcinoma in the salivary gland
Authors: Sasahira T , Oue N , Kirita T , Luo Y , Bhawal U K , Fujii K , Yasui W , Kuniyasu H 
Published: November 2008

Aims:  Regenerating islet‐derived family, member 4 (Reg IV) is associated with the progression of various cancers. The aim was to examine Reg IV expression in adenoid cystic carcinomas (ACCs) in salivary glands.Methods and results:  Reg IV expression was detected by immunohistochemistry and compared with clinicopathological parameters. Expression of phosphorylated epidermal growth factor receptor (pEGFR), phosphorylated AKT (pAKT) and MUC2 was examined by immunohistochemistry. Reg IV function was assessed with Reg IV antisense S‐oligodeoxynucleotides (AS) in ACC3 human ACC cells. Reg IV was expressed by salivary duct epithelia and acinus myoepithelia, but not in squamous epithelia. Reg IV expression was found in 41% (17/41) of ACCs, but in none of 40 oral squamous cell carcinomas (OSCCs) and was associated with nodal metastasis (P = 0.047) and poor prognosis (P = 0.012) in ACCs. Reg IV expression was associated with pEGFR (14/17, 82%) in Reg IV+ ACCs, but had no relationship with pAKT or MUC2 expression in ACCs. Cell growth was inhibited by AS treatment in Reg IV+ ACC3 cells, but not in HSC‐4 OSCC cells, whereas in vitro invasion of neither cell types was affected by AS treatment.Conclusions:  These results suggest that Reg IV might accelerate cell growth and disease progression of ACCs.
Effect of gamma irradiation and sulphitation treatments on keeping quality of white button mushroom Agaricus bisporus (J. Lge)
Authors: Wani Ali M. , Hussain Peerzada R. , Meena Raghuveer S. , Dar Mohmad A. , Mir Mohmad A. 
Published: November 2008

SummaryGamma irradiation, alone and in combination with sulphitation, was tested for preventing the browning and maintaining the quality attributes of the white button mushrooms. Mushrooms were subjected to treatment of gamma irradiation in the dose range of 0.5–2.0 kGy and to combination treatments of sulphitation at a concentration of 0.1% potassium metabisulphite (KMS) and gamma irradiation (dose range 0.5–2.0 kGy) followed by storage at 10 ± 2 °C (RH 85%). A dose of 2.0 kGy significantly reduced the weight loss, prevented browning and mould growth. Cap and veil opening of mushrooms was delayed by 9 days and shelf life was extended by 12 days at a dose level of 2.0 kGy. Sulphitation alone at a concentration of 0.1% KMS was effective in controlling browning only upto 3 days, beyond which both browning and cap opening increased significantly (P ≤ 0.05) and the samples were unacceptable after 6 days of storage. No synergistic effect of sulphitation and irradiation was observed with respect to the shelf‐life extension of mushroom.