bluuebunny/crossref_metadata_2025_split huggingface dataset:
Summary of talks and papers at ISCB-Asia/SCCG 2012
Authors: Tretyakov Konstantin , Goldberg Tatyana , Jin Victor X , Horton Paul 
Published: April 2013

Abstract
The second ISCB-Asia conference of the International Society for Computational Biology took place December 17-19, 2012, in Shenzhen, China. The conference was co-hosted by BGI as the first Shenzhen Conference on Computational Genomics (SCCG).
45 talks were presented at ISCB-Asia/SCCG 2012. The topics covered included software tools, reproducible computing, next-generation sequencing data analysis, transcription and mRNA regulation, protein structure and function, cancer genomics and personalized medicine. Nine of the proceedings track talks are included as full papers in this supplement.
In this report we first give a short overview of the conference by listing some statistics and visualizing the talk abstracts as word clouds. Then we group the talks by topic and briefly summarize each one, providing references to related publications whenever possible. Finally, we close with a few comments on the success of this conference.
Multicenter comparison of PEG-IFN α2a or α2b plus ribavirin for treatment-naïve HCV patient in Korean population
Authors: Jin Young-Joo , Lee Jin-Woo , Lee Jung il , Park Sang Hoon , Park Choong Kee , Kim Young Seok , Jeong Sook-Hyang , Kim Yun Soo , Kim Ju Hyun , Hwang Seong Gyu , Rim Kyu Sung , Yim Hyung Joon , Cheong Jae Youn , Cho Sung Won , Lee June Sung , Park Young Min , Jang Jeong Won , Lee Chun Kyon , Sohn Joo Hyun , Yang Jin Mo , Han Seungbong 
Published: April 2013

AbstractBackgroundTwo recent Italian studies suggested that Pegylated-interferon (PEG-IFN) alfa-2a achieves a higher sustained virological response (SVR) rate than PEG-IFN alfa-2b. We intended to compare the efficacy and safety of PEG-IFN alfa-2a with those of PEG-IFN alfa-2b in Korean patients with chronic hepatitis C virus (HCV).MethodsThis retrospective, multi-center trial was conducted on 661 treatment-naïve chronic HCV patients. Patients received PEG-IFN alfa-2a (180 μg/week; n=402) or PEG-IFN alfa-2b (1.5 μg/kg/week; n=259) with ribavirin (800–1200 mg/day) for 24 or 48 weeks according to HCV genotypes.ResultsEarly virologic response and sustained virologic response (SVR) rates were not significantly different between two PEG-IFN groups both in patients with HCV genotype 1 (allP-values>0.05) and 2/3 (allP-values>0.05). SVR rates were not different between two groups in each categorized baseline characteristics: age (years) (≤50 and >50), HCV viral load (IU/mL) (≤7×105and >7×105), and hepatic fibrosis (F0-2 and F3-4) (allP-values >0.05). In additional analysis for 480 patients who sufficiently complied with treatment doses and duration (80/80/80 rule) and propensity-score matched analysis, SVR rates were not different between two groups both in patients with HCV genotype 1 and 2/3 (allP-values >0.05). Adverse event rates were similar between two groups.ConclusionsUnlike the Western data, efficacy and safety of PEG-IFN alfa-2a were similar to those of PEG-IFN alfa-2b in chronically HCV-infected Korean patients regardless of age, HCV viral load, and hepatic fibrosis.
Public awareness of three major infectious diseases in rural Zhejiang province, China: a cross-sectional study
Authors: Liu He , Li Mei , Jin Mingjuan , Jing Fangyuan , Wang Hui , Chen Kun 
Published: April 2013

Abstract

Background
This study aimed to investigate the level of awareness of and factors associated with major infectious diseases in rural China and to provide the most recent baseline data for the prevention and control of these diseases.

Methods
This cross-sectional study was carried out in Zhejiang province between December 2010 and April 2011. Participants were recruited from 36 villages and interviewed by doctors from the community health service using a structured questionnaire.

Results
The study sample consisted of 36,377 subjects aged 15 to 80 years old. Study results showed that knowledge of HIV was adequate in 44.21% of rural residents; knowledge of TB was adequate in 52.66% of respondents; and knowledge of HBV was adequate in 60.18% of respondents. People in older age groups and with lower education levels were more likely to have low levels of awareness of these three infectious diseases. Participants in the farming industry had poorer awareness of HIV and HBV, while students and factory workers knew little of TB. The proportions of people reporting being fully satisfied with the control policies for HIV, TB and HBV were 37.70%, 34.25% and 36.12%, respectively.

Conclusions
The level of awareness of HIV, TB and HBV is still low among rural residents. Further national disease control plans for major infectious diseases should emphasise effective and comprehensive health education campaigns to increase public awareness of these diseases in rural areas of China.
Pheochromocytoma of the urinary bladder: a systematic review of the contemporary literature
Authors: Beilan Jonathan A , Lawton Adrienne , Hajdenberg Julio , Rosser Charles J 
Published: April 2013

AbstractBackgroundPheochromocytoma (paraganglioma) of the urinary bladder is a rare tumor. Herein we sought to review the contemporary literature on pheochromocytomas of the urinary bladder in order to further illustrate the presentation, treatment options and outcomes of patients diagnosed with these tumors.MethodsA comprehensive review of the current literature was conducted according to the PRISMA guidelines by accessing the NCBI PubMed database and using the search terms “paraganglioma, pheochromocytoma, bladder.” This search resulted in the identification of 186 articles published between January 1980 and April 2012 of which 80 articles were ultimately included in our analysis.ResultsPheochromocytomas usually occurred in young adult Caucasians (mean age, 43.3 years; range,11–84 years). According to the literature, the most common symptoms and signs of pheochromocytomas of the urinary bladder were hypertension, headache, and hematuria. Of the 77 cases that commented on catecholamine production, 65 patients had biochemically functional tumors. Approximately 20% of patients were treated by transurethral resection alone, 70% by partial cystectomy and 10% by radical cystectomy. The 75 patients with follow-up information had a mean follow-up of 35 months. At the time of last follow-up, 15 (14.2%) had disease recurrence, 10 (9.4%) had metastasis, and 65 (61.3%) were alive.ConclusionsPheochromocytomas of the urinary bladder tend to be functional and occur mostly in young adult Caucasians. Patients with localized tumors have an extremely favorable prognosis and may be managed by less aggressive modalities, whereas patients with metastatic disease have a significant reduction in survival rates despite aggressive treatment.
Extract of Scutellaria baicalensis inhibits dengue virus replication
Authors: Zandi Keivan , Lim Tong-Hye , Rahim Nor-Aziyah , Shu Meng-Hooi , Teoh Boon-Teong , Sam Sing-Sin , Danlami Mohammed-Bashar , Tan Kim-Kee , Abubakar Sazaly 
Published: April 2013

AbstractBackgroundScutellaria baicalensis(S. baicalensis) is one of the traditional Chinese medicinal herbs that have been shown to possess many health benefits. In the present study, we evaluated thein vitroantiviral activity of aqueous extract of the roots ofS. baicalensisagainst all the four dengue virus (DENV) serotypes.MethodsAqueous extract ofS. baicalensiswas prepared by microwave energy steam evaporation method (MEGHE™), and the anti-dengue virus replication activity was evaluated using the foci forming unit reduction assay (FFURA) in Vero cells. Quantitative real-time polymerase chain reaction (qRT-PCR) assay was used to determine the actual dengue virus RNA copy number. The presence of baicalein, a flavonoid known to inhibit dengue virus replication was determined by mass spectrometry.ResultsThe IC50values for theS. baicalensisextract on Vero cells following DENV adsorption ranged from 86.59 to 95.19 μg/mL for the different DENV serotypes. The IC50values decreased to 56.02 to 77.41 μg/mL when cells were treated with the extract at the time of virus adsorption for the different DENV serotypes. The extract showed potent direct virucidal activity against extracellular infectious virus particles with IC50that ranged from 74.33 to 95.83 μg/mL for all DENV serotypes. Weak prophylactic effects with IC50values that ranged from 269.9 to 369.8 μg/mL were noticed when the cells were pre-treated 2 hours prior to virus inoculation. The concentration of baicalein in theS. baicalensisextract was ~1% (1.03 μg/gm dried extract).ConclusionsOur study demonstrates thein vitroanti-dengue virus replication property ofS. baicalensisagainst all the four DENV serotypes investigated. The extract reduced DENV infectivity and replication in Vero cells. The extract was rich in baicalein, and could be considered for potential development of anti-DENV therapeutics.
Conversion of algorithms by releasing projection for minimization problems
Authors: Yao Yonghong , Liou Yeong-Cheng , Kang Shin Min 
Published: April 2013

Abstract
The projection methods for solving the minimization problems have been extensively considered in many practical problems, for example, the least-square problem. However, the computational difficulty of the projection might seriously affect the efficiency of the method. The purpose of this paper is to construct two algorithms by releasing projection for solving the minimization problem with the feasibility sets such as the set of fixed points of nonexpansive mappings and the solution set of the equilibrium problem.

MSC:47J05, 47J25, 47H09, 65J15.
Fixed point of a pair of contractive dominated mappings on a closed ball in an ordered dislocated metric space
Authors: Arshad Muhammad , Shoaib Abdullah , Beg Ismat 
Published: April 2013

AbstractCommon fixed point results for mappings satisfying locally contractive conditions on a closed ball in an ordered complete dislocated metric space have been established. The notion of dominated mappings is applied to approximate the unique solution of nonlinear functional equations. Our results improve several well-known conventional results.MSC:46S40, 47H10, 54H25.
Fixed point theorems for nonlinear non-self mappings in Hilbert spaces and applications
Authors: Takahashi Wataru , Wong Ngai-Ching , Yao Jen-Chih 
Published: April 2013

Abstract
Recently, Kawasaki and Takahashi (J. Nonlinear Convex Anal. 14:71-87, 2013) defined a broad class of nonlinear mappings, called widely more generalized hybrid, in a Hilbert space which contains generalized hybrid mappings (Kocourek et al. in Taiwan. J. Math. 14:2497-2511, 2010) and strict pseudo-contractive mappings (Browder and Petryshyn in J. Math. Anal. Appl. 20:197-228, 1967). They proved fixed point theorems for such mappings. In this paper, we prove fixed point theorems for widely more generalized hybrid non-self mappings in a Hilbert space by using the idea of Hojo et al. (Fixed Point Theory 12:113-126, 2011) and Kawasaki and Takahashi fixed point theorems (J. Nonlinear Convex Anal. 14:71-87, 2013). Using these fixed point theorems for non-self mappings, we proved the Browder and Petryshyn fixed point theorem (J. Math. Anal. Appl. 20:197-228, 1967) for strict pseudo-contractive non-self mappings and the Kocourek et al. fixed point theorem (Taiwan. J. Math. 14:2497-2511, 2010) for super hybrid non-self mappings. In particular, we solve a fixed point problem.

MSC:Primary 47H10; secondary 47H05.
Race, genetic determinism and the media: An exploratory study of media coverage of genetics and Indigenous Australians
Authors: Kowal Emma , Frederic Gerald 
Published: April 2013

Abstract
Social scientists and Indigenous people have voiced concerns that media messages about genetics and race may increase the public's belief in genetic determinism and even increase levels of racism. The degree of genetic determinism in media messages has been examined as a determining factor. This study is the first to consider the implications of this area of scholarship for the indigenous minority in Australia. A search of the last two decades of major Australian newspapers was undertaken for articles that discussed Indigenous Australians and genetics. The review found 212 articles, of which 58 concerned traits or conditions that were presented in a genetically deterministic or antideterministic fashion. These 58 articles were analysed by topic, slant, and time period. Overall, 23 articles were anti-deterministic, 18 were deterministic, 14 presented both sides and three were ambiguous. There was a spike in anti-deterministic articles in the years after the Human Genome Diversity Project, and a parallel increase in deterministic articles since the completion of the Human Genome Project in 2000. Potential implications of the nature of media coverage of genetics for Indigenous Australians is discussed. Further research is required to test directly the impact of these messages on Australians.
Renal epithelioid angiomyolipoma with a negative premelanosome marker immunoprofile: a case report and review of the literature
Authors: Hohensee Samantha E , La Rosa Francisco G , Homer Petra , Suby-Long Thomas , Wilson Shandra , Lucia M Scott , Iczkowski Kenneth A 
Published: April 2013

Abstract

Introduction
The rare variant of renal epithelioid/pleomorphic angiomyolipoma has been reported in approximately 120 cases. One of the most important characteristics to differentiate these tumors from other renal cell neoplasms is their typical reactivity to premelanosome antigens. If such a tumor does not stain for HMB-45 or Melan-A, a specific diagnosis of epithelioid pleomorphic angiomyolipoma cannot be made with certainty.

Case presentation
We present here what is, to the best of our knowledge, the first case of epithelioid/pleomorphic angiomyolipoma of the kidney in a 50-year-old Caucasian man with no history of tuberous sclerosis, and with a tumor marker profile negative for several premelanosome antigens. The tumor was composed of sheets of pleomorphic, round to polygonal epithelioid cells with prominent eosinophilic cytoplasm, large nuclei, many multinucleated, and very prominent nucleoli. There were prominent vessels and rare interspersed smooth muscle fibers, but adipocytes were not identified. A tumor marker profile showed tumor cell reactivity for CD68, calponin and focally for CD10. Intervening smooth muscle was reactive with smooth muscle actin. The tumor lacked reactivity for melanin-associated antigens HMB-45 and Melan-A, and for CD31, pan-cytokeratin (AE1/3) and desmin. Electron microscopic examination of tumor cells confirmed the presence of premelanosome-like granules.

Conclusions
Based on the characteristic microscopic appearance of this tumor, and its overall tumor marker profile, we concluded this was a renal epithelioid/pleomorphic angiomyolipoma with a negative premelanosome antigen phenotype.
Unexplained cyanosis revealing hepatopulmonary syndrome in a child with asymptomatic congenital hepatic fibrosis: a case report
Authors: Abdul Wahab Atqah , Al-Mansoori Maryam , El-Hawli Mariam , Kini Vishwanatha 
Published: April 2013

Abstract

Introduction
Hepatopulmonary syndrome is a rare disease that affects patients of any age with acute or chronic liver disease. Liver transplantation is the only therapeutic option of proved benefit, and can result in substantial improvement or total improvement in postoperative gas exchange abnormalities.

Case presentation
We report the case of a cyanotic 13-year-old Pakistani boy whose chest computed tomography scan showed normal lung fields and mediastinum with incidental findings of a prominent liver surface with a collateral vein connecting a portal cavernoma to the dilated terminal inferior vena cava. Sonography of his abdomen along with a portal venous Doppler study showed multiple collateral veins replacing the portal vein. A liver biopsy revealed congenital hepatic fibrosis. Contrast-enhanced echocardiography with agitated saline and a 99m Technetium-macroaggregated albumin perfusion lung scan confirmed intrapulmonary shunting. The patient underwent a successful liver transplantation that resulted in improved gas exchange.

Conclusions
Hepatopulmonary syndrome should be included in the differential diagnosis of unexplained hypoxemia with an evaluation of possible portal hypertension or liver disease even in the absence of other clinical symptoms.
Clinical course and visual outcome in patients with diabetes mellitus and uveitis
Authors: Oswal Kadambari S , Sivaraj Ramesh R , Murray Philip I , Stavrou Panagiota 
Published: April 2013

Abstract

Purpose
We report the clinical course and visual outcome of patients with diabetes mellitus (DM) who subsequently developed uveitis from any cause.

Methods
Longitudinal, retrospective case note review.

Results
A total of 36 patients (M/F: 18/18, 58 eyes) were included, Of the 36 patients, 35 had Type 2 DM and one had Type 1 DM. Mean age of onset of DM was 49 years and uveitis 55 years. The uveitis was bilateral in 22 (61%) patients. There were 19 patients with anterior uveitis, 12 with panuveitis and 5 with intermediate uveitis. Mean follow up was 4.4 years (range 1-18). Mean number of uveitis recurrences was 3 (range 1-7). Causes of vision of 6/18 or worse appeared related to the uveitis in 9 eyes and diabetes in 4 eyes. Cataract occurred in 22 eyes, glaucoma in 17 eyes, and cystoid macular oedema in 10 eyes. Diabetic retinopathy was detected in 38 (65.5%) eyes (29 non-proliferative including 6 with clinically significant macular oedema, and 9 proliferative). Progression of diabetic retinopathy to proliferative stage occurred in 7 eyes of 4 patients over a mean duration of 4.4 years. In 10 patients with active uveitis the mean HbA1c was 80 mmol/mol [9.5%], (range 49-137 [6.6-14.7]), and 67 mmol/mol [8.3%] (range 46-105 [6.4-11.8]) when the uveitis was quiescent, p = 0.01. Better glycaemic control was required in 10 patients during episodes of uveitis.

Conclusions
Patients with DM who develop uveitis may have a high complication rate, reduced vision and poor glycaemic control. Checking blood glucose during episodes of uveitis is important.
A test-retest fMRI dataset for motor, language and spatial attention functions
Authors: Gorgolewski Krzysztof J , Storkey Amos , Bastin Mark E , Whittle Ian R , Wardlaw Joanna M , Pernet Cyril R 
Published: April 2013

Abstract

Background
Since its inception over twenty years ago, functional magnetic resonance imaging (fMRI) has been used in numerous studies probing neural underpinnings of human cognition. However, the between session variance of many tasks used in fMRI remains understudied. Such information is especially important in context of clinical applications. A test-retest dataset was acquired to validate fMRI tasks used in pre-surgical planning. In particular, five task-related fMRI time series (finger, foot and lip movement, overt verb generation, covert verb generation, overt word repetition, and landmark tasks) were used to investigate which protocols gave reliable single-subject results. Ten healthy participants in their fifties were scanned twice using an identical protocol 2–3 days apart. In addition to the fMRI sessions, high-angular resolution diffusion tensor MRI (DTI), and high-resolution 3D T1-weighted volume scans were acquired.

Findings
Reliability analyses of fMRI data showed that the motor and language tasks were reliable at the subject level while the landmark task was not, despite all paradigms showing expected activations at the group level. In addition, differences in reliability were found to be mostly related to the tasks themselves while task-by-motion interaction was the major confounding factor.

Conclusions
Together, this dataset provides a unique opportunity to investigate the reliability of different fMRI tasks, as well as methods and algorithms used to analyze, de-noise and combine fMRI, DTI and structural T1-weighted volume data.
Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium
Authors: Meier-Abt Fabienne , Milani Emanuela , Roloff Tim , Brinkhaus Heike , Duss Stephan , Meyer Dominique S , Klebba Ina , Balwierz Piotr J , van Nimwegen Erik , Bentires-Alj Mohamed 
Published: April 2013

Abstract
Introduction
Early pregnancy has a strong protective effect against breast cancer in humans and rodents, but the underlying mechanism is unknown. Because breast cancers are thought to arise from specific cell subpopulations of mammary epithelia, we studied the effect of parity on the transcriptome and the differentiation/proliferation potential of specific luminal and basal mammary cells in mice.

Methods
Mammary epithelial cell subpopulations (luminal Sca1-, luminal Sca1+, basal stem/progenitor, and basal myoepithelial cells) were isolated by flow cytometry from parous and age-matched virgin mice and examined by using a combination of unbiased genomics, bioinformatics, in vitro colony formation, and in vivo limiting dilution transplantation assays. Specific findings were further investigated with immunohistochemistry in entire glands of parous and age-matched virgin mice.

Results
Transcriptome analysis revealed an upregulation of differentiation genes and a marked decrease in the Wnt/Notch signaling ratio in basal stem/progenitor cells of parous mice. Separate bioinformatics analyses showed reduced activity for the canonical Wnt transcription factor LEF1/TCF7 and increased activity for the Wnt repressor TCF3. This finding was specific for basal stem/progenitor cells and was associated with downregulation of potentially carcinogenic pathways and a reduction in the proliferation potential of this cell subpopulation in vitro and in vivo. As a possible mechanism for decreased Wnt signaling in basal stem/progenitor cells, we found a more than threefold reduction in the expression of the secreted Wnt ligand Wnt4 in total mammary cells from parous mice, which corresponded to a similar decrease in the proportion of Wnt4-secreting and estrogen/progesterone receptor-positive cells. Because recombinant Wnt4 rescued the proliferation defect of basal stem/progenitor cells in vitro, reduced Wnt4 secretion appears to be causally related to parity-induced alterations of basal stem/progenitor cell properties in mice.

Conclusions
By revealing that parity induces differentiation and downregulates the Wnt/Notch signaling ratio and the in vitro and in vivo proliferation potential of basal stem/progenitor cells in mice, our study sheds light on the long-term consequences of an early pregnancy. Furthermore, it opens the door to future studies assessing whether inhibitors of the Wnt pathway may be used to mimic the parity-induced protective effect against breast cancer.
EMu: probabilistic inference of mutational processes and their localization in the cancer genome
Authors: Fischer Andrej , Illingworth Christopher JR , Campbell Peter J , Mustonen Ville 
Published: April 2013

AbstractThe spectrum of mutations discovered in cancer genomes can be explained by the activity of a few elementary mutational processes. We present a novel probabilistic method, EMu, to infer the mutational signatures of these processes from a collection of sequenced tumors. EMu naturally incorporates the tumor-specific opportunity for different mutation types according to sequence composition. Applying EMu to breast cancer data, we derive detailed maps of the activity of each process, both genome-wide and within specific local regions of the genome. Our work provides new opportunities to study the mutational processes underlying cancer development. EMu is available at http://www.sanger.ac.uk/resources/software/emu/.