bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of ischemia before vein grafting on early hyperplasia of the graft and the dynamic changes of the intima after grafting
Authors: Zou RongJiang , Sun MingJuan , Lu ZhiQian , Guo QingKui 
Published: September 2012

Abstract

Background
To investigate both the influence of ischemia before grafting on early hyperplasia of the vein grafts, and the dynamic changes of the intima after grafting in a rabbit model of vein graft disease.

Methods
We performed paired vein graft experiments under different ischemic conditions (15 vs. 60 min; 15 vs. 90 min) in the neck of the rabbits and compared the differences between the grafts. Clopidogrel, an anti-platelet agent, was administered before and after surgery. Twenty-eight days after the grafting procedure, the veins were evaluated microscopically. The dynamic changes of the intima after grafting were evaluated by scanning electron microscopy over time.

Results
The vein grafts subjected to 60- or 90-min ischemia exhibited no differences compared to those subjected to 15-min ischemia in terms of the mean thickness of the intimal, medial, and adventitial layers of the graft. Similarly, there was no difference in the Ki-67 labeling index (proliferation marker) between the vein grafts. Vein grafts with 15-min ischemia lost endothelial cells (ECs) but healed by 3 days post graft, whereas vein grafts with 90-min ischemia suffered serious EC loss, which was restored with new ECs during days 2 to 14 post graft.

Conclusions
Ninety-minute ischemia before vein grafting can cause serious EC loss, but does not increase early intimal hyperplasia when clopidogrel is administered. Protecting the vein from ischemia and reperfusion injury preserves ECs.
Reduced elastogenesis: a clue to the arteriosclerosis and emphysematous changes in Schimke immuno-osseous dysplasia?
Authors: Morimoto Marie , Yu Zhongxin , Stenzel Peter , Clewing J Marietta , Najafian Behzad , Mayfield Christy , Hendson Glenda , Weinkauf Justin G , Gormley Andrew K , Parham David M , Ponniah Umakumaran , André Jean-Luc , Asakura Yumi , Basiratnia Mitra , Bogdanović Radovan , Bokenkamp Arend , Bonneau Dominique , Buck Anna , Charrow Joel , Cochat Pierre , Cordeiro Isabel , Deschenes Georges , Fenkçi M Semin , Frange Pierre , Fründ Stefan , Fryssira Helen , Guillen-Navarro Encarna , Keller Kory , Kirmani Salman , Kobelka Christine , Lamfers Petra , Levtchenko Elena , Lewis David B , Massella Laura , McLeod D Ross , Milford David V , Nobili François , Saraiva Jorge M , Semerci C Nur , Shoemaker Lawrence , Stajić Nataša , Stein Anja , Taha Doris , Wand Dorothea , Zonana Jonathan , Lücke Thomas , Boerkoel Cornelius F 
Published: September 2012

Abstract

Background
Arteriosclerosis and emphysema develop in individuals with Schimke immuno-osseous dysplasia (SIOD), a multisystem disorder caused by biallelic mutations in SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1). However, the mechanism by which the vascular and pulmonary disease arises in SIOD remains unknown.

Methods
We reviewed the records of 65 patients with SMARCAL1 mutations. Molecular and immunohistochemical analyses were conducted on autopsy tissue from 4 SIOD patients.

Results
Thirty-two of 63 patients had signs of arteriosclerosis and 3 of 51 had signs of emphysema. The arteriosclerosis was characterized by intimal and medial hyperplasia, smooth muscle cell hyperplasia and fragmented and disorganized elastin fibers, and the pulmonary disease was characterized by panlobular enlargement of air spaces. Consistent with a cell autonomous disorder, SMARCAL1 was expressed in arterial and lung tissue, and both the aorta and lung of SIOD patients had reduced expression of elastin and alterations in the expression of regulators of elastin gene expression.

Conclusions
This first comprehensive study of the vascular and pulmonary complications of SIOD shows that these commonly cause morbidity and mortality and might arise from impaired elastogenesis. Additionally, the effect of SMARCAL1 deficiency on elastin expression provides a model for understanding other features of SIOD.
PathNet: a tool for pathway analysis using topological information
Authors: Dutta Bhaskar , Wallqvist Anders , Reifman Jaques 
Published: September 2012

Abstract

Background
Identification of canonical pathways through enrichment of differentially expressed genes in a given pathway is a widely used method for interpreting gene lists generated from high-throughput experimental studies. However, most algorithms treat pathways as sets of genes, disregarding any inter- and intra-pathway connectivity information, and do not provide insights beyond identifying lists of pathways.

Results
We developed an algorithm (PathNet) that utilizes the connectivity information in canonical pathway descriptions to help identify study-relevant pathways and characterize non-obvious dependencies and connections among pathways using gene expression data. PathNet considers both the differential expression of genes and their pathway neighbors to strengthen the evidence that a pathway is implicated in the biological conditions characterizing the experiment. As an adjunct to this analysis, PathNet uses the connectivity of the differentially expressed genes among all pathways to score pathway contextual associations and statistically identify biological relations among pathways. In this study, we used PathNet to identify biologically relevant results in two Alzheimer’s disease microarray datasets, and compared its performance with existing methods. Importantly, PathNet identified de-regulation of the ubiquitin-mediated proteolysis pathway as an important component in Alzheimer’s disease progression, despite the absence of this pathway in the standard enrichment analyses.

Conclusions
PathNet is a novel method for identifying enrichment and association between canonical pathways in the context of gene expression data. It takes into account topological information present in pathways to reveal biological information. PathNet is available as an R workspace image fromhttp://www.bhsai.org/downloads/pathnet/.
Gastric lipoma presenting as a giant bulging mass in an oligosymptomatic patient: a case report
Authors: Neto Francisco Américo Fernandes , Ferreira Maria Cristina Furian , Bertoncello Luiz Carlos Nascimento , Neto André Amate , de Aveiro Wilson Chubassi , Bento Caroline Agnelli , Cecchino Gustavo Nardini , Rocha Marco Antonio Mendes 
Published: September 2012

Abstract

Introduction
Lipomas of the gastrointestinal tract are a rare condition. Only 5% are of gastric origin, and this corresponds to 2% to 3% of all benign tumors of the stomach and less than 1% of all gastric neoplasms. It is our purpose to report an unusual presentation of a giant gastric lipoma in an oligosymptomatic patient and highlight the importance of discussing differential diagnosis in this situation. A review of the literature has shown that this is one of the largest gastric lipomas described.

Case presentation
We describe a rare case of a benign gastric tumor with uncommon features in a 63-year-old Caucasian woman. She was admitted with abdominal discomfort, nausea, and upper abdominal fullness after eating. The lesion was suspicious of malignancy because of its dimension and central contrast enhancement on computed tomography. Conventional upper digestive endoscopy revealed a large bulging mass in the gastric posterior wall and three ulcerated areas. In this procedure, a technical limitation due to the location of the mass in the submucosa prevented an adequate biopsy from being obtained. The fragments obtained from the ulcers revealed nothing but necrotic mucosa. Our patient underwent a subtotal gastrectomy and D1 lymphadenectomy with a Roux-en-Y reconstruction. Macroscopic findings revealed a 12 × 8 × 6cm mass with a volume of 576cm3, and the histological pattern demonstrated well-differentiated mature adipose tissue surrounded by a fibrous capsule, confirming the diagnosis of gastric submucosal lipoma.

Conclusions
Gastric lipoma is a rare benign disease that eventually simulates a malignant tumor.
Transcriptomic analysis of the oleaginous microalga Neochloris oleoabundans reveals metabolic insights into triacylglyceride accumulation
Authors: Rismani-Yazdi Hamid , Haznedaroglu Berat Z , Hsin Carol , Peccia Jordan 
Published: September 2012

AbstractBackgroundThe lack of sequenced genomes for oleaginous microalgae limits our understanding of the mechanisms these organisms utilize to become enriched in triglycerides. Here we report thede novotranscriptome assembly and quantitative gene expression analysis of the oleaginous microalgaNeochloris oleoabundans, with a focus on the complex interaction of pathways associated with the production of the triacylglycerol (TAG) biofuel precursor.ResultsAfter growth under nitrogen replete and nitrogen limiting conditions, we quantified the cellular content of major biomolecules including total lipids, triacylglycerides, starch, protein, and chlorophyll. Transcribed genes were sequenced, the transcriptome was assembledde novo, and the expression of major functional categories, relevant pathways, and important genes was quantified through the mapping of reads to the transcriptome. Over 87 million, 77 base pair high quality reads were produced on the Illumina HiSeq sequencing platform. Metabolite measurements supported by genes and pathway expression results indicated that under the nitrogen-limiting condition, carbon is partitioned toward triglyceride production, which increased fivefold over the nitrogen-replete control. In addition to the observed overexpression of the fatty acid synthesis pathway, TAG production during nitrogen limitation was bolstered by repression of the β-oxidation pathway, up-regulation of genes encoding for the pyruvate dehydrogenase complex which funnels acetyl-CoA to lipid biosynthesis, activation of the pentose phosphate pathway to supply reducing equivalents to inorganic nitrogen assimilation and fatty acid biosynthesis, and the up-regulation of lipases—presumably to reconstruct cell membranes in order to supply additional fatty acids for TAG biosynthesis.ConclusionsOur quantitative transcriptome study reveals a broad overview of how nitrogen stress results in excess TAG production inN. oleoabundans, and provides a variety of genetic engineering targets and strategies for focused efforts to improve the production rate and cellular content of biofuel precursors in oleaginous microalgae.
LibKiSAO: a Java library for Querying KiSAO
Authors: Zhukova Anna , Adams Richard , Laibe Camille , Le Novère Nicolas 
Published: September 2012

Abstract

Background
The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of Systems Biology models, their characteristics, parameters and inter-relationships. KiSAO enables the unambiguous identification of algorithms from simulation descriptions. Information about analogous methods having similar characteristics and about algorithm parameters incorporated into KiSAO is desirable for simulation tools. To retrieve this information programmatically an application programming interface (API) for KiSAO is needed.

Findings
We developed libKiSAO, a Java library to enable querying of the KiSA Ontology. It implements methods to retrieve information about simulation algorithms stored in KiSAO, their characteristics and parameters, and methods to query the algorithm hierarchy and search for similar algorithms providing comparable results for the same simulation set-up. Using libKiSAO, simulation tools can make logical inferences based on this knowledge and choose the most appropriate algorithm to perform a simulation. LibKiSAO also enables simulation tools to handle a wider range of simulation descriptions by determining which of the available methods are similar and can be used instead of the one indicated in the simulation description if that one is not implemented.

Conclusions
LibKiSAO enables Java applications to easily access information about simulation algorithms, their characteristics and parameters stored in the OWL-encoded Kinetic Simulation Algorithm Ontology. LibKiSAO can be used by simulation description editors and simulation tools to improve reproducibility of computational simulation tasks and facilitate model re-use.
Technical and clinical analysis of microEEG: a miniature wireless EEG device designed to record high-quality EEG in the emergency department
Authors: Omurtag Ahmet , Baki Samah G Abdel , Chari Geetha , Cracco Roger Q , Zehtabchi Shahriar , Fenton André A , Grant Arthur C 
Published: September 2012

Abstract

Background
We describe and characterize the performance of microEEG compared to that of a commercially available and widely used clinical EEG machine. microEEG is a portable, battery-operated, wireless EEG device, developed by Bio-Signal Group to overcome the obstacles to routine use of EEG in emergency departments (EDs).

Methods
The microEEG was used to obtain EEGs from healthy volunteers in the EEG laboratory and ED. The standard system was used to obtain EEGs from healthy volunteers in the EEG laboratory, and studies recorded from patients in the ED or ICU were also used for comparison. In one experiment, a signal splitter was used to record simultaneous microEEG and standard EEG from the same electrodes.

Results
EEG signal analysis techniques indicated good agreement between microEEG and the standard system in 66 EEGs recorded in the EEG laboratory and the ED. In the simultaneous recording the microEEG and standard system signals differed only in a smaller amount of 60 Hz noise in the microEEG signal. In a blinded review by a board-certified clinical neurophysiologist, differences in technical quality or interpretability were insignificant between standard recordings in the EEG laboratory and microEEG recordings from standard or electrode cap electrodes in the ED or EEG laboratory. The microEEG data recording characteristics such as analog-to-digital conversion resolution (16 bits), input impedance (>100MΩ), and common-mode rejection ratio (85 dB) are similar to those of commercially available systems, although the microEEG is many times smaller (88 g and 9.4 × 4.4 × 3.8 cm).

Conclusions
Our results suggest that the technical qualities of microEEG are non-inferior to a standard commercially available EEG recording device. EEG in the ED is an unmet medical need due to space and time constraints, high levels of ambient electrical noise, and the cost of 24/7 EEG technologist availability. This study suggests that using microEEG with an electrode cap that can be applied easily and quickly can surmount these obstacles without compromising technical quality.
OGRO: The Overview of functionally characterized Genes in Rice online database
Authors: Yamamoto Eiji , Yonemaru Jun-ichi , Yamamoto Toshio , Yano Masahiro 
Published: September 2012

Abstract

Background
The high-quality sequence information and rich bioinformatics tools available for rice have contributed to remarkable advances in functional genomics. To facilitate the application of gene function information to the study of natural variation in rice, we comprehensively searched for articles related to rice functional genomics and extracted information on functionally characterized genes.

Results
As of 31 March 2012, 702 functionally characterized genes were annotated. This number represents about 1.6% of the predicted loci in the Rice Annotation Project Database. The compiled gene information is organized to facilitate direct comparisons with quantitative trait locus (QTL) information in the Q-TARO database. Comparison of genomic locations between functionally characterized genes and the QTLs revealed that QTL clusters were often co-localized with high-density gene regions, and that the genes associated with the QTLs in these clusters were different genes, suggesting that these QTL clusters are likely to be explained by tightly linked but distinct genes. Information on the functionally characterized genes compiled during this study is now available in the O verview of Functionally Characterized G enes in R ice O nline database (OGRO) on the Q-TARO website (http://qtaro.abr.affrc.go.jp/ogro). The database has two interfaces: a table containing gene information, and a genome viewer that allows users to compare the locations of QTLs and functionally characterized genes.

Conclusions
OGRO on Q-TARO will facilitate a candidate-gene approach to identifying the genes responsible for QTLs. Because the QTL descriptions in Q-TARO contain information on agronomic traits, such comparisons will also facilitate the annotation of functionally characterized genes in terms of their effects on traits important for rice breeding. The increasing amount of information on rice gene function being generated from mutant panels and other types of studies will make the OGRO database even more valuable in the future.
The effect of Camellia Sinensis (green tea) mouthwash on plaque-induced gingivitis: a single-blinded randomized controlled clinical trial
Authors: Jenabian Niloofar , Moghadamnia Ali Akbar , Karami Elaheh , Mir A Poorsattar Bejeh 
Published: September 2012

Abstract

Abstract
Background and the purpose of the Study
Complementary medicine received high attention during last decades. We aimed to assess the efficacy of Green tea mouthwash on plaque-induced gingivitis as the most common form of periodontal disease.

Methods and materials
We designed a single blinded placebo controlled clinical trial. High school female students with chronic generalized plaque-induced gingivitis were distributed to receive either 5 ml of Green tea 5% two times/day or normal saline with the same dosage. Gingival index (Sillness & Loe), plaque index (Sillness & Loe) and bleeding index (Barnett) were recorded at baseline and five consecutive weeks. Comparisons were made by a general linear model, repeated measure ANOVA and a Bonferroni test applied for multiple comparisons.

Results
Twenty five students were recruited in each arm of the study. A significant improvement was observed in all periodontal indices during the study (P < 0.001). Two groups were contrasted by changing patterns of alteration of indices (P < 0.05). Although total amount of improvement was higher in mouthwash group, the differences did not reach a statistically significant level (P > 0.05, observed power for GI: 0.09, PI: 0.11 and BI: 0.07).

Conclusion
Green tea mouthwash may be a safe and feasible adjunct treatment for inflammatory periodontal diseases. A future larger scale study is warranted for better evaluating the effect of green tea.
Longitudinal neuroimaging and neuropsychological profiles of frontotemporal dementia with C9ORF72 expansions
Authors: Mahoney Colin J , Downey Laura E , Ridgway Gerard R , Beck Jon , Clegg Shona , Blair Melanie , Finnegan Sarah , Leung Kelvin K , Yeatman Tom , Golden Hannah , Mead Simon , Rohrer Jonathan D , Fox Nick C , Warren Jason D 
Published: September 2012

Abstract
Introduction
Frontotemporal dementia (FTD) is a common cause of early-onset dementia with a significant genetic component, as underlined by the recent identification of repeat expansions in the gene C9ORF72 as a major cause of FTD and motor neuron disease. Understanding the neurobiology and clinical phenomenology of this novel mutation is currently a major research focus. However, few data are available concerning the longitudinal evolution of this genetic disease. Here we present longitudinal neuropsychological and neuroimaging data on a cohort of patients with pathological repeat expansions in C9ORF72.

Methods
Following a review of the University College London FTD DNA database, 20 cases were retrospectively identified with a C9ORF72 expansion. Twelve cases had longitudinal neuropsychology data available and six of these cases also had longitudinal volumetric brain magnetic resonance imaging. Cortical and subcortical volumes were extracted using FreeSurfer. Rates of whole brain, hemispheric, cerebellar and ventricular change were calculated for each subject. Nonlinear fluid registration of follow-up to baseline scan was performed to visualise longitudinal intra-subject patterns of brain atrophy and ventricular expansion.

Results
Patients had low average verbal and performance IQ at baseline that became impaired (< 5th percentile) at follow-up. In particular, visual memory, naming and dominant parietal skills all showed deterioration. Mean rates of whole brain atrophy (1.4%/year) and ventricular expansion (3.2 ml/year) were substantially greater in patients with the C9ORF72 mutation than in healthy controls; atrophy was symmetrical between the cerebral hemispheres within the C9ORF72 mutation group. The thalamus and cerebellum showed significant atrophy whereas no cortical areas were preferentially affected. Longitudinal fluid imaging in individual patients demonstrated heterogeneous patterns of progressive volume loss; however, ventricular expansion and cerebellar volume loss were consistent findings.

Conclusion
Disease evolution in C9ORF72-associated FTD is linked neuropsychologically with increasing involvement of parietal and amnestic functions, and neuroanatomically with rather diffuse and variable cortical and central atrophy but more consistent involvement of the cerebellum and thalamus. These longitudinal profiles are consistent with disease spread within a distributed subcortical network and demonstrate the feasibility of longitudinal biomarkers for tracking the evolution of the C9ORF72 mutation phenotype.
Expression of IL-20 in synovium and lesional skin of patients with psoriatic arthritis: differential response to alefacept treatment
Authors: Lebre Maria C , Jonckheere Christina L , Kraan Maarten C , van Kuijk Arno WR , Bos Jan D , de Rie Menno , Gerlag Danielle M , Tak Paul P 
Published: September 2012

Abstract

Introduction

Psoriatic arthritis (PsA) is an inflammatory joint disease associated with psoriasis. Alefacept (a lymphocyte function-associated antigen (LFA)-3 Ig fusion protein that binds to CD2 and functions as an antagonist to T-cell activation) has been shown to result in improvement in psoriasis but has limited effectiveness in PsA. Interleukin-20 (IL-20) is a key proinflammatory cytokine involved in the pathogenesis of psoriasis. The effects of alefacept treatment on IL-20 expression in the synovium of patients with psoriasis and PsA are currently unknown.

Methods

Eleven patients with active PsA and chronic plaque psoriasis were treated with alefacept (7.5 mg per week for 12 weeks) in an open-label study. Skin biopsies were taken before and after 1 and 6 weeks, whereas synovial biopsies were obtained before and 4 and 12 weeks after treatment. Synovial biopsies from patients with rheumatoid arthritis (RA) (n = 10) were used as disease controls. Immunohistochemical analysis was performed to detect IL-20 expression, and stained synovial tissue sections were evaluated with digital image analysis. Double staining was performed with IL-20 and CD68 (macrophages), and conversely with CD55 (fibroblast-like synoviocytes, FLSs) to determine the phenotype of IL-20-positive cells in PsA synovium. IL-20 expression in skin sections (n = 6) was analyzed semiquantitatively.

Results

IL-20 was abundantly expressed in both PsA and RA synovial tissues. In inflamed PsA synovium, CD68+ macrophages and CD55+ FLSs coexpressed IL-20, and its expression correlated with the numbers of FLSs. IL-20 expression in lesional skin of PsA patients decreased significantly (P = 0.04) 6 weeks after treatment and correlated positively with the Psoriasis Area and Severity Index (PASI). IL-20 expression in PsA synovium was not affected by alefacept.

Conclusions

Conceivably, the relatively limited effectiveness of alefacept in PsA patients (compared with anti-tumor necrosis factor (TNF) therapy) might be explained in part by persistent FLS-derived IL-20 expression.