bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dimension reduction with redundant gene elimination for tumor classification
Authors: Zeng Xue-Qiang , Li Guo-Zheng , Yang Jack Y , Yang Mary Qu , Wu Geng-Feng 
Published: May 2008

Abstract

Background
Analysis of gene expression data for tumor classification is an important application of bioinformatics methods. But it is hard to analyse gene expression data from DNA microarray experiments by commonly used classifiers, because there are only a few observations but with thousands of measured genes in the data set. Dimension reduction is often used to handle such a high dimensional problem, but it is obscured by the existence of amounts of redundant features in the microarray data set.

Results
Dimension reduction is performed by combing feature extraction with redundant gene elimination for tumor classification. A novel metric of redundancy based on DIScriminative Contribution (DISC) is proposed which estimates the feature similarity by explicitly building a linear classifier on each gene. Compared with the standard linear correlation metric, DISC takes the label information into account and directly estimates the redundancy of the discriminative ability of two given features. Based on the DISC metric, a novel algorithm named REDISC (Redundancy Elimination based on Discriminative Contribution) is proposed, which eliminates redundant genes before feature extraction and promotes performance of dimension reduction. Experimental results on two microarray data sets show that the REDISC algorithm is effective and reliable to improve generalization performance of dimension reduction and hence the used classifier.

Conclusion
Dimension reduction by performing redundant gene elimination before feature extraction is better than that with only feature extraction for tumor classification, and redundant gene elimination in a supervised way is superior to the commonly used unsupervised method like linear correlation coefficients.
Assessment of decorin-binding protein A to the infectivity of Borrelia burgdorferi in the murine models of needle and tick infection
Authors: Blevins Jon S , Hagman Kayla E , Norgard Michael V 
Published: May 2008

AbstractBackgroundDecorin-binding proteins (Dbps) A and B ofBorrelia burgdorferi, the agent of Lyme disease, are surface-exposed lipoproteins that presumably bind to the extracellular matrix proteoglycan, decorin.B. burgdorferiinfects various tissues including the bladder, heart, joints, skin and the central nervous system, and the ability ofB. burgdorferito bind decorin has been hypothesized to be important for this disseminatory pathogenic strategy.ResultsTo determine the role of DbpBA in the infectious lifecycle ofB. burgdorferi, we created a DbpBA-deficient mutant ofB. burgdorferistrain 297 and compared the infectious phenotype of the mutant to the wild-type strain in the experimental murine model of Lyme borreliosis. The mutant strain exhibited a 4-log decrease in infectivity, relative to the wild-type strain, when needle inoculated into mice. Upon complementation of the DbpBA-mutant strain with DbpA, the wild-type level of infectivity was restored. In addition, we demonstrated that the DbpBA-deficient mutant was able to colonizeIxodes scapularislarval ticks after feeding on infected mice and persist within the ticks during the molt to the nymphal state. Moreover, surprisingly, the DbpBA-mutant strain was capable of being transmitted to naïve mice via tick bite, giving rise to infected mice.ConclusionThese results suggest that DbpBA is not required for the natural tick-transmission process to mammals, despite inferences from needle-inoculation experiments implying a requirement for DbpBA during mammalian infection. The combined findings also send a cautionary note regarding how results from needle-inoculation experiments with mice should be interpreted.
Senescence marker protein 30 in acute liver failure: validation of a mass spectrometry proteomics assay
Authors: Lv Sa , Wang Jiang-hua , Liu Feng , Gao Yan , Fei Ran , Du Shao-cai , Wei Lai 
Published: May 2008

Abstract

Background
Our previous proteomic study showed that the senescence marker protein (SMP30) is selectively present in the plasma of a murine model of acute liver failure (ALF). The aim of this study was to validate this SMP30 expression in the plasma and liver tissues of mice and humans with ALF.

Methods
After the proteomic analysis of plasma from a murine model of D-galactosamine/lipopolysaccharide (GalN/LPS)-induced ALF by two-dimensional electrophoresis (2-DE) and mass spectrometry, the expression levels of SMP30 in the plasma and liver tissues were validated by western blot and RT-PCR analyses. These results were then confirmed in plasma samples from humans.

Results
These data validate the results of 2-DE, and western blot showed that SMP30 protein levels were only elevated in the plasma of ALF mice. Further analysis revealed that GalN/LPS induced the downregulation of SMP30 protein levels in liver tissues (by approximately 25% and 16% in the GalN/LPS-treated mice and in the treated mice that survived, respectively; P < 0.01). Hepatic SMP30 mRNA levels decreased by about 90% only in the mice that survived the GalN/LPS treatment. Importantly, plasma obtained from patients with ALF also contained higher levels of SMP30, about (3.65 ± 0.34) times those observed in healthy volunteers.

Conclusion
This study shows that SMP30 is not only a potential biomarker for the diagnosis and even prognosis of ALF. It also plays a very important role in a self-protective mechanism in survival and participates in the pathophysiological processes of ALF.
Clinicopathologic significance of HIF-1α, p53, and VEGF expression and preoperative serum VEGF level in gastric cancer
Authors: Oh Sung Yong , Kwon Hyuk-Chan , Kim Sung-Hyun , Jang Jin Seok , Kim Min Chan , Kim Kyeong Hee , Han Jin-Yeong , Kim Chung Ock , Kim Su-Jin , Jeong Jin-sook , Kim Hyo-Jin 
Published: May 2008

Abstract

Background
Hypoxia influences tumor growth by inducing angiogenesis and genetic alterations. Hypoxia-inducible factor 1α (HIF-1α), p53, and vascular endothelial growth factor (VEGF) are all important factors in the mechanisms inherent to tumor progression. In this work, we have investigated the clinicopathologic significance of HIF-1α, p53, and VEGF expression and preoperative serum VEGF (sVEGF) level in gastric cancer.
We immunohistochemically assessed the HIF-1α, p53, and VEGF expression patterns in 114 specimens of gastric cancer. Additionally, we determined the levels of preoperative serum VEGF (sVEGF).

Results
The positive rates of p53 and HIF-1α (diffuse, deep, intravascular pattern) were 38.6% and 15.8%, respectively. The VEGF overexpression rate was 57.9%. p53 and HIF-1α were correlated positively with the depth of invasion (P = 0.015, P = 0.001, respectively). Preoperative sVEGF and p53 levels were correlated significantly with lymph node involvement (P = 0.010, P = 0.040, respectively). VEGF overexpression was more frequently observed in the old age group (≥ 60 years old) and the intestinal type (P = 0.013, P = 0.014, respectively). However, correlations between preoperative sVEGF level and tissue HIF-1α, VEGF, and p53 were not observed. The median follow-up duration after operation was 24.5 months. HIF-1α was observed to be a poor prognostic factor of disease recurrence or progression (P = 0.002).

Conclusion
p53, HIF-1α and preoperative sVEGF might be markers of depth of invasion or lymph node involvement. HIF-1α expression was a poor prognostic factor of disease recurrence or progression in patients with gastric cancers.
Analysis of the effects of exposure to acute hypoxia on oxidative lesions and tumour progression in a transgenic mouse breast cancer model
Authors: Kalliomäki Tuula M , McCallum Gordon , Lunt Sarah Jane , Wells Peter G , Hill Richard P 
Published: May 2008

AbstractBackgroundTumour hypoxia is known to be a poor prognostic indicator, predictive of increased risk of metastatic disease and reduced survival. Genomic instability has been proposed as one of the potential mechanisms for hypoxic tumour progression. Both of these features are commonly found in many cancer types, but their relationship and association with tumour progression has not been examined in the same model.MethodsTo address this issue, we determined the effects of 6 weekin vivoacute hypoxic exposure on the levels of mutagenic lipid peroxidation product, malondialdehyde, and 8-oxo-7,8-dihydro-2'-deoxyguanosine DNA (8-oxo-dG) lesions in the transgenic polyomavirus middle T (PyMT) breast cancer mouse model.ResultsWe observed significantly increased plasma lipid peroxidation and 8-oxo-dG lesion levels in the hypoxia-exposed mice. Consumption of malondialdehyde also induced a significant increase in the PyMT tumour DNA lesion levels, however, these increases did not translate into enhanced tumour progression. We further showed that thein vivoexposure to acute hypoxia induced accumulation of F4/80 positive tumour-associated macrophages (TAMs), demonstrating a relationship between hypoxia and macrophages in an experimental model.ConclusionThese data suggest that although exposure to acute hypoxia causes an increase in 8-oxo-dG lesions and TAMs in the PyMT tumours, these increases do not translate into significant changes in tumour progression at the primary or metastatic levels in this strong viral oncogene-driven breast cancer model.
Use of residential wood heating in a context of climate change: a population survey in Québec (Canada)
Authors: Bélanger Diane , Gosselin Pierre , Valois Pierre , Abdous Belkacem 
Published: May 2008

Abstract

Background
Wood heating is recommended in several countries as a climate change (CC) adaptation measure, mainly to increase the autonomy of households during power outages due to extreme climatic events. The aim of this study was to examine various perceptions and individual characteristics associated with wood heating through a survey about CC adaptations.

Methods
A telephone survey (n = 2,545) of adults living in the southern part of the province of Québec (Canada) was conducted in the early fall season of 2005. The questionnaire used closed questions and measured the respondents' beliefs and current adaptations about CC. Calibration weighting was used to adjust the data analysis for the respondent's age and language under stratified sampling based on health regions.

Results
More than three out of four respondents had access to a single source of energy at home, which was mainly electricity; 22.2% combined two sources or more; 18.5% heated with wood occasionally or daily during the winter. The prevalence of wood heating was higher in the peripheral regions than in the more urban regions, where there was a higher proportion of respondents living in apartments. The prevalence was also higher with participants completely disagreeing (38.5%) with the eventual prohibition of wood heating when there is smog in winter, compared to respondents somewhat disagreeing (24.2%) or agreeing (somewhat: 17.5%; completely: 10.4%) with the adoption of this strategy. It appears that the perception of living in a region susceptible to winter smog, smog warnings in the media, or the belief in the human contribution to CC, did not influence significantly wood heating practices.

Conclusion
Increased residential wood heating could very well become a maladaptation to climate change, given its known consequences on winter smog and respiratory health. It would thus be appropriate to implement a long-term national program on improved and controlled residential wood heating. This would constitute a "no-regrets" adaptation to climate change, while reducing air pollution and its associated health impacts.
Evaluation of cell types for assessment of cytogenetic damage in arsenic exposed population
Authors: Ghosh Pritha , Basu Arindam , Singh Keshav K , Giri Ashok K 
Published: May 2008

AbstractBackgroundCytogenetic biomarkers are essential for assessing environmental exposure, and reflect adverse human health effects such as cellular damage. Arsenic is a potential clastogen and aneugen. In general, the majority of the studies on clastogenic effects of arsenic are based on frequency of micronuclei (MN) study in peripheral lymphocytes, urothelial and oral epithelial cells. To find out the most suitable cell type, here, we compared cytogenetic damage through MN assay in (a) various populations exposed to arsenic through drinking water retrieved from literature review, as also (b) arsenic-induced Bowen's patients from our own survey.ResultsFor literature review, we have searched the Pubmed database for English language journal articles using the following keywords: "arsenic", "micronuclei", "drinking water", and "human" in various combinations. We have selected 13 studies consistent with our inclusion criteria that measured micronuclei in either one or more of the above-mentioned three cell types, in human samples. Compared to urothelial and buccal mucosa cells, the median effect sizes measured by the difference between people with exposed and unexposed, lymphocyte based MN counts were found to be stronger. This general pattern pooled from 10 studies was consistent with our own set of three earlier studies. MN counts were also found to be stronger for lymphocytes even in arsenic-induced Bowen's patients (cases) compared to control individuals having arsenic-induced non-cancerous skin lesions.ConclusionOverall, it can be concluded that MN in lymphocytes may be superior to other epithelial cells for studying arsenic-induced cytogenetic damage.
The value of D-dimer in the detection of early deep-vein thrombosis after total knee arthroplasty in Asian patients: a cohort study
Authors: Chen Chung-Jen , Wang Ching-Jen , Huang Chung-Cheng 
Published: May 2008

AbstractBackground and purposeThe relationship of D-dimer and deep-vein thrombosis (DVT) after total knee arthroplasty (TKA) remains controversial. The purpose of this study was to assess the value of D-dimer in the detection of early DVT after TKA.MethodsThe measurements of plasma D-dimer level were obtained preoperatively and at day 7 postoperatively in 78 patients undergoing TKA. Ascending venography was performed in 7 to 10 days after surgery. The plasma D-dimer levels were correlated statistically with the venographic DVT.ResultsVenographic DVT was identified in 40% of patients. High plasma D-dimer level >2.0 μg/ml was found in 68% of patients with DVT and 45% without DVT (P < 0.05). Therefore, high D-dimer level greater than 2.0 μg/ml showed 68% sensitivity, 55% specificity, 60% accuracy, 50% positive predictive rate and 72% negative predictive rate in the detection of early DVT after TKA.ConclusionHigh plasma D-dimer level is a moderately sensitive, but less specific marker in the detection of early of DVT after TKA. Measurement of serum D-dimer alone is not accurate enough to detect DVT after TKA. Venography is recommended in patients with elevated D-dimer and clinically suspected but asymptomatic DVT after TKA.
Closing two doors of viral entry: Intramolecular combination of a coreceptor- and fusion inhibitor of HIV-1
Authors: Kopetzki Erhard , Jekle Andreas , Ji Changhua , Rao Eileen , Zhang Jun , Fischer Stephan , Cammack Nick , Sankuratri Surya , Heilek Gabrielle 
Published: May 2008

Abstract
We describe a novel strategy in which two inhibitors of HIV viral entry were incorporated into a single molecule. This bifunctional fusion inhibitor consists of an antibody blocking the binding of HIV to its co-receptor CCR5, and a covalently linked peptide which blocks envelope mediated virus-cell fusion. This novel bifunctional molecule is highly active on CCR5- and X4-tropic viruses in a single cycle assay and a reporter cell line with IC50 values of 0.03–0.05 nM. We demonstrated that both inhibitors contribute to the antiviral activity. In the natural host peripheral blood mononuclear cells (PBMC) the inhibition of CXCR4-tropic viruses is dependant on the co-expression of CCR5 and CXCR4 receptors. This bifunctional inhibitor may offer potential for improved pharmacokinetic parameters for a fusion inhibitor in humans and the combination of two active antiviral agents in one molecule may provide better durability in controlling the emergence of resistant viruses.
Trends in prevalence of substance use among Icelandic adolescents, 1995–2006
Authors: Sigfusdottir Inga D , Kristjansson Alfgeir L , Thorlindsson Thorolfur , Allegrante John P 
Published: May 2008

Abstract

Background
Adolescent substance use continues to be of great global public health concern in many countries with advanced economies. Previous research has shown that substance use among 15–16 year-old-youth has increased in many European countries in recent years. The aim of this study was to examine trends in prevalence of daily smoking, alcohol intoxication, and illicit substance use among Icelandic adolescents.

Methods
Repeated-measures, population-based cross-sectional surveys of between 3,100 and 3,900 10th-grade students who participated in the annual Youth of Iceland studies were analyzed, with response rates of between 80% and 90%.

Results
The prevalence of daily smoking, alcohol intoxication, and illicit substance use was at a peak in 1998, with almost 23% having reported daily smoking, 42% having reported becoming intoxicated at least once during the last 30 days, and over 17% having used hashish once or more often in their lifetime. By 2006, daily smoking had declined to 12%, having become intoxicated once or more often during the last 30 days to 25%, and having ever used hashish declined to 9%.

Conclusion
The prevalence of substance use among Icelandic 10th graders declined substantially from 1995 to 2006. Proportions of adolescents who smoke cigarettes, had become intoxicated during the last 30 days, as well as those admitting to hashish use all decreased to a great deal during the period under study. The decline in prevalence of adolescent substance use in Iceland is plausibly the result of local community collaboration where researchers, policy makers and practitioners who work with young people have combined their efforts.
Regulation of survival in adult hippocampal and glioblastoma stem cell lineages by the homeodomain-only protein HOP
Authors: De Toni Arianna , Zbinden Marie , Epstein Jonathan A , Altaba Ariel Ruiz i , Prochiantz Alain , Caillé Isabelle 
Published: May 2008

Abstract
Background
Homeodomain proteins play critical roles in shaping the development of the embryonic central nervous system in mammals. After birth, neurogenic activities are relegated to stem cell niches, which include the subgranular layer of the dentate gyrus of the hippocampus. Here, we have analyzed the function of HOP (Homeodomain only protein) in this stem cell niche and in human glioblastomas.

Results
We find that HOP is strongly expressed by radial astrocytes of the dentate gyrus in mice, which are stem cells that give rise to hippocampal granular neurons throughout adulthood. Deletion or down-regulation of HOP results in a decrease of apoptosis of these stem cells without changes in proliferation, and in an increase in the number of newly formed granule neurons. We also find that human glioblastomas largely lack HOP expression and that reintroduction of HOP function in glioma cells cultured as gliomaspheres leads to enhanced apoptosis in a subset of cases. In these cells, HOP function decreases clonogenicity.

Conclusion
These data suggest that HOP participates in the regulation of the adult mouse hippocampal stem cell niche by negatively affecting cell survival. In addition, HOP may work as a tumor suppressor in a subset of glioblastomas. HOP function thus appears to be critical in the adult brain in a region of continued plasticity, and its deregulation may contribute to disease.
Whole genome identification of Mycobacterium tuberculosisvaccine candidates by comprehensive data mining and bioinformatic analyses
Authors: Zvi Anat , Ariel Naomi , Fulkerson John , Sadoff Jerald C , Shafferman Avigdor 
Published: May 2008

Abstract

Background

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), infects ~8 million annually culminating in ~2 million deaths. Moreover, about one third of the population is latently infected, 10% of which develop disease during lifetime. Current approved prophylactic TB vaccines (BCG and derivatives thereof) are of variable efficiency in adult protection against pulmonary TB (0%–80%), and directed essentially against early phase infection.

Methods
A genome-scale dataset was constructed by analyzing published data of: (1) global gene expression studies under conditions which simulate intra-macrophage stress, dormancy, persistence and/or reactivation; (2) cellular and humoral immunity, and vaccine potential. This information was compiled along with revised annotation/bioinformatic characterization of selected gene products and in silico mapping of T-cell epitopes. Protocols for scoring, ranking and prioritization of the antigens were developed and applied.

Results
Cross-matching of literature and in silico-derived data, in conjunction with the prioritization scheme and biological rationale, allowed for selection of 189 putative vaccine candidates from the entire genome. Within the 189 set, the relative distribution of antigens in 3 functional categories differs significantly from their distribution in the whole genome, with reduction in the Conserved hypothetical category (due to improved annotation) and enrichment in Lipid and in Virulence categories. Other prominent representatives in the 189 set are the PE/PPE proteins; iron sequestration, nitroreductases and proteases, all within the Intermediary metabolism and respiration category; ESX secretion systems, resuscitation promoting factors and lipoproteins, all within the Cell wall category. Application of a ranking scheme based on qualitative and quantitative scores, resulted in a list of 45 best-scoring antigens, of which: 74% belong to the dormancy/reactivation/resuscitation classes; 30% belong to the Cell wall category; 13% are classical vaccine candidates; 9% are categorized Conserved hypotheticals, all potentially very potent T-cell antigens.

Conclusion
The comprehensive literature and in silico-based analyses allowed for the selection of a repertoire of 189 vaccine candidates, out of the whole-genome 3989 ORF products. This repertoire, which was ranked to generate a list of 45 top-hits antigens, is a platform for selection of genes covering all stages of M. tuberculosis infection, to be incorporated in rBCG or subunit-based vaccines.