bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology
Authors: Xu Tao , Gu JianLei , Zhou Yan , Du LinFang 
Published: August 2009

Abstract

Background
Gene set analysis based on Gene Ontology (GO) can be a promising method for the analysis of differential expression patterns. However, current studies that focus on individual GO terms have limited analytical power, because the complex structure of GO introduces strong dependencies among the terms, and some genes that are annotated to a GO term cannot be found by statistically significant enrichment.

Results
We proposed a method for enriching clustered GO terms based on semantic similarity, namely cluster enrichment analysis based on GO (CeaGO), to extend the individual term analysis method. Using an Affymetrix HGU95aV2 chip dataset with simulated gene sets, we illustrated that CeaGO was sensitive enough to detect moderate expression changes. When compared to parent-based individual term analysis methods, the results showed that CeaGO may provide more accurate differentiation of gene expression results. When used with two acute leukemia (ALL and ALL/AML) microarray expression datasets, CeaGO correctly identified specifically enriched GO groups that were overlooked by other individual test methods.

Conclusion
By applying CeaGO to both simulated and real microarray data, we showed that this approach could enhance the interpretation of microarray experiments. CeaGO is currently available at http://chgc.sh.cn/en/software/CeaGO/.
Cross-breed comparisons identified a critical 591-kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and the Ile-442-Met substitution in NCAPG as a positional candidate
Authors: Setoguchi Kouji , Furuta Masako , Hirano Takashi , Nagao Tomoko , Watanabe Toshio , Sugimoto Yoshikazu , Takasuga Akiko 
Published: August 2009

AbstractBackgroundGrowth-related traits have been mapped on bovine chromosome 6 (BTA 6) in various bovine breed populations. We previously mapped a significant quantitative trait locus (QTL) for carcass and body weight (CW-2) between 38 and 55 cM on BTA 6 using a Japanese Black half-sib family. Additional QTL mapping studies detected four QTL for body or carcass weight that overlapped withCW-2in Japanese Black and Japanese Brown half-sib families. To map the region in greater detail, we applied cross-breed comparisons of haplotypes that have been shown to be powerful in canine.ResultsWe used 38 microsatellite markers to search for a sharedQ(increasing carcass and/or body weight) haplotype within the 17-cMCW-2region among five sires. Linkage disequilibrium mapping using maternal alleles of the offspring showed that an 815-kb sharedQhaplotype was associated with body or carcass weight in both breeds. The addition of 43 single nucleotide polymorphism (SNP) markers narrowed the region to 591 kb containing 4 genes. The SNP changing Ile-442 to Met inNCAPG(chromosome condensation protein G) was significantly associated with carcass weight (p< 1.2 × 10-11) in a large Japanese Black population as well as in the five families. TheQallele of the SNP was also associated with a larger longissimus muscle area and thinner subcutaneous fat thickness in steers of all five families, indicating that theCW-2locus is pleiotropic and favorable for marker-assisted selection of beef cattle.ConclusionA 591-kb critical region forCW-2was identified. The SNP changing Ile-442 to Met inNCAPG(chromosome condensation protein G) can be used as a positional candidate ofCW-2for marker-assisted selection.
Photonic plasmid stability of transformed Salmonella Typhimurium: A comparison of three unique plasmids
Authors: Moulton Keesla , Ryan Peter , Lay Donald , Willard Scott 
Published: August 2009

Abstract

Background
Acquiring a highly stable photonic plasmid in transformed Salmonella Typhimurium for use in biophotonic studies of bacterial tracking in vivo is critical to experimental paradigm development. The objective of this study was to determine stability of transformed Salmonella Typhimurium (S. typh-lux) using three different plasmids and characterize their respective photonic properties.

Results
In presence of ampicillin (AMP), S. typh-lux with pCGLS-1, pAK1-lux and pXEN-1 plasmids exhibited 100% photon-emitting colonies over a 10-d study period. Photon emitters of S. typh-lux with pCGLS-1, pAK1-lux and pXEN-1 without AMP selection decreased over time (P < 0.05), representing only 11 ± 1%, 35 ± 1% and 43 ± 1%, respectively, of original photon emitting properties of the bacterial population by d 10. Photonic emissions were positively correlated with bacterial concentration (P < 0.05) for pAK1-lux, pCGLS-1 and pXEN-1 (r = 0.96, 0.98 and 0.82, respectively). When stratified by high, medium and low density bacteria concentrations, photonic emissions for high density populations containing pAK1-lux, pCGLS-1 and pXEN-1 resulted in differences of photonic emissions across a range of bacterial concentrations (1 × 107 to 1 × 109 CFU, P < 0.05) with positive correlations (P < 0.05) of (r = 0.72, 0.46 and 0.72, respectively). The correlation of photonic emissions with bacterial concentrations for samples with medium and low density bacteria (pAK1-lux, pCGLS-1, and pXEN-1 plasmids) imaged in tubes were also positively correlated (medium; r = 0.69, 0.49, 0.46, low; r = 0.90, 0.71, 0.68, respectively; P > 0.05); although photonic emissions across a range of bacterial concentrations were not different (1 × 104 to 1 × 106 CFU, P > 0.05). For very low density bacterial concentrations imaged in 96 well plates photonic emissions were positively correlated with bacterial concentration (P < 0.05) for pAK1-lux, pCGLS-1, and pXEN-1 plasmids (r = 0.99, 0.99, and 0.96, respectively), and photonic emissions across a range of bacterial concentrations (1 × 103 to 1 × 105 CFU) low to high were different in the 96-well plate format (P < 0.05).

Conclusion
These data characterize photon stability properties for S. typh-lux transformed with three different photon generating plasmids that may facilitate real-time Salmonella tracking using in vivo or in situ biophotonic paradigms.
Number of addictive substances used related to increased risk of unnatural death: A combined medico-legal and case-record study
Authors: Brådvik Louise , Berglund Mats , Frank Arne , Lindgren Anna , Löwenhielm Peter 
Published: August 2009

Abstract

Background
Substance use disorders have repeatedly been found to lead to premature death, i.e. drug-related death by disease, fatal intoxications, or trauma (accidents, suicide, undetermined suicide, and homicide). The present study examined the relationship between multi-drug substance use and natural and unnatural death.

Methods
All consecutive, autopsied patients who had been in contact with the Addiction Centre in Malmö University Hospital from 1993 to 1997 inclusive were investigated. Drug abuse was investigated blindly in the case records and related to the cause of death in 387 subjects.

Results
Every substance apart from alcohol used previously in life added to the risk of unnatural death in a linear way. There were independent increased risks of fatal heroin overdoses or undetermined suicide. Death by suicide and violent death were unrelated to additional abuse.

Conclusion
The number of drugs used was related to an increased risk of unnatural death by undetermined suicide (mainly fatal intoxications) and heroin overdose.
Anti-collagenase, anti-elastase and anti-oxidant activities of extracts from 21 plants
Authors: Thring Tamsyn SA , Hili Pauline , Naughton Declan P 
Published: August 2009

Abstract

Background
Owing to their roles in tissue remodelling in health and disease, several studies have reported investigations on plant extracts as inhibitors of proteinases and as anti-oxidants.

Methods
The anti-ageing and anti-oxidant properties of 23 plant extracts (from 21 plant species) were assessed as anti-elastase and anti-collagenase activities and in selected anti-oxidant assays along with phenolic content.

Results
Anti-elastase activities were observed for nine of the extracts with inhibitory activity in the following order: white tea (~89%), cleavers (~58%), burdock root (~51%), bladderwrack (~50%), anise and angelica (~32%). Anti-collagenase activities were exhibited by sixteen plants of which the highest activity was seen in white tea (~87%), green tea (~47%), rose tincture (~41%), and lavender (~31%). Nine plant extracts had activities against both elastase (E) and collagenase (C) and were ranked in the order of white tea (E:89%, C:87%) > bladderwrack (E:50%, C:25%) > cleavers (E:58%, C:7%) > rose tincture (E:22%, C:41%) > green tea (E:10%: C:47%) > rose aqueous (E: 24%, C:26%) > angelica (E:32%, C:17%) > anise (E:32%, C:6%) > pomegranate (E:15%, C:11%).
Total phenolic content varied between 0.05 and 0.26 mg gallic acid equivalents (GAE)/mL with the exception of white tea (0.77 mg GAE/mL). For anti-oxidant assessment, the Trolox equivalent anti-oxidant capacity (TEAC) assay revealed activity for all extracts. White tea had the highest activity equivalent to ~21 μM Trolox for a 6.25 μg aliquot. In addition, seven extracts exhibited activities = 10 μM Trolox with witch hazel (6.25 μg = 13 μM Trolox) and rose aqueous (6.25 μg = 10 μM Trolox) showing very high activities at low concentrations. A high activity for white tea was also found in the superoxide dismutase (SOD) assay in which it exhibited ~88% inhibition of reduction of nitroblue tetrazolium. High activities were also observed for green tea (86.41%), rose tincture (82.77%), witch hazel (82.05%) and rose aqueous (73.86%).

Conclusion
From a panel of twenty three plant extracts, some one dozen exhibit high or satisfactory anti-collagenase or anti-elastase activities, with nine having inhibitory activity against both enzymes. These included white tea which was found to have very high phenolic content, along with high TEAC and SOD activities.
Utilization of acute and long-term care in the last year of life: comparison with survivors in a population-based study
Authors: Pot Anne Margriet , Portrait France , Visser Geraldine , Puts Martine , van Groenou Marjolein I Broese , Deeg Dorly JH 
Published: August 2009

Abstract

Background
It is well-known that the use of care services is most intensive in the last phase of life. However, so far only a few determinants of end-of-life care utilization are known. The aims of this study were to describe the utilization of acute and long-term care among older adults in their last year of life as compared to those not in their last year of life, and to examine which of a broad range of determinants can account for observed differences in care utilization.

Methods
Data were used from the Longitudinal Aging Study Amsterdam (LASA). In a random, age and sex stratified population-based cohort of 3107 persons aged 55 – 85 years at baseline and representative of the Netherlands, follow-up cycles took place at 3, 6 and 9 years. Those who died within one year directly after a cycle were defined as the "end-of-life group" (n = 262), and those who survived at least three years after a cycle were defined as the "survivors". Utilization of acute and long-term care services, including professional and informal care, were recorded at each cycle, as well as a broad range of health-related and psychosocial variables.

Results
The end-of-life group used more care than the survivors. In the younger-old this difference was most pronounced for acute care, and in the older-old, for long-term care. Use of both acute and long-term home care in the last year of life was fully accounted for by health problems. Use of institutional care at the end of life was partly accounted for by health problems, but was not fully explained by the determinants included.

Conclusion
This study shows that severity of health problems are decisive in the explanation of the increase in use of care services towards the end-of-life. This information is essential for an appropriate allocation of professional health care to the benefit of older persons themselves and their informal caregivers.
Sri Lankan tsunami refugees: a cross sectional study of the relationships between housing conditions and self-reported health
Authors: Turner Alex , Pathirana Sameera , Daley Amanda , Gill Paramjit S 
Published: August 2009

Abstract

Background
On the 26th December 2004 the Asian tsunami devastated the Sri Lankan coastline. More than two years later, over 14,500 families were still living in transitional shelters. This study compares the health of the internally displaced people (IDP), living in transitional camps with those in permanent housing projects provided by government and non-government organisations in Sri Lanka.

Methods
This study was conducted in seven transitional camps and five permanent housing projects in the south west of Sri Lanka. Using an interviewer-led questionnaire, data on the IDPs' self-reported health and housing conditions were collected from 154 participants from transitional camps and 147 participants from permanent housing projects. Simple tabulation with non-parametric tests and logistic regression were used to identify and analyse relationships between housing conditions and the reported prevalence of specific symptoms.

Results
Analysis showed that living conditions were significantly worse in transitional camps than in permanent housing projects for all factors investigated, except 'having a leaking roof'. Transitional camp participants scored significantly lower on self-perceived overall health scores than those living in housing projects. After controlling for gender, age and marital status, living in a transitional camp compared to a housing project was found to be a significant risk factor for the following symptoms; coughs OR: 3.53 (CI: 2.11–5.89), stomach ache 4.82 (2.19–10.82), headache 5.20 (3.09–8.76), general aches and pains 6.44 (3.67–11.33) and feeling generally unwell 2.28 (2.51–7.29). Within transitional camp data, the only condition shown to be a significant risk factor for any symptom was household population density, which increased the risk of stomach aches 1.40 (1.09–1.79) and headaches 1.33 (1.01–1.77).

Conclusion
Internally displaced people living in transitional camps are a vulnerable population and specific interventions need to be targeted at this population to address the health inequalities that they report to be experiencing. Further studies need to be conducted to establish which aspects of their housing environment predispose them to poorer health.
Transcriptional activation of the Lats1 tumor suppressor gene in tumors of CUX1 transgenic mice
Authors: Siam Rania , Harada Ryoko , Cadieux Chantal , Battat Robert , Vadnais Charles , Nepveu Alain 
Published: August 2009

Abstract

Background

Lats1 (large tumor suppressor 1) codes for a serine/threonine kinase that plays a role in the progression through mitosis. Genetic studies demonstrated that the loss of LATS1 in mouse, and of its ortholog wts (warts) in Drosophila, is associated with increased cancer incidence. There are conflicting reports, however, as to whether overexpression of Lats1 inhibits cell proliferation. CUX1 is a transcription factor that exists in different isoforms as a result of proteolytic processing or alternative transcription initiation. Expression of p110 and p75 CUX1 in transgenic mice increases the susceptibility to cancer in various organs and tissues. In tissue culture, p110 CUX1 was shown to accelerate entry into S phase and stimulate cell proliferation.

Results
Genome-wide location arrays in cell lines of various cell types revealed that Lats1 was a transcriptional target of CUX1. Scanning ChIP analysis confirmed that CUX1 binds to the immediate promoter of Lats1. Expression of Lats1 was reduced in cux1-/- MEFs, whereas it was increased in cells stably or transiently expressing p110 or p75 CUX1. Reporter assays confirmed that the immediate promoter of Lats1 was sufficient to confer transcriptional activation by CUX1. Lats1 was found to be overexpressed in tumors from the mammary gland, uterus and spleen that arise in p110 or p75 CUX1 transgenic mice. In tissue culture, such elevated LATS1 expression did not hinder cell cycle progression in cells overexpressing p110 CUX1.

Conclusion
While inactivation of Lats1/wts in mouse and Drosophila can increase cancer incidence, results from the present study demonstrate that Lats1 is a transcriptional target of CUX1 that can be overexpressed in tumors of various tissue-types. Interestingly, two other studies documented the overexpression of LATS1 in human cervical cancers and basal-like breast cancers. We conclude that, similarly to other genes involved in mitotic checkpoint, cancer can be associated with either loss-of-function or overexpression of Lats1.
MyD88 and TRIF mediate the cyclic adenosine monophosphate (cAMP) induced corticotropin releasing hormone (CRH) expression in JEG3 choriocarcinoma cell line
Authors: Uh Andy , Simmons Charles F , Bresee Catherine , Khoury Nasif , Gombart Adrian F , Nicholson Richard C , Kocak Hande , Equils Ozlem 
Published: August 2009

Abstract

Background
Classically protein kinase A (PKA) and transcription factor activator protein 1 (AP-1) mediate the cyclic AMP (cAMP) induced-corticotrophin releasing hormone (CRH) expression in the placenta. However enteric Gram (-) bacterial cell wall component lipopolysaccharide (LPS) may also induce-CRH expression via Toll like receptor (TLR)4 and its adaptor molecule Myd88. Here we investigated the role of MyD88, TRIF and IRAK2 on cAMP-induced CRH promoter activation in JEG3 cells in the absence of LPS/TLR4 stimulation.

Methods
JEG3 cells were transfected with CRH-luciferase and Beta-galactosidase expression vectors and either empty or dominant-negative (DN)-MyD88, DN-TRIF or DN-IRAK2 vectors using Fugene6 (Roche). cAMP-induced CRH promoter activation was examined by using a luminometer and luciferase assay. Calorimetric Beta-galactosidase assays were performed to correct for transfection efficiency. Luciferase expression vectors of cAMP-downstream molecules, CRE and AP-1, were used to further examine the signaling cascades.

Results
cAMP stimulation induced AP-1 and CRE promoter expression and led to dose-dependent CRH promoter activation in JEG3 cells. Inhibition of MyD88 signaling blocked cAMP-induced CRE and CRH promoter activation. Inhibition of TRIF signaling blocked cAMP-induced CRH but not CRE expression, while inhibition of IRAK2 did not have an effect on cAMP-induced CRH expression.

Conclusion
MyD88 and TRIF exert direct regulatory effect on cAMP-induced CRH promoter activation in JEG3 cells in the absence of infection. MyD88 most likely interacts with molecules upstream of IRAK2 to regulate cAMP-induced CRH expression.
Transforming growth factor beta isoforms regulation of Akt activity and XIAP levels in rat endometrium during estrous cycle, in a model of pseudopregnancy and in cultured decidual cells
Authors: Caron Pierre-Luc , Fréchette-Frigon Guylaine , Shooner Carl , Leblanc Valérie , Asselin Eric 
Published: August 2009

Abstract

Background
During the estrous cycle, the rat uterine endometrium undergoes many changes such as cell proliferation and apoptosis. If implantation occurs, stromal cells differentiate into decidual cells and near the end of pregnancy, a second wave of apoptosis occurs. This process called decidual regression, is tightly regulated as is it crucial for successful pregnancy. We have previously shown that TGF-beta1, TGF-beta2 and TGF-beta3 are expressed in the endometrium during decidual basalis regression, but although we had demonstrated that TGF- beta1 was involved in the regulation of apoptosis in decidual cells, the ability of TGF- beta2 and TGF-beta3 isoforms to trigger apoptotic mechanisms in these cells remains unknown. Moreover, we hypothesized that the TGF-betas were also present and regulated in the non-pregnant endometrium during the estrous cycle. The aim of the present study was to determine and compare the specific effect of each TGF-β isoform in the regulation of apoptosis in sensitized endometrial stromal cells in vitro, and to investigate the regulation of TGF-beta isoforms in the endometrium during the estrous cycle in vivo.

Methods
Rats with regular estrous cycle (4 days) were killed at different days of estrous cycle (diestrus, proestrus, estrus and metestrus). Pseudopregnancy was induced with sex steroids in ovariectomized rats and rats were killed at different days (days 1–9). Uteri were collected and either fixed for immunohistochemical staining (IHC) or processed for RT-PCR and Western analyses. For the in vitro part of the study, rats were ovariectomized and decidualization was induced using sex steroids. Endometrial stromal decidual cells were purified, cultured and treated with different concentrations of TGF-beta isoforms.

Results
Our results showed that all three TGF-beta isoforms are present, but are localized differently in the endometrium during the estrous cycle and their expression is regulated differently during pseudopregnancy. In cultured stromal cells, we found that TGF-beta3 isoform induced Smad2 phosphorylation, indicating that the Smad pathway is activated by TGF-beta3 in these cells. Furthermore, TGF-beta2 and TGF-beta3 induced a dose-dependant increase of apoptosis in cultured stromal cells, as demonstrated by Hoechst nuclear staining. Noteworthy, TGF-beta2 and TGF-beta3 reduced the level of the anti-apoptotic XIAP protein, as well as the level of phosphorylated/active Akt, a well known survival protein, in a dose-dependent manner.

Conclusion
Those results suggest that TGF-beta might play an important role in the remodelling endometrium during the estrous cycle and in the regulation of apoptosis in rat decidual cells, in which inhibition of Akt survival pathway might be an important mechanism involved in the regulation of apoptosis.
Increased urine IgM excretion predicts cardiovascular events in patients with type 1 diabetes nephropathy
Authors: Tofik Rafid , Torffvit Ole , Rippe Bengt , Bakoush Omran 
Published: August 2009

Abstract

Background
Diabetic nephropathy, a major complication of diabetes, is characterized by progressive renal injury and increased cardiovascular mortality. An increased urinary albumin excretion due dysfunction of the glomerular barrier is an early sign of diabetic nephropathy. An increased urinary excretion of higher molecular weight proteins such as IgM appears with progression of glomerular injury. We aim here to study the prognostic significance of urine IgM excretion in patients with type 1 diabetes mellitus (type 1 diabetic nephropathy).

Methods
This is an observational study of 139 patients with type1 diabetes mellitus (79 males and 60 females) under routine care at the diabetic outpatient clinic at the Lund University Hospital. The median follow-up time was 18 years (1 to 22) years. Urine albumin and urine IgM concentration were measured at time of recruitment.

Results
Overall 32 (14 male and 18 female) patients died in a cardiovascular event and 20 (11 male and 9 female) patients reached end-stage renal disease. Univariate analysis indicated that patient survival and renal survival were inversely associated with urine albumin excretion (RR = 2.9 and 5.8, respectively) and urine IgM excretion (RR = 4.6 and 5.7, respectively). Stratified analysis demonstrated that in patients with different degrees of albuminuria, the cardiovascular mortality rate and the incidence of end-stage renal disease was approximately three times higher in patients with increased urine IgM excretion.

Conclusion
An increase in urinary IgM excretion in patients with type 1 diabetes is associated with an increased risk for cardiovascular mortality and renal failure, regardless of the degree of albuminuria.
A synopsis of eukaryotic Nα-terminal acetyltransferases: nomenclature, subunits and substrates
Authors: Polevoda Bogdan , Arnesen Thomas , Sherman Fred 
Published: August 2009

Abstract
We have introduced a consistent nomenclature for the various subunits of the NatA-NatE N-terminal acetyltransferases from yeast, humans and other eukaryotes.