bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting the effects of selection at the population level in six bovine immune genes
Authors: Freeman Abigail R , Lynn David J , Murray Caitriona , Bradley Daniel G 
Published: October 2008

AbstractBackgroundThe capacity of a species or population to respond to and survive novel infectious disease challenge is one of the most significant selective forces shaping genetic diversity and the period following animal domestication was likely one of the most important in terms of newly emerging diseases. Inter-specific genome-wide comparison has suggested that genes, including cluster of differentiation 2 (CD2), ADP-ribosyltransferase 4 (ART4), tyrosine kinase binding protein (TYROBP) and interleukins IL2, IL5, IL13, may have undergone positive selection during the evolution of the bovine lineage. Past adaptive change implies that more recent variation may have also been subject to selective forces.ResultsIn this paper, we re-sequence each of these genes in cattle cohorts from Europe, Africa and Asia to investigate patterns of polymorphism at the population level. Patterns of diversity are higher withinBos indicussuggesting different demographic history to that ofBos taurus. Significant coding polymorphism was observed within each of the cell-surface receptors. In particular, CD2 shows two divergent haplotypes defined by a series of six derived nonsynonymous substitutions that are significantly clustered on the extracellular surface of the protein and give significant values for Fay and Wu'sH, strongly suggesting a recent adaptive history. In contrast, the signaling molecules (especially IL13) display outlying allele frequency spectra which are consistent with the effects of selection, but display negligible coding polymorphism.ConclusionWe present evidence suggestive of recent adaptive history in bovine immune genes; implying some correspondence between intra- and inter-specific signals of selection. Interestingly, three signaling molecules have negligible nonsynonymous variation but show outlying test statistics in contrast to three receptors, where it is protein sequence diversity that suggests selective history.
A comparative computational analysis of nonautonomous Helitron elements between maize and rice
Authors: Sweredoski Michael , DeRose-Wilson Leah , Gaut Brandon S 
Published: October 2008

Abstract

Background

Helitrons are DNA transposable elements that are proposed to replicate via a rolling circle mechanism. Non-autonomous helitron elements have captured gene fragments from many genes in maize (Zea mays ssp. mays) but only a handful of genes in Arabidopsis (Arabidopsis thaliana). This observation suggests very different histories for helitrons in these two species, but it is unclear which species contains helitrons that are more typical of plants.

Results
We performed computational searches to identify helitrons in maize and rice genomic sequence data. Using 12 previously identified helitrons as a seed set, we identified 23 helitrons in maize, five of which were polymorphic among a sample of inbred lines. Our total sample of maize helitrons contained fragments of 44 captured genes. Twenty-one of 35 of these helitrons did not cluster with other elements into closely related groups, suggesting substantial diversity in the maize element complement. We identified over 552 helitrons in the japonica rice genome. More than 70% of these were found in a collinear location in the indica rice genome, and 508 clustered as a single large subfamily. The japonica rice elements contained fragments of only 11 genes, a number similar to that in Arabidopsis. Given differences in gene capture between maize and rice, we examined sequence properties that could contribute to differences in capture rates, focusing on 3' palindromes that are hypothesized to play a role in transposition termination. The free energy of folding for maize helitrons were significantly lower than those in rice, but the direction of the difference differed from our prediction.

Conclusion
Maize helitrons are clearly unique relative to those of rice and Arabidopsis in the prevalence of gene capture, but the reasons for this difference remain elusive. Maize helitrons do not seem to be more polymorphic among individuals than those of Arabidopsis; they do not appear to be substantially older or younger than the helitrons in either species; and our analyses provided little evidence that the 3' hairpin plays a role.
Determination of the mimic epitope of the M-like protein adhesin in swine Streptococcus equi subsp. zooepidemicus
Authors: Fan Hongjie , Wang Yongshan , Tang Fuyu , Lu Chengping 
Published: October 2008

AbstractBackgroundThe M-like protein, also known as SzP, is expressed on the surface ofStreptococcus equisubsp. zooepidemicus(S. zooepidemicus). Previous studies demonstrated that SzP is similar to M protein of group AStreptococcusin the structure and characteristics of antiphagocytosis. The M protein is an adhesin that can bind to the host cells, however it is not known whether the SzP ofS. zooepidemicusalso functions as an adhesin. We conducted an investigation to determine SzP as an adhesin, and one SzP epitope was identified to be responsible for mediating binding to HEp-2 cells.MethodsThe gene encoding SzP was expressed inE. coli, and the purified recombinant SzP (rSzP) was recognized by rabbit anti-S. zooepidemicusantibodies using immunoblot. Furthermore, the adherence ofS. zooepidemicusto HEp-2 cells was inhibited by anti-rSzP antibodies in a dose-dependent manner. We employed a random 12-peptide phage display library for screening of immunodominant mimics of the SzP, which were recognized by an anti-SzP specific monoclonal antibody (mAb 2C8). Initial positive phage clones were identified by ELISA, followed by assays to determine the adherence-inhibiting ability of the peptide.ResultsTen out of fourteen selected positive clones showed high reactivity that effectively inhibited the binding of mAb 2C8 to rSzP. The motif XSLSRX was highly conserved among six of the ten clones.ConclusionCollectively, our findings suggest that the motif XSLSRX may represent an immunodominant mimic epitope of the SzP ofS. zooepidemicusstrain ATCC 35246, and that the same epitope may be used to mediate SzP binding to HEp-2 cells.
Sulphur metabolism and cellulase gene expression are connected processes in the filamentous fungus Hypocrea jecorina (anamorph Trichoderma reesei)
Authors: Gremel Gabriela , Dorrer Marcel , Schmoll Monika 
Published: October 2008

Abstract

Background
Sulphur compounds like cysteine, methionine and S-adenosylmethionine are essential for the viability of most cells. Thus many organisms have developed a complex regulatory circuit that governs the expression of enzymes involved in sulphur assimilation and metabolism. In the filamentous fungus Hypocrea jecorina (anamorph Trichoderma reesei) little is known about the participants in this circuit.

Results
Analyses of proteins binding to the cellulase activating element (CAE) within the promotor of the cellobiohydrolase cbh2 gene led to the identification of a putative E3 ubiquitin ligase protein named LIMPET (LIM1), which is an orthologue of the sulphur regulators SCON-2 of Neurospora crassa and Met30p of Saccharomyces cerevisiae. Transcription of lim1 is specifically up-regulated upon sulphur limitation and responds to cellulase inducing conditions. In addition, light dependent stimulation/shut down of cellulase gene transcription by methionine in the presence of sulphate was observed. Further, lim1 transcriptionally reacts to a switch from constant darkness to constant light and is subject to regulation by the light regulatory protein ENVOY. Thus lim1, despite its function in sulphur metabolite repression, responds both to light as well as sulphur- and carbon source. Upon growth on cellulose, the uptake of sulphate is dependent on the light status and essential for growth in light. Unlike other fungi, growth of H. jecorina is not inhibited by selenate under low sulphur conditions, suggesting altered regulation of sulphur metabolism. Phylogenetic analysis of the five sulphate permeases found in the genome of H. jecorina revealed that the predominantly mycelial sulphate permease is lacking, thus supporting this hypothesis.

Conclusion
Our data indicate that the significance of the sulphate/methionine-related signal with respect to cellulase gene expression is dependent on the light status and reaches beyond detection of sulphur availability.
The accuracy of symptoms, signs and diagnostic tests in the diagnosis of left ventricular dysfunction in primary care: A diagnostic accuracy systematic review
Authors: Madhok V , Falk G , Rogers A , Struthers AD , Sullivan FM , Fahey T 
Published: October 2008

Abstract

Background
To assess the accuracy of findings from the clinical history, symptoms, signs and diagnostic tests (ECG, CXR and natriuretic peptides) in relation to the diagnosis of left ventricular systolic dysfunction (LVSD) in a primary care setting.

Methods
Diagnostic accuracy systematic review, we searched Medline (1966 to March 2008), EMBASE (1988 to March 2008), Central, Cochrane and ZETOC using a diagnostic accuracy search filter. We included cross-sectional or cohort studies that assess the diagnostic utility of clinical history, symptoms, signs and diagnostic tests, against a reference standard of echocardiography. We calculated pooled positive and negative likelihood ratios and assessed heterogeneity using the I2 index.

Results
24 studies incorporating 10,710 patients were included. The median prevalence of LVSD was 29.9% (inter-quartile range 14% to 37%). No item from the clinical history or symptoms provided sufficient diagnostic information to "rule in" or "rule out" LVSD. Displaced apex beat shows a convincing diagnostic effect with a pooled positive likelihood ratio of 16.0 (8.2–30.9) but this finding occurs infrequently in patients. ECG was the most widely studied diagnostic test, the negative likelihood ratio ranging from 0.06 to 0.6. Natriuretic peptide results were strongly heterogeneous, with negative likelihood ratios ranging from 0.02 to 0.80.

Conclusion
Findings from the clinical history and examination are insufficient to "rule in" or "rule out" a diagnosis of LVSD in primary care settings. BNP and ECG measurement appear to have similar diagnostic utility and are most useful in "ruling out" LVSD with a normal test result when the probability of LVSD is in the intermediate range.
Restoration of tumor suppressor miR-34 inhibits human p53-mutant gastric cancer tumorspheres
Authors: Ji Qing , Hao Xinbao , Meng Yang , Zhang Min , DeSano Jeffrey , Fan Daiming , Xu Liang 
Published: October 2008

Abstract

Background
MicroRNAs (miRNAs), some of which function as oncogenes or tumor suppressor genes, are involved in carcinogenesis via regulating cell proliferation and/or cell death. MicroRNA miR-34 was recently found to be a direct target of p53, functioning downstream of the p53 pathway as a tumor suppressor. miR-34 targets Notch, HMGA2, and Bcl-2, genes involved in the self-renewal and survival of cancer stem cells. The role of miR-34 in gastric cancer has not been reported previously. In this study, we examined the effects of miR-34 restoration on p53-mutant human gastric cancer cells and potential target gene expression.

Methods
Human gastric cancer cells were transfected with miR-34 mimics or infected with the lentiviral miR-34-MIF expression system, and validated by miR-34 reporter assay using Bcl-2 3'UTR reporter. Potential target gene expression was assessed by Western blot for proteins, and by quantitative real-time RT-PCR for mRNAs. The effects of miR-34 restoration were assessed by cell growth assay, cell cycle analysis, caspase-3 activation, and cytotoxicity assay, as well as by tumorsphere formation and growth.

Results
Human gastric cancer Kato III cells with miR-34 restoration reduced the expression of target genes Bcl-2, Notch, and HMGA2. Bcl-2 3'UTR reporter assay showed that the transfected miR-34s were functional and confirmed that Bcl-2 is a direct target of miR-34. Restoration of miR-34 chemosensitized Kato III cells with a high level of Bcl-2, but not MKN-45 cells with a low level of Bcl-2. miR-34 impaired cell growth, accumulated the cells in G1 phase, increased caspase-3 activation, and, more significantly, inhibited tumorsphere formation and growth.

Conclusion
Our results demonstrate that in p53-deficient human gastric cancer cells, restoration of functional miR-34 inhibits cell growth and induces chemosensitization and apoptosis, indicating that miR-34 may restore p53 function. Restoration of miR-34 inhibits tumorsphere formation and growth, which is reported to be correlated to the self-renewal of cancer stem cells. The mechanism of miR-34-mediated suppression of self-renewal appears to be related to the direct modulation of downstream targets Bcl-2, Notch, and HMGA2, indicating that miR-34 may be involved in gastric cancer stem cell self-renewal/differentiation decision-making. Our study suggests that restoration of the tumor suppressor miR-34 may provide a novel molecular therapy for p53-mutant gastric cancer.
Family caregiver quality of life in multiple sclerosis among Kuwaitis: a controlled study
Authors: Alshubaili Asmahan F , Ohaeri Jude U , Awadalla Abdel W , Mabrouk Asser A 
Published: October 2008

AbstractBackgroundResearch interest in the quality of life (QOL) of persons with multiple sclerosis (MS) has been spurred by the need to broaden outcome measures. Far less of this interest has been directed at the family caregivers, who bear most of the burden of care. The objectives of the study were: First, to compare the subjective QOL of family caregivers of persons with relapsing remitting and progressive MS, with those of a matched general population sample and caregivers of diabetes and psychiatric patients. Second, to assess the relationship of QOL with caregiver attitudes to MS and patient's variables.MethodsConsecutive MS clinic attendees were assessed with the 26 – item WHOQOL Instrument, and for depression and disability. Similarly, caregivers independently rated their own QOL as well as their impression of patients' QOL and attitudes to patients' illness.ResultsThe 170 caregivers, mean age 35.7 years, had no significant diagnostic differences in QOL domain scores and attitudes to MS. Caregivers had significantly lower QOL than the general population control group for five out of six domains and the general facet (P < 0.01), but higher QOL than the patients. When the scores were corrected for patients' depression and disability, caregivers had similar QOL with the general population group for four domains. Using corrected scores, MS caregivers had lower scores than diabetic and psychiatric caregivers in the physical, psychological and social relations domains. Majority expressed negative attitudes to MS. Caregiver QOL was more affected by their fear of having MS than their feelings about the illness and caregiving role. Caregiver attitudes had mostly no significant impact on their proxy ratings of patients' QOL. The significant predictor of caregivers' overall QOL was their impression of patients' QOL.ConclusionCaregivers need specific attention if they are less educated, unemployed, afraid of having MS and caring for patients with longer duration of illness and less education. In particular, attention to patients' depression and disability could improve caregivers' QOL. Caregivers need specific programs to address fear of having MS, negative attitudes to illness and their unmet needs.
A conserved acidic patch in the Myb domain is required for activation of an endogenous target gene and for chromatin binding
Authors: Ko Emily Ray , Ko Dennis , Chen Carolyn , Lipsick Joseph S 
Published: October 2008

Abstract
The c-Myb protein is a transcriptional regulator initially identified by homology to the v-Myb oncoprotein, and has since been implicated in human cancer. The most highly conserved portion of the c-Myb protein is the DNA-binding domain which consists of three imperfect repeats. Many other proteins contain one or more Myb-related domains, including a number of proteins that do not bind directly to DNA. We performed a phylogenetic analysis of diverse classes of Myb-related domains and discovered a highly conserved patch of acidic residues common to all Myb-related domains. These acidic residues are positioned in the first of three alpha-helices within each of the three repeats that comprise the c-Myb DNA-binding domain. Interestingly, these conserved acidic residues are present on a surface of the protein which is distinct from that which binds to DNA. Alanine mutagenesis revealed that the acidic patch of the third c-Myb repeat is essential for transcriptional activity, but neither for nuclear localization nor DNA-binding. Instead, these acidic residues are required for efficient chromatin binding and interaction with the histone H4 N-terminal tail.
Fast quantitative determination of microbial rhamnolipids from cultivation broths by ATR-FTIR Spectroscopy
Authors: Leitermann Frank , Syldatk Christoph , Hausmann Rudolf 
Published: October 2008

AbstractBackgroundVibrational spectroscopic techniques are becoming increasingly important and popular because they have the potential to provide rapid and convenient solutions to routine analytical problems. Using these techniques, a variety of substances can be characterized, identified and also quantified rapidly.ResultsThe rapid ATR-FTIR (Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy)in timetechnique has been applied, which is suitable to quantify the concentrations of microbial rhamnolipids in a typical cultivation process. While the usually applied HPLC analysis requires an extensive and time consuming multi step extraction protocol for sample preparation, the ATR-FTIR-method allows the quantification of the rhamnolipids within 20 minutes. Accuracies between 0.5 g/l – 2.1 g/l for the different analytes were determined by cross validation of the calibration set. Even better accuracies between 0.28 g/l – 0.59 g/l were found for independent test samples of an arbitrarily selected cultivation.ConclusionATR-FTIR was found to be suitable for the rapid analysis of rhamnolipids in a biotechnological process with good reproducibility in sample determination and sufficient accuracy. An improvement in accuracy through continuous expansion and validation of the reference spectra set seems very likely.
Readmission to a surgical intensive care unit: incidence, outcome and risk factors
Authors: Kaben Axel , Corrêa Fabiano , Reinhart Konrad , Settmacher Utz , Gummert Jan , Kalff Rolf , Sakr Yasser 
Published: October 2008

Abstract
Introduction
We investigated the incidence of, outcome from and possible risk factors for readmission to the surgical intensive care unit (ICU) at Friedrich Schiller University Hospital, Jena, Germany.

Methods
We conducted an analysis of prospectively collected data from all patients admitted to the postoperative ICU between September 2004 and July 2006.

Results
Of 3169 patients admitted to the ICU during the study period, 2852 were discharged to the hospital floor and these patients made up the study group (1828 male (64.1%), mean patient age 62 years). The readmission rate was 13.4% (n = 381): 314 (82.4%) were readmitted once, 39 (10.2%) were readmitted twice and 28 (7.3%) were readmitted more than twice. The first readmission to the ICU occurred within a median of seven days (range 5 to 14 days). Patients who were readmitted to the ICU had a higher simplified acute physiology II score (37 +/- 16 versus 33 +/- 16; p < 0.001) and sequential organ failure score (6 +/- 3 versus 5 +/- 3; p = 0.001) on initial admission to the ICU than those who were not readmitted. In-hospital mortality was significantly higher in patients readmitted to the ICU (17.1% versus 2.9%; p < 0.001) than in other patients. In a multivariate analysis, age (odds ratio (OR) = 1.13 per 10 years; 95% confidence interval (CI) = 1.03 to 1.24; p = 0.04), maximum sequential organ failure score (OR = 1.04 per point; 95% CI = 1.01 to 1.08; p = 0.04) and C-reactive protein levels on the day of discharge to the hospital floor (OR = 1.02; 95% CI = 1.01 to 1.04; p = 0.035) were independently associated with a higher risk of readmission to the ICU.

Conclusions
In this group of surgical ICU patients, readmission to the ICU was associated with a more than five-fold increase in hospital mortality. Older age, higher maximum sequential organ failure score and higher C-reactive protein levels on the day of discharge to the hospital floor were independently associated with a higher risk of readmission to the ICU.
Tamoxifen Use and Osteoporotic Fracture Risk: A Population-Based Analysis
Authors: Cooke Andrew L. , Metge Colleen , Lix Lisa , Prior Heather J. , Leslie William D. 
Published: October 2008

Purpose Although tamoxifen has been shown to increase bone mineral density in clinical trials, it is less clear whether this significantly affects fracture rates. Even fewer data are available on skeletal outcomes when tamoxifen is used outside of the context of a clinical trial. A population-based case-control study was undertaken to determine whether tamoxifen use is associated with osteoporotic fractures in routine clinical practice. Patients and Methods Population-based administrative data for the Province of Manitoba, Canada, were examined for tamoxifen use and nontraumatic fracture codes in women 50 years of age or older. Women with osteoporotic fractures (vertebral, wrist or hip; n = 11,096) from 1996 to 2004 were each compared with three controls without fracture, matched for age, ethnicity, and comorbidity (n = 33,209). Tamoxifen use was classified as never, past use, or current use. Results Lower osteoporotic fracture rates were associated with current tamoxifen use (univariate odds ratio [OR] = 0.68; 95% CI, 0.55 to 0.84). After controlling for demographic and medical diagnoses known to affect fracture risk, current use was associated with a significantly reduced overall osteoporotic fracture risk (adjusted OR = 0.68; 95% CI, 0.55 to 0.88) and of hip fractures (adjusted OR = 0.47; 95% CI, 0.28 to 0.77). Neither recent nor remote past tamoxifen use was associated with reduced osteoporotic fracture risk. Breast cancer was not independently associated with osteoporotic fractures (adjusted OR = 0.95; 95% CI, 0.81 to 1.12). Conclusion In a population-based case-control study, current tamoxifen use was associated with a substantial reduction in osteoporotic fractures.