Miracle-dz/UniFAR-FTUs huggingface dataset:
Terminal Restriction Fragment Length Polymorphism Data Analysis for Quantitative Comparison of Microbial Communities

ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) is a culture-independent method of obtaining a genetic fingerprint of the composition of a microbial community. Comparisons of the utility of different methods of (i) including peaks, (ii) computing the difference (or distance) between profiles, and (iii) performing statistical analysis were made by using replicated profiles of eubacterial communities. These samples included soil collected from three regions of the United States, soil fractions derived from three agronomic field treatments, soil samples taken from within one meter of each other in an alfalfa field, and replicate laboratory bioreactors. Cluster analysis by Ward's method and by the unweighted-pair group method using arithmetic averages (UPGMA) were compared. Ward's method was more effective at differentiating major groups within sets of profiles; UPGMA had a slightly reduced error rate in clustering of replicate profiles and was more sensitive to outliers. Most replicate profiles were clustered together when relative peak height or Hellinger-transformed peak height was used, in contrast to raw peak height. Redundancy analysis was more effective than cluster analysis at detecting differences between similar samples. Redundancy analysis using Hellinger distance was more sensitive than that using Euclidean distance between relative peak height profiles. Analysis of Jaccard distance between profiles, which considers only the presence or absence of a terminal restriction fragment, was the most sensitive in redundancy analysis, and was equally sensitive in cluster analysis, if all profiles had cumulative peak heights greater than 10,000 fluorescence units. It is concluded that T-RFLP is a sensitive method of differentiating between microbial communities when the optimal statistical method is used for the situation at hand. It is recommended that hypothesis testing be performed by redundancy analysis of Hellinger-transformed data and that exploratory data analysis be performed by cluster analysis using Ward's method to find natural groups or by UPGMA to identify potential outliers. Analyses can also be based on Jaccard distance if all profiles have cumulative peak heights greater than 10,000 fluorescence units.
Psychological predictors for health-related quality of life and disability in persons with chronic obstructive pulmonary disease (COPD)

Objective: Individuals with chronic obstructive pulmonary disease (COPD) exhibit low physical and mental health-related quality of life (HRQL) and high susceptibility to disability. We investigated the influence of psychological factors on HRQL and disability in COPD individuals recruited from the general population. In line with Leventhal’s common sense model, we expected psychological factors to be associated with HRQL and disability even after controlling for medical status. Methods: Individuals with COPD (n = 502; 59.7 years old; GOLD grades were I: 3%, II: 17%, III: 34%, IV: 46%) were assessed through an online survey administered via COPD patient organisations in Germany. Individuals filled in the Short Form Health Survey (SF-12), COPD Assessment Test, Patient Health Questionnaire (modules: GAD-2, PHQ-15, PHQ-9), Brief Illness Perception Questionnaire, a questionnaire that assesses causal illness attributions, and the internal illness-related locus of control scale of the ‘KKG questionnaire for the assessment of control beliefs about illness and health’. Multiple linear regressions were calculated. Results: The investigated factors explained high variances (disability = 56%, physical HRQL = 28%, mental HRQL = 63%, p ≤ .001). Better mental health, more optimistic illness perceptions, attribution to psychological causes, and stronger internal locus of control were associated with lower disability and better HRQL. Comorbid somatic symptoms contributed to high disability and low quality of life. Conclusion: Psychological factors, such as illness perception, attribution and internal locus of control, were associated with disability and HRQL. These factors should be considered when designing treatments for individuals with COPD, and adequate interventions should be provided to enhance illness understanding and self-management skills.
Better anticoagulation control improves survival after valve replacement.

OBJECTIVE We sought to assess the effect of anticoagulation control on long-term survival after valve replacement with the Medtronic Hall valve (Medtronic, Inc, Minneapolis, Minn). METHODS Prospective follow-up data, including 82,297 international normalized ratios, were collected for 1476 patients undergoing single valve replacement with the Medtronic Hall valve between 1979 and 1994, with follow-up to the end of 1998. After excluding 204 patients who either died within 30 days or had fewer than 10 international normalized ratios recorded beyond 30 days, there were 10,203 patient years of follow-up for analysis. Anticoagulation variability was measured as the percentage of international normalized ratios outside a target range of 2.0 to 4.0 for each patient. RESULTS Linearized rates for late death rose progressively with increasing deciles of anticoagulation variability for both aortic and mitral valve replacement (2.7% and 3.3% per year, respectively, in deciles 1 and 2 up to 9.5% and 14.6% per year, respectively, in deciles 6-10; P <.001). Survival at 15 years after aortic valve replacement was 59% for low anticoagulation variability (deciles 1 and 2), 55% for intermediate anticoagulation variability (decile 3), and 28% for high anticoagulation variability (deciles 4-10); survivals at 15 years after mitral valve replacement were 56%, 42%, and 24%, respectively (P <.001 between low-intermediate anticoagulation variability and high anticoagulation variability for both aortic and mitral valve replacement). On multivariate analysis, significant predictors of reduced survival were anticoagulation variability per 20% increase (hazard ratio, 1.8), diabetes (hazard ratio, 1.6), decade of age (hazard ratio, 1.6), concomitant coronary artery bypass grafting (hazard ratio, 1.5), male sex (hazard ratio, 1.4), hypertension (hazard ratio, 1.4), New York Heart Association class III or IV (hazard ratio, 1.3), and non-sinus rhythm (hazard ratio, 1.2). Patients with low anticoagulation variability who were in sinus rhythm and did not have diabetes, coronary bypass grafting, or hypertension had survivals equal to those of the age- and sex-matched general population at 15 years. The incidence of valve-related deaths was significantly higher with high anticoagulation variability compared with the incidence with low-intermediate anticoagulation variability for both aortic (1.4% vs 0.5% per year, P <.001) and mitral valve replacement (1.5% vs 0.5% per year, P <.001). By means of univariate analysis, high anticoagulation variability was significantly associated with New York Heart Association class III or IV at 5 years postoperatively (P <.001) and with age of greater than 60 years at the time of the operation (P =.002). CONCLUSIONS High anticoagulation variability is the most important independent predictor of reduced survival after valve replacement with a mechanical valve. Better anticoagulation control should improve survival.
Productive interaction between the chromosome partitioning proteins, ParA and ParB, is required for the progression of the cell cycle in Caulobacter crescentus

In Caulobacter crescentus the partitioning proteins ParA and ParB operate a molecular switch that couples chromosome partitioning to cytokinesis. Homologues of these proteins have been shown to be important for the stable inheritance of F‐plasmids and the prophage form of bacteriophage P1. In C. crescentus, ParB binds to sequences adjacent to the origin of replication and is required for the initiation of cell division. Additionally, ParB influences the nucleotide‐bound state of ParA by acting as a nucleotide exchange factor. Here we have performed a genetic analysis of the chromosome partitioning protein ParB. We show that C. crescentus ParB, like its plasmid homologues, is composed of three domains: a carboxyl‐terminal dimerization domain; a central DNA‐binding, helix–turn–helix domain; and an amino‐terminal domain required for the interaction with ParA. In vivo expression of amino‐terminally deleted parB alleles has a dominant lethal effect resulting in the inhibition of cell division. Fluorescent in situ hybridization experiments indicate that this phenotype is not caused by a chromosome partitioning defect, but by the reversal of the amounts of ATP‐ versus ADP‐ bound ParA inside the cell. We present evidence suggesting that amino‐terminally truncated and full‐length, wild‐type ParB form heterodimers which fail to interact with ParA, thereby reversing the intracellular ParA‐ATP to ParA‐ADP ratio. We hypothesize that the amino‐terminus of ParB is required to regulate the nucleotide exchange of ParA which, in turn, regulates the initiation of cell division.
Cerebrospinal T-cell responses aid in the diagnosis of tuberculous meningitis in a human immunodeficiency virus- and tuberculosis-endemic population.

RATIONALE Current tools for the rapid diagnosis of tuberculous meningitis (TBM) are suboptimal. We evaluated the clinical utility of a quantitative RD-1 IFN-gamma T-cell enzyme-linked immunospot (ELISPOT) assay (T-SPOT.TB), using cerebrospinal fluid cells for the rapid immunodiagnosis of TBM. OBJECTIVES To evaluate the diagnostic utility of the RD1 antigen- specific ELISPOT assay for the diagnosis of tuberculous meningitis. METHODS The ELISPOT assay was evaluated in 150 patients with suspected TBM who were categorized as definite-TBM, probable-TBM, and non-TBM. Culture or polymerase chain reaction positivity for Mycobacerium tuberculosis served as the reference standard. To determine the diagnostic value of the ELISPOT assay, a clinical prediction rule was derived from baseline clinical and laboratory parameters using a multivariable regression model. MEASUREMENTS AND MAIN RESULTS A total of 140 patients (81% HIV-infected; median CD4 count, 160 cells/mm(3)) were included in the final analysis. When comparing the definite-TBM (n = 38) and non-TBM groups (n = 48), the ELISPOT assay (cut point of > or =228 spot-forming cells per 1 million mononuclear cells) was a useful rule-in test: sensitivity 58% (95% confidence interval [CI], 41-74); specificity 94% (95% CI, 83-99). However, ELISPOT outcomes improved when other rapid tests were concurrently used to exclude bacterial (Gram stain) and cryptococcal meningitis (latex-agglutination test) within the non-TBM group. Using this approach, the ELISPOT assay (cut point of > or =46 spot-forming cells) was an excellent rule-in test: sensitivity 82% (95% CI, 66-92); specificity 100% (95% CI, 78-100); positive predictive value, 100% (95% CI, 89-100); negative predictive value, 68% (95% CI, 45-86); area under the curve, 0.90. The ELISPOT assay had incremental diagnostic value compared with the clinical prediction rule. CONCLUSIONS The RD-1 ELISPOT assay, using cerebrospinal fluid mononuclear cells and in conjunction with other rapid confirmatory tests (Gram stain and cryptococcal latex-agglutination test), is an accurate rapid rule-in test for TBM in a TB and HIV endemic setting.
Exhaustive analysis of BH 4 and dopamine biosynthesis genes in patients with Dopa-responsive dystonia

Exhaustive analysis of BH4 and dopamine biosynthesis genes in patients with Dopa-responsive dystonia Fabienne Clot,* David Grabli,* Cécile Cazeneuve, Emmanuel Roze, Pierre Castelnau, Brigitte Chabrol, Pierre Landrieu, Karine Nguyen, Gérard Ponsot, Myriem Abada, Diane Doummar, Philippe Damier, Roger Gil, Stéphane Thobois, Alana J. Ward, Michael Hutchinson, Annick Toutain, Fabienne Picard, Agnès Camuzat, Estelle Fedirko, Chankannira Sân, Delphine Bouteiller, Eric LeGuern, Alexandra Durr, Marie Vidailhet, Alexis Brice and the French Dystonia Network
Cell‐specific Localization of the CholecystokininA Receptor in the Porcine Pancreas

Cholecystokinin (CCK) produced in the mucosa of the upper small intestine exerts several biological functions. Its secretion in physiological amounts is modulated by the interaction of extracellular regulators and by binding to intracellular receptors of the target cells. The relative affinity of CCK to its receptor has been characterized in various biological and pharmacological studies and it is now well established that CCK has a higher affinity to the CCKA than to the CCKB receptor. Furthermore CCK influences the secretion of pancreatic enzymes in several species but very little is known about the relationship between CCK and the islet hormone‐producing cells in the pig pancreas. The localization of this receptor at the cellular level showed conflicting results in animal studies and has not been described in pigs. The aim of the present study was to characterize the precise cellular location of the CCKA receptor in the porcine pancreas. Polyclonal antiserum was raised against the N‐terminal epitope of the CCKA receptor molecule and used for localization studies. Using immunohistochemistry on methanol/acetic acid‐fixed, paraffin‐embedded pancreas, the CCKA receptor could successfully be localized in islet cells. Parallel staining of serial sections with antibodies directed against insulin and glucagon revealed colocalization with glucagon in alpha cells. No immunoreaction was found in the exocrine pancreas. Our results support the concept that in the porcine species the stimulation of the exocrine pancreas is mediated by the CCKB rather than the CCKA receptor, as it is known for the rat species.
School-enrollment rates and trends, gender, and fertility: a cross-national analysis.

The analysis of the association between educational status and fertility decline is performed 1) by examining the rates of enrollment in primary and secondary schools by gender and 2) by assessing the effects of the change/spread in rates of enrollment between 1965 and 1986. 59 countries were involved in the cross-sectional analysis. Variables included the logged crude birth rate, total enrollment rates, enrollment rates by gender, male-female ratios, the growth rate for each educational measure by world system status (core, peripheral, and semiperipheral countries), control variables (economic growth, family planning, multinational corporate penetration, women's labor force participation, child mortality rate, social insurance programs), and enrollment changes. The evidence reflects a strong association between levels of enrollment of girls in primary and secondary school and gender inequality and fertility declines. Caldwell's theory of the flows of wealth and the spread of education effect was found to have little support. High levels of female enrollment and low levels of gender inequality in access to schooling are associated with fertility declines. Caldwell's theory is that this indicates a decline in patriarchy, change in women's familial roles and a shift to a more egalitarian family structure. Increases in female education mean higher status and more power for women.
Orthotopic transplantation of immortalized mesencephalic progenitors (CSM14.1 cells) into the substantia nigra of hemiparkinsonian rats induces neuronal differentiation and motoric improvement

Neural progenitor cell grafting is a promising therapeutic option in the treatment of Parkinson's disease. In previous experiments we grafted temperature‐sensitive immortalized CSM14.1 cells, derived from the ventral mesencephalon of E14‐rats, bilaterally in the caudate putamen of adult hemiparkinsonian rats. In these studies we were not able to demonstrate either a therapeutic improvement or neuronal differentiation of transplanted cells. Here we examined whether CSM14.1 cells grafted bilaterally orthotopically in the substantia nigra of hemiparkinsonian rats have the potential to differentiate into dopaminergic neurons. Adult male rats received 6‐hydroxydopamine into the right medial forebrain bundle, and successful lesions were evaluated with apomorphine‐induced rotations 12 days after surgery. Two weeks after a successful lesion the animals received bilateral intranigral grafts consisting of either about 50 000 PKH26‐labelled undifferentiated CSM14.1 cells (n = 16) or a sham‐graft (n = 9). Rotations were evaluated 3, 6, 9 and 12 weeks post‐grafting. Animals were finally perfused with 4% paraformaldehyde. Cryoprotected brain slices were prepared for immunohistochemistry using the freeze‐thaw technique to preserve PKH26‐labelling. Slices were immunostained against neuronal epitopes (NeuN, tyrosine hydroxylase) or glial fibrillary acidic protein. The CSM14.1‐cell grafts significantly reduced the apomorphine‐induced rotations 12 weeks post‐grafting compared to the sham‐grafts (P < 0.05). There was an extensive mediolateral migration (400–700 µm) of the PKH26‐labelled cells within the host substantia nigra. Colocalization with NeuN or glial fibrillary acidic protein in transplanted cells was confirmed with confocal microscopy. No tyrosine hydroxylase‐immunoreactive grafted cells were detectable. The therapeutic effect of the CSM14.1 cells could be explained either by their glial cell‐derived neurotrophic factor‐expression or their neural differentiation with positive effects on the basal ganglia neuronal networks.
Association between perceived level of stress, clinical characteristics and psychopathological symptoms in women with systemic lupus erythematosus.

OBJECTIVES To evaluate psychopathological status and stress level from a sample with SLE; compare mental functioning and stress levels between women with SLE and healthy women; determine whether disease duration, disease activity, cumulative organ damage and stress have an influence on psychopathological symptoms in SLE patients; and evaluate whether perception of stress is related to SLE severity. METHODS We conducted a cross-sectional study of 425 participants; 202 women with SLE, with an average age (SD) of 36.61 (10.15), and 223 healthy women, with age-matched controls. The assessment included the clinical characteristics (disease duration, SLE activity, cumulative organ damage, pharmacotherapy), the Symptom Checklist-90-Revised (SCL-90-R) and the Perceived Stress Scale. Descriptive, comparative, univariate and multivariate analysis were performed. RESULTS SLE patients showed psychopathological alterations in the somatisation, obsessive-compulsive and positive discomfort subscales of SCL-90-R. Women with SLE reported significantly higher scores on the psychopathological dimensions and perceived stress compared to healthy women, except for paranoid ideation. Disease duration, SLE activity, cumulative organ damage, and perceived stress were shown to be significant predictors of psychopathological manifestations, explaining a range, between 20 and 43%, of variance across SCL-90-R dimensions. Moreover, perceived stress was related to SLE activity, after controlling for psychopathological dimensions. CONCLUSIONS The psychopathological manifestations in SLE appeared to be influenced by perceived stress, disease duration, disease activity and cumulative organ damage. In turn, perceived stress was associated with disease severity. This knowledge may contribute to a more comprehensive perspective of these manifestations in the SLE population in the clinical setting.
Association of Risk Estimates of Three Different Cardiovascular Risk Assessment Tools with Carotid Intima Media Thickness in Patients with Type 2 Diabetes.

INTRODUCTION Risk assessment tools used to calculate the Cardiovascular Disease (CVD) risk such as the Framingham Risk Score (FRS), United Kingdom Prospective Diabetes study (UKPDS) risk engine and the World Health Organization (WHO) risk score have not been tested on their ability to detect subclinical atherosclerosis in most developing countries. AIM To study the association between the calculated CVD risk scores using each of these tools and Carotid Intima Medial Thickness (CIMT), a surrogate marker of atherosclerosis, in a group of patients with Type 2 diabetes (T2DM) in Sri Lanka. MATERIALS AND METHODS We calculated CVD risk scores of 68 randomly selected patients with T2DM with no history or symptoms of CVD and measured their CIMT using B-mode ultrasonography (USS). Carotid USS was considered positive when the maximum carotid IMT was 0.9mm or when arteriosclerotic plaques were detected. The 10-year CVD risk was calculated using the FRS, the UKPDS risk engine and the WHO risk score. Pearson correlation was used to study the association between CVD risk scores with CIMT. RESULTS Of the 68 patients studied, 50% were males and their mean age (SD) was 56.9 (±9.6) years. The mean age at onset and duration of diabetes were 44.3(±9.1) and 12.2(±7.6) years respectively. Of the scoring methods, UKPDS tool had weak, but significantly positive (r = 0.26, p < 0.05) and FRS had positive but not significant association (r= 0. 21) with CIMT. There was a negative association between CIMT and WHO risk score (r= - 0.07). CONCLUSION Of the three CVD risk assessment tools, both UKPDS risk engine and FRS have almost equal ability (former being marginally superior) in predicting underlying atherosclerotic vascular disease in patients with T2DM. Negative association of the WHO risk score with CIMT argues against its utility for CVD screening. These findings highlight the need for developing more sensitive and reliable CVD risk assessment tools for developing countries.
Ultrastructure of oocyte migration through the mouse ovarian surface epithelium during neonatal development

Previous studies using light microscopy have described the presence of oocytes within the ovarian surface epithelium (OSE) of the neonate ovary and their subsequent release into the periovarian space. The ultrastructural examination and quantitative estimate of oocyte migration through the OSE is described in this study. The surface of the mouse ovary is covered by a simple squamous to simple cuboidal epithelium resting on a distinct basal lamina. Healthy, non‐atretic primordial follicles located in the periphery of the ovarian cortex interact with the OSE. Oocytes within the primordial follicles are large (50–70 μm), spherical cells surrounded by a single layer of squamour granulosa cells. Migratory oocytes initially display a ruffled border and extended pseudopodia like cellular extensions towards the OSE. These processes subsequently compromise the basal lamina of the OSE and extend between the epithelial cells. Granulosa cells retract as junctional complexes between them and the oocyte are no longer observed. The oocyte migrates between the OSE cells and passes into the periovarian space without the loss of either OSE or granulosa cells. The rate of oocyte migration reaches a peak during the first week of neonatal development and then gradually diminishes until by day 28 of development no oocyte migration was observed.