Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparisons of Different Hypervariable Regions of rrs Genes for Use in Fingerprinting of Microbial Communities by PCR-Denaturing Gradient Gel Electrophoresis

ABSTRACT Denaturing gradient gel electrophoresis (DGGE) has become a widely used tool to examine microbial diversity and community structure, but no systematic comparison has been made of the DGGE profiles obtained when different hypervariable (V) regions are amplified from the same community DNA samples. We report here a study to make such comparisons and establish a preferred choice of V region(s) to examine by DGGE, when community DNA extracted from samples of digesta is used. When the members of the phylogenetically representative set of 218 rrs genes archived in the RDP II database were compared, the V1 region was found to be the most variable, followed by the V9 and V3 regions. The temperature of the lowest-melting-temperature (Tm(L)) domain for each V region was also calculated for these rrs genes, and the V1 to V4 region was found to be most heterogeneous with respect to Tm(L). The average Tm(L) values and their standard deviations for each V region were then used to devise the denaturing gradients suitable for separating 95% of all the sequences, and the PCR-DGGE profiles produced from the same community DNA samples with these conditions were compared. The resulting DGGE profiles were substantially different in terms of the number, resolution, and relative intensity of the amplification products. The DGGE profiles of the V3 region were best, and the V3 to V5 and V6 to V8 regions produced better DGGE profiles than did other multiple V-region amplicons. Introduction of degenerate bases in the primers used to amplify the V1 or V3 region alone did not improve DGGE banding profiles. Our results show that DGGE analysis of gastrointestinal microbiomes is best accomplished by the amplification of either the V3 or V1 region of rrs genes, but if a longer amplification product is desired, then the V3 to V5 or V6 to V8 region should be targeted.
Culture-Independent Analysis of Indomethacin-Induced Alterations in the Rat Gastrointestinal Microbiota

ABSTRACT Nonsteroidal anti-inflammatory drugs (NSAIDs) are commonly prescribed for a variety of inflammatory conditions; however, the benefits of this class of drugs are accompanied by deleterious side effects, most commonly gastric irritation and ulceration. NSAID-induced ulceration is thought to be exacerbated by intestinal microbiota, but previous studies have not identified specific microbes that contribute to these adverse effects. In this study, we conducted a culture-independent analysis of ∼1,400 bacterial small-subunit rRNA genes associated with the small intestines and mesenteric lymph nodes of rats treated with the NSAID indomethacin. This is the first molecular analysis of the microbiota of the rat small intestine. A comparison of clone libraries and species-specific quantitative PCR results from rats treated with indomethacin and untreated rats revealed that organisms closely related to Enterococcus faecalis were heavily enriched in the small intestine and mesenteric lymph nodes of the treated rats. These data suggest that treatment of NSAID-induced ulceration may be facilitated by addressing the microbiological imbalances.
Delayed eosinophil apoptosis in asthma.

BACKGROUND Eosinophilic inflammation of the airways is a key characteristic of asthma. A defect in apoptosis might contribute to the chronic tissue eosinophilia associated with asthma. OBJECTIVE Our purpose was to examine whether the rate of apoptosis differs between peripheral blood eosinophils from asthmatic patients and healthy volunteers. METHODS Peripheral blood was obtained from volunteers with asthma and from control volunteers. Eosinophils were isolated by CD16-negative selection to >99% purity and were cultured for 48 hours. The number of apoptotic eosinophils in the culture was assessed by flow cytometric analysis of relative DNA content in propidium iodide-stained cells. Eosinophil apoptosis is expressed as apoptosis index (number of apoptotic cells/total number of cells). RESULTS Eosinophils from asthmatic patients not taking steroid medication survived longer (apoptosis index 0.25) than those of healthy control subjects (apoptosis index 0.40, P <.05). In contrast, the rate of apoptosis in eosinophils from patients concurrently taking steroids (apoptosis index 0.46) is higher than that of those not using steroids (P <.01) and not different from that of healthy subjects. To assess whether endogenous IL-3, IL-5, and GM-CSF production contributes to the delayed eosinophil apoptosis, the effects of the corresponding neutralizing antibodies were studied on eosinophil longevity. Neutralization of GM-CSF, but not of IL-3 or IL-5, increased slightly but significantly (P <.01) the rate of apoptosis in eosinophils obtained from patients with asthma. To assess whether beta(2)-agonist medication could contribute to the observed differences, we determined the in vitro effects of albuterol, fenoterol, and salmeterol on eosinophil apoptosis. All beta(2)-agonists inhibited eosinophil apoptosis by 12% to 19%. A possibility existed that a prior in vivo exposure to IL-5, GM-CSF, or beta(2)-agonists would explain the observed difference. To study this, eosinophils were incubated with GM-CSF, IL-5, and albuterol for 2 to 3 hours, followed by washout of the added compounds, and were subsequently cultured for 48 hours. However, an exposure to GM-CSF (7 pmol/L) or IL-5 (10 pmol/L) for 15 to 180 minutes was not a sufficient signal to prevent eosinophil apoptosis. In contrast, exposure to albuterol (100 nmol/L) for 120 minutes was sufficient to induce a significant (P <.05) decrease in eosinophil apoptosis. CONCLUSIONS The results suggest that eosinophil apoptosis is delayed in asthma. This delay may be partly explained by production of GM-CSF. The in vitro effects of beta(2)-agonists suggest that beta(2)-agonist use might contribute to the prolonged eosinophil survival through inhibition of apoptosis and thus may worsen eosinophilia in asthmatic patients. Use of inhaled glucocorticoids seems to totally reverse the delayed eosinophil apoptosis in asthma.
Deficiency of CPEB2-Confined Choline Acetyltransferase Expression in the Dorsal Motor Nucleus of Vagus Causes Hyperactivated Parasympathetic Signaling-Associated Bronchoconstriction

Cytoplasmic polyadenylation element binding protein 2 (CPEB2) is an RNA-binding protein and translational regulator. To understand the physiological function of CPEB2, we generated CPEB2 knock-out (KO) mice and found that most died within 3 d after birth. CPEB2 is highly expressed in the brainstem, which controls vital functions, such as breathing. Whole-body plethysmography revealed that KO neonates had aberrant respiration with frequent apnea. Nevertheless, the morphology and function of the respiratory rhythm generator and diaphragm neuromuscular junctions appeared normal. We found that upregulated translation of choline acetyltransferase in the CPEB2 KO dorsal motor nucleus of vagus resulted in hyperactivation of parasympathetic signaling-induced bronchoconstriction, as evidenced by increased pulmonary acetylcholine and phosphorylated myosin light chain 2 in bronchial smooth muscles. Specific deletion of CPEB2 in cholinergic neurons sufficiently caused increased apnea in neonatal pups and airway hyper-reactivity in adult mice. Moreover, inhalation of an anticholinergic bronchodilator reduced apnea episodes in global and cholinergic CPEB2-KO mice. Together, the elevated airway constriction induced by cholinergic transmission in KO neonates may account for the respiratory defect and mortality. SIGNIFICANCE STATEMENT This study first generated and characterized cpeb2 gene-deficient mice. CPEB2-knock-out (KO) mice are born alive but most die within 3 d after birth showing no overt defects in anatomy. We found that the KO neonates showed severe apnea and altered respiratory pattern. Such respiratory defects could be recapitulated in mice with pan-neuron-specific or cholinergic neuron-specific ablation of the cpeb2 gene. Further investigation revealed that cholinergic transmission in the KO dorsal motor nucleus of vagus was overactivated because KO mice lack CPEB2-suppressed translation of the rate-limiting enzyme in the production of acetylcholine (i.e., choline acetyltransferase). Consequently, increased parasympathetic signaling leads to hyperactivated bronchoconstriction and abnormal respiration in the KO neonates.
Synapses made by axons of callosal projection neurons in mouse somatosensory cortex: Emphasis on intrinsic connections

This is one of a series of papers aimed at identifying the synaptic output patterns of the local and distant projections of subgroups of pyramidal neurons. The subgroups are defined by the target site to which their main axon projects. Pyramidal neurons in areas 1 and 40 of mouse cerebral cortex were labeled by the retrograde transport of horseradish peroxidase (HRP) transported from severed callosal axons in the contralateral hemisphere. Terminals of the local axon collaterals of these neurons (“intrinsic” terminals) were identified in somatosensory areas 1 and 40, and their distribution and synaptic connectivity were examined. Also examined were the synaptic connections of “extrinsic” callosal axon terminals labeled by lesion induced degeneration consequent to the severing of callosal fibers. A post‐lesion survival time of 3 days was chosen because by this time the extrinsic terminals were all degenerating, whereas the intrinsic terminals were labeled by HRP.
Disease burden in The Netherlands due to infections with Shiga toxin-producing Escherichia coli O157

Surveys carried out between 1990 and 2000 indicated that the incidence of STEC O157-associated gastroenteritis in The Netherlands was 1250 cases/year (median), of which 180 visited a general practitioner, 40 are reported and 0·6 are fatal, mainly in the elderly. There are approximately 20 cases of STEC O157-associated haemolytic–uraemic syndrome (HUS) per year, mainly in children. There are 2·5 HUS patients per year who develop end-stage renal disease (ESRD). There are an estimated 2 HUS-related and 0·5 ESRD-related fatalities per year. The mean disease burden associated with STEC O157 in the Dutch population is 116 (90% confidence interval 85–160) Disability Adjusted Life Years (DALYs) per year. Mortality due to HUS (58 DALYs), and ESRD (21 DALYs) and dialysis due to ESRD (21 DALYs) constitute the main determinants of disease burden. Sensitivity analysis indicates that uncertainty associated with model assumptions did not have a major effect on these estimates.
Monitoring Northern Fowl Mites (Acari: Macronyssidae) in Caged Laying Hens: Feasibility of an Egg-Based Sampling System

Abstract Northern fowl mites were monitored on a caged-layer operation in southern California for 22 mo. Three experienced observers underestimated actual numbers of mites in the vent region ≈80% of the time. Errors were higher for heavy infestations. Observer estimates were highly correlated with each other (r > 0.89, P < 0.01) and with mite numbers estimated by vent feather removal (r > 0.82, P < 0.01). Mites on hens varied between houses and over time. Molting consistently reduced mite numbers, but did not eliminate them in a flock. Long-term monitoring of individual sentinel hens demonstrated that some hens would support high numbers of mites for several months or more. Use of a new sequential hen sampling plan required ≈1 min per hen, if mite numbers were estimated. At this site, treatment decisions often could be reached in <20 min per house. Mite scores (index of estimated mites per hen) were well correlated with percentage of hens infested in both test houses. In a chronically infested house, prevalence of mites on eggs averaged 8.5%, with a range of 0–55%. Applications of tetrachlorvinphos-dichlorvos by the producer appeared to be based on mites on > about 20% of eggs. The chemical was marginal for controlling mites on hens (25% reduction in percentage of hens infested), but effectively reduced mites on eggs (95% fewer mites on eggs at 1 wk and 90% at 2 wk). When data were grouped by mite index score on hens, there was a strong relationship (r 2 = 0.83, P < 0.01) between mite prevalence on eggs and the scores of the hens which laid them. Sampling 100 eggs evenly spaced in a house required <7 min, and adult mites were easily seen. Sampling mites on eggs appears to be useful to localize at least high-level infestations, and egg-based sampling for mites merits further investigation.
Evaluative Indices Assigned to Contraceptive Methods by University Undergraduates

Abstract Background: Preordinate attitudes and beliefs about contraception may influence acceptance or rejection of a particular method. Purpose: We examined the attitudes about contraception methods held by undergraduate students (N=792) at two large southeastern universities in the United States. Methods: Twelve methods were rated on 40 semantic differential scales. Means of the scale sum scores for men and women were compared using t-tests. Results: Among women the most favorably rated methods were: abstinence, oral contraceptive, male condom, Nuva ring, contraceptive patch, emergency contraception, male sterilization, female sterilization, diaphragm and female condom, each yielding a mean above the scale midpoint. The most negatively rated methods were withdrawal and douche. For men, the ratings in descending order were: oral contraceptive, male condom, abstinence, contraceptive patch, emergency contraception, female sterilization, Nuva ring, female condom, diaphragm, withdrawal, male sterilization and douche. There were four statistically significant (P < 0.05) gender differences, with abstinence, male condom, male sterilization and Nuva ring all rated more favorably by women. Discussion: These evaluative indices suggest that contraceptive methods elicit varied responses among potential users that theoretically could manifest themselves in acceptance or rejection of a particular method. Improved understanding of the traits by which potential users judge contraception may be beneficial in fostering communication between potential users and practitioners who provide relevant advice. Translation to Health Education Practice: Health educators and other practitioners engaged in contraception counseling must consider that persons may already hold strong feelings about some methods before they enter the clinical setting.
Perceived work stress, overcommitment, and self-reported musculoskeletal pain: Across-sectional investigation

The objectiveofthis study was to analyze associations of three indicators of perceived work stress (physical job demand, low control at work, andan imbalance between effort and reward), and of overcommitment, a personal pattern of coping with work demands, with musculoskeletal pain. A standardized questionnaire measuring these conditions in addition to self-reported musculoskeletal pain at different locations was administered to a group of 316 male and female employees of a public transport enterprise. After we adjusted for confounding effects of age, sex, socioeconomic status, shift work, and negative affectivity, we observed elevated prevalence odds ratios in employees who scored high on overcommitment, who were exposed to physical job demand, and, to a lesser extent, who reported psychosocial work stress. Results have implications for a more comprehensive approach to primary and secondary prevention of musculoskeletal pain.
Muscle tone in different joint positions and at submaximal isometric torque levels

The aim was to evaluate the tone and electric activity of the quadriceps muscle at rest and different torque levels. The second aim was to study whether thickness of soft tissues and change in the joint position would affect muscle tone. Eighteen healthy subjects participated. Computerized muscle tonometer (CMT) and surface electromyography (sEMG) measurements were performed: seated, first at rest with leg straight and then with the knee at 60°. Thereafter measurements were obtained at levels of 80, 60, 40 and 20% of the maximum isometric torque at the same knee angle. Thickness of skin, subcutis and muscle was measured by ultrasound. The CMT values taken were the depth the indenter travelled and the work it did while compressing the right rectus femoris and vastus intermedius muscles. Expressed as mean (SD) depth the change in muscle tone changed from 29.2 (3.6) mm in the relaxed position to 16.9 (5.2) mm at 80% of maximal torque, and expressed as work the values were from 1589 (150) mJ to 739 (149) mJ respectively. The correlation between CMT, sEMG and torque measurements varied from r = −0.52 to −0.71 (p < 0.01). CMT was able to detect a change of 20% in torque production and 4% in tone. Tone values, at each torque level, were significantly separate from the values at the other force levels (p < 0.001–0.04). Soft tissue thickness explained most of the tone results at rest (57%). The repeatability of the CMT measures was good (ICCs 0.75–0.99). Both depth and work correlated with electric activity and muscle torque, but the correlation with work was higher. In conclusion, muscle activity, length and thickness have to be taken into account when evaluating muscle tone.
KSHV/HHV8‐associated lymphomas

This review looks at the current state of knowledge on primary effusion lymphoma (PEL) and other Kaposi sarcoma herpesvirus (KSHV)/human herpesvirus 8 (HHV8)‐associated lymphomas. In 1995, KSHV DNA sequences were identified within a distinct subgroup of acquired immunodeficiency syndrome‐related non‐Hodgkin lymphomas localized in body cavities and presenting as pleural, peritoneal and pericardial lymphomatous effusions. Subsequently, the spectrum of KSHV/HHV8‐associated lymphomas has been expanded by the identification of cases of extracavitary solid lymphomas without serous effusions. Despite the diversification in the clinical presentation of KSHV/HHV8‐associated lymphomas, the majority of the cases reported demonstrated similar morphology, immunophenotype and KSHV/HHV8 viral status. KSHV/HHV8 infection is also in multicentric Castleman disease‐associated plasmablastic lymphoma. The exact oncogenic mechanisms of KSHV/HHV8 are not clearly defined. The prognosis for KSHV/HHV8‐associated lymphomas is poor. Novel approaches for therapy, outside traditional chemotherapy with CHOP (cyclophosphamide, doxorubicin, prednisone, vincristine), have been suggested. These include the addition of antiviral therapy as well as inhibition of specific cellular targets.
Characteristics of Schizophrenic Patients and the Outcome of Fluphenazine and of Electroconvulsive Treatments*

We examined the outcome with fluphenazine treatment and ECT in a group of 120 patients according to the incidence of psychopathological symptoms, the patients’ status on a variety of sociodemographic and anamnestic variables, and their diagnoses according to 13 systems for diagnosing schizophrenia. All had previously been considered to be schizophrenic patients at least once in hospital settings. The outcome with fluphenazine was better in patients with passivity feelings, auditory hallucinations and other hallucinations and delusions. The outcome with patients who had ECT, as judged from the hospital files, was better in those who were preoccupied with delusions or hallucinations and less successful in those who had been diagnosed as having schizophrenia on the first previous occasion when they had been discharged from the hospital.
High-grade Gliomas

Purpose of Review:This article reviews the standard treatment of patients with high-grade glioma primary brain tumors and discusses promising new therapeutic advances. Recent Findings:While surgery and radiation remain critical components of the management of patients with high-grade gliomas, chemotherapy has recently been proven to improve the overall survival of patients with glioblastomas and anaplastic oligodendrogliomas. Molecular markers are complementing clinical prognostic factors and, in some cases, are able to guide treatment decisions. Despite aggressive treatment, high-grade gliomas eventually progress, emphasizing the importance of continued development of novel therapies for the treatment of this deadly disease. Summary:The care of patients with high-grade gliomas is challenging, but the experience is highly rewarding. Rapidly developing technology allows for the use of molecular data for improved classification of high-grade gliomas and is beginning to improve our understanding of the pathogenesis and drivers of this disease. Collaboration among investigators will be critical to effectively validate prognostic biomarkers and identify tumors that might benefit from specific therapies.
Biases in the Evaluation of Psychiatric Clinical Evidence

Abstract The evolution of medical research has vaulted randomized clinical trials to the status of current gold standard of clinical evidence. In parallel, the evolution of the science of decision-making has revealed human beings’ universal tendency to make biased judgments and systematic errors in their evaluation of information and choices. As a result of numerous psychological biases, randomized clinical trials are more prone to error, misinterpretation, and faulty judgment than is often acknowledged. Interdisciplinary fields of experimental psychology, economics, and social science are drawn upon to examine psychological biases in the interpretation of clinical evidence. A number of these are postulated to be important, both for the investigators generating clinical evidence and for the clinical observers interpreting clinical trials. This study focuses on the field of psychiatry and on the potentially significant implications of evidence biases for psychiatric practice and clinical understanding.
Capacitative calcium entry channels

In the phospholipase C signaling system, Ca2+ is mobilized from intracellular stores by an action of inositol 1,4,5‐trisphosphate. The depletion of intracellular calcium stores activates a calcium entry mechanism at the plasma membrane called capacitative calcium entry. The signal for activating the entry is unknown but likely involves either the generation or release, or both, from the endoplasmic reticulum of some diffusible signal. Recent research has focused on mammalian homologues of the Drosophila TRP protein as potential candidates for capacitative calcium entry channels. This review summarizes current knowledge about the nature of capacitative calcium entry signals, as well as the potential role of mammalian TRP proteins as capacitative calcium entry channel molecules. BioEssays 21:38–46, 1999. Published 1999 John Wiley & Sons, Inc.
Prevalence of depression in patients with coronary artery disease in a tertiary care hospital in Pakistan.

OBJECTIVE To determine the prevalence of depression in patients with coronary artery disease (CAD) in a tertiary care hospital setting in Pakistan. METHODS One hundred and fifty four patients of CAD (115 males and 39 females) were randomly selected from the outpatient department and wards of the National Institute of Cardiovascular Diseases, Karachi and were scored for depression via the Hospital Anxiety and Depression Scale. Basic demographic data and disease variables were also collected. RESULTS The point prevalence of depression in the sample was 37% (31.3% males and 53.8% females). Female sex, income level below Rs. 5000 per month, low education level, outpatient, single earning family member and hypertension were few variables associated positively with depression (p < 0.05). Only one patient was receiving treatment for depression by his cardiologist. CONCLUSION Depression is prevalent in CAD patients in Pakistan. Economic conditions may pose an additional threat on these patients. Treating physicians (especially cardiologists) need to be aware of this co-morbidity so as to be able to diagnose and adequately manage such patients.