Miracle-dz/UniFAR-FTUs huggingface dataset:
Differentiation of Phylogenetically Related Slowly Growing Mycobacteria Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences

ABSTRACT Interspecific polymorphisms of the 16S rRNA gene (rDNA) are widely used for species identification of mycobacteria. 16S rDNA sequences, however, do not vary greatly within a species, and they are either indistinguishable in some species, for example, in Mycobacterium kansasii and M. gastri, or highly similar, for example, in M. malmoense and M. szulgai. We determined 16S-23S rDNA internal transcribed spacer (ITS) sequences of 60 strains in the genus Mycobacterium representing 13 species (M. avium, M. conspicuum, M. gastri, M. genavense, M. kansasii,M. malmoense, M. marinum, M. shimoidei, M. simiae, M. szulgai,M. triplex, M. ulcerans, and M. xenopi). An alignment of these sequences together with additional sequences available in the EMBL database (for M. intracellulare, M. phlei, M. smegmatis, and M. tuberculosis) was established according to primary- and secondary-structure similarities. Comparative sequence analysis applying different treeing methods grouped the strains into species-specific clusters with low sequence divergence between strains belonging to the same species (0 to 2%). The ITS-based tree topology only partially correlated to that based on 16S rDNA, but the main branching orders were preserved, notably, the division of fast-growing from slowly growing mycobacteria, separate branching for M. simiae, M. genavense, and M. triplex, and distinct branches for M. xenopi and M. shimoidei. Comparisons of M. gastri with M. kansasii and M. malmoense with M. szulgairevealed ITS sequence similarities of 93 and 88%, respectively.M. marinum and M. ulcerans possessed identical ITS sequences. Our results show that ITS sequencing represents a supplement to 16S rRNA gene sequences for the differentiation of closely related species. Slowly growing mycobacteria show a high sequence variation in the ITS; this variation has the potential to be used for the development of probes as a rapid approach to mycobacterial identification.
Presence of NAP‐1/IL‐8 in Synovial Fluids Indicates a Possible Pathogenic Role in Rheumatoid Arthritis

The synovial fluid in affected joints of rheumatoid arthritis (RA) patients contains many cells, in numbers strongly correlated with the severity of disease. As the disease worsens and the cell count increases, the polymorphonuclear leucocyte becomes the predominant cell type. Although the inflammatory cytokines interleukin 1 (IL‐I) and tumour necrosis factor (TNF) have no direct neutrophil‐attractant activity, they are both potent inducers of interleukin 8(IL‐8) in a variety of cell types, Chemotactic attraction of neutrophils is a major activity of IL‐8.
Psychological strains and depression in Chinese rural populations

Objective: The aim of this study is to explore the relationship between psychological strains and depression and to further test the Strain Theory of Suicide and Mental Disorders. Method: Data for the current study were from a large psychological autopsy (PA) study in Chinese rural populations with a case-control design to investigate the environmental and other characteristics of rural young suicides and controls. Subjects (N = 1618) for the current study were the informants in the PA interviews. The center for epidemiologic studies depression scale was used to assess the respondents’ depression level. Chi-square , t test, t′ test, and general linear regression model were used to analyse the data by SPSS software. Results: Value strain and deprivation strain are positively correlated with the depression level for both men and women of the Chinese rural population. Religion is another strong risk factor for depression and marriage is not a protective factor for depression in this sample. Conclusions: The study verifies that there is strong correlation between the psychological strains and depression in Chinese rural populations. It is suggested that reducing psychological strains may be a possible approach to reduce the prevalence of depression so as to help bring down the suicide risk in rural China.
Clinical dose–response for a broad set of biological products: A model-based meta-analysis

Characterizing clinical dose–response is a critical step in drug development. Uncertainty in the dose–response model when planning a dose-ranging study can often undermine efficiency in both the design and analysis of the trial. Results of a previous meta-analysis on a portfolio of small molecule compounds from a large pharmaceutical company demonstrated a consistent dose–response relationship that was well described by the maximal effect model. Biologics are different from small molecules due to their large molecular sizes and their potential to induce immunogenicity. A model-based meta-analysis was conducted on the clinical efficacy of 71 distinct biologics evaluated in 91 placebo-controlled dose–response studies published between 1995 and 2014. The maximal effect model, arising from receptor occupancy theory, described the clinical dose–response data for the majority of the biologics (81.7%, n = 58). Five biologics (7%) with data showing non-monotonic trend assuming the maximal effect model were identified and discussed. A Bayesian model-based hierarchical approach using different joint specifications of prior densities for the maximal effect model parameters was used to meta-analyze the whole set of biologics excluding these five biologics (n = 66). Posterior predictive distributions of the maximal effect model parameters were reported and they could be used to aid the design of future dose-ranging studies. Compared to the meta-analysis of small molecules, the combination of fewer doses, narrower dosing ranges, and small sample sizes further limited the information available to estimate clinical dose–response among biologics.
Dorzolamide Influences the Autoregulation of Major Retinal Vessels Caused by Artificial Intraocular Pressure Elevation in Patients with POAG: A Clinical Study

Purpose: The study investigated whether dorzolamide influences the autoregulatory behavior of major retinal arterioles in glaucoma patients via a moderate perfusion pressure reduction. Methods: The study included one eye each of 12 untreated patients with a primary open-angle glaucoma (POAG) (age 60.8 ± 8.3, IOP 22.3 ± 6.5 mmHg). Changes in the diameter of a retinal artery segment before (120 s), during (100 s), and after (380 s) artificial IOP elevation to 38 mmHg for 100 s were recorded continuously by means of a Retinal Vessel Analyzer. The measurement was repeated after 4-week treatment with dorzolamide eye drops t.i. d. Results: Ocular perfusion pressure (mmHg) was reduced by the intraocular pressure (IOP) elevation from 58 (± 10) to 41 (± 11) in the pretreatment examination and from 60 (± 8) to 40 (± 8) posttreatment (differences between the examinations n.s.). Before IOP elevation, the arterial diameter was found to be +1.7 ± 3.5% greater in the posttreated eyes than in the pretreated eyes (p < 0.02). During IOP elevation, the arterial diameter decreased by −1.8% ± 3.8 in the pretreated eyes, whereas dilatation by +1.4% ± 2.5 was observed in the posttreated eyes (p = 0.02). At the end of the observation period following IOP elevation, the vessel diameter in the pretreated eyes had increased by +1.8% ± 4.2, whereas in the posttreated eyes it had decreased by −1.7% ± 3.0. On average, dorzolamide reduced IOP by −5.6 mmHg (p = 0.001). Conclusions: The arterial diameter dilatation during IOP elevation in dorzolamide-treated eyes could be an accelerated counter-regulation on the induced elevated IOP and could constitute an additional therapeutic effect.
LONG-TERM PERSONAL EXPOSURE TO TRAFFIC-RELATED AIR POLLUTION AMONG SCHOOL CHILDREN, A VALIDATION STUDY

Several recent studies suggest an association between long-term exposure to traffic-related air pollution and health. Most studies use indicators of exposure such as outdoor air pollution or traffic density on the street of residence. Little information is available about the validity of these measurements as an estimate of long-term personal exposure to traffic-related air pollution. In this pilot study, we assessed outdoor and personal exposure to traffic-related air pollution in children living in homes on streets with different degree of traffic intensity. The personal exposure of 14 children aged 9-12 years to 'soot', NO(x) (NO and NO(2)) was assessed in Amsterdam between March and June 2003. Each child's personal exposure was monitored during four repeated 48-h periods. Concurrently, in- and outdoor NO(x) measurements were carried out at the school and at the home of each participating child. Measurements were supplemented by a questionnaire on time activity patterns and possible indoor sources. Flow-controlled battery operated pumps in a made-to-fit backpack were used to sample personal exposure to 'soot', determined from the reflectance of PM(2.5) filters. Exposure to NO(x) was assessed using Ogawa passive samplers. Children living near busy roads were found to have a 35% higher personal exposure to 'soot' than children living at an urban background location, despite that all children attended the same school that was located away from busy roads. Smaller contrasts in personal exposure were found for NO (14%), NO(2) (15%) and NO(x) (14%). This finding supports the use of 'living near a busy road' as a measure of exposure in epidemiological studies on the effects of traffic-related air pollution in children.
On the performability of on-board train networks with fault-tolerant controllers

This paper studies a mixed load of control and entertainment on top of Gigabit Ethernet on-board a train wagon. The control load is comprised of sensors and actuators of different sampling periods. There is a dedicated server for control and a dedicated server for entertainment. It is proven that the system can tolerate the failure of one controller, shifting both entertainment and control loads to the remaining controller while guaranteeing correct performance. The maximum acceptable entertainment load is found. Enhancements to the network are introduced in order to minimize degradation of entertainment service due to a controller failure. OPNET simulations are used to study packet transmission/reception and end-to-end delay. Finally, a performability model is developed; this model will help system designers determine the cost- effectiveness of architectural features aiming at increasing performance.
Performance Comparison of Affymetrix SNP6.0 and Cytogenetic 2.7M Whole-Genome Microarrays in Complex Cancer Samples

The Affymetrix cytogenetic 2.7M whole-genome microarray (Cyto2.7M) detects genomic aberrations. The Cyto2.7M array has increased coverage in regions with cancer-related genes, ∼4-fold reduced processing time, and 5-fold reduced input requirements (100 ng) compared to the commonly used Affymetrix SNP6.0 genome-wide microarray (SNP6.0). We set out to compare the performance of these microarrays on cancer samples containing complex genomic changes. We analyzed genomic DNA from 8 lymphoma samples and 1 blood sample using both SNP6.0 and Cyto2.7M microarrays. We compared the arrays with respect to 4 parameters, including detection of copy number variations (CNV), CNV boundaries, the actual copy number (CN) assigned to the aberrations, and loss of heterozygosity. The CN state of selected regions was validated by quantitative PCR. Very high consistency between arrays on all parameters tested was observed, hence only 30 of 224 aberrations disagreed on the CN state, corresponding to a total of ∼12 Mb or 0.06% of the analyzed base pairs. Thus, the SNP6.0 and Cyto2.7M arrays are equally well suited to detect genomic aberrations in complex samples such as cancer samples. With reduced processing time and lower input requirements, the Cyto2.7M array enables genomic analysis of samples where only limited DNA is available.
Scanning and transmission electron microscopy of Ruffini endings in the periodontal ligament of rat incisors

The Ruffini organ is an arborized axon ending categorized as a low‐threshold stretch receptor. We have previously shown that the lingual periodontal ligament of rat incisors is densely innervated with Ruffini endings. In the present study, fine structures in the surface of the periodontal Ruffini endings and their topographical relationship with the surrounding collagen fibers were observed by a combination of scanning and transmission electron microscopy to analyze the mechanism of the stretch reception. The entire length of the branches of the Ruffini endings, excepting their terminal portions, corresponded well with those depicted by previous investigators in the following points: (1) their cylindrical appearance covered by Schwann cell processes; (2) the presence of numerous axon fingers protruding through gaps in the Schwann sheath and; (3) their isolation from collagen fibers by multilayered basal lamina. On the other hand, tips of the axon branches—together with their Schwann sheaths—became attenuated and projected into tight bundles of collagen, indicating their susceptibility to mechanical deformations of the surrounding tissue. Margins of the axon terminals were conspicuously ruffled with long tongue‐like projections of Schwann cells. The Schwann cell tongues twined around collagen bundles in their distal portions, and associated closely with fine axon projections in their proximal portions, suggesting their involvement in the mechanical transmission of stimuli to axon terminals. J. Comp. Neurol. 389:177–184, 1997. © 1997 Wiley‐Liss, Inc.
Prevalence of harassment and discrimination among residents in three training hospitals in Saudi Arabia

BACKGROUND AND OBJECTIVES Multiple surveys of medical residents have shown a high incidence of harassment and discrimination in academic health centers. Harassment has a negative effects on residents’ health and on their ability to function. No previous study has documented the prevalence of harassment and discrimination among residents in Saudi Arabia. We aimed in this study to assess the prevalence of harassment and discrimination among residents at a tertiary care academic hospitals in Saudi Arabia. DESIGN AND SETTING Cross-sectional survey conducted at National Guard Hospitals in Riyadh, Jeddah and Al-Ahsa’a from 27 July to 20 August 2010. SUBJECTS AND METHODS The survey included questions on the prevalence of harassment of different types, inlcuding verbal, academic, physical and sexual harassment, as well as discrimination on the basis of gender, region of origin or physical appearance. RESULTS Of 380 residents, 213 (56%) returned a completed questionnaire (123 male, 57.8%). At least one of type of harassment and discrimination was reported by 83.6% of respondents. The most frequently reported forms were verbal harassment and gender discrimination (61.5% and 58.3%, respectively). Sexual harassment was commonly reported (19.3%) and was experienced significantly more often by female residents than by male residents (P=.0061). CONCLUSION Harassment and discrimination of Saudi residents is common with more than three-quarters reporting having had such an experience. Identification of the risk factors is a necessary first step in clarifying this issue and could be used when planning strategies for prevention.
Transforaminal epidural steroid injection via a preganglionic approach for lumbar spinal stenosis and lumbar discogenic pain with radiculopathy.

BACKGROUND Epidural steroid injection (ESIs) is one of the treatment modalities for chronic low back pain (CLBP) with various degrees of success. AIM We analyzed the efficacy of fluoroscopically guided transforaminal epidural steroid injections (TFESIs) via a preganglionic approach in patients with foraminal stenosis due to lumbar spinal stenosis and lumbar discogenic pain with radiculopathy. MATERIALS AND METHODS We analyzed the data of 40 patients (February 2008 and April 2009) with the diagnosis of CLBP and treated by fluoroscopically guided TFESIs via a preganglionic approach. Patients were followed-up at one month (short term), six months (midterm) and one year (long term) after injections. Follow-up data collection included the Visual Numeric Pain Scale (VNS) and North American Spine Society (NASS) patient satisfaction scores. RESULTS The mean age of the patients was 59.87 +/- 15.06 years (range 30 - 89 years, 25 women). Average follow-up period was 9.22 +/- 3.56 months. Statistically significant differences were observed between the pre-procedure and post-procedure VNSs (P < 0.01, Pearson Correlation Test). Improvements in VNS scores were correlated with improvements in the NASS scores. When the VNS scores were evaluated with respect to the age of patient, level numbers, gender, pre-procedure symptom duration and pre-procedure VNS, no significant differences were found (P < 0.05, linear regression test). At short term evaluation in post treatment (one month), 77.78 % of patients were found to have a successful outcome and 22.22 % were deemed failures. Overall patient satisfaction was 67.23 % in the midterm period. Additionally, 54.83 % of patients (N/n: 15/8) had a successful long-term outcome at a follow-up of one year. CONCLUSION Our data suggest that fluoroscopically guided TFESIs via a preganglionic approach, in patients with foraminal stenosis due to lumbar spinal stenosis and lumbar discogenic pain with radiculopathy, has effective outcome and patients responding to injection have significantly lower post-injection pain scores.
Report of the Expert Committee on the Diagnosis and Classification of Diabetes Mellitus

the growth of knowledge regarding the etiology and pathogenesis of diabetes has led many individuals and groups in the diabetes community to express the need for a revision of the nomenclature, diagnostic criteria, and classification of diabetes. As a consequence, it was deemed essential to develop an appropriate, uniform terminology and a functional, working classification of diabetes that reflects the current knowledge about the disease. (1)
Association between intestinal permeability and faecal microbiota composition in Italian children with beta cell autoimmunity at risk for type 1 diabetes

Pancreatic organ‐specific autoimmunity in subjects at risk for type 1 diabetes (T1D) is associated with increased intestinal permeability and an aberrant gut microbiota, but these factors have not yet been simultaneously investigated in the same subjects. Thus, the aim of this study was to assess both intestinal permeability and gut microbiota composition in an Italian sample of children at risk for T1D.
Étude de l'agrosystème rizicole en Camargue dans ses relations avec le milieu et le système cultural : aspects particuliers de la fertilité

En camargue, les contraintes du milieu, liees au ec2s d'eau et de sel, imposent a l'agriculteur des systemes de culture originaux. La riziculture inondee permet de valoriser la quantite d'eau necessaire du dessalement du sol et d'introduire dans la rotation d'autres especes sensibles au sel. Le riz jour ainsi un role de pivot du systeme de culture. L'analyse dans l'espace et dans le temps de la variabilite des peuplements du riz, l'examen de l'evolution des systemes techniques, mettent en evidence les relations entre le riz et les systemes culturaux. Ces relations s'expriment particulierement a travers certaines variables indicatrices qui caracterisent l'etat du milieu. L'etude de l'evolution des etats physiques du sol, des principaux elements mineraux et des adventices, conduit a proposer un systeme de culture ou la rotation riz-culture pluviale, doit permettre d'exterioriser le potentiel productif du milieu tout en preservant les equilibres biologiques fragiles
Foot sole and ankle muscle inputs contribute jointly to human erect posture regulation

1 In order to assess the relative contribution and the interactions of the plantar cutaneous and muscle proprioceptive feedback in controlling human erect posture, single or combined vibratory stimuli were applied to the forefoot areas and to the tendons of the tibialis anterior muscles of nine standing subjects using various vibration frequency patterns (ranging from 20 to 80 Hz). 2 The variations in the centre of foot pressure, ankle angle and the EMG activities of the soleus and tibialis anterior muscles of each subject were recorded and analysed. 3 Separate stimulation of the plantar forefoot zones or the tibialis anterior muscles always resulted in whole‐body tilts oppositely directed backwards and forwards, respectively, the amplitude of which was proportional to the vibration frequency. EMG activity of ankle muscles also varied according to the direction of the postural responses. However, the same vibration frequency did not elicit equivalent postural responses: in the low frequency range, tactile stimulation induced stronger postural effects than proprioceptive stimulation, and the converse was the case for the higher frequency range. 4 Under sensory conflict conditions, i.e. foot sole‐flexor ankle muscle co‐stimulation, the direction of the body tilts also varied according to the difference and the absolute levels of the vibration frequencies. In all cases, the resulting postural shifts always corresponded to the theoretical sum of the isolated effects observed upon vibrating each of these two sensory channels. 5 We proposed that tactile and proprioceptive information from the foot soles and flexor ankle muscles might be co‐processed following a vector addition mode to subserve the maintenance of erect stance in a complementary way.
Hepatic Glucose Production Is Regulated Both by Direct Hepatic and Extrahepatic Effects of Insulin in Humans

The present study examines the effect of the route of insulin delivery on glucose turnover in humans. By using a new noninvasive in vivo method, the acute effect of insulin secreted by the pancreas can be compared with that of insulin delivered by a peripheral vein. Three euglycemic-hyperinsulinemic studies were performed in lean healthy men. In the first study (n = 10), constant portal hyperinsulinemia was produced using a programmed intravenous tolbutamide infusion algorithm, and the insulin secretion rate was mathematically derived by deconvolution from peripheral plasma C-peptide levels. In the second study (n = 10), exogenous insulin was infused by peripheral vein at the same rate as that determined in the first study. In the third study (n = 7), the peripheral insulin levels in the first study were matched by infusing exogenous insulin into a peripheral vein at half that rate. Peripheral insulin levels were higher (P < 0.001) with the full-rate peripheral insulin infusion (266.3 ± 28.1 pmol/l) than with the portal delivery of insulin (171.1 ± 30.4 pmol/l) or the half-rate peripheral insulin infusion (158.6 ± 7.4 pmol/l) (portal versus half-rate peripheral insulin infusion, NS). Calculated hepatic insulin levels were higher (P < 0.001) in the portal insulin study (443.1 ± 52.6 pmol/l) than in the full-rate peripheral insulin study (303.6 ± 30.9 pmol/l) or in the half-rate peripheral insulin study (204.5 ± 9.8 pmol/l). Hepatic glucose production (HGP) was suppressed to a greater extent with the full-rate peripheral insulin infusion (69.3 ± 7.8%, P < 0.001 vs. portal or half-rate peripheral insulin) than portal (50.3 ± 9.8%) or half-rate peripheral insulin infusion (36.8 ± 3.8%). In the portal insulin study, however, suppression was > in the half-rate peripheral insulin study (P < 0.01), in spite of equal peripheral insulin levels. The assumption that tolbutamide, when used in this fashion, has no independent effect on glucose turnover, glucagon, or gluconeogenic precursor and energy substrates for gluconeogenesis was validated in five C-peptide-negative patients with IDDM. We conclude that in nondiabetic humans, 1) peripheral effects of insulin are important in suppressing HGP, as evidenced by the greater suppression of HGP with equivalent rate peripheral versus portal insulin delivery, and 2) because HGP was suppressed to a greater extent with portal verus peripheral insulin delivery at half the rate when peripheral insulin levels were matched, insulin-induced suppression of HGP is also partly mediated by a direct hepatic effect.