Miracle-dz/UniFAR-FTUs huggingface dataset:
Clonal Relationship and Differentiation among Mycobacterium abscessus Isolates as Determined Using the Semiautomated Repetitive Extragenic Palindromic Sequence PCR-Based DiversiLab System

ABSTRACT Mycobacterium abscessus is a rapidly growing mycobacterium that causes respiratory tract infections in predisposed patients, such as those with cystic fibrosis and nosocomial skin and soft tissue infections. In order to investigate the clonal relationships between the strains causing epidemic episodes, we evaluated the discriminatory power of the semiautomated DiversiLab (DL) repetitive extragenic palindromic sequence PCR (REP-PCR) test for M. abscessus genotyping. Since M. abscessus was shown to be composed of subspecies (M. abscessus subsp. massiliense, M. abscessus subsp. bolletii, and M. abscessus subsp. abscessus), we also evaluated the ability of this technique to differentiate subspecies. The technique was applied to two collections of clinical isolates, (i) 83 M. abscessus original isolates (43 M. abscessus subsp. abscessus, 12 M. abscessus subsp. bolletii, and 28 M. abscessus subsp. massiliense) from infected patients and (ii) 35 repeated isolates obtained over 1 year from four cystic fibrosis patients. The DL REP-PCR test was standardized for DNA extraction, DNA amplification, and electrophoresis pattern comparisons. Among the isolates from distinct patients, 53/83 (62%) isolates showed a specific pattern, and 30 were distributed in 11 clusters and 6 patterns, with 2 to 4 isolates per pattern. The clusters and patterns did not fully correlate with multilocus sequence typing (MLST) analysis results. This revealed a high genomic diversity between patients, with a discriminatory power of 98% (Simpson's diversity index). However, since some isolates shared identical patterns, this raises the question of whether it is due to transmission between patients or a common reservoir. Multiple isolates from the same patient showed identical patterns, except for one patient infected by two strains. Between the M. abscessus subspecies, the indexes were <70%, indicating that the DL REP-PCR test is not an accurate tool for identifying organisms to the subspecies level. REP-PCR appears to be a rapid genotyping method that is useful for investigating epidemics of M. abscessus infections.
Optimal Design of Adjustable Air-Gap, Two-Speed, Capacitor-Run, Single-Phase Axial Flux Induction Motors

-In this paper, a new optimized structure for two-speed, capacitor-run, single-phase axial flux induction motor (AFIM) for direct-drive operation is presented. Although, there are many advantages for direct-drive systems, their axial forces between the stator and rotor increases with reduction in air-gap length and is of serious concern. An increase in the air-gap length will result in the deterioration of performance characteristics of the motor. In this paper, a new construction technique is proposed to fabricate an AFIM with adjustable air-gap length. After presenting a comprehensive design algorithm, all geometrical dimensions and electrical equivalent circuit parameters are analytically calculated. Then, a multiobjective and multivariable optimization for a high efficiency and power factor with minimum usage of core materials is carried out. Optimization process is verified using three-dimensional, time-stepping finite-element analyses, and finally, the prototype of the optimal motor is fabricated and tested. Good agreements between analytic, finite element, and experimental results show the success of the proposed design.
Factors Related to Coping with Severe Mental Illness in the Latter Half of Life

Abstract Adapting to severe mental illness (SMI) can be a lifelong endeavor. This study examined mental illness coping versus general life stress coping among older SMI sufferers. Eighty-five middle-aged and older adults with SMI completed a coping questionnaire as part of a larger study on SMI in late life. Participants described significantly more strategies for coping with mental illness-related stressors than with other stressors, but used similar types of strategies. Older participants reported fewer coping strategies for mental illness coping, and women reported more strategies than men. Age differences were not explained by length of illness experience. Despite the added coping burden of mental illness, adults in this sample were experiencing similar stressors, and coping similarly, as their same-aged peers without mental illness.
Experimental intrarenal reflux and blood pressure.

The effect on the blood pressure of experimental vesico-ureteric reflux was investigated in adult female Wistar rats. In 6 rats, reflux with isotonic saline produced a transient rise in systemic blood pressure followed by a fall, with return to normal within 2 min (mean BP readings: 121-130-93 mmHg). In 6 rats during water diuresis, reflux with distilled water produced similar changes (114-120-79 mmHg). In 6 rats in which the ureters were divided before reflux, no rise in blood pressure occurred although in 2 of these the pressure showed a marked fall. The pattern of blood pressure changes which occurred as a result of reflux was similar to that produced by a rapid i.v. injection of a corresponding volume of saline and it was concluded that the changes accompanying reflux are due to pyelovenous backflow. This was confirmed by producing reflux with 5% lissamine green which appeared in the peripheral capillaries within 4 s of the reflux in 3 rats. Slow dilatation of the pelvis with saline in 9 rats showed that rupture of the pelvic epithelium occurred at a mean pressure of 99 mmHg.
Clinical features and prognostic implications of familial hypertrophic cardiomyopathy related to the cardiac myosin-binding protein C gene.

BACKGROUND Little information is available on phenotype-genotype correlations in familial hypertrophic cardiomyopathy that are related to the cardiac myosin binding protein C (MYBPC3) gene. The aim of this study was to perform this type of analysis. METHODS AND RESULTS We studied 76 genetically affected subjects from nine families with seven recently identified mutations (SASint20, SDSint7, SDSint23, branch point int23, Glu542Gln, a deletion in exon 25, and a duplication/deletion in exon 33) in the MYBPC3 gene. Detailed clinical, ECG, and echocardiographic parameters were analyzed. An intergene analysis was performed by comparing the MYBPC3 group to seven mutations in the beta-myosin heavy-chain gene (beta-MHC) group (n=52). There was no significant phenotypic difference among the different mutations in the MYBPC3 gene. However, in the MYBPC3 group compared with the beta-MHC group, (1) prognosis was significantly better (P<0.0001), and no deaths occurred before the age of 40 years; (2) the age at onset of symptoms was delayed (41+/-19 versus 35+/-17 years, P<0.002); and (3) before 30 years of age, the phenotype was particularly mild because penetrance was low (41% versus 62%), maximal wall thicknesses lower (12+/-4 versus 16+/-7 mm, P<0.03), and abnormal T waves less frequent (9% versus 45%, P<0.02). CONCLUSIONS These results are consistent with specific clinical features related to the MYBPC3 gene: onset of the disease appears delayed and the prognosis is better than that associated with the beta-MHC gene. These findings could be particularly important for the purpose of clinical management and genetic counseling in familial hypertrophic cardiomyopathy.
Fully Automatic Anatomical, Pathological, and Functional Segmentation from CT Scans for Hepatic Surgery

Objective: To improve the planning of hepatic surgery, we have developed a fully automatic anatomical, pathological, and functional segmentation of the liver derived from a spiral CT scan. Materials and Methods: From a 2 mm-thick enhanced spiral CT scan, the first stage automatically delineates skin, bones, lungs, kidneys, and spleen by combining the use of thresholding, mathematical morphology, and distance maps. Next, a reference 3D model is immersed in the image and automatically deformed to the liver contours. Then an automatic Gaussian fitting on the imaging histogram estimates the intensities of parenchyma, vessels, and lesions. This first result is next improved through an original topological and geometrical analysis, providing an automatic delineation of lesions and veins. Finally, a topological and geometrical analysis based on medical knowledge provides hepatic functional information that is invisible in medical imaging: portal vein labeling and hepatic anatomical segmentation according to the Couinaud classification. Results: Clinical validation performed on more than 30 patients shows that delineation of anatomical structures by this method is often more sensitive and more specific than manual delineation by a radiologist. Conclusion: This study describes the methodology used to create the automatic segmentation of the liver with delineation of important anatomical, pathological, and functional structures from a routine CT scan. Using the methods proposed in this study, we have confirmed the accuracy and utility of the creation of a 3D liver model compared with the conventional reading of the CT scan by a radiologist. This work may allow improved preoperative planning of hepatic surgery by more precisely delineating liver pathology and its relationship to normal hepatic structures. In the future, this data may be integrated with computer-assisted surgery and thus represents a first step towards the development of an augmented-reality surgical system.
Bounds for Learning the Kernel: Rademacher Chaos Complexity

In this paper we develop a novel probabilistic generalization bound for regularized kernel learning algorithms. First, we show that generalization analysis of kernel learning algorithms reduces to investigation of the suprema of homogeneous Rademacher chaos process of order two over candidate kernels, which we refer to it as Rademacher chaos complexity. Our new methodology is based on the principal theory of U-processes. Then, we discuss how to estimate the empirical Rademacher chaos complexity by well-established metric entropy integrals and pseudo-dimension of the set of candidate kernels. Finally, we establish satisfactory generalization bounds and misclassiflcation error rates for learning Gaussian kernels and general radial basis kernels.
Role of Tissue Factor in Mycobacterium tuberculosis-Induced Inflammation and Disease Pathogenesis

Tuberculosis (TB) is a chronic lung infectious disease characterized by severe inflammation and lung granulomatous lesion formation. Clinical manifestations of TB include hypercoagulable states and thrombotic complications. We previously showed that Mycobacterium tuberculosis (M.tb) infection induces tissue factor (TF) expression in macrophages in vitro. TF plays a key role in coagulation and inflammation. In the present study, we investigated the role of TF in M.tb-induced inflammatory responses, mycobacterial growth in the lung and dissemination to other organs. Wild-type C57BL/6 and transgenic mice expressing human TF, either very low levels (low TF) or near to the level of wild-type (HTF), in place of murine TF were infected with M.tb via aerosol exposure. Levels of TF expression, proinflammatory cytokines and thrombin-antithrombin complexes were measured post M.tb infection and mycobacterial burden in the tissue homogenates were evaluated. Our results showed that M.tb infection did not increase the overall TF expression in lungs. However, macrophages in the granulomatous lung lesions in all M.tb-infected mice, including low TF mice, showed increased levels of TF expression. Conspicuous fibrin deposition in the granuloma was detected in wild-type and HTF mice but not in low TF mice. M.tb infection significantly increased expression levels of cytokines IFN-γ, TNF-α, IL-6 and IL-1ß in lung tissues. However, no significant differences were found in proinflammatory cytokines among the three experimental groups. Mycobacterial burden in lungs and dissemination into spleen and liver were essentially similar in all three genotypes. Our data indicate, in contrast to that observed in acute bacterial infections, that TF-mediated coagulation and/or signaling does not appear to contribute to the host-defense in experimental tuberculosis.
Maximum a posteriori adaptation of subspace Gaussian mixture models for cross-lingual speech recognition

This paper concerns cross-lingual acoustic modeling in the case when there are limited target language resources. We build on an approach in which a subspace Gaussian mixture model (SGMM) is adapted to the target language by reusing the globally shared parameters estimated from out-of-language training data. In current cross-lingual systems, these parameters are fixed when training the target system, which can give rise to a mismatch between the source and target systems. We investigate a maximum a posteriori (MAP) adaptation approach to alleviate the potential mismatch. In particular, we focus on the adaptation of phonetic subspace parameters using a matrix variate Gaussian prior distribution. Experiments on the GlobalPhone corpus using the MAP adaptation approach results in word error rate reductions, compared with the cross-lingual base-line systems and systems updated using maximum likelihood, for training conditions with 1 hour and 5 hours of target language data.
CREB Binding Protein Is Required for Both Short-Term and Long-Term Memory Formation

CREB binding protein (CBP) is a transcriptional coactivator with histone acetyltransferase activity. Our prior study suggested that CBP might be a key target of presenilins in the regulation of memory formation and neuronal survival. To elucidate the role of CBP in the adult brain, we generated conditional knock-out (cKO) mice in which CBP is completely inactivated in excitatory neurons of the postnatal forebrain. Histological analysis revealed normal neuronal morphology and absence of age-dependent neuronal degeneration in the CBP cKO cerebral cortex. CBP cKO mice exhibited robust impairment in the formation of spatial, associative, and object-recognition memory. In addition to impaired long-term memory, CBP cKO mice also displayed deficits in short-term associative and object-recognition memory. Administration of a histone deacetylase inhibitor, trichostatin A, rescued the reduction of acetylated histones in the CBP cKO cortex but failed to rescue either short- or long-term memory deficits, suggesting that the memory impairment may not be caused by general reduction of histone acetyltransferase activity in CBP cKO mice. Further microarray and Western analysis showed decreased expression of calcium-calmodulin-dependent kinase isoforms and NMDA and AMPA receptor subunits in the cerebral cortex of CBP cKO mice. Collectively, these findings suggest a crucial role for CBP in the formation of both short- and long-term memory.
Predicting Effects of Climate Change on Habitat Suitability of Red Spruce (Picea rubens Sarg.) in the Southern Appalachian Mountains of the USA: Understanding Complex Systems Mechanisms through Modeling

Alpine, subalpine and boreal tree species, of low genetic diversity and adapted to low optimal temperatures, are vulnerable to the warming effects of global climate change. The accurate prediction of these species’ distributions in response to climate change is critical for effective planning and management. The goal of this research is to predict climate change effects on the distribution of red spruce (Picea rubens Sarg.) in the Great Smoky Mountains National Park (GSMNP), eastern USA. Climate change is, however, conflated with other environmental factors, making its assessment a complex systems problem in which indirect effects are significant in causality. Predictions were made by linking a tree growth simulation model, red spruce growth model (ARIM.SIM), to a GIS spatial model, red spruce habitat model (ARIM.HAB). ARIM.SIM quantifies direct and indirect interactions between red spruce and its growth factors, revealing the latter to be dominant. ARIM.HAB spatially distributes the ARIM.SIM simulations under the assumption that greater growth reflects higher probabilities of presence. ARIM.HAB predicts the future habitat suitability of red spruce based on growth predictions of ARIM.SIM under climate change and three air pollution scenarios: 10% increase, no change and 10% decrease. Results show that suitable habitats shrink most when air pollution increases. Higher temperatures cause losses of most low-elevation habitats. Increased precipitation and air pollution produce acid rain, which causes loss of both low- and high-elevation habitats. The general prediction is that climate change will cause contraction of red spruce habitats at both lower and higher elevations in GSMNP, and the effects will be exacerbated by increased air pollution. These predictions provide valuable information for understanding potential impacts of global climate change on the spatiotemporal distribution of red spruce habitats in GSMNP.
Hydrogen sulfide replacement therapy protects the vascular endothelium in hyperglycemia by preserving mitochondrial function

The goal of the present studies was to investigate the role of changes in hydrogen sulfide (H2S) homeostasis in the pathogenesis of hyperglycemic endothelial dysfunction. Exposure of bEnd3 microvascular endothelial cells to elevated extracellular glucose (in vitro “hyperglycemia”) induced the mitochondrial formation of reactive oxygen species (ROS), which resulted in an increased consumption of endogenous and exogenous H2S. Replacement of H2S or overexpression of the H2S-producing enzyme cystathionine-γ-lyase (CSE) attenuated the hyperglycemia-induced enhancement of ROS formation, attenuated nuclear DNA injury, reduced the activation of the nuclear enzyme poly(ADP-ribose) polymerase, and improved cellular viability. In vitro hyperglycemia resulted in a switch from oxidative phosphorylation to glycolysis, an effect that was partially corrected by H2S supplementation. Exposure of isolated vascular rings to high glucose in vitro induced an impairment of endothelium-dependent relaxations, which was prevented by CSE overexpression or H2S supplementation. siRNA silencing of CSE exacerbated ROS production in hyperglycemic endothelial cells. Vascular rings from CSE−/− mice exhibited an accelerated impairment of endothelium-dependent relaxations in response to in vitro hyperglycemia, compared with wild-type controls. Streptozotocin-induced diabetes in rats resulted in a decrease in the circulating level of H2S; replacement of H2S protected from the development of endothelial dysfunction ex vivo. In conclusion, endogenously produced H2S protects against the development of hyperglycemia-induced endothelial dysfunction. We hypothesize that, in hyperglycemic endothelial cells, mitochondrial ROS production and increased H2S catabolism form a positive feed-forward cycle. H2S replacement protects against these alterations, resulting in reduced ROS formation, improved endothelial metabolic state, and maintenance of normal endothelial function.
Aprendizaje y práctica de la conciencia plena en estudiantes de bachillerato para potenciar la relajación y la autoeficacia en el rendimiento escolar

El objetivo este estudio fue analizar los efectos que produce un programa psicoeducativo de entrenamiento en conciencia plena (mindfulness) sobre la autoeficacia en el rendimiento escolar y los estados de relajacion (Estados-R), en adolescentes estudiantes de bachillerato. Se realizo un diseno controlado y aleatorizado con un grupo experimental y un grupo control en lista de espera con medicion pretest-postest. Los instrumentos de medida empleados fueron el Cuestionario de Cartagena (Cartagena, 2008) y el Cuestionario SRSI-3 (Smith, 2005a). Los analisis estadisticos muestran la existencia de mejoras significativas en el grupo experimental en comparacion con el grupo control, en los niveles de autoeficacia en el rendimiento escolar, asi como en los estados de relajacion basica, conciencia plena y energia positiva; ademas, se obtuvo una reduccion significativa en el grupo experimental en comparacion con el grupo control en la dimension de estres percibido.
The PLAN score: a bedside prediction rule for death and severe disability following acute ischemic stroke.

BACKGROUND We sought to develop and validate a simple clinical prediction rule for death and severe disability after acute ischemic stroke that can be used by general clinicians at the time of hospital admission. METHODS We analyzed data from a registry of 9847 patients (4943 in the derivation cohort and 4904 in the validation cohort) hospitalized with acute ischemic stroke and included in the Registry of the Canadian Stroke Network (July 1, 2003, to March 31, 2008; 11 regional stroke centers in Ontario, Canada). Outcome measures were 30-day and 1-year mortality and a modified Rankin score of 5 to 6 at discharge. RESULTS Overall 30-day mortality was 11.5% (derivation cohort) and 13.5% (validation cohort). In the final multivariate model, we included 9 clinical variables that could be categorized as preadmission comorbidities (5 points for preadmission dependence [1.5], cancer [1.5], congestive heart failure [1.0], and atrial fibrillation [1.0]), level of consciousness (5 points for reduced level of consciousness), age (10 points, 1 point/decade), and neurologic focal deficit (5 points for significant/total weakness of the leg [2], weakness of the arm [2], and aphasia or neglect [1]). Maximum score is 25. In the validation cohort, the PLAN score (derived from preadmission comorbidities, level of consciousness, age, and neurologic deficit) predicted 30-day mortality (C statistic, 0.87), death or severe dependence at discharge (0.88), and 1-year mortality (0.84). The PLAN score also predicted favorable outcome (modified Rankin score, 0-2) at discharge (C statistic, 0.80). CONCLUSIONS The PLAN clinical prediction rule identifies patients who will have a poor outcome after hospitalization for acute ischemic stroke. The score comprises clinical data available at the time of admission and may be determined by nonspecialist clinicians. Additional studies to independently validate the PLAN rule in different populations and settings are required.
Text-independent speaker verification based on relation of MFCC components

GMM is prevalent for speaker verification. It performs very well but needs a background model to give a reference value, which greatly influences the error rate. In order to get a better generalization result, a large database with lots of people is needed to train the background model. In this paper, a new method without background model is proposed, which is called the correlation and kernel function method (CK method). In the CK method, the correlation and uncorrelation of MFCC are used to identify individuals, and a kernel function is used to work out the likelihood of two models. It works more than 30 times as fast as GMM method does, but requires fewer data to train and less space to store the model. But its performance is nearly identical to that of GMM. So it is suitable for real-time computation.
Review: Rebuilding engagement through the arts : responding to disaffected students

Title: Rebuilding engagement through the arts : responding to disaffected students Author/Editor: John Finney, Richard Hickman, Morag Morrison, Bill Nicholl and Jean Ruddock Publisher: Pearson Publishing Publication Date: 2005 ISBN: 1-85749-858-5 Reviewed by: Andy Mitchell, The Design and Technology Association
Culture, innovation and successful development of new medicines ‐ an exploratory study of the pharmaceutical industry

Reports on a pilot study carried out to investigate methods for determining corporate culture in the pharmaceutical industry and its effect on innovation and development of new medicines. The results showed that it is possible to use a questionnaire‐based approach for this type of investigation to demonstrate cultural differences between companies and between departments. Furthermore, the results could be related to factors most suited to fast development and to innovation.