Miracle-dz/UniFAR-FTUs huggingface dataset:
Global Study of IS6110 in a Successful Mycobacterium tuberculosis Strain: Clues for Deciphering Its Behavior and for Its Rapid Detection

ABSTRACT The Mycobacterium tuberculosis insertion sequence IS6110, besides being a very useful tool in molecular epidemiology, seems to have an impact on the biology of bacilli. In the present work, we mapped the 12 points of insertion of IS6110 in the genome of a successful strain named M. tuberculosis Zaragoza (which has been referred to as the MTZ strain). This strain, belonging to principal genetic group 3, caused a large unsuspected tuberculosis outbreak involving 85 patients in Zaragoza, Spain, in 2001 to 2004. The mapping of the points of insertion of IS6110 in the genome of the Zaragoza strain offers clues for a better understanding of the adaptability and virulence of M. tuberculosis. Surprisingly, the presence of one copy of IS6110 was found in Rv2286c, as was recently described for a successful Beijing sublineage. As a result of this analysis, a rapid method for detecting this particular M. tuberculosis strain has been designed.
Surgical Treatment for Double Outlet Right Ventricle With Pulmonary Outflow Tract Obstruction

Background: Double outlet right ventricle (DORV) is a conotruncal anomaly that is a defining element of many types of complex congenital heart disease. Because of a big variety of pathology, there are still some controversies with respect to the definition, classification, and surgical treatment. We report our experience with surgical treatment for DORV (as defined by the “90% rule”) with pulmonary outflow tract obstruction (POTO). Methods: From July 2005 to July 2015, 90 patients underwent surgical treatment of DORV with POTO at the First Hospital of Tsinghua University. There were 55 males and 35 females whose age varies from 3 months to 36 years (mean age 7.1 ± 9.0 years old), and body weights ranged from 5 to 63 kg (mean weight 20.4 ± 16.6 kg). Besides DORV, ventricular septal defect, and POTO, this group of patients includes some with additional associated cardiac abnormalities. Results: Fourteen patients (15.6%) died. The main cause of death was low cardiac output syndrome. Conclusions: The DORV is usually associated with a variety of cardiac abnormalities and POTO is a common defining feature. Acceptable surgical results can be achieved by individualized surgical treatment of most patients. Some patients may require reoperation, and a close follow-up is needed.
Gene polymorphism profiles of drug-metabolising enzymes GSTM1, GSTT1 and GSTP1 in an Argentinian population

Abstract Background: Glutathione S-transferases (GSTs) are drug-metabolising enzymes involved in biotransformation of carcinogens, drugs, xenobiotics and oxygen free radicals. Polymorphisms of GST genes contribute to inter-individual and population variability in the susceptibility to environmental risk factors, cancer predisposition and pharmacotherapy responses. However, data about GST variability in Argentina are lacking. Aim: The purpose was to determine the prevalence of GSTM1, GSTT1 and GSTP1 polymorphisms in the general population from a central region of Argentina and to perform inter-population comparisons. Subjects and methods: GSTM1 and GSTT1 gene deletions and GSTP1 c.313A > G were genotyped by PCR assays in 609 healthy and unrelated Argentinians. Results: The frequencies of variant genotypes in Argentinians were GSTM1-null (45%), GSTT1-null (17%) and GSTP1-GG (11%). GSTM1-present genotype was significantly associated with GSTP1-AG or GSTP1-GG variants (p = 0.037; p = 0.034, respectively). Comparison with worldwide populations demonstrated that the GST distributions in Argentina are similar to those reported for Italy and Spain, whereas significant differences were observed regarding Asian and African populations (p < 0.001). Conclusion: This study has determined, for the first time, the normative profile of three pharmacogenetically relevant polymorphisms (GSTM1, GSTT1 and GSTP1) in the largest Argentinian cohort described to date, providing the basis for further epidemiological and pharmacogenetic studies in this country.
Fine specificity of cellular immune responses in humans to human cytomegalovirus immediate-early 1 protein

Cell-mediated immunity is important in maintaining the virus-host equilibrium in persistent human cytomegalovirus (HCMV) infection. The HCMV 72-kDa major immediate early 1 protein (IE1) is a target for CD8+ cytotoxic T cells in humans, as is the equivalent 89-kDa protein in mouse. Less is known about responses against this protein by CD4+ T cells, which may be important as direct effector cells or helper cells for antibody and CD8+ responses. Proliferative-T-cell responses to HCMV IE1 were studied in normal seropositive subjects. Peripheral blood mononuclear cells from 85% of seropositive subjects proliferated in response to HCMV from infected fibroblasts, and of these, 73% responded to recombinant baculovirus IE1. Responding cells were predominantly CD3+ CD4+. IE1 antigen preparations, including baculovirus recombinant protein, transfected rat cell nuclei, and synthetic peptides, induced IE1-specific T-cell lines which cross-reacted between the preparations. The fine specificity of these IE1-specific T-cell lines was studied by using overlapping synthetic peptides encompassing the entire sequence of the IE1 protein. The regions of the IE1 molecule recognized were identified and these varied between individuals, possibly reflecting differences in major histocompatibility complex (MHC) class II haplotype. In one subject, the peptide specificities of proliferative and MHC class I-restricted cytotoxic determinants on IE1 were spatially distinct. Thus, no single immunodominant T-cell determinant within HCMV IE1 was identified, suggesting that multiple peptides or a region of the 72-kDa IE1 protein would be required to induce specific T-cell responses in humans.
Molecular Characterization of the Mycoplasma gallisepticum pvpA Gene Which Encodes a Putative Variable Cytadhesin Protein

ABSTRACT A putative cytadhesin-related protein (PvpA) undergoing variation in its expression was identified in the avian pathogen Mycoplasma gallisepticum. The pvpA gene was cloned, expressed inEscherichia coli, and sequenced. It exhibits 54 and 52% homology with the P30 and P32 cytadhesin proteins of the human pathogens Mycoplasma pneumoniae and Mycoplasma genitalium, respectively. In addition, 50% homology was found with the MGC2 cytadhesin of M. gallisepticum and 49% homology was found with a stretch of 205 amino acids of the cytadherence accessory protein HMW3 of M. pneumoniae. The PvpA molecule possesses a proline-rich carboxy-terminal region (28%) containing two identical directly repeated sequences of 52 amino acids and a tetrapeptide motif (Pro-Arg-Pro-X) which is repeated 14 times. Genetic analysis of several clonal isolates representing different expression states of the PvpA product ruled out chromosomal rearrangement as the mechanism for PvpA phase variation. The molecular basis of PvpA variation was revealed in a short tract of repeated GAA codons, encoding five successive glutamate resides, located in the N-terminal region and subject to frequent mutation generating an in-frame UAA stop codon. Size variation of the PvpA protein was observed among M. gallisepticum strains, ranging from 48 to 55 kDa and caused by several types of deletions occurring at the PvpA C-terminal end and within the two directly repeated sequences. By immunoelectron microscopy, the PvpA protein was localized on the mycoplasma cell surface, in particular on the terminal tip structure. Collectively, these findings suggest that PvpA is a newly identified variable surface cytadhesin protein of M. gallisepticum.
A 300°C, SOI transimpedance amplifier with application to capacitive temperature sensing

This paper reports a high-temperature, wide gain-bandwidth SOI-CMOS transimpedance (Rm) amplifier that is well suited for application to MEMS-based impedance sensors. The amplifier was fabricated using a fully depleted 0.5-μm technology and achieves a gain-bandwidth of 8 MΩ by 1.2 MHz at room temperature while drawing 0.66 mW from a 3.3-V supply. Gain and bandwidth remain above 2 MΩ and 0.3 MHz, respectively, at all temperatures up to 300oC, while power consumption remains under 1 mW. Measured input-referred noise current is just 3.0 pA/√Hz at 100 kHz; consistent with simulation. The amplifier requires one off-chip capacitor but otherwise employs only CMOS transistors; die area is 8500 μm2. A novel temperature sensor was constructed using a MEMS-based capacitive strain sensor, which was glued to a 2-mil thick stainless steel (17-4-PH) base using high-temperature epoxy. The mismatch in coefficient of thermal expansion (CTE) between the two materials (~8.7 ppm/°C) generates a sensor displacement when temperature is varied, which results in a capacitance change. An FEA model predicted that the structure can deliver a sensitivity of 10.7 μ-strain/oC, which produces a -1.12 fF/oC capacitance change in the strain sensor. The transimpedance amplifier was packaged in the same DIP as the capacitive temperature sensor; and this active sensor was stimulated using a 100 kHz, differential sinusoid and heated to temperatures as high as 250 °C. The amplified sensor output was measured using a spectrum analyzer, and the differential capacitance of the sensor was found to be +0.28 pF at room temperature, with a temperature coefficient of approximately -1 fF/oC, in good agreement with the predicted model.
Accuracy of Point-of-Care Blood Glucose Measurements in Critically Ill Patients in Shock

Background: A widely used method in monitoring glycemic status of ICU patients is point-of-care (POC) monitoring devices. A possible limitation to this method is altered peripheral blood flow in patients in shock, which may result in over/underestimations of their true glycemic status. Methods: This study aims to determine the accuracy of blood glucose measurements with a POC meter compared to laboratory methods in critically ill patients in shock. POC blood glucose was measured with a glucose-1-dehydrogenase-based reflectometric meter. The reference method was venous plasma glucose measured by a clinical chemistry analyzer (glucose oxidase-based). Outcomes assessed were concordance to ISO 15197:2003 minimum accuracy criteria for glucose meters, bias in glucose measurements obtained by the 2 methods using Bland–Altman analysis, and clinical accuracy through modified error grid analysis. Results: A total of 186 paired glucose measurements were obtained. ISO 2003 accuracy criteria were met in 95.7% and 79.8% of POC glucose values in the normotensive and hypotensive group, respectively. Mean bias for the normotensive group was –12.4 mg/dL, while mean bias in the hypotensive group was –34.9 mg/dL. Conclusions: POC glucose measurements within the target zone for clinical accuracy were 90.2% and 79.8% for the normotensive and hypotensive group, respectively. POC blood glucose measurements were significantly less accurate in the hypotensive subgroup of ICU patients compared to the normotensive group. We recommend a lower threshold in confirming POC blood glucose with a central laboratory method if clinically incompatible. In light of recently updated accuracy standards, we also recommend alternative methods of glucose monitoring for the ICU population as a whole regardless of blood pressure status.
Lipopolysaccharide-Induced Tumor Necrosis Factor Alpha Production by Human Monocytes Involves the Raf-1/MEK1-MEK2/ERK1-ERK2 Pathway

ABSTRACT During gram-negative sepsis, human monocytes are triggered to produce large quantities of proinflammatory cytokines such as tumor necrosis factor alpha (TNF-α) in response to endotoxin (lipopolysaccharide [LPS]). Several studies have identified signal transduction pathways that are activated by LPS, including activation of nuclear factor-κB (NF-κB) and activation of mitogen-activated protein kinases (MAPKs), including ERK1 and ERK2, c-Jun N-terminal kinase, and p38. In this study, the relevance of ERK1 and ERK2 activation for LPS-induced TNF-α production by primary human monocytes has been addressed with PD-098059, which specifically blocks activation of MAPK kinase (MEK) by Raf-1. TNF-α levels in the monocyte culture supernatant, induced by 10 ng of LPS/ml, were reduced by PD-098059 (50 μM). In addition, PD-098059 also reduced TNF-α mRNA expression when cells were stimulated for 1 h with LPS. On the other hand, LPS-induced interleukin-10 (IL-10) levels in the monocyte supernatant were only slightly inhibited by PD-098059. Ro 09-2210, a recently identified MEK inhibitor, completely abrogated TNF-α levels at nanomolar concentrations. IL-10 levels also were strongly reduced. To show the efficacy of PD-098059 and Ro 09-2210, ERK1 and -2 activation was monitored by Western blotting with an antiserum that recognizes the phosphorylated (i.e., activated) forms of ERK1 and ERK2. Addition of LPS to human monocytes resulted in activation of both ERK1 and ERK2 in a time- and concentration (50% effective concentration between 1 and 10 ng of LPS/ml)-dependent manner. Activation of ERK2 was blocked by PD-098059 (50 μM), whereas ERK1 seemed to be less affected. Ro 09-2210 completely prevented LPS-induced ERK1 and ERK2 activation. LPS-induced p38 activation also was prevented by Ro 09-2210. These data further support the view that the ERK signal transduction pathway is causally involved in the synthesis of TNF-α by human monocytes stimulated with LPS.
The carriage of Candida species on the dorsal surface of the tongue: the correlation with the dental, periodontal and prosthetic status in elderly subjects.

OBJECTIVES To screen the carriage status of Candida species, especially Candida albicans and its genotype in an epidemiological survey and to investigate its correlation with the dental, periodontal and prosthetic status of healthy elderly subjects. MATERIALS AND METHODS Microbiological samples were collected from the dorsum of the tongue of 366 subjects, aged 75, and cultured on CHROMagar medium. The carriage status of Candida spp. and the distribution of C. albicans genotypes by a polymerase chain reaction (PCR) method were analysed and compared with the dental, periodontal and prosthetic status of the subjects. RESULTS A high carriage rate (68.6%) of Candida spp. and the predominant species of C. albicans (72.1%) were found in this study. The prevalence, density and multi-species of Candida spp. were significantly related to the presence of a dental prosthesis. In C. albicans, genotype A predominated (56.4%) and genotype D showed a higher prevalence (12.5%) than previous reports. When comparing Candida spp. carriage with the oral status, significant positive correlations were found with the presence of any dental prosthesis, missing teeth, the number of retained roots and the percentage of sites showing bleeding on probing (BOP), while significant negative correlations were found with the number of teeth present, sound and filled teeth. CONCLUSIONS Candida carriage on the dorsum of the tongue in healthy elderly is significantly associated with the dental, periodontal and prosthetic status, especially the presence of a dental prosthesis. As the complexity of the prosthesis being worn increased, the relative risk of Candida carriage and the numbers and multi-species of Candida increased accordingly.
Low-power consumption ternary full adder based on CNTFET

This paper presents low-power circuits to implement ternary full adder (TFA) using carbon nanotube field-effect transistors (CNTFETs). Besides the unique characteristics of the CNTs, the threshold voltage simple control is the best property to implement ternary logic circuits. Low-complexity, low-power consumption and low-power delay product (PDP) are the benefits of the proposed circuits in comparison with all previous presented designs of TFA. The final proposed TFA is robust and has proper noise margins. The structure of the final proposed TFA is more appropriate to use in ripple adders, since the first ternary half sum generators (THSGs) in all cells produce their outputs in parallel (in the final proposed TFA, the output of the first THSG of the sum-generation unit is also used in the carry-generation unit). The proposed circuits are simulated using HSPICE with 32 nm-CNTFET technology. According to simulation results, the final proposed TFA has reduced the power consumption significantly and results in 86.92 and 97% reductions in terms of the PDP in comparison with two recent proposed designs.
Adaptive refinement of higher order method of moment applied to surface integral equations

Optimal choice of expansion orders for currents is of crucial importance for efficient use of higher order basis functions in method of moment solution of surface integral equations. In this paper it is shown that accuracy of a solution for a given set of expansion orders can be estimated using the residuum of the system of linear equations, obtained by increasing expansion orders by one. Based on such estimation, an iterative procedure is proposed for determination of a minimum set of basis functions needed for given accuracy. In the first iteration 1st order is adopted for all patches. In each iteration patches having insufficient order of current expansion are detected and their orders are increased in the next iteration. Iterative procedure is stopped when a sufficient order of current expansion is detected. The method is illustrated on examples of a cube and a fighter airplane scatterer.
Serum carotenoids as biomarkers of fruit and vegetable consumption in the New York Women's Health Study

Abstract Objective: To investigate the usefulness of serum carotenoids as biomarkers of fruit and vegetable consumption. Design: Reproducibility study on three repeat measurements of serum carotenoids. Correlation analysis of carotenoids and dietary food intake, and regression analysis of potential predictive parameters for serum carotenoid levels. Setting: New York, USA. Subjects: Women participating in the New York Women's Health Study, a prospective study of sex hormones, diet and breast cancer. Forty-eight women with three repeat blood samples and 302 women having a blood sample and a dietary history questionnaire. Results: Serum carotenoid concentrations were highly reproducible between one- and two-year repeat samples. Estimated fruit and vegetable consumption was positively correlated with serum carotenoid concentrations but correlation coefficients were low. Consumption of fruit was predictive for serum levels of beta-carotene, alpha-carotene and beta-cryptoxanthin, while vegetable consumption was predictive for serum beta-carotene, lutein, zeaxanthin and lycopene. Serum concentrations of cholesterol and triglycerides were predictive for serum carotenoids but adjustment for their levels had little or no influence on the correlation between fruit and vegetable consumption and serum carotenoid concentrations. Conclusions: One single serum measurement of alpha-carotene, beta-carotene and lutein can accurately rank subjects according to their usual serum level. Serum concentrations, however, correlate only moderately with estimated dietary intake of fruits or vegetables and should therefore be used with caution as biomarkers of fruit and vegetable intake.
Suicide Risk Assessment in Adolescents – C-SSRS, K10, and READ

Background: Assessment and screening are often the first step in planning interventions to help adolescents at risk of suicide. Causes of suicidal thoughts and behavior are multifaceted and it is important for clinical work that assessment reflects this complexity. Aims: To investigate whether a general psychological Resilience Scale for Adolescents (READ) is associated with a validated suicide rating scale (C-SSRS). Method: An observational study of self-reported suicidality (C-SSRS), psychological distress (K10), and resiliency (READ) in three adolescent samples: suicide clinic (N = 147); general psychiatric clinic (N = 85); and a nonclinical sample (N = 92). Results: Resiliency scores were significantly higher (p < .05) in the nonclinical compared with the clinic samples on all READ scales. READ scores were similar in the two clinic samples apart from the family cohesion subscale, which was significantly lower in the suicide clinic sample. READ was predictive of levels of suicidality within all samples independently of general psychological distress (K10). Limitations: The study did not examine other early childhood factors that may contribute to individual resiliency or suicidality. Conclusion: READ provides a reliable and valid assessment of individual resilience for both clinical and nonclinical settings. Evaluation of protective resources is a useful adjunct to the assessment and treatment of suicidal behavior.
Driver headway: How close is too close on a motorway?

Driver headway has recently become an important question with much attention being given to unsafe headways or ‘tailgating’. This paper reviews a series of recent studies undertaken at the University of Southampton, which have sought to measure and model distance keeping, demonstrating how following distance depends on a wide range of factors, some of which are only recently being explored. These include variations in following distance for any particular driver and the relationship with time to collision, variations in following distances of drivers of differing nationalities and the ability of the driver to ‘read the road ahead’, which may be affected by interaction with different vehicle types. It is demonstrated that providing clear unequivocal statements regarding car following and safety levels, even after such studies, is still far from straightforward.
Identification of Residues in a Hydrophilic Loop of the Papaver rhoeas S Protein That Play a Crucial Role in Recognition of Incompatible Pollen

The self-incompatibility response involves S allele–specific recognition between stigmatic S proteins and incompatible pollen. This response results in pollen inhibition. Defining the amino acid residues within the stigmatic S proteins that participate in S allele–specific inhibition of incompatible pollen is essential for the elucidation of the molecular basis of the self-incompatibility response. We have constructed mutant derivatives of the S1 protein from Papaver rhoeas by using site-directed mutagenesis and have tested their biological activity. This has enabled us to identify amino acid residues in the stigmatic S proteins of P. rhoeas that are required for S-specific inhibition of incompatible pollen. We report here the identification of several amino acid residues in the predicted hydrophilic loop 6 of the P. rhoeas stigmatic S1 protein that are involved in the inhibition of S1 pollen. Mutation of the only hypervariable amino acid, which is situated in this loop, resulted in the complete loss of ability of the S protein to inhibit S1 pollen. This clearly demonstrates that this residue plays a crucial role in pollen recognition and may also participate in defining allelic specificity. We have also established the importance of highly conserved amino acids adjacent to this hypervariable site. Our studies demonstrate that both variable and conserved amino acids in the region of the S protein corresponding to surface loop 6 are key elements that play a role in the recognition and inhibition of incompatible pollen in the pollen–pistil self-incompatibility reaction.