Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Translocator 18 KDa Ligands in the Activation of Leukotriene B4 Activated G-Protein Coupled Receptor and Toll Like Receptor-4 Pathways in Neutrophils

TSPO (Translocator 18 KDa; tryptophan-rich sensory protein oxygen sensor) is a constitutive outer mitochondrial membrane protein overexpressed in inflammatory cells during local or systemic processes. Despite its expression is characterized, role of TSPO in inflammation remains elusive. For this study, we investigated the role of TSPO ligands on neutrophil functions elicited by two different inflammatory pathways. Peritoneal neutrophils were isolated from male Balb-C mice, treated with TSPO ligand diazepam, Ro5-4864 or PK11195 (1,100 or 1000 nM; 2 h) and further stimulated with lipopolysaccharide from Escherichia coli (LPS), a binding for Toll-Like Receptor-4 (TLR4), or leukotriene B4 (LTB4), a G-protein coupled receptor (GPCR) ligand. LPS treatment did not lead to overexpression of TSPO on neutrophils, and pre-treatment with any TSPO ligand did not alter cytokine expression, adhesion molecule expression, or the production of reactive oxygen and nitrogen species caused by LPS stimulation. Conversely, all TSPO ligands impaired LTB4’s actions, as visualized by reductions in L-selectin shedding, β2 integrin overexpression, neutrophil chemotaxis, and actin filament assembly. TSPO ligands showed distinct intracellular effects on LTB4-induced neutrophil locomotion, with diazepam enhancing cofilin but not modifying Arp2/3 expression, and Ro5-4864 and PK11195 reducing both cofilin and Arp2/3 expression. Taken together, our data exclude a direct role of TSPO ligands in TLR4-elicited pathways, and indicate that TSPO activation inhibits GPCR inflammatory pathways in neutrophils, with a relevant role in neutrophil influx into inflammatory sites.
Activation of mitochondrial ERK protects cancer cells from death through inhibition of the permeability transition

We studied human cancer cell models in which we detected constitutive activation of ERK. A fraction of active ERK was found to be located in mitochondria in RWPE-2 cells, obtained by v-Ki-Ras transformation of the epithelial prostate RWPE-1 cell line; in metastatic prostate cancer DU145 cells; and in osteosarcoma SAOS-2 cells. All these tumor cells displayed marked resistance to death caused by apoptotic stimuli like arachidonic acid and the BH3 mimetic EM20-25, which cause cell death through the mitochondrial permeability transition pore (PTP). PTP desensitization and the ensuing resistance to cell death induced by arachidonic acid or EM20-25 could be ablated by inhibiting ERK with the drug PD98059 or with a selective ERK activation inhibitor peptide. ERK inhibition enhanced glycogen synthase kinase-3 (GSK-3)-dependent phosphorylation of the pore regulator cyclophilin D, whereas GSK-3 inhibition protected from PTP opening. Neither active ERK in mitochondria nor pore desensitization was observed in non-transformed RWPE-1 cells. Thus, in tumor cells mitochondrial ERK activation desensitizes the PTP through a signaling axis that involves GSK-3 and cyclophilin D, a finding that provides a mechanistic basis for increased resistance to apoptosis of neoplastic cells.
Model selection using dimensionality reduction of time series characteristics

To find the best forecasting model, several methods are usually tried on training dataset and the best one is selected to forecast the testing dataset. In this paper, we propose a model which selects a forecasting method based on its previous performance on similar dataset assuming that we have historical database of predictor’s performance. Thus, we need to obtain the characteristics of time series for similarity measure. Since not all of time series characteristics may necessarily be used to identify certain time series, we reduce the dimensionality of those characteristics using Principal Component Analysis. We use diverse forecasting methods ranging from simple to sophisticated ones, measure as Random Walk, ARIMA, interpolation, S-curve, and Multiple Kernel Learning. To cope with large dataset, we utilize clustering and similarity measure to select only a subset of training dataset. We use the 3003 dataset from M3 competition to construct the historical database which acts as training dataset and 111 from the M1 competition as testing dataset. Our experimental results indicate that our model selection may perform well compared to each individual predictor. The advantage of our method lies in its ability to select suitable predictors without trying all of them on current dataset.
Estimation et analyse du taux de substitution adaptatif chez les animaux

Comprendre les determinants du taux d’adaptation est une question primordiale en evolution moleculaire. En particulier, l’influence de la taille efficace de population sur la selection positive, ainsi que la nature des changements d’acides amines qui menent a de l’adaptation sont des questions encore debattues. Pour y repondre, la methode DFE-α, derivee du test fondateur de McDonald & Kreitman, est un outil puissant pour mesurer le taux de substitution adaptatif. Elle est neanmoins sensible a certains biais. Au cours de cette these, nous avons identifie deux biais majeurs de cette methode, les fluctuations de long-terme du regime de selection-derive via des fluctuations demographiques, et la conversion genique biaisee vers GC (gBGC). Via des simulations, nous avons montre que divers scenarios plausibles de fluctuations demographiques peuvent mener a une sur-estimation du taux de substitution adaptatif. Nous avons aussi obtenu des indications empiriques que le regime de selection-derive recent ne reflete pas le regime de selection-derive de long-terme chez diverses especes animales, ce qui represente une violation d’une hypothese forte de la methode DFE-α. D’autre part, nous avons montre que la gBGC entraine une sur-estimation du taux de substitution adaptatif chez les primates et les oiseaux. Via un jeu de donnees de neuf taxons de metazoaires et un total de 40 especes, nous avons d’une part initie une analyse visant a identifier la nature des changements d’acides amines qui menent a l’adaptation, et montre que les changements radicaux sont soumis a une plus forte selection purificatrice que les changements conservatifs. D’autre part, nous avons pu evaluer le lien entre la taille efficace et le taux de substitution adaptatif tout en prenant en compte les deux sources de biais explorees precedemment. Nous avons mis en evidence pour la premiere fois une relation negative entre le taux de substitution adaptatif et des traits d’histoire de vie representatifs de la taille de population de long-terme. Ce resultat va a l’encontre de l’hypothese canonique d’une adaptation plus efficace en grandes populations.
Diagnostic utility of PCR-enzyme immunoassay, culture, and serology for detection of Chlamydia pneumoniae in symptomatic and asymptomatic patients

To assess the utility of PCR-enzyme immunoassay (EIA) for diagnosis of acute infection with Chlamydia pneumoniae, we compared tissue culture, PCR-EIA, direct fluorescent-antibody (DFA) stain, and serology in studies with 56 patients with respiratory symptoms and 80 asymptomatic persons. Thirty-five patients were positive by either culture or PCR-EIA, and 101 were negative by both assays. Thirty specimens from symptomatic patients and one from an asymptomatic patient were culture positive; 23 of these were also PCR-EIA positive. Of the eight culture-positive, PCR-EIA-negative specimens, five were DFA negative and three were DFA positive. Four additional specimens were culture negative and PCR-EIA positive; of these, three were DFA positive and one was DFA negative. When we used culture- and/or DFA-positive results as a reference or "gold standard," the sensitivity and specificity of PCR were 76.5 and 99.0%, respectively. When we used PCR- and/or DFA-positive results as the reference, the sensitivity of culture was 87.5%. On the basis of single acute serum specimens, only 8 of these 35 patients had diagnostic antibody titers. Of the asymptomatic patients, 75% had immunoglobulin G or immunoglobulin M antibody to C. pneumoniae; 15 (18.8%) of these had antibody levels considered to be diagnostic of acute infection. This multicenter study indicates that culture and/or PCR-EIA is more reliable for prompt diagnosis of C. pneumoniae infection than single-point serology alone.
Self-perception regarding the need for orthodontic treatment among impoverished schoolchildren in Brazil.

AIM The objectives of the present study were to assess predictive factors associated to self-perception regarding the need for orthodontic treatment among 170 impoverished schoolchildren. MATERIALS AND METHODS A cross- sectional study was conducted in public schools in the city of Belo Horizonte-MG (Brazil). Children's self-perception regarding the need for treatment was assessed using the Aesthetic Component of the Index of Orthodontic Treatment Need (IOTN-AC) and a questionnaire addressing biopsychosocial factors. The chi-square test and multiple logistic regression were used in the data analysis. RESULTS The predictive factors for the self-perception of orthodontic treatment need on the part of the impoverished schoolchildren included ridicule from persons close to the children regarding the appearance of the teeth (OR 2.81; 95%CI 1.2 to 6.4), dissatisfaction with oral aesthetics due to the alignment of the teeth (OR 2.45; 95%CI 1.1 to 5.4) and missing teeth (OR 3.02; 95%CI 1.0 to 9.23). CONCLUSION The alignment of the teeth, missing teeth and ridicule from others regarding the appearance of the teeth are the factors that most strongly influence self- perception regarding the need for orthodontic treatment among impoverished schoolchildren.
PROBABILISTIC APPROACH FOR VULNERABILITY ANALYSIS USING GNAVE ALGORITHM FOR NODE CAPTURE ATTACKS IN WSN

The impact of node capture attacks on the confidentiality and integrity of network traffic, where it is attempted to map the compromise of network traffic to the flow of current through an electric circuit and propose a metric for quantifying the vulnerability of the traffic using the circuit mapping. It computes the vulnerability metric as a function of the routing and the cryptographic protocols used to secure the network traffic and formulate the minimum cost node capture attack problem as a nonlinear integer programming problem. Due to the NPhardness of the minimization problem, a greedy heuristic is implemented that approximates the minimum cost attack by providing examples of node capture attacks using the vulnerability metric and show that the adversary can expand significantly less resources to compromise target traffic by exploiting information leakage from the routing and cryptographic protocols. Finally, the framework is targeted to design where it can formalize node capture attacks using the vulnerability metric as a nonlinear integer programming minimization problem and with the proposed GNAVE algorithm, a Greedy Node capture Approximation using Vulnerability Evaluation with a discussion on the availability of security parameters to the adversary and show that unknown parameters can be estimated using probabilistic analysis.
Mitochondrial Genetic Disorders: Challenges & Opportunities

Due to the close proximity of the mitochondrial genome to the respiratory chain complex producing ATP, it is believed to be more susceptible to get damaged by the reactive oxygen species (ROS) than nuclear DNA. In addition to this, the poorly developed mitochondrial DNA (mtDNA) repair machinery and the lack of protective histones, unlike in nuclear genome are also believed to be the major factors for high mutation rate [6-8].
Application of a Mycoplasma group-specific PCR for monitoring decontamination of Mycoplasma-infected Chlamydia sp. strains

Mycoplasma contamination of biological materials remains a major problem. Most contaminations are caused by the use of Mycoplasma-contaminated cell lines. We adapted a Mycoplasma group-specific PCR to detect Mycoplasma contamination in cell lines and demonstrate its use in monitoring decontamination procedures with Mycoplasma-contaminated suspensions of Chlamydia spp. Three different methods were investigated: the use of Mycoplasma-specific antiserum in cell culture, physical separation by the combined use of enzymatic treatment and differential centrifugation, and the use of detergents. With these methods only incubation with Triton X-100 resulted in decontamination of Mycoplasma-contaminated suspensions of several laboratory strains of Chlamydia pneumoniae, C. pecorum, and C. trachomatis. Only one C. pneumoniae strain, UZG-1, was sensitive to Triton X-100 treatment. Since 39 of 40 throat swabs from patients with symptoms of an upper respiratory tract infection had positive reactions in the Mycoplasma group-specific PCR, this procedure could also have clinical significance in attempts to propagate C. pneumoniae strains from clinical specimens.
Cis-regulation of IRF 5 expression is unable to fully account for systemic lupus erythematosus association : analysis of multiple experiments with lymphoblastoid cell lines

Introduction: Interferon regulatory factor 5 gene (IRF5) polymorphisms are strongly associated with several diseases, including systemic lupus erythematosus (SLE). The association includes risk and protective components. They could be due to combinations of functional polymorphisms and related to cis-regulation of IRF5 expression, but their mechanisms are still uncertain. We hypothesised that thorough testing of the relationships between IRF5 polymorphisms, expression data from multiple experiments and SLE-associated haplotypes might provide useful new information. Methods: Expression data from four published microarray hybridisation experiments with lymphoblastoid cell lines (57 to 181 cell lines) were retrieved. Genotypes of 109 IRF5 polymorphisms, including four known functional polymorphisms, were considered. The best linear regression models accounting for the IRF5 expression data were selected by using a forward entry procedure. SLE-associated IRF5 haplotypes were correlated with the expression data and with the best cis-regulatory models. Results: A large fraction of variability in IRF5 expression was accounted for by linear regression models with IRF5 polymorphisms, but at a different level in each expression data set. Also, the best models from each expression data set were different, although there was overlap between them. The SNP introducing an early polyadenylation signal, rs10954213, was included in the best models for two of the expression data sets and in good models for the other two data sets. The SLE risk haplotype was associated with high IRF5 expression in the four expression data sets. However, there was also a trend towards high IRF5 expression with some protective and neutral haplotypes, and the protective haplotypes were not associated with IRF5 expression. As a consequence, correlation between the cis-regulatory best models and SLE-associated haplotypes, regarding either the risk or protective component, was poor. Conclusions: Our analysis indicates that although the SLE risk haplotype of IRF5 is associated with high expression of the gene, cis-regulation of IRF5 expression is not enough to fully account for IRF5 association with SLE susceptibility, which indicates the need to identify additional functional changes in this gene.
The regulatory/cytotoxic infiltrating T cells in early renal surveillance biopsies predicts acute rejection and survival.

BACKGROUND To analyze the immune phenotype of T-lymphocyte infiltrations in surveillance renal biopsies with stable renal function early post-transplantation (median time 40 days, range from 18 to 85 days). METHODS One hundred and twenty-five surveillance biopsies with interstitial T-lymphocyte infiltration between non-atrophic tubules in the cortex (14 with subclinical rejection, 32 with borderline change and 79 with only interstitial T-lymphocyte infiltration but no obvious pathological abnormalities according to Banff criteria) were enrolled. All cases were classified into two groups: regulatory phenotype (RP) group, which was dominated by FOXP3-positive T lymphocytes in surveillance biopsies, and cytotoxic phenotype (CP) group, which was dominated by Granzyme B-positive T lymphocytes. RESULTS The RP group includes 83.2% (104/125) cases, none of which developed acute rejection during nearly 5 years of follow-up. The CP group includes 16.8% (21/125) cases, all of which developed biopsy-proven acute rejection or clinical diagnostic acute rejection within 1 year after biopsy. Glomerular filtration rate and cumulative graft survival time were superior in the RP group than in the CP group (P<0.001). CONCLUSION Analyzing the immunophenotype of graft-infiltrating T cells in renal surveillance biopsies during early post-transplantation could predict acute rejection and survival.
A Feasibility study on Combining Internet-Based Cognitive Behaviour Therapy with Physical Exercise as Treatment for Panic Disorder—Treatment Protocol and Preliminary Results

Internet-based cognitive behaviour therapy (ICBT) is a recommended, cost-effective and efficacious treatment for panic disorder (PD). However, treatment effects in psychiatric settings indicate that a substantial proportion fail to achieve remission. Physical exercise improves symptoms in patients with PD, and acts through mechanisms that can augment the effect of ICBT. The feasibility of combining these two interventions has not previously been investigated, and this was the aim of this study. The intervention comprised guided ICBT combined with one weekly session of supervised and two weekly sessions of unsupervised physical exercise for a total of 12 weeks. Treatment rationale, procedures and protocols are presented together with preliminary results for four patients with PD who have currently finished treatment. Quantitative and qualitative results are reported on the feasibility of adhering to the treatments, treatment outcome as assessed by clinician rating and estimation of reliable and clinically significant change for outcome measures, and participants' satisfactions with the combined treatment. The preliminary results indicate that the combined treatment is feasible to complete, and that the combination is perceived by the participants as beneficial.
High Recurrence Rates of Squamous Cell Carcinoma after Mohs' Surgery in Patients with Chronic Lymphocytic Leukemia

BACKGROUND Cutaneous cancers exhibit a much higher incidence in patients with chronic lymphocytic leukemia than in nonleukemic patients. Squamous and basal cell carcinomas also exhibit greater subclinical tumor extension in patients with chronic lymphocytic leukemia. OBJECTIVE The purpose of this study was to estimate and compare the recurrence rates of squamous cell carcinoma after Mohs' surgery in patients with chronic lymphocytic leukemia compared with those in controls and to evaluate differences among squamous cell carcinoma size and histologic grade. METHODS We retrospectively assessed the clinical histories, postoperative notes, and surgical photographs of patients with chronic lymphocytic leukemia and controls matched (2:1) for age, sex, and surgical year. Both patients and controls underwent Mohs' surgery for squamous cell carcinoma of the head and neck at the Mayo Clinic between March 1988 and April 1999. RESULTS Twenty-eight patients who underwent Mohs' surgery for 57 squamous cell carcinomas had 7 recurrences. The cumulative incidence of recurrence on a per-tumor basis was 4.3% at 1 year, 14.8% at 3 years, and 19.0% at 5 years. Squamous cell carcinoma was seven times more likely to recur in patients with chronic lymphocytic leukemia than in controls (p= .003). The distribution of tumor histologic grade was not significantly different between patients and controls (p= .39). Maximum preoperative tumor diameters were clinically similar between patients and controls (median 15 mm vs 14 mm; p= .04). CONCLUSION The recurrence rates of squamous cell carcinoma were significantly higher in patients with chronic lymphocytic leukemia. Squamous cell carcinomas in patients with chronic lymphocytic leukemia did not exhibit a significant difference in histologic grade or clinical difference in preoperative tumor size. Close surveillance for squamous cell carcinoma recurrence is warranted in patients with chronic lymphocytic leukemia.
Comparative Study of Children With ADHD Only, Autism Spectrum Disorder + ADHD, and Chronic Multiple Tic Disorder + ADHD

Objective: Identification of differences among children with ADHD only, autism spectrum disorder (ASD)+ADHD, and chronic multiple tic disorder (CMTD)+ADHD may lead to better understanding of clinical phenotypes. Method: Children were evaluated using the parent- and teacher-completed questionnaires. Results: All three groups were highly similar in severity of oppositional defiant disorder and conduct disorder symptoms; however, the ASD+ADHD group generally exhibited the most severe anxiety, although the CMTD+ADHD group had the most severe generalized anxiety. The two comorbid groups had the most involved medical histories and the greatest likelihood of a family history of psychopathology. Conclusion: Groups differed in clinically meaningful ways, and the apparent association between tics and anxiety may explain in part the elevated levels of anxiety in both comorbid groups. Collectively, results suggest that ADHD may be better conceptualized as a family of interrelated syndromes defined in part by comorbid conditions and that continued research is clearly warranted. (J. of Att. Dis. 2009; 12(5) 474-485)
Effect of Formaldehyde on the Immunochemical and Biological Activity of Staphylococcal Endotoxin B

Staphylococcal enterotoxin B was treated with 0.15 or 0.3% formaldehyde at 37 C and pH 7.3. As early as 8 hr after addition of HCHO, the toxin was unable to precipitate as much antibody from antiserum as untreated toxin; greater amounts of treated toxin were required to reach equivalence and to inhibit precipitation. With increasing time, its reactivity decreased so that at 32 weeks it could precipitate only 20% as much antibody as untreated toxin. When other factors were kept constant, the degree of inactivation increased as the HCHO concentration increased from 0.6 to 1.4%. Treated toxin gave a “reaction of partial identity” by the Ouchterlony double-immunodiffusion technique. The emetic effect of the toxin for the monkey remained essentially unchanged for about 48 hr of treatment, but the amount required to cause death by the intravenous route increased from 25 to over 1,000 μg/kg of body weight. HCHO destroyed the pyrogenic effect for rabbits. The treated toxin remained immunogenic for rabbits even after 4 to 5 weeks of exposure to 0.3% HCHO at 37 C.
A segmentation based global iterative censoring scheme for ship detection in synthetic aperture radar image.doc

This letter depicts a ship detection scheme for synthetic aperture radar images, utilizing a segmentation based global iterative censoring algorithm. In the proposed scheme, the fuzzy local information c-means clustering (RFLICM) algorithm is adopted to partition the inhomogeneous SAR image into numerous homogeneous sub-regions, thereby eliminating the performance degradation caused by SAR image inhomogeneity. Subsequently, successively applying the GIC algorithm base on a parametric clutter model database to the sub-regions, the optimal clutter models and the initial outlier map of the sub-regions are generated. A sliding window CFAR detector based on the selected clutter models and the initial outlier map is utilized to detect ships in the SAR image. In our experiment, we tested the proposed method on spaceborne SAR data, and its effectiveness was successfully demonstrated.