Miracle-dz/UniFAR-FTUs huggingface dataset:
A Deubiquitinating Activity Is Conserved in the Large Tegument Protein of the Herpesviridae

ABSTRACT The largest tegument protein of herpes simplex virus 1 (HSV-1), UL36, contains a novel deubiquitinating activity embedded in it. All members of the Herpesviridae contain a homologue of HSV-1 UL36, the N-terminal segments of which show perfect conservation of those residues implicated in catalysis. For murine cytomegalovirus and Epstein-Barr virus, chosen as representatives of the beta- and gammaherpesvirus subfamilies, respectively, we here show that the homologous modules indeed display deubiquitinating activity in vitro. The conservation of this activity throughout all subfamilies is indicative of an important, if not essential, function.
Lysine acetylation stoichiometry and proteomics analyses reveal pathways regulated by sirtuin 1 in human cells

Lysine acetylation is a widespread posttranslational modification affecting many biological pathways. Recent studies indicate that acetylated lysine residues mainly exhibit low acetylation occupancy, but challenges in sample preparation and analysis make it difficult to confidently assign these numbers, limiting understanding of their biological significance. Here, we tested three common sample preparation methods to determine their suitability for assessing acetylation stoichiometry in three human cell lines, identifying the acetylation occupancy in more than 1,300 proteins from each cell line. The stoichiometric analysis in combination with quantitative proteomics also enabled us to explore their functional roles. We found that higher abundance of the deacetylase sirtuin 1 (SIRT1) correlated with lower acetylation occupancy and lower levels of ribosomal proteins, including those involved in ribosome biogenesis and rRNA processing. Treatment with the SIRT1 inhibitor EX-527 confirmed SIRT1's role in the regulation of pre-rRNA synthesis and processing. Specifically, proteins involved in pre-rRNA transcription, including subunits of the polymerase I and SL1 complexes and the RNA polymerase I-specific transcription initiation factor RRN3, were up-regulated after SIRT1 inhibition. Moreover, many protein effectors and regulators of pre-rRNA processing needed for rRNA maturation were also up-regulated after EX-527 treatment with the outcome that pre-rRNA and 28S rRNA levels also increased. More generally, we found that SIRT1 inhibition down-regulates metabolic pathways, including glycolysis and pyruvate metabolism. Together, these results provide the largest data set thus far of lysine acetylation stoichiometry (available via ProteomeXchange with identifier PXD005903) and set the stage for further biological investigations of this central posttranslational modification.
Changing Epidemiology of Group B Streptococcal Colonization

Objectives. To define factors influencing vertical transmission of and neonatal colonization with group B streptococci (GBS) in neonates representing ethnically and economically diverse populations, and to determine the serotype distribution of isolates, especially new types IV–VIII. Study Design. Prospective, cross-sectional study of neonates born to women evaluated for GBS colonization at admission for delivery to one of four hospitals between January 1994 and February 1995. Cultures of throat, umbilicus, and rectum were obtained from 24- to 48-hour-old infants for isolation of GBS. Isolates were classified by capsular polysaccharide (I-VIII) and C protein (α and β) antigen components. Results. Colonization was detected in 28% of 546 mothers, was higher in blacks than whites (40.6% vs 20.3%) and Hispanics (26.9%), and was not influenced by socioeconomic status. Overall, ethnic origin did not seem to be related to GBS serotype, but whites were more likely to carry the new type V strain than blacks (6 out of 24 [25%] vs 1 out of 43 [2%]). Vertical transmission of GBS to neonates was significantly diminished when their mothers had intrapartum antibiotics (0% vs 52%), rupture of membranes <12 hours before delivery (38.4% vs 73.3%), or delivery by cesarean section (25.9% vs 45.2%). Colonization with GBS was found in 13.8% of 549 neonates, was acquired vertically in 97%, and was less frequent in neonates at the private hospitals (4% vs 20%) where intrapartum antibiotics were given more frequently (34.7% vs 17.3%). Among isolates from neonates, serotype Ia predominated (31.6%) followed by types II (25%), III (22.4%), and V (11.8%); ∼40% of strains contained C protein antigen. Conclusions. Changes in the epidemiology of GBS colonization included diminished rates in some populations associated with use of maternal intrapartum antibiotics, and a shift in serotype prevalence, with Ia as predominant and V, in addition to II and III, as common.
Factors that predict morbidity and mortality in patients with perforated peptic ulcers.

BACKGROUND The demographic changes of perforated peptic ulcer disease were assessed in a well-defined population in northern Finland. The high mortality from perforated peptic ulcer underlines the importance of risk stratification, and clinical variables and three scoring systems were therefore tested for their ability to predict the probability of morbidity and mortality. METHODS Two hundred and eighty patients admitted to a university hospital with peptic ulcer perforation during the 22-year period 1979-2000 were identified using a computer database, and their clinical data were reviewed from the database and patient records. RESULTS The annual operation rate for ulcer perforation has varied from 2.7/100,000 in 1979 to 6.2 in 1985 and 3.6 in 2000 without any significant changes during the examination period. More operations have been performed for duodenal (157) than for gastric (123) ulcer perforations, but their incidence rates were quite similar at the beginning and the end of the period. Of the clinical variables, two or more associated illnesses, duration of symptoms for more than 24 hours, the amount of abdominal liquid, and low albumin concentration predicted morbidity, while a long duration of symptoms and the amount of abdominal liquid were independent risk factors for mortality. The MPI score correctly predicted 96% of postoperative complications and all the three scores, i.e. the Boey score, the MPI score and the ASA score, were good predictors of mortality. CONCLUSION The incidence of peptic ulcer perforation has not changed during the 22-year period in northern Finland. All the three scores, i.e. the Boey score, the MPI score and the ASA score, predict mortality in patients with peptic ulcer perforation and are suitable for risk stratification preoperatively in the surgical ward.
Tire Defect Detection Using Image Component Decomposition

This study presents a component decomposition based method for fast tire defect detection, which is motivated by the fact that defective tire images mainly consist of three components: texture, background and defect. Thus the proposed method exploits three steps to separate the defect component from the defective image. At the first step, the local total variation filtering is used to extract the texture. Then the background is estimated by the vertical mean filtering. Finally, the defect is detected by thresholding the residual image. Experimental results show that the proposed method is more accurate in locating the defects.
Least Squares Fuzzy One-class Support Vector Machine for Imbalanced Data

Based on fuzzy one-class support vector machine (SVM) and least squares (LS) one-class SVM, we propose an LS fuzzy one-class SVM to deal with the class imbalanced problem. The LS fuzzy one-class SVM applies a fuzzy membership to each sample and attempts to solve the modified primal problem. Hence, we just need to solve a system of linear equations as opposed solving the quadratic programming problem (QPP) in fuzzy one-class SVM, which leads to an extremely simple and fast algorithm. Numerical experiments on several benchmark data sets demonstrate the feasibility and effectiveness of the proposed algorithm.
Flow cytometric analysis of protease activities in vital cells.

The analysis of lysosomal proteases in cell lysates is complicated by pH-dependent and oxidative changes of their activity and complex formation with cytosolic inhibitors. Therefore, new flow cytometric methods were developed for the intracellular measurement of protease activities in viable cells. Intracellular cleavage of substrates such as Z-Arg-Arg-4-trifluoromethylcoumarinyl-7-amide to green fluorescent 7-amino-4-trifluoromethylcoumarin (AFC) in viable neutrophils and monocytes was only detected following phagocytosis of Escherichia coli. A measurement of the cysteine or serine proteinase activities in resting human leukocytes was, however, not possible with AFC derivatives as the overlapping blue fluorescence of the substrates reduces sensitivity. Nonfluorescent bis-substituted peptide derivatives of rhodamine 110 (R110), which are intracellularly cleaved to green fluorescent mono-substituted R110 and free R110 proved to be more sensitive substrates. The activity of the lysosomal cysteine proteinases of human monocytes or rat macrophages, i.e. cathepsin B and L, was specifically measured with (Z-Arg-Arg)2-R110, (Z-Phe-Arg)2-R110, or (Z-Ala-Arg-Arg)2-R110. Fluorescence generation was completely inhibited by Z-Phe-Ala-diazomethane or E-64. The serine proteinases of human neutrophils were analyzed with Elastase-substrates such as (Z-Ala-Ala)2-R110 or (Z-Ala-Ala-Ala)2-R110. Specificity was shown by inhibition with diisopropylfluorophosphate.
Methyl tert‐butyl ether (MTBE)‐induced cytotoxicity and oxidative stress in isolated rat spermatogenic cells

Methyl tert‐butyl ether (MTBE) is a class of synthetic organic chemical. In the USA, MTBE pollution is regarded as a serious environmental problem. The objective of the present study was to investigate the cytotoxic effects and oxidative stress induced by MTBE in isolated rat spermatogenic cells. In cytotoxic experiments, spermatogenic cells isolated from the testes of adult Sprague‐Dawley rats by a mechanical procedure without the use of trypsin were incubated with medium alone (control), 0.5, 5, 50 mm MTBE, respectively, for 6, 12 and 18 h. MTT assay, staining with fluorescein diacetate (FDA) and propidium iodide (PI) and flow cytometric analyses were used. In oxidative stress experiments, the spermatogenic cells were incubated with medium alone (control) and with 0.5, 50 μm, 5 mm MTBE. For 1, 2, 6, 12, 18 h incubation, ROS production was tested using a 2′,7′‐dichlorofluorescein diacetate (DCHF‐DA) probe; for 1, 3, 6, 12, 18 h incubation, cytosolic superoxide dismutase (SOD) and extracellular SOD (SODEX) activity was assessed; and for 18 h incubation, lipid peroxidation was assessed. The results showed that MTBE at high doses significantly decreased the spermatogenic cell viability and increased plasma membrane damage and the ratio of necrotic cells compared with the control. Assessment of the MTBE‐induced oxidative stress revealed that MTBE increased the production of reactive oxygen species (ROS) and enhanced lipid peroxidation. In addition, although SODEX activity increased at a high dose level, cytosolic SOD activity decreased. These results suggest that an increase of MTBE‐induced ROS production and an enhancement of membrane lipid peroxidation may play an important role in its cytotoxicity in isolated rat spermatogenic cells. Copyright © 2006 John Wiley & Sons, Ltd.
Determination of selenium by X-ray fluorescence spectrometry using dispersive solid-phase microextraction with multiwalled carbon nanotubes as solid sorbent

A dispersive solid-phase microextraction (DSPME) with multiwalled carbon nanotubes (MWCNTs) as solid sorbent and ammonium pyrrolidinedithiocarbamate (APDC) as chelating agent was developed for determination of selenium. In the proposed procedure, the Se(IV)–APDC complex is adsorbed on MWCNTs dispersed in aqueous samples. After the adsorption process, the aqueous samples are filtered and MWCNTs with selenium chelate are collected onto a filter. The loaded filters are directly measured using X-ray fluorescence (XRF) spectrometry. In order to obtain high recovery of the Se ions on MWCNTs, the proposed procedure was optimized for various analytical parameters such as pH, amounts of MWCNTs and APDC, sample volume and time of the sorption process. Under optimized conditions Se ions can be determined with very good recovery (97 ± 3%), precision (RSD = 3.2%) and detection limits (from 0.06 to 0.2 ng mL−1, depending on counting time and XRF equipment). The effect of common coexisting ions was also investigated. Se(IV) can be determined in the presence of heavy metal ions and alkali metals. The chemical interferences observed for high concentrations of Cu(II), Fe(III), and Zn(II) can be completely eliminated using precipitation with NaOH. The proposed method was applied for the determination of Se in mineral water and biological samples (Lobster Hepatopancreas). The proposed method can also be applied for selenium speciation. The concentration of selenate can be obtained as the difference between the concentration of selenite after and before prereduction of selenate to selenite.
Bone Mass in Middle‐Aged Osteoporotic Men and Their Relatives: Familial Effect

Severe idiopathic osteoporosis in middle‐aged men is still poorly understood. The aim of this study was to assess the contribution of genetic factors in these patients. We studied 38 men (mean age ± SD, 50 ± 11 years) presenting with vertebral or peripheral bone fractures due to primary osteoporosis and 73 of their relatives divided into four subgroups: 19 brothers, 22 sisters, 13 sons, and 19 daughters. The control group comprised 199 age‐matched subjects. In all subjects, we measured bone mineral density (BMD) and calculated the Z score at the lumbar spine (LS) and femoral neck (FN) based on the fitted BMD value in the controls. LS BMD values were lower in each of the four subgroups compared with the age‐matched controls. The mean Z score for the overall group of 73 relatives was decreased compared with the age‐matched controls (−1.28 ± 1.48 at the LS and −1.03 ± 1.19 at the FN) and was not influenced by gender or by whether the relatives were siblings or children. An LS Z score < −1) was found in 54.8% of the relatives of osteoporotic patients versus 17.4% of the control subjects (risk ratio, 3.2). Alcohol and tobacco abuse are well‐known risk factors for osteoporosis in men. Among the 38 osteoporotic patients, 7 were heavy smokers (>20 pack‐years), 8 were both heavy smokers and drinkers (>80 g/day for at least 10 years and γGT > 40 UI/l), and 23 had neither of these risk factors. BMD, Z score, and anthropometric data were the same in patients with and without risk factors. Decreases in LS and FN Z scores were similar in relatives of patients with and without risk factors. In conclusion, low BMD is observed in relatives of osteoporotic men with or without risk factors for osteoporosis, indicating that familial factors contribute to primary osteoporosis in middle‐aged men.
Determination of MIC distribution of colistin, fosfomycin, and tigecyclin antibiotics against carbapenem resistant enterobacteriaceae

Introduction: There are limited treatments options for carbapenem resistant Enterobacteriaceae (CRE) species and especially colistin, fosfomycin and tigecyclin are used for treatment. Therefore, in this study, we aimed for determining the rates of antibiotic susceptibility against colisting, fosfomycin and tigecyclin in CRE isolates with microdilution method. Material and Method: In our study, a total of 63 isolates, which were isolated from blood, urine and tracheal aspirate samples. Bacteria identification of the isolates was made with MALDI-TOF MS (Bruker Biotyper; Germany) device. Imipenem, meropenem and ertapenem susceptibilities were determined with the gradient strip test (Liofilchem, Italy) method and genotypic properties were determined with the PCR method. Colistin (0.06-32 μg/ml), fosfomycin (0.06-32 μg/ml) and tigecyclin (0.25-256 μg/ml) M? K values were determined with the microdilution method. Results: Of the isolates included in the study, 60 isolates (95.24%) were defined as Klebsiella pneumoniae, 2 (3.17%) as Escherichia coli and 1 (1.59%) as Enterobacter cloacae. 57 isolates (90.48%) had OXA-48, 4 (6.35%) had NDM and 2 (3.17%) had OXA-48 and NDM resistant genotypes. M? K50 values for colistin, fosfomycin and tigecyclin were 0.50, 4 and 0.25 M? K90 values were 1, 16 and 1, respectively. Two isolates (3.17%) had resistance to colistin, 23 (63.51%) to fosfomycin and 18 (28.57%) to tigecyclin. Conclusion: Under the light of the findings of the study, we believe colistin, fosfomycin and tigecyclin can be alternatives for CRE treatment, however, local and national level surveillance studies are important and treatment protocols should be organized and dosage should be arranged based on this surveillance data.
Robust attitude control for a tail-sitter aircraft

Many challenges of modeling and control exist in the tail-sitter aircraft, including parameter uncertainty, highly coupling, nonlinearity, and external disturbance. In this paper, the model of a tail-sitter aircraft is simplified at the nominal condition to obtain the nominal linear invariant model. Then a robust controller based on the H∞ control theory is proposed to deal with the attitude tracking control problem and decrease the effects of multiple uncertainties. It is proved that the closed-loop system has robust stability, and the tracking error can converge to stability. It is shown that the proposed robust controller can maintain the attitude angle adjustment accuracy and robustness to the model uncertainty and external disturbance.
PTGS 2 ( Cyclooxygenase-2 ) Expression and Survival among Colorectal Cancer Patients : A Systematic Review

Background: Studies have examined whether tumor expression of PTGS2 (also known as COX-2), an enzyme inhibited by nonsteroidal anti-inflammatory drugs such as aspirin, is associated with prognosis in patients with colorectal cancer. However, results to date have been mixed. Methods:Using terms for PTGS2 and colorectal cancer, theMedline, Embase, andWeb of Science databases were systematically searched for studies published, in any language, until December 2011. Random effects meta-analyses were used to calculate pooled HRs [95% confidence intervals (CI)] for the association between PTGS2 expression and tumor recurrence, colorectal cancer–specific survival, and overall survival. Results: In total, 29 studies, which had prognostic data on 5,648 patients, met the inclusion criteria. PTGS2positive patients were at an increased risk of tumor recurrence (n 1⁄4 9 studies; HR, 2.79; 95% CI, 1.76–4.41; P < 0.001) and had poorer colorectal cancer–specific survival (n 1⁄4 7; HR, 1.36; 95% CI, 1.02–1.82; P 1⁄4 0.04). However, there was funnel plot asymmetry, possibly due to publication bias, for the association with cancerspecific survival but less so for recurrence. PTGS2 expressionwas not associatedwith overall survival [(n1⁄4 16; pooledunadjustedHR, 1.30; 95%CI, 0.94–1.79;P1⁄4 0.11) and (n1⁄4 9; pooled adjustedHR, 1.02; 95%CI, 0.72–1.45; P 1⁄4 0.91)]. Conclusions: PTGS2 expression was associated with an increased risk of tumor recurrence and poorer colorectal cancer–specific survival but not overall survival among patients with colorectal cancer. However, confounding by tumor characteristics such as tumor stage seems likely. Impact: There is insufficient evidence to recommend PTGS2 expression as a prognostic marker in patients with colorectal cancer. Furthermore, studies providing adjusted results are required. Cancer Epidemiol Biomarkers Prev; 22(9); 1490–7. 2013 AACR.
Detecting Early Risk of Depression from Social Media User-generated Content

This paper presents the systems developed by the UQAM team for the CLEF eRisk Pilot Task 2017. The goal was to predict as early as possible the risk of mental health issues from user-generated content in social media. Several approaches based on supervised learning and information retrieval methods were used to estimate the risk of depression for a user given the content of its posts in reddit. Among the five systems evaluated, the experiments show that combining information retrieval and machine learning approaches gives the best results.
Inability of IL-12 to Down-Regulate IgE Synthesis Due to Defective Production of IFN-γ in Atopic NC/Nga Mice1

NC/Nga mice raised in nonsterile circumstances spontaneously suffer from atopic dermatitis-like skin lesions with IgE hyperproduction. We investigated effects of rIL-12 on the IgE production in NC/Nga mice. rIL-12 administration was successful to suppress the increase of IgE levels in BALB/c mice immunized with OVA and aluminum hydroxide, but failed to abrogate that in NC/Nga mice. Both in vivo and in vitro IFN-γ production induced by rIL-12 was less in NC/Nga mice than in BALB/c mice. Addition of rIFN-γ to rIL-4 and LPS completely abrogated IgE production by B cells of BALB/c mice, but was insufficient to suppress it by B cells of NC/Nga mice. In splenic cells pretreated with Con A, STAT4 was phosphorylated at the tyrosine residue by addition of rIL-12, which was more weakly inducible in NC/Nga mice than in BALB/c mice. Finally, we examined the preventive ability of rIL-12 on the clinical aspects of atopic dermatitis in NC/Nga mice. rIL-12 administration resulted in exacerbation of development of the skin lesions and IgE production in NC/Nga mice raised in nonsterile circumstances. These results suggest that defective production of IFN-γ by T cells less sensitive to IL-12 and low responsiveness of B cells to IFN-γ may contribute to IgE hyperproduction in NC/Nga mice, and that IL-12 may have no ability to improve the clinical aspects of NC/Nga mice.
The relationship between condom use and herpes simplex virus acquisition

Abstract Objectives To assess the impact on risk of pre-eclampsia of genes that work through the mother, and genes of paternal origin that work through the fetus. Design Population based cohort study. Setting Registry data from Norway. Participants Linked generational data from the medical birth registry of Norway (1967-2003): 438 597 mother-offspring units and 286 945 father-offspring units. Main outcome measures Pre-eclampsia in the second generation. Results The daughters of women who had pre-eclampsia during pregnancy had more than twice the risk of pre-eclampsia themselves (odds ratio 2.2, 95% confidence interval 2.0 to 2.4) compared with other women. Men born after a pregnancy complicated by pre-eclampsia had a moderately increased risk of fathering a pre-eclamptic pregnancy (1.5, 1.3 to 1.7). Sisters of affected men or women, who were themselves born after pregnancies not complicated by pre-eclampsia, also had an increased risk (2.0, 1.7 to 2.3). Women and men born after pre-eclamptic pregnancies were more likely to trigger severe pre-eclampsia in their own (or their partner's) pregnancy (3.0, 2.4 to 3.7, for mothers and 1.9, 1.4 to 2.5, for fathers). Conclusions Maternal genes and fetal genes from either the mother or father may trigger pre-eclampsia. The maternal association is stronger than the fetal association. The familial association predicts more severe pre-eclampsia.
Utilization of Low Distortion Power Electronics Current Sources in Generator of Spatial Magnetic Field

The paper considers Generator of the Spatial Magnetic Field for medicine purposes. One of essential blocks there is three-channel power electronics current source, powering set of space oriented induction coils (electromagnets) ¿ sources of magnetic field. The control module utilizes DSP based microcomputer for power electronics applications. The microcomputer is integrated with industrial PC in form of PCI card. The execution block utilizes three power electronics inverters, utilizing PWM strategy. The paper describes fundamentals of current source control algorithms and test results of laboratory model of generator.