Miracle-dz/UniFAR-FTUs huggingface dataset:
Antigens of Actinobacillus actinomycetemcomitans recognized by patients with juvenile periodontitis and periodontally normal subjects

Most juvenile periodontitis patients respond to infection by Actinobacillus actinomycetemcomitans by producing serum antibodies. Specific antigens inducing the humoral immune response have not been identified, nor has the role of the resulting antibodies in disease progression been determined. Adsorbed and unadsorbed sera from juvenile periodontitis patients and normal subjects were analyzed by enzyme-linked immunosorbent assay and Western blots (immunoblots), using digested and undigested bacterial sonicates and French pressure cell fractions to determine the biochemical class, cross-reactivity, and cellular location of the antigens in different A. actinomycetemcomitans serotypes. Antigens detected by using high-titer sera included the following: (i) serotype-specific nonprotein material located on the cell surface, (ii) soluble-fraction proteins showing highly variable antibody binding, (iii) cross-reactive proteins, and (iv) a protein present in soluble and cell wall fractions and immunopositive for all sera tested. In addition, one apparently nonprotein component that was enriched in the cell wall fraction was observed. Sera with high immunoglobulin G titers to one, two, three, or none of the three A. actinomycetemcomitans serotypes were observed. There was a high degree of variation from one patient to another in the humoral immune response to serotype-specific and cross-reactive antigens. As demonstrated by whole-cell adsorption experiments, the serotype-specific surface antigen accounted for approximately 72 to 90% of the total antibody-binding activity for sera with titers greater than 100-fold above background, while cross-reactive antigen accounted for less than 28%. Antibody binding the whole-cell sonicate for high-titer sera was inhibited 90% by lipopolysaccharide from the same serotype, strongly suggesting that lipopolysaccharide is the immunodominant antigen class.
Improvement in adiposity with oligofructose is modified by antibiotics in obese rats

Given the intimate link between gut microbiota and host physiology, there is growing interest in understanding the mechanisms by which diet influences gut microbiota and affects human metabolic health. Using antibiotics and the prebiotic oligofructose, which has been shown to counteract excess fat mass, we explored the gut microbiota‐dependent effects of oligofructose on body composition and host metabolism. Diet‐induced obese male Sprague Dawley rats, fed a background high‐fat/sucrose diet, were randomized to one of the following diets for 6 wk: 1) high‐energy control; 2) 10% oligofructose; 3) ampicillin; 4) ampicillin + 10% oligofructose; 5) ampicillin/neomycin; or 6) ampicillin/neomycin + 10% oligofructose. Combining oligofructose with ampicillin treatment blunted the decrease in adiposity seen with oligofructose. Although ampicillin did not affect total bacteria, ampicillin impeded oligofructose‐induced increases in Bifidobacterium and Lactobacillus. In contrast, the combination of ampicillin and neomycin reduced total bacteria but did not abrogate the oligofructose‐induced decrease in adiposity. Oligofructose‐mediated effects on host adiposity and metabolic health appear to be in part dependent on the presence of specific microbial species within the gut. —Bomhof, M. R. , Paul, H. A. , Geuking, M. B. , Eller, L. K. , Reimer, R. A. Improvement in adiposity with oligofructose is modified by antibiotics in obese rats. FASEB J. 30, 2720‐2732 (2016). www.fasebj. org
A silicon based Fourier transform spectrometer base on an open-loop controlled electrothermal MEMS mirror

This paper reports a compact Fourier transform spectrometer system with a large-stroke electrothermal MEMS mirror and other optical components all integrated on a micro-machined silicon base with the dimension of 2cm×2cm. The overall size of the system is reduced dramatically from the prior work [1]. The linear optical path difference (OPD) scan range is increased to 440μm and the mirror plate tilting is compensated down to ±0.002° during the full OPD scan using a new open-loop control method. A spectral resolution of 1.1nm at 532nm is achieved.
Mycobacterium bovis BCG-induced human T-cell clones from BCG-vaccinated healthy subjects: antigen specificity and lymphokine production

A total of 121 human T-cell clones were raised from nine Mycobacterium bovis BCG-vaccinated healthy individuals. Three clones were autoreactive, 74 responded to BCG in the presence of antigen-presenting cells, and the others required in addition exogenous interleukin 2. Only one clone was CD8+ CD4-, and the rest were CD4+ CD8-. Testing with a panel of mycobacteria suggested that the clones were recognizing epitopes of varied specificity. Out of 44 clones tested, 15 were specific to BCG and Mycobacterium tuberculosis, 22 showed limited cross-reactivity, and 8 were broadly cross-reactive. None of the 22 BCG responder clones could differentiate between Danish, French, Prague, and Moreau strains of BCG. BCG and M. tuberculosis H37Rv also paralleled very closely; however, 6 of 18 BCG- and M. tuberculosis H37Rv-responding clones did not proliferate to Mycobacterium africanum. BCG- and M. tuberculosis H37Rv-specific as well as cross-reactive T-cell clones could be induced to produce interleukin 2, gamma interferon, and granulocyte-macrophage colony-stimulating factor activity.
Expression of miRNA-124a in CD4 Cells Reflects Response to a Multidisciplinary Treatment Program in Patients With Chronic Low Back Pain.

STUDY DESIGN A prospective evaluation of microRNA (miRNA) expression in patients with chronic low back pain (CLBP). OBJECTIVE The aim of this study was to evaluate whether pain- and T cell-related miRNAs are differentially expressed in CLBP when compared with healthy volunteers and whether these miRNAs may distinguish between responders and nonresponders to a multidisciplinary treatment program. SUMMARY OF BACKGROUND DATA CLBP is a common health problem worldwide. Multidisciplinary pain treatment programs have been proven as an effective treatment option. miRNAs are known to be important mediators of gene regulation in various processes, including pathophysiology of pain. The expression of miRNAs in CLBP and changes due to a multidisciplinary treatment programs are still unknown. METHODS Thirty-four patients with CLBP were enrolled (46.5 ± 12.7 yrs). CLBP was defined as low back pain with an average intensity of numerical rating scale (NRS) ≥3 during the last 4 weeks, persisting longer than 6 months, and not attributable to a recognized specific pathological condition. Expression of pain- and T cell-related miRNAs in human CD4 cells were determined using TaqMan assays and RealTime PCR. MiRNA expression in patients with CLBP was compared with the expression in healthy volunteers before a multidisciplinary treatment program started. The multidisciplinary outpatient program (4 weeks, 5 days a week, 8 h per day) is a clinically established outpatient program and comprises medical (examination, education), physical (exercise), work-related, and psychological therapy components. After the program, differentially expressed miRNAs in CLBP (before treatment) were analyzed once more. Expression of these miRNAs in patients who respond to the treatment (n = 14) was compared with those who did not respond (n = 20). Response to therapy was defined as reduction of pain of ≥50% (NRS) from baseline. RESULTS MiRNA-124a (patients: 0.79 ± 0.63 vs. healthy volunteers: 0.30 ± 0.16; P < 0.001), miRNA-150 (patients: 0.75 ± 0.21 vs. healthy volunteers: 0.56 ± 0.20; P = 0.025), and miRNA-155 (patients: 0.55 ± 0.14 vs. healthy volunteers: 0.38 ± 0.16; P = 0.017) were significantly upregulated in CLBP patients when compared with healthy volunteers. After the multidisciplinary treatment program, patients who respond to the treatment showed only an increase of miRNA-124a expression (before treatment: 0.54 ± 0.26 vs. after treatment: 1.05 ± 0.56, P = 0.007). CONCLUSION MiRNA-124a upregulation is associated with therapy response in a multidisciplinary treatment programs and might help to identify more specific and mechanism-based treatment strategies for CLBP. LEVEL OF EVIDENCE 3.
Bluejay: A Highly Scalable and Integrative Visual Environment for Genome Exploration

Many questions that biologists want to answer using the information available from completely sequenced genomes are complex. A graphical environment allows users to visually explore and operate on a sequence. Sequence and annotation data exists in bewildering varieties of types and levels of detail. The graphical environment therefore needs to adapt to this variation to provide the user the best possible visual representation of genomic data in a given context. As more and more online tools and services become available for biologists, mediating software should also be able to integrate and link to them. The Bluejay browser is a Java-based visual environment for exploring biological sequences. Uniquely, Bluejay fully integrates existing gene expression software into a genomic context. Bluejay also differentiates itself from most form-based HTML sequence browsers because it: (i) is highly scalable so that it can visualize a wide range of genomic objects ranging from a large whole genome down to individual nucleotides by using data-transformational Web services; and (ii) dynamically discovers and provides links to disparate resources such as gene annotation data (via XLinks) and semantically- described biological Web Services (via the BioMOBY protocol).
The effect of magnesium sulfate treatment on blood biochemistry and bleeding time in patients with severe preeclampsia.

OBJECTIVE The objective of this study was to observe the effects of magnesium sulfate on various blood biochemical parameters and coagulation status of patients with preeclampsia. METHODS During a period of 4 years, 50 patients with severe or mild preeclampsia progressing to severe preeclampsia were included in the cross-sectional study. Prothrombine (PT), activated limited thromboplastin time (aPTT), magnesium level, biochemistry parameters, systolic, and diastolic blood pressure (BP) were measured. These parameters were remeasured in the second hour of magnesium sulfate treatment. RESULTS After magnesium sulfate therapy; creatinine levels are decreased (p < 0.05), bleeding time is increased and serum magnesium levels are increased (p < 0.01), systolic and diastolic BP values decreased significantly (p < 0.01). PT, aPTT, platelet levels, and coagulation time did not change after treatment. CONCLUSION Magnesium sulfate infusion prolonged bleeding time in patients with severe preeclampsia. This is clinically important because it worsens the present condition and causes possible complications.
Business Confidence and International Tourism Demand: Evidence from a Global Panel of Experts

In 2003, the United Nations agency for tourism (UNWTO), established a Panel of Tourism Experts, to collect regular information on the short-term development of tourism. Experts’ opinions are since used to estimate a confidence index, which offers fairly accurate information on the current and future development of the tourism sector worldwide and by macro-regions. The significance of this instrument became evident during the 2008/2009 economic and financial crisis, when indications about the impact and duration of the crisis were scarce, but particularly relevant to a sector having experience virtually uninterrupted growth until then. As the crisis unfolded, the constant revision of key explanatory variables of tourism demand, such as GDP and inflation, jeopardized the accurateness of model-based forecasts, while soft information collected through the Panel provided accurate indications about the evolution of the crisis. This occurrence renewed interest in the value of such a simple, but effective forecasting tool (Croce, Wober et al. 2015, Croce 2016).
Antibacterial activity of wine phenolic compounds and oenological extracts against potential respiratory pathogens

Aims: To investigate the effect of seven wine phenolic compounds and six oenological phenolic extracts on the growth of pathogenic bacteria associated with respiratory diseases (Pseudomonas aeruginosa, Staphylococcus aureus, Moraxella catarrhalis, Enterococcus faecalis, Streptococcus sp Group F, Streptococcus agalactiae and Streptococcus pneumoniae).
How oxygen reacts with oxygen-tolerant respiratory [NiFe]-hydrogenases

Significance Mass spectrometry experiments with a nickel-containing respiratory hydrogenase from Escherichia coli provide conclusive proof that it catalyzes the four-electron reduction of oxygen by hydrogen, a reaction analogous to combustion. Hydrogenase-1 is a membrane-bound enzyme that oxidizes hydrogen in the periplasm to reduce respiratory-chain quinones. If oxygen is present and enters the buried active site, a package of electrons, derived from hydrogen oxidation and held in the iron–sulfur cluster relay system, transfers back to convert it cleanly to water. The enzyme thus avoids production of reactive oxygen intermediates that would otherwise cause inactivation. This study establishes the basis of the oxygen tolerance in respiratory nickel–iron hydrogenases and demonstrates biology’s unexpected use of nickel in the active site of a four-electron oxidase. An oxygen-tolerant respiratory [NiFe]-hydrogenase is proven to be a four-electron hydrogen/oxygen oxidoreductase, catalyzing the reaction 2 H2 + O2 = 2 H2O, equivalent to hydrogen combustion, over a sustained period without inactivating. At least 86% of the H2O produced by Escherichia coli hydrogenase-1 exposed to a mixture of 90% H2 and 10% O2 is accounted for by a direct four-electron pathway, whereas up to 14% arises from slower side reactions proceeding via superoxide and hydrogen peroxide. The direct pathway is assigned to O2 reduction at the [NiFe] active site, whereas the side reactions are an unavoidable consequence of the presence of low-potential relay centers that release electrons derived from H2 oxidation. The oxidase activity is too slow to be useful in removing O2 from the bacterial periplasm; instead, the four-electron reduction of molecular oxygen to harmless water ensures that the active site survives to catalyze sustained hydrogen oxidation.
Proteasome modulator 9 and depression in type 2 diabetes.

BACKGROUND The chromosome 12q24 locus is linked to bipolar disorder, depression, and type 2 diabetes (T2D). PSMD9 lies in the 12q24 locus and is linked to MODY3, T2D, T2D-nephropathy, T2D-neuropathy, retinopathy, macrovascular pathology, hypertension, and hypercholesterolemia in Italian families. Interestingly, PSMD9 gene common variants contribute to the therapeutic response to anti-depressant treatment. Further, PSMD9 is implicated in a model of prediction to susceptibility to depression. AIMS Our goal was to determine whether PSMD9 is linked to depression in 200 T2D Italian families. METHODS We characterized the Italian families' members for presence and/or absence of depression using the diagnostic criteria of DSM-IV. The phenotype was described as unknown in all cases in which the diagnosis was unclear or data were not available. We tested in the 200 Italians families for evidence of linkage of the PSMD9 single nucleotide polymorphisms (SNPs) IVS3+nt460 A > G, IVS3+nt437 T > C and E197G A > G with the depression phenotype. The non-parametric linkage analysis was performed by using the Merlin software. To rule out results due to random chance, 1000 replicates were executed. RESULTS The PSMD9 gene SNPs studied and/or any gene variants in linkage disequilibrium with them are linked to depression in our Italian families. CONCLUSIONS This is the first report of PSMD9 linkage to depression. This finding highlights the pleiotropic effects of PSMD9.
Liver expression of proteins controlling interferon‐mediated signalling as predictive factors in the response to therapy in patients with hepatitis C virus infection

Combination therapy with interferon‐alpha (IFNα) and ribavirin is the current treatment of choice for hepatitis C virus (HCV) infection. However, an important number of patients fail to respond to this therapeutic strategy. Factors determining IFN responsiveness are not well understood, and assessment of biomarkers that predict the response to IFN therapy in HCV patients is necessary. Several studies show that particular HCV proteins are able to block IFN function through interaction with important IFN‐signal mediators, such as signal transducers and activators of transcription (STATs). We performed immunostaining analysis of STATs in liver tissue from IFN‐responder vs. non‐responder HCV patients in order to compare the expression profile of these proteins between both groups. Tissue arrays of liver biopsies were used to study the expression of STAT1, STAT2, STAT5 and PIAS1 (protein inhibitor of activated STAT1). Robust and higher expression levels of STAT1, STAT2 and STAT5 in liver tissue from HCV patients were found when compared with samples from healthy donors. However, no significant differences were observed between IFN‐responder and ‐non‐responder groups, but rather increasing levels of STAT1, STAT2 and STAT5 paralleled the degree of liver injury. Importantly, PIAS1 expression in the nucleus of most hepatocytes in HCV tissue biopsy sections, particularly of non‐responder HCV patients, strongly indicated a regulatory effect on STAT1–DNA binding, likely affecting the IFN late signalling. In conclusion, our evidence indicates that intense PIAS1 nuclear staining, widely distributed in hepatocytes of infected livers, could be a good predictive factor of a defective response to IFN treatment, and a biomarker that is easily detectable by immunostaining during standard histopathological liver biopsy analysis. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Quantifying the Physician Contribution to Managed Care Pharmacy Expenses: A Random Effects Approach

Background. Despite the availability of more sophisticated techniques, few alternatives to ordinary least squares (OLS) regression have been utilized to profile physician prescribing in managed care. It is not known to what extent the modest R2 values derived from OLS models reflect incomplete risk adjustment or widely varying physician prescribing patterns. Objectives. To quantify the role of interphysician variability relative to overall variability in managed care pharmacy expenses, and to examine the extent to which different statistical approaches generate meaningful differences in profile results. Research Design. Comparison of three basic statistical modeling approaches: OLS, fixed effects regression, and random effects (ie, hierarchical) regression models. Setting. Two managed care populations that differed more than 2-fold in per member pharmacy expenditures in 1999, one from the Midwestern United States, the other from three Western States. Main Outcome Measures. The intraclass correlation coefficient (ICC, the proportion of variability in expenses attributable to differences among physicians) and the range of projected expenses attributed to each physician’s prescribing style. Results. The ICCs were small for aggregated pharmacy expenditures, 0.04 or less in both populations. As determined by OLS, the most costly physician contributed $94,399 in excess expenses to the organization whereas the most parsimonious saved $89,940. When derived from random effects models, the range in performance was 63% of that derived from OLS. Conclusions. In the populations studied, systematic prescribing differences among physicians were small relative to the overall variability in pharmacy expenses, suggesting other factors were more likely driving these costs. Random effects models generated smaller estimates of the individual physicians’ contribution to costs, sometimes considerably, relative to those derived from OLS and fixed effects approaches.
Train monitoring using GSM-R based passive radar

Train detection technologies are universal to all modern railway signal and control systems. They are essential for managing the movement of vehicles across entire transport networks, and to ensure their safe operation. In this paper we investigate the feasibility of a new train monitoring capability based on passive radar technology. The system exploits signal transmissions from the railways' GSM-Railway (GSM-R) radio communications infrastructure, and has the potential to determine the positions and velocities of trains over any section of a railway network where there is GSM-R coverage. A theoretical ambiguity function analysis on directly measured GSM-R waveforms suggest that targets can be detected with axial range resolutions of approximately 850 m, and velocities down to less than 1 mph. To demonstrate proof-of-concept, a series of experiments were carried out using a software-defined GSM-R passive radar system. The results show the first detections of trains at bistatic ranges of just over 1 km moving at various speeds. There are now hundreds of thousands of miles of railway track covered by GSM-R globally, with many more countries planning to rollout systems nationally. The results therefore imply that GSM-R based passive radar technology could be used to develop low-cost train monitoring capabilities worldwide alongside the existing GSM-R radio communications infrastructure.
The American Association for Thoracic Surgery ( AATS ) consensus guidelines : Surgical treatment of infective endocarditis : Executive summary

From the Departments of Thor Medicine, and Infectious Dise of Cardiothoracic Surgery, and of Medicine; Texas Heart Inst This work was supported by instit Clinic editorial staff. Received for publication May 9, 2 publication Sept 16, 2016. Address for reprints: G€osta B. Pett diovascular Surgery, Cleveland 44195 (E-mail: petterg@ccf.or J Thorac Cardiovasc Surg 2017;0022-5223/$36.00 Copyright 2017 by The Ameri http://dx.doi. org/10.1016/j.jtcvs. 2 €osta B. Pettersson, MD, PhD, and oseph S. Coselli, MD
Comparison of Capture Immunoglobulin M (IgM) and IgG Enzyme-Linked Immunosorbent Assay (ELISA) and Nonstructural Protein NS1 Serotype-Specific IgG ELISA for Differentiation of Primary and Secondary Dengue Virus Infections

ABSTRACT We have found that NS1 serotype-specific immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA) can be used to differentiate primary and secondary dengue virus infections. This is due to the fact that the NS1-specific IgG antibody cannot be detected before day 9 of illness for primary infection, so the NS1-specific IgG antibodies measured in acute-phase sera must come from previous infection. Comparison of NS1 serotype-specific IgG ELISA with envelope- and membrane-specific capture IgM and IgG ELISA in the differentiation of primary and secondary dengue virus infections showed good correlation (95.90% agreement). Most important, we have found that the serotype of the dengue virus from the majority of patients with primary infection could be correctly identified when convalescent-phase or postinfection sera were analyzed by NS1 serotype-specific IgG ELISA. These findings suggested that NS1 serotype-specific IgG ELISA could be reliably applied for serodiagnosis and seroepidemiological study of dengue virus infection.