Miracle-dz/UniFAR-FTUs huggingface dataset:
Induction of cytokine production in human T cells and monocytes by highly purified lipoteichoic acid: involvement of Toll-like receptors and CD14.

BACKGROUND The pro-inflammatory potential of lipoteichoic acid (LTA) from Staphylococcus aureus is controversial. The present study was undertaken to examine the ability of highly purified and characterized S. aureus LTA to stimulate the production of pro-inflammatory cytokines in human leukocytes at both mRNA and protein level, and to study the involvement of Toll-like receptors (TLRs) and CD14 in this response. MATERIAL/METHODS Purified LTA was administered to whole human blood ex-vivo (or primary adherent monocytes) and the cytokine response assessed in plasma by EIA. Cytokine mRNA was measured by RT-PCR on leukocyte subsets isolated following stimulation. To study the involvement of specific receptors for LTA signaling, CHO cells transfected with CD14 and/or TLR2, TLR4 were used, as well as antibodies directed against these receptors. RESULTS Addition of highly purified LTA to human whole blood or primary adherent human monocytes elicited a time and concentration dependent release of tumor necrosis factor alpha (TNF-alpha), interleukin-1 beta (IL-1 beta), IL-6 and IL-8. Messenger RNA encoding TNF-alpha, IL-1 beta and IL-6 seemed to be accumulated in monocytes and T cells, but not in granulocytes and B cells. Expression of TLR2, but not TLR4, in chinese hamster ovary cells conferred responsiveness to LTA. However, antibodies directed towards TLR2 (clone TL2.1) or TLR4 (clone HTA125) failed to inhibit TNF-a release induced by LTA in both the whole blood model and in adherent monocytes. In contrast, blockade of the CD14 receptor with MAb18D11 strongly attenuated the LTA induced release of TNF-alpha in both models. CONCLUSIONS We propose that (i) LTA from S. aureus triggers the release of cytokines during staphylococcal infections, and (ii) both monocytes and T cells contribute to cytokine production induced by LTA. TLR2 may mediate cellular activation by LTA, but the functional significance of this receptor during staphylococcal infections remains elusive.
Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair

Improper DNA double-strand break (DSB) repair results in complex genomic rearrangements (CGRs) in many cancers and various congenital disorders in humans. Trinucleotide repeat sequences, such as (GAA)n repeats in Friedreich's ataxia, (CTG)n repeats in myotonic dystrophy, and (CGG)n repeats in fragile X syndrome, are also subject to double-strand breaks within the repetitive tract followed by DNA repair. Mapping the outcomes of CGRs is important for understanding their causes and potential phenotypic effects. However, high-resolution mapping of CGRs has traditionally been a laborious and highly skilled process. Recent advances in long-read DNA sequencing technologies, specifically Nanopore sequencing, have made possible the rapid identification of CGRs with single base pair resolution. Here, we have used whole-genome Nanopore sequencing to characterize several CGRs that originated from naturally occurring DSBs at (GAA)n microsatellites in Saccharomyces cerevisiae. These data gave us important insights into the mechanisms of DSB repair leading to CGRs.
Performance evaluation and optimizations of hidden vector encryption

As security is an important concern, the usage of encrypted communication is increasing. As a result, techniques that allow complex operations on such data streams are of importance. Searchable encryption allows entities to evaluate predicates on encrypted data without disclosing any other information except the outcome of the operation. We focus on Hidden Vector Encryption, which allows the usage of a wide set of predicate types on cyphertext of small length. This paper presents an evaluation of this technique in order to assess its practicability. We also provide optimizations that reduce the computational requirements for each operation at the cost of extra memory usage.
The Effects of Macroprudential Policy on Borrower Leverage

This Economic Letter explores the effects of the recent macroprudential measures in the mortgage market on the leverage of Irish borrowers. Using loan-by-loan data from before and after the measures, we test how loan-to-income (LTI) and loan-to-value (LTV) ratios have changed for First Time Buyers (FTBs) and Second and Subsequent Buyers (SSBs). A number of findings emerge. The average (mean) LTV and LTI ratios increased slightly after the introduction of the regulations for both FTBs and SSBs. However, the opposite pattern is observed for high leverage borrowers. For FTBs with an LTV of 80 per cent or above, the average borrower registered a small reduction in their LTV after the regulations. This result was only present for higher income borrowers, i.e. FTBs at the lower end of the income distribution had the same average. LTV pre- and post-regulations. SSBs with an LTV of 80 per cent and above also had a lower LTV after the regulations, but the effect was more pronounced than for FTBs. Few borrowers experienced a tightening of LTIs following the measures; we find only a limited effect among high leverage SSB borrowers.
Model-based Testing Without a Model: Assessing Portability in the Seattle Testbed

Despite widespread OS, network, and hardware heterogeneity, there has been a lack of research into quantifying and improving portability of a programming environment. We have constructed a distributed testbed called Seattle built on a platform-independent programming API that is implemented on different operating systems and architectures. Our goal is to show that applications written to our API will be portable. In this work, we use an instrumented version of the programming environment for testing purposes. The instrumentation allows us to gather traces of actual program behavior from a running implementation. These traces can be used across different versions of the implementation exactly as if they were test cases generated offline from a model program, so we can commence testing using model based testing tools, without constructing a model program. Such offline testing is only effective in scenarios where traces are expected to be reproducible (deterministic). Where reproducibility is not expected, for instance due to nondeterminism in the network environment, we must resort to on-the-fly testing, which does require a model program. To validate this model program, we can use the recorded traces of actual behavior. Validating with captured traces should provide greater coverage than we could achieve by validating only with traces constructed a priori.
The Effect of China’s Pork Reserve Program on Pork Price Volatility

China introduced a systematic pork reserve program in 2009 to decrease pork price volatility. The price stabilization effectiveness of the reserve program is unknown. Two econometric procedures are used to analyze the effectiveness of the program in reducing pork price volatility. The first approach is an autoregressive conditionally heteroskedastic (ARCH) regression model estimated using monthly national average wholesale pork price data for January 2000 to July 2015. Price volatility is modeled as the difference in monthly price in consecutive months. The ARCH procedure controls for domestic production, consumer income and seasonality. A difference in difference (DD) regression procedure, compliments the ARCH procedure, to further investigate the relationship between the reserve policy and price volatility. Two DD analyses are conducted. The first analysis measures monthly price volatility in terms of absolute differences, and the second in absolute percentage change differences. Both the ARCH and DD approaches find that pork price volatility increased, not decreased, after the introduction of the reserve program.
Do the symptoms of obstructive sleep apnea syndrome exist in highly trained Malay security personnel?

OBJECTIVE Obstructive Sleep Apnea Syndrome (OSAS) has been associated with excessive daytime sleepiness, which may lead to reduced alertness. This study determines the distribution of OSAS among highly trained Malay male security personnel, an occupation that requires constant alertness. METHODS Berlin questionnaires (Malay version) were distributed and the body mass index (BMI) and neck circumference were measured. This questionnaire asked for symptoms indicative of OSAS and consists of three categories: snoring, excessive daytime sleepiness/fatigue, and the presence of obesity or hypertension. RESULTS In total, 661 respondents were involved in this study. There was a range of prevalence of the main symptoms of OSAS with 45 subjects (6.8%, 95%CI: 5.0-9.0) categorized in the high risk group for OSAS. There was no significant difference in age, but the BMI and neck circumference were significantly higher in the high risk group (p<0.001). CONCLUSION The presence of OSAS symptoms in highly trained security personnel found in this study suggests the need to screen for this syndrome in individuals involved in high risk occupations.
Long-term (4 years) efficacy of lopinavir/ritonavir monotherapy for maintenance of HIV suppression.

OBJECTIVES Data are scarce on the long-term efficacy of lopinavir/ritonavir monotherapy for the maintenance of HIV suppression. Four years of results of patients randomized to monotherapy in the Only Kaletra (OK) pilot clinical trial are presented. PATIENTS AND METHODS Twenty-one HIV-infected patients with suppressed HIV replication (<50 copies/mL) for at least 6 months and without previous failure while receiving a protease inhibitor-based regimen started lopinavir/ritonavir monotherapy. Follow-up was performed within the OK pilot clinical trial during the first 2 years and according to routine clinical practice during the 3rd and 4th years. RESULTS Fourteen patients (67%) remain on monotherapy and with RNA <50 copies/mL (intention-to-treat analysis, with missing patients scored as failures). Five patients (24%) had virological rebound and all of them were successfully re-suppressed by adding two nucleosides. No major protease inhibitor mutations were found. CONCLUSIONS Our data support the long-term efficacy and safety of lopinavir/ritonavir monotherapy for the maintenance of HIV suppression, a finding that must be confirmed in larger studies.
Collaboration in Global Governance: the un and indigenous Peoples

Global governance today is a complicated process of governmental and non-governmental bodies' interaction in order to make decisions that should be implemented all over the world. On the global level the leadership of the collaborative governance in many cases belongs to the United Nations Organization. Being criticized for its mainly governmental nature, absence of ordinary people influence on decision-making process, the UN is trying to promote collaboration with separate governmental bodies, individuals, and organizations representing different structures and levels of the global civil society. One of the most interesting examples of such collaboration is the influence and involvement of the Global Indigenous Movement (GIM) in UN activities, joint work on elaborating principles and approaches that lead to the recognition of the fact that special measures are required to protect their rights in order to help them to maintain their way of life and traditional cultures. Though the GIM is just one of several global social movements to have developed close relations to the UN it is considered to be the most successful.
Analysis of Farmers’ Willingness to Adopt Genetically Modified Insect-resistant Rice in China

Genetically modified (GM) crops, particularly GM grain crops, have been controversial since their commercialization in 1996. However, only a few studies have investigated farmers’ attitudes toward adopting GM grain crops in China. This study explores farmers’ willingness to adopt GM insect-resistant rice prior to its commercial release in China and determines the factors that affect farmers’ prospective adoption decisions. The analysis is based on data collected by using a questionnaire. The results of econometric analyses show that increasing output and income, and simplicity in crop management, have positive effects on prospective adoption, whereas the high seed price of GM rice has a significantly negative effect. Health implications also have a significantly positive effect on the farmers’ decision to adopt GM grain crops. A comparative analysis of ordered and binary probit models also demonstrates that farmers are more deliberate in their decisions when they have fewer choices.
Gendered Perceptions of Power and Decision‐Making in Rural Kenya

Development policies and programmes rest on assumptions about what constitutes power and how to change power dynamics. However, they rarely consider local understandings of power. In this article we ask how these common assumptions correspond with socially and culturally specific ideas about what power is, who can hold power, and how power can be transferred, in rural communities in Kenya's lake region. We find that men and women are constantly negotiating for power in the household, within the bounds of their gendered limitations. And the predominant zeroâ€ sum conception of power may undermine common development approaches to empowerment. However, the results also highlight some exceptions to this conceptualization, as well as the value of taking a wholeâ€ family approach to empowerment.
Optimization of SMES-FCL for Augmenting FRT Performance and Smoothing Output Power of Grid-Connected DFIG Wind Turbine

Fault-ride-through (FRT) performance and output power variation are crucial issues of the grid-connected wind turbine with the doubly fed induction generator (DFIG). To overcome these problems, the optimal parameters tuning of the superconducting magnetic energy storage and the fault-current limiter (SMES-FCL) with the common part of the superconducting coil (SC) is proposed. In addition to the alleviation of the DFIG output power, the SC behaves as the short-circuit current limiter to enhance the FRT capability. The tuning of the SC inductance and the controller parameters of converters is optimally conducted, so that the DFIG terminal voltage deviation and the power fluctuation during faults are at their minimum. By simulation study, the utilized power and energy of the SC for the grid stabilization are curtailed, whereas the dynamic performance of the SMES-FCL is higher than a single SMES unit.
Overnight Orthokeratology: Preliminary Results of the Lenses and Overnight Orthokeratology (LOOK) Study

Background. The Lenses and Overnight Orthokeratology (LOOK) study is a pilot study designed to learn the procedures of orthokeratology lens fitting in preparation for a planned larger clinical trial and to obtain data with which to calculate a sample size for that larger study. Data are presented for the first 3 months of the LOOK study. Methods. Sixty subjects were enrolled in this multicenter pilot study to evaluate the success and safety of treatment with overnight orthokeratology contact lenses. Refractive error, corneal topography, and biomicroscopic data were collected to determine the amount of refractive error change achieved, corneal changes, and a safety profile of overnight wear of reverse geometry rigid gas permeable lenses for orthokeratology. Results. Of the 60 subjects enrolled, 46 completed the 1-month visit, and 31 completed the 3-month visit. The mean change in spherical equivalent manifest refraction from baseline to the morning 3-month visit was 2.08 ± 1.11 D in the right eye and 2.16 ± 1.05 D in the left eye. At the 3-month morning visit, 74% of right eyes and 61% of left eyes had 20/20 unaided visual acuity. No corneal infiltrates or ulcers were noted in any subjects. Observations of fluorescein staining of the cornea, imprinting, and microcysts were noted in some patients at the 3-month visit. Conclusions. The preliminary results of the LOOK study indicate that improvement in unaided visual acuity can be attained for at least 6 h after lens removal. The short-term safety and efficacy of the procedure appear to be favorable; however, future studies are needed to determine the long-term outcomes of treatment.
Absence of hepatitis C virus transmission in a prospective cohort of heterosexual serodiscordant couples

Objective: To analyse hepatitis C virus (HCV) transmission in a cohort of heterosexual couples who are discordant both for HIV and for HCV. Methods: We followed an open cohort of 171 people, 152 women and 19 men, who were not initially infected by either HIV or HCV, and whose steady heterosexual partner presented antibodies to both viruses (index case). Other risk exposures were excluded. Every 6 months clinical, epidemiological, and risk behaviour information was collected, and antibodies to both viruses were determined. Results: During 529 person years of follow up more than 40 000 vaginal or anal penetrations were recorded. 74 partners (43.3%) had vaginal and/or anal intercourse without condoms with the index case; another 15.8%, who always used condoms, declared breaking or slipping episodes during intercourse; and another 22.2% had unprotected orogenital exposures. During the follow up, over 5800 unprotected vaginal and anal contacts with the index case were estimated, as well as more than 25 000 unprotected orogenital contacts. 31 women became pregnant (two were index cases), and seroconversion to HIV occurred for one woman (1.7 per 10 000 unprotected contacts; 95% CI, 0 to 9.5), but there was no seroconversion to HCV (95% CI, 0–6.3 per 10 000 unprotected contacts). Conclusion: These results are consistent with a low or null transmissibility of HCV in heterosexual relations, even when the index case is HIV co-infected.
The effect of nonsurgical periodontal treatment on the severity of drug-induced gingival overgrowth in transplant patients.

OBJECTIVE Immunosuppressive drugs may induce an increase of the gingival connective tissue in the extracellular matrix. The aim of this study was to assess the effectiveness of nonsurgical periodontal treatment in reducing gingival overgrowth (GO) in transplant patients taking cyclosporin A (CsA) or tacrolimus (Tcr). METHOD AND MATERIALS An observational cohort study employing 68 transplant patients with diagnosis of GO, 51 taking CsA and 17 in therapy with Tcr, was performed at the Periodontal Unit of the School of Dental Sciences (University of Trieste, Italy). Percentages of plaque index (PI), bleeding on probing (BoP), sites with probing depth (PD) > 3 mm, and hypertrophy index (HI) were registered at baseline, 90 days, 180 days, and at 1 year after nonsurgical periodontal therapy. Furthermore, HI at baseline and after 1 year was investigated by multiple linear regression. RESULTS Both groups have significantly improved their clinical parameters: CsA group: PIbaseline = 41.67%; PIyear = 33%; BoPbaseline = 13.88%; BoPyear = 6.94%; PD > 3 mmbaseline = 18.6%; PD > 3 mmyear = 12.96%; HIbaseline = 22%; HIyear = 10%; Tcr group: PIbaseline = 40.73%; PIyear = 38.54%; BoPbaseline = 20.78%; BoPyear = 12.5%; PD > 3 mmbaseline = 21.53%; PD > 3 mmyear = 13.19%; HIbaseline = 12%; HIyear = 6.5%. Age showed a statistical negative correlation with HI at baseline (P < .05), while PD > 3 mm was positively correlated to the baseline HI (P < .001). Only HI at baseline showed a statistically significant negative relation with HI at 1 year (P < .001). CONCLUSION After nonsurgical periodontal therapy no patients needed additional periodontal surgery. Nonsurgical periodontal treatment itself represents an efficacious therapy in transplant patients treated with CsA and Tcr.
Impact of Conformational Flexibility on Three-Dimensional Similarity Searching Using Correlation Vectors

Many three-dimensional (3D) virtual screening concepts, like automated docking or pharmacophore searching, rely on the calculation of a "bioactive" or "receptor-relevant" conformation of a molecule to assess its biological activity. We investigated the dependence of the presence of conformations near the "bioactive" conformation on three-dimensional similarity searching with pharmacophore-based correlation vectors (CATS3D approach). Cocrystal structures of 11 target classes served as queries for virtual screening of a database of annotated ligands. Different numbers of conformations were calculated. Single 3D structures were obtained using the 3D structure generator CORINA and conformational ensembles by the conformation generation program ROTATE. This approach was able to reproduce conformations for high resolution cocrystal structures. For virtual screening we found that using only the CORINA-generated single conformation already resulted in a significant enrichment of isofunctional molecules having the same biological property profile. This observation was also made for ligand classes with many rotatable bonds. Although more similar conformations were considered to be more similar in the CATS3D description, the impact of using multiple conformations on the enrichment of actives was not as high as expected. CATS3D provides an alignment-free three-dimensional virtual screening approach that is less dependent on the presence of conformations which are close to the "bioactive" conformation of a molecule compared to methods that rely on an explicit three-dimensional alignment of molecules.
An accurate coarse-grained model for chitosan polysaccharides in aqueous solution

Computational models can provide detailed information about molecular conformations and interactions in solution, which is currently inaccessible by other means in many cases. Here we describe an efficient and precise coarse-grained model for long polysaccharides in aqueous solution at different physico-chemical conditions such as pH and ionic strength. The Model is carefully constructed based on all-atom simulations of small saccharides and metadynamics sampling of the dihedral angles in the glycosidic links, which represent the most flexible degrees of freedom of the polysaccharides. The model is validated against experimental data for Chitosan molecules in solution with various degree of deacetylation, and is shown to closely reproduce the available experimental data. For long polymers, subtle differences of the free energy maps of the glycosidic links are found to significantly affect the measurable polymer properties. Therefore, for titratable monomers the free energy maps of the corresponding links are updated according to the current charge of the monomers. We then characterize the microscopic and mesoscopic structural properties of large chitosan polysaccharides in solution for a wide range of solvent pH and ionic strength, and investigate the effect of polymer length and degree and pattern of deacetylation on the polymer properties.
Early depth determination algorithm for enhancement layer intra coding of SHVC

In this paper, an improved low complexity algorithm for the scalable extension of the HEVC (SHVC) is proposed by using the information of rate-distortion cost (RD cost) of the coding unit at the co-located position in the base layer and the neighboring coding unit in the enhancement layer. The proposed algorithm in our previous work used an early determination of the depth decision by adaptively selecting an optimal threshold value on the basis of RD cost. However, the threshold value become a low accuracy value because RD cost and the coding unit depth in different resolutions depend on the quantization parameter. Therefore, the relationship of the quantization parameter in different resolutions is evaluated. Based on the evaluation results, an improved algorithm focused on the complexity reduction of the enhancement layer is proposed. The proposed algorithm is evaluated by the reference software of SHVC(SHM6.0). The simulation results show that the proposed algorithm can achieve over 48% computation complexity reduction comparing to the original SHVC algorithm.