Miracle-dz/UniFAR-FTUs huggingface dataset:
Endothelial Cell Amplification of Regulatory T Cells Is Differentially Modified by Immunosuppressors and Intravenous Immunoglobulin

Immunosuppressive treatment is a prerequisite for both organ transplantation and tolerance of the allograft. However, long-term immunosuppression has been associated with a higher incidence of malignancies and infections. Immunosuppressors mainly target circulating immune cells and little is known of their “off-target” effects, such as their impact on endothelial cells (ECs). In chronic antibody-mediated rejection (AMR), the allograft endothelium is a target of damage, histologically detected as transplant glomerulopathy, and which correlates with poor graft survival. Under inflammatory conditions, EC expression of HLA class II antigens can lead to CD4+-T lymphocyte alloactivation and selective expansion of pro-inflammatory Th17 and pro-tolerance Treg subsets. This response can be modified and preactivation of the EC by HLA-DR antibody binding promoted a proinflammatory Th17 response. However, whether or not immunosuppressors alter EC immunogenicity has not been examined. In alloimmunized patients with AMR, cyclosporine A (CsA) and mycophenolic acid (MPA) are often combined with intravenous immunoglobulins (IVIgs). This study reports changes in the microvascular EC phenotype and function after treatment with CsA, MPA, or IVIg. Both CsA and MPA decreased HLA-DR and increased CD54 expression, whereas IVIg increased HLA-DR expression. Interleukin 6 secretion was reduced by all three immunomodulators. Preincubation of ECs with CsA or MPA limited, while IVIg amplified, Treg expansion. Because CsA, MPA, and IVIg are known for their ability to act upon leukocytes, we confirmed that ECs maintained their immunoregulatory role when allogeneic leukocytes were pretreated with CsA, MPA, or IVIg. The results reveal that individual immunosuppressors, used in the induction and maintenance of renal allograft tolerance, had direct and distinct effects on ECs. Results of experiments associating IVIg with either CsA or MPA underlined the differences observed using individual immunosuppressors. Paradoxically, CsA or MPA may increase EC mediated inflammatory responses and long-term exposure may contribute to limitation of allograft tolerance. In contrast, IVIg interaction with the endothelium may mediate some of its immunosuppressive effects through promotion of Treg expansion, contributing to the maintenance of allograft tolerance.
Towards a Behavioral Public Choice: Guilt-Aversion and Accountability in the Lab

Mimicking standard features of electoral accountability and selection models, we conduct a computerized laboratory experiment in order to identify the influence of other-regarding preferences on democratic outcomes. We find that elected candidates are more pro-social towards their constituency the more favorable approval rates are. In contrast, this systematic positive relationship is not observed if the appointment is unintentionally determined by computer. These results suggest that a substantial fraction of candidates is motivated by guilt aversion. We discuss the implications of these findings for the design of democratic institutions.
Exploring difficult morning awakening in Delayed Sleep Phase Syndrome using polysomnography

Objective: Difficult morning awakening is an important symptom of delayed sleep phase syndrome (DSPS), but there is little knowledge about this phenomenon. The first aim of this study was to test the hypothesis that DSPS patients have more slow wave sleep (SWS) during the latter half of the night than what is normally observed. The second aim of the study was to examine whether the difficult awakening had any relation to a specific sleep stage upon awakening and sleep inertia. The third aim was to test if cognitive performance was reduced upon awakening.Methods: Six patients diagnosed with DSPS and four healthy controls were recruited. The subjects kept a sleep diary for 14 days and underwent actigraphy recording for seven days prior to an experimental night at the sleep laboratory where a polysomnography (PSG) recording took place. In addition, saliva samples were collected for dim light melatonin onset (DLMO) testing.Results: The PSG analysis showed that the DSPS patients do not have more SWS during the latter half of the night. In fact, the controls were observed to have more SWS than the patients during the latter half of the night. All subjects woke up from either stage Nl, N2 or REM. Two of the patients were difficult to wake up from REM sleep. No significant differences were observed between the groups regarding sleep inertia. Likewise, no significant difference was found in the patients' cognitive performance when tested in the afternoon compared to immediately after awakening.Conclusions: The most interesting finding is the difficult awakening from REM sleep in two of the patients. This yields for further investigation. As no differences were observed regarding cognitive performance, it is possible to conclude that the patients in this study did not experience any major temporary cognitive impairment upon awakening.
Bacterial etiology in acute hospitalized chronic obstructive pulmonary disease exacerbations

Introduction. The most common cause of acute COPD exacerbation (AECOPD) is the respiratory tract infections. We sought to determine the bacteriological etiology of hospitalized acute exacerbations of COPD requiring hospitalization in consecutive two years. Methods. We aimed to determine the bacteriological etiology underlying in patients whom admitted to Uludag University Faculty of Medicine, Department of Pulmonary Medicine and hospitalized with AECOPD in the last two years. Medical records of the study participants were screened retrospectively and sociodemographic characteristics, routine laboratory tests and sputum culture results were analyzed. Results. A total of 242 patients hospitalized for AECOPD were enrolled. Of these 86.4% (n=209) were male. The mean age of the group was 66.6±11 years old. Sputum cultures were available in the 45 % (n=109) of the study group. The most frequent bacteria isolated from the sputum cultures of the study group were Pseudomonas aeruginosa, Streptococcus pneumonia , Haemophilus influenzae and Acinetobacter baumanii . Length of stay was longer in patients with the A. baumanii isolate than the rest of the group ( p =0.024). Length of stay in hospital was independently associated with in-hospital mortality (OR: 1.37, 95% CI: 1.05–1.78). Isolation of A. baumanii and/or Staphylococcus aureus in sputum culture were identified as independent risk factors for prolonged length of stay in-hospital (b=0.26, p =0.008; b=15.40, p =0.003). Conclusion. Our study shows that P. aeruginosa, S. pneumonia , H. influenzae are common sputum isolates in AECOPD patients requiring hospitalization. Isolation of A. baumanii and/or S. aureus in sputum culture is associated with prolonged length of stay in hospital, which is an independent risk factor for in-hospital mortality.
Temporal Dynamics of the Saccharopolyspora erythraea Phosphoproteome*

Actinomycetes undergo a dramatic reorganization of metabolic and cellular machinery during a brief period of growth arrest (“metabolic switch”) preceding mycelia differentiation and the onset of secondary metabolite biosynthesis. This study explores the role of phosphorylation in coordinating the metabolic switch in the industrial actinomycete Saccharopolyspora erythraea. A total of 109 phosphopeptides from 88 proteins were detected across a 150-h fermentation using open-profile two-dimensional LC-MS proteomics and TiO2 enrichment. Quantitative analysis of the phosphopeptides and their unphosphorylated cognates was possible for 20 pairs that also displayed constant total protein expression. Enzymes from central carbon metabolism such as putative acetyl-coenzyme A carboxylase, isocitrate lyase, and 2-oxoglutarate dehydrogenase changed dramatically in the degree of phosphorylation during the stationary phase, suggesting metabolic rearrangement for the reutilization of substrates and the production of polyketide precursors. In addition, an enzyme involved in cellular response to environmental stress, trypsin-like serine protease (SACE_6340/NC_009142_6216), decreased in phosphorylation during the growth arrest stage. More important, enzymes related to the regulation of protein synthesis underwent rapid phosphorylation changes during this stage. Whereas the degree of phosphorylation of ribonuclease Rne/Rng (SACE_1406/NC_009142_1388) increased during the metabolic switch, that of two ribosomal proteins, S6 (SACE_7351/NC_009142_7233) and S32 (SACE_6101/NC_009142_5981), dramatically decreased during this stage of the fermentation, supporting the hypothesis that ribosome subpopulations differentially regulate translation before and after the metabolic switch. Overall, we show the great potential of phosphoproteomic studies to explain microbial physiology and specifically provide evidence of dynamic protein phosphorylation events across the developmental cycle of actinomycetes.
Automatic Geometric Processing for Very High Resolution Optical Satellite Data Based on Vector Roads and Orthophotos

In response to the increasing need for fast satellite image processing SPACE-SI developed STORM—a fully automatic image processing chain that performs all processing steps from the input optical images to web-delivered map-ready products for various sensors. This paper focuses on the automatic geometric corrections module and its adaptation to very high resolution (VHR) multispectral images. In the automatic ground control points (GCPs) extraction sub-module a two-step algorithm that utilizes vector roads as a reference layer and delivers GCPs for high resolution RapidEye images with near pixel accuracy was initially implemented. Super-fine positioning of individual GCPs onto an aerial orthophoto was introduced for VHR images. The enhanced algorithm is capable of achieving accuracy of approximately 1.5 pixels on WorldView-2 data. In the case of RapidEye images the accuracies of the physical sensor model reach sub-pixel values at independent check points. When compared to the reference national aerial orthophoto the accuracies of WorldView-2 orthoimages automatically produced with the rational function model reach near-pixel values. On a heterogeneous set of 41 RapidEye images the rate of automatic processing reached 97.6%. Image processing times remained under one hour for standard-size images of both sensor types.
Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective

With the growth of aging population all over the world, a rising incidence of Alzheimer's disease (AD) has been recently observed. In contrast to FDA-approved western drugs, herbal medicines, featured as abundant ingredients and multi-targeting, have been acknowledged with notable anti-AD effects although the mechanism of action (MOA) is unknown. Investigating the possible MOA for these herbs can not only refresh but also extend the current knowledge of AD pathogenesis. In this study, clinically tested anti-AD herbs, their ingredients as well as their corresponding target proteins were systematically reviewed together with applicable bioinformatics resources and methodologies. Based on above information and resources, we present a systematically target network analysis framework to explore the mechanism of anti-AD herb ingredients. Our results indicated that, in addition to the binding of those symptom-relieving targets as the FDA-approved drugs usually do, ingredients of anti-AD herbs also interact closely with a variety of successful therapeutic targets related to other diseases, such as inflammation, cancer and diabetes, suggesting the possible cross-talks between these complicated diseases. Furthermore, pathways of Ca(2+) equilibrium maintaining upstream of cell proliferation and inflammation were densely targeted by the anti-AD herbal ingredients with rigorous statistic evaluation. In addition to the holistic understanding of the pathogenesis of AD, the integrated network analysis on the MOA of herbal ingredients may also suggest new clues for the future disease modifying strategies.
Background Selection as Baseline for Nucleotide Variation across the Drosophila Genome

The constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites (a process called Background Selection, BGS). Population genetic studies, however, often ignore BGS effects when investigating demographic events or the presence of other types of selection. To obtain a more realistic evolutionary expectation that incorporates the unavoidable consequences of deleterious mutations, we generated high-resolution landscapes of variation across the Drosophila melanogaster genome under a BGS scenario independent of polymorphism data. We find that BGS plays a significant role in shaping levels of variation across the entire genome, including long introns and intergenic regions distant from annotated genes. We also find that a very large percentage of the observed variation in diversity across autosomes can be explained by BGS alone, up to 70% across individual chromosome arms, thus indicating that BGS predictions can be used as baseline to infer additional types of selection and demographic events. This approach allows detecting several outlier regions with signal of recent adaptive events and selective sweeps. The use of a BGS baseline, however, is particularly appropriate to investigate the presence of balancing selection and our study exposes numerous genomic regions with the predicted signature of higher polymorphism than expected when a BGS context is taken into account. Importantly, we show that these conclusions are robust to the mutation and selection parameters of the BGS model. Finally, analyses of protein evolution together with previous comparisons of genetic maps between Drosophila species, suggest temporally variable recombination landscapes and thus, local BGS effects that may differ between extant and past phases. Because genome-wide BGS and temporal changes in linkage effects can skew approaches to estimate demographic and selective events, future analyses should incorporate BGS predictions and capture local recombination variation across genomes and along lineages.
Trematodes of herons (Aves: Ciconiiformes) in the Czech Republic

SummaryA survey of 29 species of trematodes found in the Czech Republic in 530 herons of 8 species: Ardea cinerea 436 species examined (21 species of digeneas determined), A. purpurea 2 (4), Egretta alba 34 (7), E. garzetta 2 (3), Nycticorax nycticorax 28 (2), Ixobrychus minutus 19 (0), Botaurus stellaris 8 (5), Ardeola ralloides 1 (3) is presented. The species recorded for the first time in the Central Europe — Clinostomum heluans, Nephrostomum ramosum and Pygorchis affixus which has been brought from the wintering grounds in Africa, Echinochasmus militaris and Saakotrema metatestis brought by juvenile birds from breeding ground in the South Europe. Ophiosoma patagiatum and Posthodiplostomum brevicaudatum found for the first time in the Czech Republic.
Automated swimming activity monitor for examining temporal patterns of toxicant effects on individual Daphnia magna

Aquatic pollutants are often biologically active at low concentrations and impact on biota in combination with other abiotic stressors. Traditional toxicity tests may not detect these effects, and there is a need for sensitive high‐throughput methods for detecting sublethal effects. We have evaluated an automated infra‐red (IR) light‐based monitor for recording the swimming activity of Daphnia magna to establish temporal patterns of toxicant effects on an individual level. Activity was recorded for 48 h and the sensitivity of the monitor was evaluated by exposing D. magna to the reference chemicals K2Cr2O7 at 15, 20 and 25 °C and 2,4‐dichlorophenol at 20 °C. Significant effects (P < 0.001) of toxicant concentrations, exposure time and incubation temperatures were observed. At 15 °C, the swimming activity remained unchanged for 48 h at sublethal concentrations of K2Cr2O7 whereas activity at 20 and 25 °C was more biphasic with decreases in activity occurring after 12–18 h. A similar biphasic pattern was observed after 2,4‐dichlorophenol exposure at 20 °C. EC50 values for 2,4‐dichlorophenol and K2Cr2O7 determined from automated recording of swimming activity showed increasing toxicity with time corresponding to decreases in EC50 of 0.03–0.07 mg l–1 h–1. EC50 values determined after 48 h were comparable or lower than EC50 values based on visual inspection according to ISO 6341. The results demonstrated that the swimming activity monitor is capable of detecting sublethal behavioural effects that are toxicant and temperature dependent. The method allows EC values to be established at different time points and can serve as a high‐throughput screening tool in toxicity testing. Copyright © 2015 John Wiley & Sons, Ltd.
High-density lipoprotein cholesterol and ischemic stroke in the elderly: the Northern Manhattan Stroke Study.

CONTEXT Elevated high-density lipoprotein cholesterol (HDL-C) levels have been shown to be protective against cardiovascular disease. However, the association of specific lipoprotein classes and ischemic stroke has not been well defined, particularly in higher-risk minority populations. OBJECTIVE To evaluate the association between HDL-C and ischemic stroke in an elderly, racially or ethnically diverse population. DESIGN Population-based, incident case-control study conducted July 1993 through June 1997. SETTING A multiethnic community in northern Manhattan, New York, NY. PARTICIPANTS Cases (n = 539) of first ischemic stroke (67% aged >/=65 years; 55% women; 53% Hispanic, 28% black, and 19% white) were enrolled and matched by age, sex, and race or ethnicity to stroke-free community residents (controls; n = 905). MAIN OUTCOME MEASURE Independent association of fasting HDL-C levels, determined at enrollment, with ischemic stroke, including atherosclerotic and nonatherosclerotic ischemic stroke subtypes. RESULTS After risk factor adjustment, a protective effect was observed for HDL-C levels of at least 35 mg/dL (0.91 mmol/L) (odds ratio [OR], 0.53; 95% confidence interval [CI], 0.39-0.72). A dose-response relationship was observed (OR, 0.65; 95% CI, 0.47-0.90 and OR, 0.31; 95% CI, 0.21-0.46) for HDL-C levels of 35 to 49 mg/dL (0.91-1.28 mmol/L) and at least 50 mg/dL (1.29 mmol/L), respectively. The protective effect of a higher HDL-C level was significant among participants aged 75 years or older (OR, 0.51; 95% CI, 0.27-0.94), was more potent for the atherosclerotic stroke subtype (OR, 0.20; 95% CI, 0.08-0.50), and was present in all 3 racial or ethnic groups studied. CONCLUSIONS Increased HDL-C levels are associated with reduced risk of ischemic stroke in the elderly and among different racial or ethnic groups. These data add to the evidence relating lipids to stroke and support HDL-C as an important modifiable stroke risk factor.
Facial Electromyogram and Heart-Rate Correlates of a Paradoxical Attitude Change to Antinuclear War Information

The effects of film images versus film descriptions of the effects of nuclear explosions (versus a no-film control) on corrugator muscle tension, heart rate, attitude and mood were investigated. The last 5 min. of the images were associated with more corrugator tension for that condition when compared to the last 5 min. of the description condition. The groups did not differ in heart rate but women in both groups showed an increase in heart rate whereas men in both groups showed a decrease in heart rate. Film groups did not differ in their significant increases in anxiety, hostility, and depression on the Multiple Adjective Affect Checklist. On the pretest there was no significant correlation between scores on Betts' Questionnaire Upon Mental Imagery and scores on Goldenring and Doctor's index of concern for nuclear war. The vivid-image film group showed a decrease in concern for nuclear war when compared to the descriptive film group and the no-film control.
What do computer science students think about software piracy?

Today, software piracy is an issue of global importance. Computer science students are the future information and communication technologies professionals and it is important to study the way they approach this issue. In this article, we attempt to study attitudes, behaviours and the corresponding reasoning of computer science students in Greece regarding software piracy. The statements taken in 56 semi-structured interviews with students indicate that computer science students in Greece make intensive use of pirated software, mention as main reason for their practice the cost of genuine software, and blame the academic environment, coincidental stereotypes and their student status for this behaviour. They acknowledge the immoral character of their actions, as well as the fact that others are affected by software piracy, but they pay little attention to this action and they practically don't care. While keeping distance from software development companies, when specifically asked, they easily adopt the role of a software developer and attempt to substantiate their current and eventually future attitude out of hand. They consider software copyright laws to be inapplicable and unrealistic and fail to argue against intellectual property rights for mere digital products, such as software.
Infrared properties of chemical-vapor deposition polycrystalline diamond windows.

Low-resolution transmittance and reflectance spectra of high-quality chemical-vapor deposition (CVD) diamond windows were measured in the infrared in the 2.5-500-mum wavelength range (20-4000 cm(-1)). High-resolution measurements on a window with nearly parallel surfaces show well defined interference fringes at low frequencies. By standard procedures the optical constants n and k of CVD diamond were determined, for the first time to the author's knowledge, in the far-infrared region. It is shown that a window with a large wedge angle, close to 1 degrees , does not produce appreciable interference fringes. Modeling of these results confirms that interference fringes can be avoided by use of properly wedged CVD diamond windows. This result is of considerable relevance to the use of CVD diamond windows in spectroscopic applications for which fringe suppression is a major requirement.