Miracle-dz/UniFAR-FTUs huggingface dataset:
Pro-inflammatory Cytokines Alter the Immunopeptidome Landscape by Modulation of HLA-B Expression

Antigen presentation on HLA molecules is a major mechanism by which the immune system monitors self and non-self-recognition. Importantly, HLA-I presentation has gained much attention through its role in eliciting anti-tumor immunity. Several determinants controlling the peptides presented on HLA have been uncovered, mainly through the study of model substrates and large-scale immunopeptidome analyses. These determinants include the relative abundances of proteins in the cell, the stability or turnover rate of these proteins and the binding affinities of a given peptide to the HLA haplotypes found in a cell. However, the regulatory principles involved in selection and regulation of specific antigens in response to tumor pro-inflammatory signals remain largely unknown. Here, we chose to examine the effect that TNFα and IFNγ stimulation may exert on the immunopeptidome landscape of lung cancer cells. We show that the expression of many of the proteins involved in the class I antigen presentation pathway are changed by pro-inflammatory cytokines. Further, we could show that increased expression of the HLA-B allomorph drives a significant change in HLA-bound antigens, independently of the significant changes observed in the cellular proteome. Finally, we observed increased HLA-B levels in correlation with tumor infiltration across the TCGA lung cancer cohorts. Taken together, our results suggest that the immunopeptidome landscape should be examined in the context of anti-tumor immunity whereby signals in the microenvironment may be critical in shaping and modulating this important aspect of host-tumor interactions.
Adherence and Utilisation Accepting the unacceptable : Medication adherence and different types of action patterns among patients with high blood pressure

Objective: To gain deep insight into what it means for patients to live with drug-treated hypertension and to understand the implications for the doctors’ influence on patients’ adherence. Methods: Group discussions with 43 drug-treated hypertensive patients. Documentary method was used for interpretative analysis. Results: Four basic phenomena were identified (fear, ignorance, reluctance to discuss matters with the doctor, impact of illness experiences), which resulted in different types of action patterns: (1) the assertive actor, (2) the unconscious avoider, and (3) the inconsistent actor. The types of action patterns do not refer to any implications for adherence. The patients’ action does not indicate their preferred model of doctor–patient interaction or their acceptance of taking medication. Conclusion: Adherence must not be seen as meaningless behaviour, which can simply be learned, but rather as the result of subjective experiences on living with hypertension and the ability to accept the diagnosis and its treatment. Practice implications: It is premature to initiate therapy straight after the diagnosis, before the patient is prepared to take the tablets. Supporting adherence means to stay in dialogue and to give the time, privacy and patience to enable patients to overcome their inhibitions of asking and to accept the therapy. 2011 Elsevier Ireland Ltd. All rights reserved.
Does Measurement Error Bias Fixed‐effects Estimates of the Union Wage Effect?

This paper compares estimates of the union wage effect using cross-section and panel estimators for male manual full-time and female employees using data from the British Household Panel Survey, 1991-97. A comparison of cross-section and panel estimates suggests that unobserved heterogeneity biases cross-section estimates upwards. However, it is also found that the divergence between estimates is overstated because measurement error biases the fixed-effects estimates downward. Reducing measurement error in the union variable by taking averages and restricting changes in union status to occur only when a change in employer and/or job takes place increases fixed-effects estimates of the union wage effect. Copyright 2001 by Blackwell Publishing Ltd
Mathematik in den Naturwissenschaften Leipzig Duality symmetry of the p-form effective action and super trace of the twisted de Rham complex by

We consider quantum p-form fields interacting with a background dilaton. We calculate the variation with respect to the dilaton of a difference of the effective actions in the models related by a duality transformation. We show that this variation is defined essentially by the supertrace of the twisted de Rham complex. The supertrace is then evaluated on a manifold of an arbitrary dimension, with or without boundary.
Trichostatin A Ameliorates Spatial Memory Deficits and Suppresses Hippocampal Pro- Inflammatory Cytokines in A Rat Model of Prenatal Stress

Introduction: Maternal stress during pregnancy leads to neuroinflammation of the fetus and cognitive disorders in children. On the other side, Trichostatin A (TSA) as a histone deacetylase inhibitor has antiinflammatory and neuroprotective effects. The aim of the present study was an evaluation of TSA effect on amelioration of spatial memory deficit and modification of pro-inflammatory cytokines in rat’s hippocampus of prenatal footshock stress model. Methods: In the present study, 24 pregnant Wistar rats were divided into 4 groups including control, PFS+Saline, PFS+TSA5, and PFS+TSA10. In order to induce prenatal footshock stress (PFS), the pregnant rats were subjected to electrical shock at 1 mA, 50 Hz for 2 seconds with 5 repetitions at 3-minute intervals from 12 to 18 days of pregnancy. Two hours before applying the shock intraperitoneal administration of TSA was performed daily. When the offsprings were one-month old, their spatial memory was assessed by the Morris water maze. Finally, the levels of pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6) were measured by ELISA method. Results: a reduction in spatial memory and an increase in the level of TNFα, IL-1β, and IL-6 were observed in PFS+Saline group compared to the control. Besides, spatial learning showed a significant increase in TSAtreated groups compared to PFS+Saline. Conclusion: TSA with anti-inflammatory effects led to the reduction of hippocampal inflammatory cytokines and amelioration of spatial memory in offsprings who were exposed to stress in the prenatal period.
Edge rotation and temperature diagnostic on the National Spherical Torus Experiment

A new diagnostic for the National Spherical Torus Experiment is described whose function is to measure ion rotation and temperature at the plasma edge. The diagnostic is sensitive to C III, C IV, and He II intrinsic emission, covering a radial region of 15 cm at the extreme edge of the outboard midplane. Thirteen chords are distributed between toroidal and poloidal views, allowing the toroidal and poloidal rotation and temperature of the plasma edge to be simultaneously measured with 10 ms resolution. Combined with the local pressure gradient and EFIT reconstructed magnetic field profile, the edge flow gives a measure of the local radial electric field.
PROPOSING AN EFFICIENT INDICATOR OF GRAZER DISTRIBUTION ON HETEROGENEOUS HILL VEGETATION

Irish and UK uplands and peatlands are of international importance but are under threat from several factors, including heavy grazing pressure. Sheep preferentially graze patches of acid grassland with short dense swards, sometimes referred to as ‘grazing lawns’, and have been implicated in damage to uplands. The aim of this study was to increase our understanding of resource selection by grazers to further inform the design and implementation of conservation strategies. Grazing lawn frequency and habitat condition were mapped and GPS collars were used to track Scottish Blackface sheep on a hill farm in Ireland. Weighted compositional analysis (multivariate analysis of variance) was used to test for random use of different categories of grazing lawn frequency and habitat condition. Grazing lawn frequency was spatially uneven and habitat condition ranged from undamaged to very severely damaged areas. Typically, selection of differing categories of habitat condition was not significant (P>0.05), although the highest selection rank was consistently for the ‘moderate-undamaged’ category. Sheep most selected 1 ha grid squares containing numerous/extensive grazing lawns (P<0.05) day, night and yearround. As a simple, efficient indicator of hill use by sheep, which would be a valuable input in models predicting grazing impact on hill vegetation, the mapping of grazing lawn frequency is suggested.
Fighting Pathogenic Bacteria on Two Fronts: Phages and Antibiotics as Combined Strategy

With the emerging threat of infections caused by multidrug resistant bacteria, phages have been reconsidered as an alternative for treating infections caused by tenacious pathogens. However, instead of replacing antibiotics, the combination of both types of antimicrobials can be superior over the use of single agents. Enhanced bacterial suppression, more efficient penetration into biofilms, and lowered chances for the emergence of phage resistance are the likely advantages of the combined strategy. While a number of studies have provided experimental evidence in support of this concept, negative interference between phages and antibiotics have been reported as well. Neutral effects have also been observed, but in those cases, combined approaches may still be important for at least hampering the development of resistance. In any case, the choice of phage type and antibiotic as well as their mixing ratios must be given careful consideration when deciding for a dual antibacterial approach. The most frequently tested bacterium for a combined antibacterial treatment has been Pseudomonas aeruginosa, but encouraging results have also been reported for Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Enterococcus faecalis, and Burkholderia cepacia. Given the immense play area of conceivable phage-antibiotic combinations and their potential excess value, it is time to recapitulate of what has been achieved so far. This review therefore gathers and compares the results from most relevant studies in order to help researchers and clinicians in their strategies to combat multidrug resistant bacteria. Special attention is given to the selected bacterial model organisms, the phage families and genera employed, and the experimental design and evaluation (e.g., in vitro vs. in vivo models, biofilm vs. planktonic culture experiments, order and frequency of administration etc.). The presented data may serve as a framework for directed further experimental approaches to ultimately achieve a resolute challenge of multidrug resistant bacteria based on traditional antibiotics and phages.
Organizational Culture from an Internal and External Stakeholders’ Perspective

A culture change within an organization may be of importance in this turbulent world. An assessment of the current and desired cultural profiles can help estimate as to whether any changes are required. In this study the organizational culture of a housing association was examined from both the staff’s and external stakeholders’ perspectives. How does the current culture compare with the desired culture? Do the external stakeholders perceive the organization’s culture in a similar way? Do the staff’s and external stakeholders’ perceptions coincide with the organization’s intended image? The results demonstrate that the external stakeholders’ perceptions of the organizational culture in this case study are similar to those of the organization’s staff. The organization’s strategy, however, does not correspond to the perceived organizational culture.
Non-suicidal self-harm amongst incarcerated men: a qualitative study

Purpose The purpose of this paper is to understand the needs and motivations of incarcerated men who self-harm with no apparent suicidal intent. These have received little attention in research and policy, despite men accounting for a high and increasing proportion of self-harm in prisons. Design/methodology/approach Semi-structured interviews were conducted with 20 adult male prisoners with a recent history or thoughts of non-suicidal self-harm. The interviews were analysed drawing on principles of thematic analysis and discourse analysis. Findings Against a backdrop of early traumatic experiences and more recent adverse events (including prison-related ones), self-harm was described by many as a desperate – but meaningful – coping strategy; both a means of releasing tension, sadness and frustration, and of being heard in an unresponsive system. Originality/value These findings echo those of research conducted with women (including women prisoners) who self-harm, but challenge some of the more negative ways in which non-suicidal male prisoner self-harm has been portrayed in the (scant) previous literature. As well as pointing to the need for greater awareness of the complex needs of men in prisons, they underscore the importance of (also) exploring – and perhaps addressing – the issue of self-harm separately from suicide, and of striving to make prisons, as well as prisoners, “healthier” and better able to cope with pressure.
Effects of in Ovo Infusion of Probiotic Strains on Performance Parameters, Jejunal Bacterial Population and Mucin Gene Expression in Broiler Chicken

ABSTRACT The objective of the present study was to evaluate the effects of in ovo infusion of probiotic strains ( Bacillus subtilis, Enterococcus faecium, and Pediococcus acidilactici ) on jejunal microbial population and mucin gene expression in broiler chicken. In a completely randomized design, 0.5 ml of mediums containing 10 7 cfu of different probiotic strains, was administered into amniotic fluid of the 480 Cobb fetus (day 18 of incubation), with four treatments, five replicates with twenty four eggs each. For mucin gene expression, samples from the jejunum were taken on day 21 of incubation and day 3 post-hatch. Microbial profile was determined for total lactobacillus and E. coli by sampling jejunal contents on days 1 and 3 of age. Expression of the mucin gene in the jejunum was higher (p 0.05). There were no significant differences among treatments for performance parameters at different periods and the whole period. It was concluded that infusion of probiotic bacteria during the late of incubation has no effect on feed intake, gain and feed conversion ratio, but has a positive effect on mucin gene expression in the jejunum. The best probiotic strain for mucin gene expression was
Robust covariance matrix estimation and multivariate outlier detection

A severe limitation for the application of robust position and scale estimators having a high breakdown point is a consequence of their high computational cost. In this paper we present and analyze several inexpensive robust estimators for the co variance matrix, based on information obtained from projections onto certain sets of directions. The properties of these estimators (breakdown point, computational cost, bias) are analyzed and compared with those of the Stahel-Donoho estimator, through simulation studies. These studies show a clear improvement both on the computational requirements and the bias properties of the Stahel-Donoho estimator. The same ideas are also applied to the construction of procedures to detect outliers in multivariate samples. Their performance is analyzed by applying them to a set of test cases.
Characterization of Methanobrevibacter arboriphilicus SA Isolated from a Paddy Field Soil and DNA-DNA Hybridization among M. arboriphilicus strains

We isolated a methanogenic strain, designated strain SA (= DSM 7056), from an enrichment culture inoculated with a Japanese paddy field soil. Cells of this strain were strictly anaerobic, nonmotile, short rods and stained gram positive. The strain was able to use H2-CO2or formate as a methanogenic substrate. It required vitamins, but not acetate, for growth. Growth was fastest at 35 to 40°C. Methane was produced most rapidly at pH 6.0 to 7.5. The cellular lipid composition of strain SA was similar to that of M. arboriphilicus A2 (= DSM 2462). The G+C content of the DNA was 26.4 mol%. Strain SA had DNA-DNA hybridization values of more than 70% with M. arboriphilicus DH1T(= DSM 1125T). On the basis of phenotypic and genotypic characteristics, we identified strain SA as M. arboriphilicus. In the course of our identification work, the genetic heterogeneity of M. arboriphilicus was revealed by the results of DNA-DNA hybridization experiments. Although strain AZ (= DSM 744) should be classified as a member of a species distinct from the species containing the other four strains studied (DH1T, A2, DC [= DSM 1536], and SA), further phenotypic characterization will be required before a new species can be proposed.
Working with Orthopedic Oncologists: When to Offer Immediate and when and why to Delay Definitive Reconstruction of an Extremity

A review of patients that were treated jointly by the plastic and the orthopedic surgery teams from 2011 to 2015 to evaluate the timing of definitive reconstruction of extremity defects was undertaken. The cohort consists of 81 patients, of which 4 presented with either a high-risk lesion or an advanced squamous cell carcinoma and of which the remaining 77 patients presented with different types of extremity sarcomas. In 58 cases, immediate-definitive reconstruction was performed, while in 23 cases the definitive procedure was delayed. Immediate definitive reconstruction, concurrent with ablative procedures, was offered whenever possible. In 16 cases, delayed reconstruction was due to diagnostic uncertainty (uncertain diagnosis per se or non-established negative margins). In 6 cases, delayed reconstruction was performed because of infection, in 1 case a bleeding disorder necessitated workup and in another, the intraoperative histology necessitated a plan-change, wound temporization and preparation of an arteriovenous fistula for microsurgical reconstruction. Indications for delayed reconstruction can be related to systemic conditions, donor or recipient site issues (infection, suspicion of margin-problems or tumor “not in continuity”). Although frozen sections have an overall diagnostic accuracy of 90%, changes in management were related to the inadequacy of frozen material, sampling errors resulting from heterogeneity or non-appositional growth of malignancy. A high rate (28%) of delayed reconstruction corresponds with new data reaffirming an old paradigm (radically excised margins “make a difference”), and with objectives dictated by customized, personalized, multimodal approaches. Wound temporization was offered whenever definitive reconstruction couldn’t be performed immediately. Limb sparing, with the utilization of temporary spacers or distractors, mega-prostheses, or trials of re-implanting formerly tumorous bone autografts, which have been sterilized to eliminate malignant cells – may all necessitate temporary coverage or staged repair. Authors’ clinical experience was evaluated in the context whether the rationale behind immediate versus delayed reconstruction was optimal.
Automata-Guided Hierarchical Reinforcement Learning for Skill Composition

Skills learned through (deep) reinforcement learning often generalizes poorly across domains and re-training is necessary when presented with a new task. We present a framework that combines techniques in \textit{formal methods} with \textit{reinforcement learning} (RL). The methods we provide allows for convenient specification of tasks with logical expressions, learns hierarchical policies (meta-controller and low-level controllers) with well-defined intrinsic rewards, and construct new skills from existing ones with little to no additional exploration. We evaluate the proposed methods in a simple grid world simulation as well as a more complicated kitchen environment in AI2Thor
RADIOPROTECTIVE ACTIVITY OF FICUS RACEMOSA ETHANOL EXTRACT AGAINST ELECTRON BEAM INDUCED DNA DAMAGE IN VITRO, IN VIVO AND IN SILICO

Objective: To investigate the radioprotective effect of Ficus racemosa (Fr) ethanol stem bark extract against electron beam radiation (EBR) induced DNA damage using in vitro, in vivo and in silico models. Methods: The extract of Fr was tested against radiation induced DNA damage by exposing pBR322 plasmid to different EBR dose rates. Comet assay was conducted using mice which were exposed at 6Gy EBR. In silico study was performed by inhibiting p53 protein C-chain (1TUP C) using phyto chemicals of Fr. Results: The in vitro results revealed that, Fr at lower concentration (50µg) showed inhibitory effect on radiation induced DNA damage compared with control. Exposure of mice to 6Gy EBR increased comet parameters like TL (Tail length), OTM (Olive tail moment) and %T (percentage of DNA in the tail) of blood lymphocytes. Fr ethanol extract given orally prior to irradiation at a dose of 400 mg/kg body weight protected the DNA from the radiation damage. The phytochemicals of Fr showed clear interaction with p53 protein chain C, specifically binding to Arginine 248 (ARG248) and Arginine 273 (ARG273) amino acid residues thereby inhibiting the p53 protein-DNA interaction upon radiation. Conclusion: The present study indicates that Fr ethanol extract significantly reduced radiation induced DNA damage in vivo and in vitro. It also showed that the biologically active compounds of Fr have ability to inhibit wild p53 protein which is responsible for apoptosis; these compounds can be used as radioprotectors during chemotherapy to protect normal tissues surrounding cancerous tissue. Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:. 0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}
Bayesian Stochastic Blockmodeling

This chapter provides a self-contained introduction to the use of Bayesian inference to extract large-scale modular structures from network data, based on the stochastic blockmodel (SBM), as well as its degree-corrected and overlapping generalizations. We focus on nonparametric formulations that allow their inference in a manner that prevents overfitting, and enables model selection. We discuss aspects of the choice of priors, in particular how to avoid underfitting via increased Bayesian hierarchies, and we contrast the task of sampling network partitions from the posterior distribution with finding the single point estimate that maximizes it, while describing efficient algorithms to perform either one. We also show how inferring the SBM can be used to predict missing and spurious links, and shed light on the fundamental limitations of the detectability of modular structures in networks.