Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a FPGA based RF Control System for the S-DALINAC

The Superconducting DArmstadt electron LINear ACcelerator S-DALINAC has a maximum energy of 130 MeV and beam currents of up to 60 µA. To reach this energy conveniently in cw superconducting cavities with a high Q at a frequency of 3 GHz are used. In order to achieve a minimum energy spread, the amplitude and phase of the cavities have to be controlled strictly in order to compensate the impact of microphonic perturbations. The existing analogue RF control system based on a self exited loop, converts the 3 GHz signals down to the base band. This concept will also be followed by the new digital system currently under design. It is based on a FPGA in the low frequency part, giving a great flexibility in the control algorithm and providing additional diagnostics. The low level RF system is controlled via CAN bus. We will report on the design concept, the status and the latest results measured with a prototype.
Stress Response Protein BolA Influences Fitness and Promotes Salmonella enterica Serovar Typhimurium Virulence

ABSTRACT The intracellular pathogen Salmonella enterica serovar Typhimurium has emerged as a major cause of foodborne illness, representing a severe clinical and economic concern worldwide. The capacity of this pathogen to efficiently infect and survive inside the host depends on its ability to synchronize a complex network of virulence mechanisms. Therefore, the identification of new virulence determinants has become of paramount importance in the search of new targets for drug development. BolA-like proteins are widely conserved in all kingdoms of life. In Escherichia coli, this transcription factor has a critical regulatory role in several mechanisms that are tightly related to bacterial virulence. Therefore, in the present work we used the well-established infection model Galleria mellonella to evaluate the role of BolA protein in S. Typhimurium virulence. We have shown that BolA is an important player in S. Typhimurium pathogenesis. Specifically, the absence of BolA leads to a defective virulence capacity that is most likely related to the remarkable effect of this protein on S. Typhimurium evasion of the cellular response. Furthermore, it was demonstrated that BolA has a critical role in bacterial survival under harsh conditions since BolA conferred protection against acidic and oxidative stress. Hence, we provide evidence that BolA is a determining factor in the ability of Salmonella to survive and overcome host defense mechanisms, and this is an important step in progress to an understanding of the pathways underlying bacterial virulence. IMPORTANCE BolA has been described as an important protein for survival in the late stages of bacterial growth and under harsh environmental conditions. High levels of BolA in stationary phase and under stresses have been connected with a plethora of phenotypes, strongly suggesting its important role as a master regulator. Here, we show that BolA is a determining factor in the ability of Salmonella to survive and overcome host defense mechanisms, and this is an important step in progress to an understanding of the pathways underlying bacterial virulence. This work constitutes a relevant step toward an understanding of the role of BolA protein and may have an important impact on future studies in other organisms. Therefore, this study is of utmost importance for understanding the genetic and molecular bases involved in the regulation of Salmonella virulence and may contribute to future industrial and public health care applications.
Inverse Reinforcement Learning via Deep Gaussian Process

We propose a new approach to inverse reinforcement learning (IRL) based on the deep Gaussian process (deep GP) model, which is capable of learning complicated reward structures with few demonstrations. Our model stacks multiple latent GP layers to learn abstract representations of the state feature space, which is linked to the demonstrations through the Maximum Entropy learning framework. Incorporating the IRL engine into the nonlinear latent structure renders existing deep GP inference approaches intractable. To tackle this, we develop a non-standard variational approximation framework which extends previous inference schemes. This allows for approximate Bayesian treatment of the feature space and guards against overfitting. Carrying out representation and inverse reinforcement learning simultaneously within our model outperforms state-of-the-art approaches, as we demonstrate with experiments on standard benchmarks ("object world","highway driving") and a new benchmark ("binary world").
Usability Evaluation of Domain-Specific Languages

Domain-Specific Languages (DSLs) are claimed to bring important productivity improvements to developers, when compared to General-Purpose Languages (GPLs). The increased Usability is regarded as one of the key benefits of DSLs when compared to GPLs, and has an important impact on the achieved productivity of the DSL users. So, it is essential to build in good usability while developing the DSL. The purpose of this proposal is to contribute to the systematic activity of Software Language Engineering by focusing on the issue of the Usability evaluation of DSLs. Usability evaluation is often skipped, relaxed, or at least omitted from papers reporting development of DSLs. We argue that a systematic approach based on User Interface experimental validation techniques should be used to assess the impact of new DSLs. For that purpose, we propose to merge common Usability evaluation processes with the DSL development process. In order to provide reliable metrics and tools we should reuse and identify good practices that exist in Human-Computer Interaction community.
Neuropsychological performance in solvent-exposed vehicle collision repair workers in New Zealand

Objectives To assess whether contemporary solvent exposures in the vehicle collision repair industry are associated with objectively measured neuropsychological performance in collision repair workers. Methods The RBANS battery and additional tests were administered to 47 vehicle collision repair and 51 comparison workers randomly selected from a previous questionnaire study. Results Collision repair workers performed lower on tests of attention (digit span backwards: -1.5, 95% CI -2.4, -0.5; digit span total: -1.7, CI -3.3, -0.0; coding: -6.1, CI -9.9, -2.8; total attention scale: -9.3, CI -15.9, -2.8) and the RBANS total scale (-5.1, CI -9.1, -1.2). Additional tests also showed deficits in visual attention and reaction time (Trails B: -11.5, CI -22.4, -0.5) and motor speed/dexterity (coin rotation dominant hand & non-dominant: -2.9, CI -5.3, -0.4 and -3.1, CI -5.6, -0.7 respectively). The strongest associations were observed in panel beaters. Applying dichotomised RBANS outcomes based on the lowest percentile scores of a normative comparison group showed strongly increased risks for attention (5th percentile: OR 20.1, 95% CI 1.5, 263.3; 10th percentile: 8.8, CI 1.7, 46.2; and 20th percentile: 5.1, CI 1.5, 17.6, respectively). Those employed in the industry for ≤ 17 years (the median work duration) generally had lower scores in the attention domain scale and RBANS total scale compared to those employed >17 years suggesting a healthy worker survivor bias, but trends were inconsistent for other domains. Conclusions This study has found significant deficits in cognitive performance in collision repair workers despite low current airborne exposures in New Zealand.
Alterations in Brain Structure and Functional Connectivity in Alcohol Dependent Patients and Possible Association with Impulsivity

Background Previous studies have documented that heightened impulsivity likely contributes to the development and maintenance of alcohol use disorders. However, there is still a lack of studies that comprehensively detected the brain changes associated with abnormal impulsivity in alcohol addicts. This study was designed to investigate the alterations in brain structure and functional connectivity associated with abnormal impulsivity in alcohol dependent patients. Methods Brain structural and functional magnetic resonance imaging data as well as impulsive behavior data were collected from 20 alcohol dependent patients and 20 age- and sex-matched healthy controls respectively. Voxel-based morphometry was used to investigate the differences of grey matter volume, and tract-based spatial statistics was used to detect abnormal white matter regions between alcohol dependent patients and healthy controls. The alterations in resting-state functional connectivity in alcohol dependent patients were examined using selected brain areas with gray matter deficits as seed regions. Results Compared with healthy controls, alcohol dependent patients had significantly reduced gray matter volume in the mesocorticolimbic system including the dorsal posterior cingulate cortex, the dorsal anterior cingulate cortex, the medial prefrontal cortex, the orbitofrontal cortex and the putamen, decreased fractional anisotropy in the regions connecting the damaged grey matter areas driven by higher radial diffusivity value in the same areas and decreased resting-state functional connectivity within the reward network. Moreover, the gray matter volume of the left medial prefrontal cortex exhibited negative correlations with various impulse indices. Conclusions These findings suggest that chronic alcohol dependence could cause a complex neural changes linked to abnormal impulsivity.
THE SPECIATION HISTORY OF THE PHYSCOMITRIUM—PHYSCOMITRELLA SPECIES COMPLEX

A central problem in evolutionary biology is identifying factors that promote the evolution of reproductive isolation. Among mosses, biogeographic evidence indicates that the potential for migration is great, suggesting that biological factors other than geographic isolation may be critical for speciation in this group. The moss Physcomitrella patens (Funariaceae) has long been used as a model for interspecies hybridization and has recently emerged as an important model system for comparative genomics. We report genealogical analyses of six loci from several populations of P. patens and related species in the genus Physcomitrium. These results unambiguously indicate that the so‐called genus Physcomitrella arose at least three times from distinct ancestors within the genus Physcomitrium. In spite of the evidence for natural hybridization in the Physcomitrella–Physcomitrium complex, genealogical and experimental hybridization data indicate that the taxonomically defined species are reproductively isolated. However, these analyses suggest that Physcomitrium eurystomum was formed from a hybridization event between two early diverging lineages in the complex, and that the ancestral population size of these lineages was much smaller than the current population sizes. We discuss these findings in the context of the inferred mating system in the Physcomitrella–Physcomitrium complex and patterns of speciation and diversification.
Unrealized Global Temperature Increase: Implications of Current Uncertainties

Unrealized increase in global mean surface air temperature (GMST) may result from the climate system not being in steady state with forcings and/or from cessation of negative aerosol forcing that would result from decreases in emissions. An observation‐constrained method is applied to infer the dependence of Earth's climate sensitivity on forcing by anthropogenic aerosols within the uncertainty on that forcing given by the Fifth (2013) Assessment Report of the Intergovernmental Panel on Climate Change. Within these uncertainty ranges the increase in GMST due to temperature lag for future forcings held constant is slight (0.09–0.19 K over 20 years; 0.12–0.26 K over 100 years). However, the incremental increase in GMST that would result from a hypothetical abrupt cessation of sources of aerosols could be quite large but is highly uncertain, 0.1–1.3 K over 20 years. Decrease in CO2 abundance and forcing following abrupt cessation of emissions would offset these increases in GMST over 100 years by as little as 0.09 K to as much as 0.8 K. The uncertainties quantified here greatly limit confidence in projections of change in GMST that would result from any strategy for future reduction of emissions.
MPI-NeTSim: A Network Simulation Module for MPI

Programs that execute in parallel across a network often use the Message Passing Interface (MPI) library for communication. The network requirements of an MPI program are often unclear because of the difficulty in exploring alternative network configurations as well as obtaining packet level information about the communication. MPI-NeTSim is an execution environment to emulate MPI programs on simulated networks to allow users to better explore the impact of the network on the performance of MPI programs. We describe the design of MPI-NeTSim and the integration of OMNeT++’s INET framework into MPICH2’s MPI middleware. We introduce a novel technique for uniformly slowing down the execution of the system to allow the discrete event network simulator to keep up with the execution and provide a consistent view of the communication. We validate our technique with synthetic programs as well as the standard NAS benchmarks. We demonstrate MPI-NeTSim’s usefulness in analyzing the effect of the network on communication by using our environment to study the impact of a slow-link on the NAS benchmarks.
Surface impact on nanoparticle-based magnetic resonance imaging contrast agents

Magnetic resonance imaging (MRI) is one of the most widely used diagnostic tools in the clinic. To improve imaging quality, MRI contrast agents, which can modulate local T1 and T2 relaxation times, are often injected prior to or during MRI scans. However, clinically used contrast agents, including Gd3+-based chelates and iron oxide nanoparticles (IONPs), afford mediocre contrast abilities. To address this issue, there has been extensive research on developing alternative MRI contrast agents with superior r1 and r2 relaxivities. These efforts are facilitated by the fast progress in nanotechnology, which allows for preparation of magnetic nanoparticles (NPs) with varied size, shape, crystallinity, and composition. Studies suggest that surface coatings can also largely affect T1 and T2 relaxations and can be tailored in favor of a high r1 or r2. However, the surface impact of NPs has been less emphasized. Herein, we review recent progress on developing NP-based T1 and T2 contrast agents, with a focus on the surface impact.
Hill-Robertson Interference Reduces Genetic Diversity on a Young Plant Y-Chromosome

X and Y chromosomes differ in effective population size (Ne), rates of recombination, and exposure to natural selection, all of which can affect patterns of genetic diversity. On Y chromosomes with suppressed recombination, natural selection is expected to eliminate linked neutral variation, and lower the Ne of Y compared to X chromosomes or autosomes. However, female-biased sex ratios and high variance in male reproductive success can also reduce Y-linked Ne, making it difficult to infer the causes of low Y-diversity. Here, we investigate the factors affecting levels of polymorphism during sex chromosome evolution in the dioecious plant Rumex hastatulus (Polygonaceae). Strikingly, we find that neutral diversity for genes on the Y chromosome is, on average, 2.1% of the value for their X-linked homologs, corresponding to a chromosome-wide reduction of 93% compared to the standard neutral expectation. We demonstrate that the magnitude of this diversity loss is inconsistent with reduced male Ne caused by neutral processes. Instead, using forward simulations and estimates of the distribution of deleterious fitness effects, we show that Y chromosome diversity loss can be explained by purifying selection acting in aggregate over a large number of genetically linked sites. Simulations also suggest that our observed level of Y-diversity is consistent with the joint action of purifying and positive selection, but only for models in which there were fewer constrained sites than we empirically estimated. Given the relatively recent origin of R. hastatulus sex chromosomes, our results imply that Y-chromosome degeneration in the early stages may be largely driven by selective interference rather than by neutral genetic drift of silenced Y-linked genes.
Soft behaviour modelling of user communities

A soft modelling approach for describing behaviour in on-line user communities is introduced in this work. Behaviour models of individual users in dynamic virtual environments have been described in the literature in terms of timed transition automata; they have various drawbacks. Soft multi/agent behaviour automata are defined and proposed to describe multiple user behaviours and to recognise larger classes of user group histories, such as group histories which contain unexpected behaviours. The notion of deviation from the user community model allows defining a soft parsing process which assesses and evaluates the dynamic behaviour of a group of users interacting in virtual environments, such as e-learning and e-business platforms. The soft automaton model can describe virtually infinite sequences of actions due to multiple users and subject to temporal constraints. Soft measures assess a form of distance of observed behaviours by evaluating the amount of temporal deviation, additional or omitted actions contained in an observed history as well as actions performed by unexpected users. The proposed model allows the soft recognition of user group histories also when the observed actions only partially meet the given behaviour model constraints. This approach is more realistic for real-time user community support systems, concerning standard boolean model recognition, when more than one user model is potentially available, and the extent of deviation from community behaviour models can be used as a guide to generate the system support by anticipation, projection and other known techniques. Experiments based on logs from an e-learning platform and plan compilation of the soft multi-agent behaviour automaton show the expressiveness of the proposed model.
Consensus guidance for the use of debridement techniques in the UK

All authors were members of the consensus meeting panel; * Chair of the panel. Full author details in Box 1 In Autumn 2010, a multidisciplinary group of clinicians met in Manchester to discuss the issue of debridement in wound management. There are various debridement techniques available in the UK, but facilities and skills vary. This paper, resulting from the meeting, briefly outlines the differing techniques used, the levels of skill required to use them and the wound types for which they are appropriate. It is important that clinicians practising debridement are aware of the variations in method, and the limitations of their own skills and competency so that, if appropriate, the patient can be referred to receive timely and appropriate intervention.
Flow shear stress in the co-extrusion of polymer multilayer film: variations and effects on interfacial instability

Abstract Multilayer co-extrusion combines two or more layers of materials in a single extrusion process. To improve the quality of multilayered film products fabricated by co-extruding two polymers with different rheological properties, suppressing interfacial instability is vital. This study designed and fabricated a mould with layer-multiplying sets to increase the number of layers in co-extruded polymer multilayer films. Flow pressure drops were measured by two pressure sensors set sequentially on the mould wall along the flow direction. Pressure drops in the flow were measured to calculate flow shear stress. Variations of shear stress are then used to analyse interface slipping. Experiments were performed using polypropylene (PP) and polycaprolactam (PA6). Extrusion rate was experimentally increased to raise the pressure within the flow. The experiments showed that, when shear stress reaches a certain threshold, a large number of interfaces causes interfacial slip, which leads to a decline in shear stress. Increasing the number of interfaces increases interfacial slip. A large interfacial slip results in much lower shear stress on the mould wall.
MafB Is Critical for Glucagon Production and Secretion in Mouse Pancreatic α Cells In Vivo

ABSTRACT The MafB transcription factor is expressed in pancreatic α and β cells during development but becomes exclusive to α cells in adult rodents. Mafb-null (Mafb−/−) mice were reported to have reduced α- and β-cell numbers throughout embryonic development. To further analyze the postnatal function of MafB in the pancreas, we generated endocrine cell-specific (MafbΔEndo) and tamoxifen-dependent (MafbΔTAM) Mafb knockout mice. MafbΔEndo mice exhibited reduced populations of insulin-positive (insulin+) and glucagon+ cells at postnatal day 0, but the insulin+ cell population recovered by 8 weeks of age. In contrast, the Arx+ glucagon+ cell fraction and glucagon expression remained decreased even in adulthood. MafbΔTAM mice, with Mafb deleted after pancreas maturation, also demonstrated diminished glucagon+ cells and glucagon content without affecting β cells. A decreased Arx+ glucagon+ cell population in MafbΔEndo mice was compensated for by an increased Arx+ pancreatic polypeptide+ cell population. Furthermore, gene expression analyses from both MafbΔEndo and MafbΔTAM islets revealed that MafB is a key regulator of glucagon expression in α cells. Finally, both mutants failed to respond to arginine, likely due to impaired arginine transporter gene expression and glucagon production ability. Taken together, our findings reveal that MafB is critical for the functional maintenance of mouse α cells in vivo, including glucagon production and secretion, as well as in development.
Monitoring of Cytomegalovirus (CMV)-Specific Cell-Mediated Immunity in Heart Transplant Recipients: Clinical Utility of the QuantiFERON-CMV Assay for Management of Posttransplant CMV Infection

ABSTRACT The clinical utility of the QuantiFERON-CMV (QFN-CMV) assay in heart transplant recipients was assessed. Forty-four cytomegalovirus (CMV)-seropositive patients were enrolled: 17 received antiviral prophylaxis, and 27 were managed preemptively. CMV-DNAemia monitoring was performed by the use of a quantitative real-time PCR assay. The QFN-CMV assay was retrospectively performed on blood samples collected at five posttransplant time points. A higher proportion of patients with an indeterminate QFN-CMV result after the suspension of prophylaxis than of patients who showed a global T-cell responsiveness developed CMV infection (P = 0.036). Patients who reconstituted a CMV-specific response following the first CMV-DNAemia-positive result (42.9%) showed a median CMV-DNAemia peak 1 log of magnitude lower than that seen with patients with indeterminate results, and all controlled viral replication spontaneously. The 25% of patients with an indeterminate result developed CMV disease. In the preemptive strategy group, no differences in the development of subsequent infection, magnitude of viral load, and viral control were observed on the basis of QFN-CMV measurements performed before and after the first CMV-DNAemia-positive result. Considering both CMV prevention strategies, viral relapse was associated with the failure to reconstitute CMV-specific cell-mediated immunity (CMI) after the resolution of the first episode of CMV infection (P = 0.032). QFN-CMV measurements can be a useful tool for identifying patients (i) at higher risk of developing infection after discontinuing antiviral prophylaxis, (ii) with late CMV infection who would benefit from appropriate antiviral interventions, and (iii) at higher risk of viral relapses. QFN-CMV measurements taken within 1 month posttransplantation (early period) are not revealing.