Miracle-dz/UniFAR-FTUs huggingface dataset:
Convergence of the NF‐κB and Interferon Signaling Pathways in the Regulation of Antiviral Defense and Apoptosis

Abstract: The ubiquitously expressed interferon regulatory factor 3 (IRF‐3) is directly activated following virus infection and functions as a key activator of the immediate‐early Type 1 interferon (IFN) genes. Using DNA microarray analysis (8,556 genes) in Jurkat T cells inducibly expressing constitutively active IRF‐3, several target genes directly regulated by IRF‐3 were identified. Among the genes upregulated by IRF‐3 were transcripts for a subset of known IFN‐stimulated genes (ISGs), including ISG56, which functions as an inhibitor of translation initiation. Phosphorylation of C‐terminal Ser/Thr residues—‐382GGASSLENTVDLHISNSHPLSLTSDQY408—is required for IRF‐3 activation. Using C‐terminal point mutations and a novel phosphospecific antibody, Ser396 was characterized as the minimal phosphoacceptor site required in vivo for IRF‐3 activation following Sendai virus (SeV) infection, expression of viral nucleocapsid, or double‐stranded RNA (dsRNA) treatment. The identity of the virus‐activated kinase (VAK) activity that targets and activates IRF‐3 and IRF‐7 has remained a critical missing link in the understanding of interferon signaling. We report that the IKK‐related kinases—IKKε/TBK‐1—are components of VAK that mediate IRF‐3 and IRF‐7 phosphorylation and thus functionally link the NF‐κB and IRF pathways in the development of the antiviral response.
Search, Inference and Opponent Modelling in an Expert-Caliber Skat Player

In this dissertation, we investigate the problems of search, inference and opponent modelling in imperfect information games through the creation of a computer player for the popular german card game skat. In so doing, we demonstrate three major contributions to the field of artificial intelligence research in games. First, we present our skat player Kermit which, using a synthesis of different techniques, decisively defeats previously existing computer players and displays playing strength comparable to human experts. Second, we propose a framework for evaluating game-playing algorithms with known theoretical flaws and explaining the success of such methods in different classes of games. Finally, we enhance Kermit with a simple but effective opponent modelling component that allows it to adapt and improve its performance against players of differing playing strength in real time.
Combining Singular Value Decomposition and Item-based Recommender in Collaborative Filtering

Recommender Systems are introduced as an intelligent technique to deal with the problem of information and product overload. Their purpose is to provide efficient personalized solutions in economic business domains. Collaborative filtering is a widely used method of providing recommendations using ratings on items from users. However, it has three major limitations, accuracy, data sparsity and scalability. This paper proposes a new collaborative filtering algorithm to solve the problems mentioned above. We utilize the results of singular value decomposition (SVD) to fill the vacant ratings and then use the item based method to produce the prediction of unrated items. Our experimental results on MovieLens dataset show that the algorithm combined SVD method and item-based method is promising, since it does not only solute some of the recorded problems of recommender systems, but also assists in increasing the accuracy of systems employing it.
Differential Modulation of Remifentanil-induced Analgesia and Postinfusion Hyperalgesia by S-Ketamine and Clonidine in Humans

Background Experimental studies and clinical observations suggest a possible role for opioids to induce pain and hyperalgesia on withdrawal. The authors used a new experimental pain model in human skin to determine the time course of analgesic and hyperalgesic effects of the &mgr;-receptor agonist remifentanil alone or in combination with the N-methyl-D-aspartate-receptor antagonist S-ketamine or the &agr;2-receptor agonist clonidine. Methods Thirteen volunteers were enrolled in this randomized, double-blind, placebo-controlled study. Transcutaneous electrical stimulation at a high current density (2 Hz, 67.3 ± 16.8 mA, mean ± SD) induced acute pain (numerical 11-point rating scale: 5–6 out of 10) and stable areas of mechanical hyperalgesia to punctate stimuli and touch (allodynia). The magnitude of pain and area of hyperalgesia were assessed before, during, and after drug infusion (remifentanil at 0.1 &mgr;g · kg−1 · min−1 and S-ketamine at 5 &mgr;g · kg−1 · min−1 over a period of 30 min, respectively; clonidine infusion at 2 &mgr;g/kg for 5 min). Results Remifentanil reduced pain and areas of punctate hyperalgesia during infusion. In contrast, postinfusion pain and hyperalgesia were significantly higher than control. During infusion of S-ketamine, pain and hyperalgesia decreased and gradually normalized after infusion. When given in combination, S-ketamine abolished postinfusion increase of punctate hyperalgesia but did not reduce increased pain ratings. Clonidine alone did not significantly attenuate pain or areas of hyperalgesia. However, when given in combination with remifentanil, clonidine attenuated postinfusion increase of pain ratings. Conclusions Opioid-induced postinfusion hyperalgesia could be abolished by S-ketamine, suggesting an N-methyl-d-aspartate-receptor mechanism. In contrast, elevated pain ratings after infusion were not reduced by ketamine but were alleviated by the &agr;2-receptor agonist clonidine. The results of this study suggest different mechanisms of opioid-induced postinfusion antianalgesia and secondary hyperalgesia.
Helicobacter pylori in out-patients of a general practitioner: prevalence and determinants of current infection

Data on prevalence and determinants of Helicobacter pylori infection in well-defined populations are scarce. We investigated the prevalence and determinants of active H. pylori infection in a population of out-patients attending a general practitioner in Southern Germany. Infection status was determined by [13C]urea breath test. In addition, information on potential risk factors and medical history was collected. Five hundred and one of the 531 eligible patients participated in the study (response rate of 94·4%). In total, 117 of the 501 patients had a positive [13C]urea breath test (23·4%). Prevalence of H. pylori infection increased with age from 10·8% (95% CI 5·7–18·1%) in the age group 15–29 years to 30·8% (95% CI 22·1–40·6%) in the age group 60–79 years and was 20·3%, 30·4% and 28·2% for the age groups 30–39, 40–49 and 50–59 years, respectively. Education and childhood living conditions, especially the number of siblings, were identified as additional independent determinants of infection.
Vasoactive intestinal peptide is involved in the inhibitory effect of interleukin-1 beta on the jejunal contractile response induced by acetylcholine.

UNLABELLED Although previous studies have shown that interleukin-1 beta (IL-1 beta) decreases acetylcholine (ACh)-induced intestinal contraction by an action on the enteric nervous system, the neuromediator(s) involved are still unknown. AIM To determine the role of nitric oxide (NO), vasoactive intestinal peptide (VIP) and/or adenosine triphosphate (ATP) in mediating this inhibitory effect. METHODS The effects of NO synthase inhibitors, VIP and ATP antagonists on motor response to the ACh were investigated before and after 90-min exposure of a rat preparation of jejunal longitudinal muscle-myenteric plexus to IL-1 beta. NG-nitro-L-arginine methyl ester, NG-nitro-L-arginine and NG-monomethyl-L-arginine were used to inhibit NO synthase, VIP (10-28) and [D-p-Cl-Phe6, Leu17] VIP to block VIP receptors, and suramin to block ATP receptors. RESULTS NO synthase inhibitors failed to block the inhibitory effect of IL-1 beta on ACh-contracted jejunum smooth muscle. Suramin also failed to affect IL-1 beta-induced inhibition, whereas VIP antagonists abolished it. Moreover, the action of IL-1 beta was partly reproduced by VIP. CONCLUSIONS While neither NO nor ATP accounts for the inhibitory effect of IL-1 beta on ACh-contracted jejunum, VIP seems to be a key-mediator of this effect.
Change Impact Analysis of a Software Process Using Process Slicing

A software process needs to be changed for various reasons during or before its enactment. To accommodate the change in the software process, it is necessary to analyze the impacts of the change. Few researches provide the methods to structurally analyze the impacts of the change for a software process or workflow with limitations. In this paper, we propose an approach to analyzing the impacts of the software process change using process slicing. Process slicing is designed to formally operate on the software process considering multi-perspectives of the software process such as behavioral, informational, and organizational perspectives. Process slicing produces the process slice, which is the part of the software process related to the change. Process slicing can be automatically performed resulting in making a project manager enable to reduce the effort to identify the impacts of the change.
Hybrid-Parallel Sparse Matrix – Vector Multiplication and Iterative Linear Solvers with the communication library GPI

We present a library of Krylov subspace iterative solvers built over the PGAS-type communication layer GPI. The hybrid pattern is here the appropriate choice to reveal the hierarchical parallelism of clusters with multiand manycore nodes. Our approach includes asynchronous communication and differs in many aspects from the classical one. We first present the GPI-based implementation of the sparse matrix-vector multiplication and then, using as a benchmark the numerical solution of a Poisson boundary value problem in a unit cube, we compare the performance on Intel/Infiniband and CRAY XE6 architectures of our GPI-based Conjugate Gradients and Richardson methods against the ones available in PETSc. The results show good scalability and performance of our approach, at least comparable to these of PETSc. Key–Words: multi-core clusters, PGAS, RDMA, GPI, hybrid-parallel iterative solvers, sparse matrix-vector multiplication, performance
Cartoon capture by key-frame based contour tracking

Traditional cartoons have been widely used in entertainment, education, and advertisement. Thus, a large amount of cartoon data is available. In this paper, we propose a new technique for capturing the motion of a character in an existing cartoon sequence. This technique tracks the contours of the cartoon character in the sequence, and key frames are used to guide the tracking. We model contour tracking as a space-time optimization problem in which an energy function including both temporal and spatial constraints is defined. First, the user labels the contours of the character on the key frames. Then, the contours on the intermediate frames are tracked by minimizing the energy function. The user may need to interactively adjust the tracking result and restart the optimization process to refine the result. Finally, an edge snapping algorithm is applied to make the tracking result more precise. Experiments show that our technique works effectively.
Geographic variation in energy storage and physiological responses to freezing in the gray treefrogs Hyla versicolor and H. chrysoscelis

SUMMARY The physiological responses supporting freeze tolerance in anurans are well known, but the evolution of this trait remains little studied. This is the first common-garden study of geographic variation in cryoprotective responses to freezing and the degree of freeze tolerance. We studied the gray treefrogs (Hyla versicolor and H. chrysoscelis) from sympatric sites in Minnesota, Indiana and Missouri. Patterns in the literature suggest that northern frogs produce more cryoprotectants upon freezing, but we found no geographic variation in cryoprotective responses or degree of freeze tolerance. The concentration of glucose produced upon freezing was higher than previously reported for this species (liver: 475 μmol g–1 dry mass). Unfrozen frogs had high levels of glycerol (liver: approx. 150μ mol g–1 dry mass), and did not produce more upon freezing. Liver glycogen content (concentration multiplied by liver mass) was highest in frogs from Minnesota and Missouri, and was stored in preference to lipids in Minnesota frogs, possibly to provide energy for the longer northern winters. Minnesota frogs accumulated more ice (53.4±1.8%) after freezing to–2.5°C than Indiana frogs (45.5±3.3%). The two species differed in body size but not in any of the physiological parameters measured. We conclude that these populations show no adaptive variation in freeze tolerance and that comparing published studies may be misleading because of different acclimation and feeding regimes.
Mental health needs of young offenders in custody and in the community

Background Research has revealed high levels of mental health needs in young offenders but many studies have been small, focusing on specific populations. Aims To evaluate the mental health and psychosocial needs of a nationally representative sample of juvenile offenders in England and Wales, including female offenders and those from Black and minority ethnic groups. Method A cross-sectional survey of 301 young offenders, 151 in custody and 150 in the community, was conducted in six geographically representative areas across England and Wales. Each young person was interviewed to obtain demographic information, mental health and social needs, and psychometric data. Results Young offenders were found to have high levels of needs in a number of different areas including mental health (31%), education/work (36%) and social relationships (48%). Young offenders in the community had significantly more needs than those in secure care and needs were often unmet. One in five young offenders was also identified as having a learning disability (IQ < 70). Conclusions Needs for young offenders were high but often unmet. This emphasises the importance of structured needs assessment within custody and community settings in conjunction with a care programme approach that improves continuity of care.
LITAO3 CHARACTERIZATION OF RUBIDIUM ON TEMPERATURE VARIATIONS

One of the studies that recently attracted the attention of physicists is research on ferroelectric material because this material is very promising for the development of new generation devices in connection with the unique properties it has. Ferroelectric materials, especially those based on a mixture of lithium tantalite (LiTaO3), are expected to be applied to the infrared sensor. Lithium tantalate (LiTaO3) is a ferroelectric material that is unique in terms of pyroelectric and piezoelectric properties that are integrated with good mechanical and chemical stability. Therefore LiTaO3 is often used for several applications such as electro-optical modulators and pyroelectric detectors. LiTaO3 is a non-hygroscopic crystal, colorless, soluble in water, has a high transmission rate and does not easily damage its optical properties. LiTaO3 is a material that has a high dielectric constant and a high load storage capacity. This research has succeeded in determining the band gap energy of the LiTaO3 film in the rubidium chamber obtained in the range of values 2.02-2.98 eV as shown in figure 4. The LiTaO3 film after the annealing process at a temperature of 650 oC, has the highest band gap energy of 2.98 eV. Large energy is needed on the electrons to be excited from the valence band to the conduction band. Whereas in the LiTaO3 film after an annealing process of 800 oC, the band gap energy obtained is 2.02 eV. This makes it easier for electrons to be excited from the valence band to the conduction band because the energy needed is not too large.
Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the GenomicEncyclopedia ofBacteria andArchaea project.
Contemporary reliance on bicarbonate acquisition predicts increased growth of seagrass Amphibolis antarctica in a high-CO2 world

We find energetically costly bicarbonate pathways exist in three temperate seagrasses and then provide evidence that indicates greater growth and photosynthetic efficiency for bicarbonate users in a high CO2 world. Greater growth might enhance the future prosperity and rehabilitation of these important habitat forming plants, which have experienced declines of global significance.
Runtime infrastructure for simulating vehicle-2-x communication scenarios

Simulations are essential to evaluate Vehicle-2-X Communication applications and to efficiently prepare their deployment. Accordingly, to enable realistic simulations of Vehicle-2-X Communication applications, different kinds of simulators have to be coupled dynamically. Running coupled simulators synchronously and exchanging simulation data among them is a challenging task. Currently, simulator couplings lack flexibility because they are designed merely for specific simulators. In this work, the runtime infrastructure VSimRTI is presented allowing a flexible combination of time-discrete simulators for Vehicle-2-X simulations. Based on the requirements of a concrete scenario, arbitrary simulators can be plugged onto the VSimRTI and are executed together.
Radiobiological risk estimates of adverse events and secondary cancer for proton and photon radiation therapy of pediatric medulloblastoma

Abstract Introduction. The aim of this model study was to estimate and compare the risk of radiation-induced adverse late effects in pediatric patients with medulloblastoma (MB) treated with either three-dimensional conformal radiotherapy (3D CRT), inversely-optimized arc therapy (RapidArc® (RA)) or spot-scanned intensity-modulated proton therapy (IMPT). The aim was also to find dose-volume toxicity parameters relevant to children undergoing RT to be used in the inverse planning of RA and IMPT, and to use in the risk estimations. Material and methods. Treatment plans were created for all three techniques on 10 pediatric patients that have been treated with craniospinal irradiation (CSI) at our institution in 2007–2009. Plans were generated for two prescription CSI doses, 23.4 Gy and 36 Gy. Risk estimates were based on childhood cancer survivor data when available and secondary cancer (SC) risks were estimated as a function of age at exposure and attained age according to the organ-equivalent dose (OED) concept. Results. Estimates of SC risk was higher for the RA plans and differentiable from the estimates for 3D CRT at attained ages above 40 years. The risk of developing heart failure, hearing loss, hypothyroidism and xerostomia was highest for the 3D CRT plans. The risks of all adverse effects were estimated as lowest for the IMPT plans, even when including secondary neutron (SN) irradiation with high values of the neutron radiation weighting factors (WRneutron). Conclusions. When comparing RA and 3D CRT treatment for pediatric MB it is a matter of comparing higher SC risk against higher risks of non-cancer adverse events. Considering time until onset of the different complications is necessary to fully assess patient benefit in such a comparison. The IMPT plans, including SN dose contribution, compared favorably to the photon techniques in terms of all radiobiological risk estimates.
Gene expression profiles in rice gametes and zygotes: identification of gamete-enriched genes and up- or down-regulated genes in zygotes after fertilization

In angiosperms, fertilization and subsequent zygotic development occur in embryo sacs deeply embedded in the ovaries; therefore, these processes are poorly elucidated. In this study, microarray-based transcriptome analyses were conducted on rice sperm cells, egg cells, and zygotes isolated from flowers to identify candidate genes involved in gametic and/or early zygotic development. Cell type-specific transcriptomes were obtained, and up- or down-regulated genes in zygotes after fertilization were identified, in addition to genes enriched in male and female gametes. A total of 325 putatively up-regulated and 94 putatively down-regulated genes in zygotes were obtained. Interestingly, several genes encoding homeobox proteins or transcription factors were identified as highly up-regulated genes after fertilization, and the gene ontology for up-regulated genes was highly enriched in functions related to chromatin/DNA organization and assembly. Because a gene encoding methyltransferase 1 was identified as a highly up-regulated gene in zygotes after fertilization, the effect of an inhibitor of this enzyme on zygote development was monitored. The inhibitor appeared partially to affect polarity or division asymmetry in rice zygotes, but it did not block normal embryo generation.
Scientific Respiratory Symposium, Paris June 2010

At a 2010 Respiratory Symposium in Paris, chaired by Professors Bousquet and Roche of the University of Paris, recent trends in research, therapy and treatment guidelines for asthma and chronic obstructive pulmonary disease (COPD) were reviewed and discussed by a faculty of expert European and US respiratory physicians. This article reviews five key clinical presentations with particular emphasis given to the importance of small airways in the pathology and treatment of asthma and COPD. Further analysis of the economics of treatment in Europe and the US shows a wide variance in direct and indirect costs.
Variant View: Visualizing Sequence Variants in their Gene Context

Scientists use DNA sequence differences between an individual's genome and a standard reference genome to study the genetic basis of disease. Such differences are called sequence variants, and determining their impact in the cell is difficult because it requires reasoning about both the type and location of the variant across several levels of biological context. In this design study, we worked with four analysts to design a visualization tool supporting variant impact assessment for three different tasks. We contribute data and task abstractions for the problem of variant impact assessment, and the carefully justified design and implementation of the Variant View tool. Variant View features an information-dense visual encoding that provides maximal information at the overview level, in contrast to the extensive navigation required by currently-prevalent genome browsers. We provide initial evidence that the tool simplified and accelerated workflows for these three tasks through three case studies. Finally, we reflect on the lessons learned in creating and refining data and task abstractions that allow for concise overviews of sprawling information spaces that can reduce or remove the need for the memory-intensive use of navigation.