Miracle-dz/UniFAR-FTUs huggingface dataset:
Azathioprine, Mercaptopurine, and 5-Aminosalicylic Acid Affect the Growth of IBD-Associated Campylobacter Species and Other Enteric Microbes

Campylobacter concisus is a bacterium that is associated with inflammatory bowel disease (IBD). Immunosuppressive drugs including azathioprine (AZA) and mercaptopurine (MP), and anti-inflammatory drug such as 5-aminosalicylic acid (5-ASA) are commonly used to treat patients with IBD. This study aimed to examine the effects of AZA, MP, and 5-ASA on the growth of IBD-associated bacterial species and to identify bacterial enzymes involved in immunosuppressive drug metabolism. A total of 15 bacterial strains of five species including 11 C. concisus strains, Bacteroides fragilis, Bacteroides vulgatus, Enterococcus faecalis, and Escherichia coli were examined. The impact of AZA, MP, and 5-ASA on the growth of these bacterial species was examined quantitatively using a plate counting method. The presence of enzymes involved in AZA and MP metabolism in these bacterial species was identified using bioinformatics tools. AZA and MP significantly inhibited the growth of all 11 C. concisus strains. C. concisus strains were more sensitive to AZA than MP. 5-ASA showed inhibitory effects to some C. concisus strains, while it promoted the growth of other C. concisus strains. AZA and MP also significantly inhibited the growth of B. fragilis and B. vulgatus. The growth of E. coli was significantly inhibited by 200 μg/ml of AZA as well as 100 and 200 μg/ml of 5-ASA. Bacterial enzymes related to AZA and MP metabolism were found, which varied in different bacterial species. In conclusion, AZA and MP have inhibitory effects to IBD-associated C. concisus and other enteric microbes, suggesting an additional therapeutic mechanism of these drugs in the treatment of IBD. The strain dependent differential impact of 5-ASA on the growth of C. concisus may also have clinical implication given that in some cases 5-ASA medications were found to cause exacerbations of colitis.
Tree compatibility and inferring evolutionary history

The tree compatibility problem is a problem concerned with evolutionary history construction. For a species set S, an S-labelled tree is a tree T along with a labelling L: S ? V(T). The tree compatibility problem asks whether a set T of S-labelled trees, each of which describes the evolution of S, is compatible in the sense that there is a single tree T from which each tree T ? T can be derived by a sequence of edge contractions. Polynomial time algorithms for the tree compatibility problem have been known to exist for a long time, with the best being the recent O(n2k) algorithm by Gusfield to determine compatibility of k trees on n species. Recently Gusfield found an O(nk) algorithm for a restricted case of the tree compatibility problem. In this paper, we will present an O(nk) algorithm for the tree compatibility problem, thus achieving linear time. The perfect phylogeny problem is another problem in evolutionary history construction, which has been recently shown to be in P for special cases but NP-complete for the general case. We will show that we can characterize each instance to the perfect phylogeny problem as an instance to the tree compatibility problem, and thus derive an algorithm for the perfect phylogeny problem. Our algorithm is superior to the other algorithms for perfect phylogeny problem for many realistic cases, such as when the species are defined by molecular data such as amino-acid sequences.
ICTs in Speech and Language Therapy

Over the past decade speech and language therapy has taken an interesting turn towards the use of information communication technologies (ICTs) for diagnosis of disorders and delivery of therapy. In many cases ICTs have worked as assistive tools to therapists, while in others as sole providers of therapy, especially in remote areas. In this report we provide a brief overview of the most representative articles for applications and assistive technologies used for assessment and intervention purposes in Speech Therapy according to the type of disorders.
Developmental Outcome of Very Low Birth Weight Infants at Four Years of Age as a Function of Biological Risk and Psychosocial Risk

The continuing contribution of early biological and psychosocial risk factors to developmental outcome of 55 very low birth weight infants (≤ 1500 g) was assessed at 4 years of age. Biological risk, assessed by the Neurobiologic Risk Score, accounted for significant portions of the variance in the perceptual-performance (17%) and motor (35%) dimensions of the McCarthy Scales of Children's Abilities. Psychosocial risk, reflected in maternal appraisals of daily stress during the newborn period, did not account for a significant portion of variance in any of the McCarthy Scales. Maternal education level, however, another measure of psychosocial risk, accounted for significant portions of variance (from 6% to 34%) on each of the McCarthy Scales. Movement from low neurobiologic risk status to poor outcome status at 4 years of age was associated with a number of psychosocial variables, including maternal education and early levels of maternal daily stress. The findings are discussed in terms of early markers for very low birth weight infants who require careful follow-up and of potential intervention targets to promote developmental outcome.
Survival of intimate partner violence as experienced by women.

AIMS AND OBJECTIVES The study set out to describe women's experiences of intimate partner violence, the consequences of such violence, the help they received and women's experiences of their survival. BACKGROUND Social and health professionals do not have sufficient ability to identify and help families who suffer from intimate partner violence. Methods for identifying and treating partner violence not have been developed adequately. METHOD The study was conducted in Finland by loosely formulated open-ended interviews with seven battered women. The data were analysed by inductive qualitative content analysis. FINDINGS Women had past experience of maltreatment and a distressing climate at their parental home. Women experienced both themselves and their spouse as having weak identities; their ideals, patterns of marriage and sexuality were different. Violence occurred in situations of disagreement. Women tried to strike a balance between independence and dependence in the relationship. The different forms of couple violence were interlinked. The women sought help when their health and social relationships got worse. An awareness of the problem, taking action, counselling and social relationships helped them survive. Religiousness was a factor that involved commitment to the couple relationship, made religious demands on women and promoted the recovery of integrity. CONCLUSIONS Intimate partner violence was associated with the family model, childhood experience of maltreatment, the partners' weak identity and conflicts between individualism and familism. Social and healthcare professionals need competence in early intervention and skills to discuss moral principles, sexuality, and violence in a way that is free of prejudice and condemning attitudes. Spiritual approaches in the context of interventions should be taken into consideration. RELEVANCE TO CLINICAL PRACTICE In a clinical context, nurses should be aware of the symptoms of violence, and they should have skills in dealing with intimate moral and spiritual issues.
Research Statement Research Overview

My research addresses performance bottlenecks in a range of large scale networked and distributed applications. In my work I identify performance issues in major applications, propose mitigating techniques, build systems incorporating my ideas, and evaluate them at large scales to demonstrate practical benefit. When possible I also leverage theoretical analysis to gain insight into the fundamental tradeoffs underlying the system design.
Improving the detection of detainees with suspected intellectual disability in police custody

Purpose – The purpose of this paper is twofold. First to ascertain the efficacy of current police reception screening to detect detainees with intellectual disability (ID). Second to assess the validity of a short targeted screen for ID among police custody detainees. Design/methodology/approach – The study comprised three stages. First, 248 police custody detainees were assessed for a range of health morbidities, including a pragmatic clinical evaluation of ID. For those with suspected ID, the police custody screens were scrutinised for evidence that this had been detected. Second, a new police health screen, incorporating a short screen for ID, was piloted. Totally, 351 detainees were assessed in the same way as in part 1 with the new screens being scrutinised for evidence that ID had been detected where relevant. Third, the new police screen for ID was validated among a sample of 64 inpatients, some with ID and some without, from forensic inpatient services. Parts 1 and 2 were carried out in the Metrop.
Capacity and coverage increase with repeaters in UMTS urban cellular mobile communication environment

In this letter, we propose to use repeaters to increase system information capacity in urban areas, where path loss exponents are higher (as much as 3.4 or more). There is at least a 10% increase in coverage area when repeaters are placed in every cell within the network to increase system capacity. The overall system information capacity is doubled at propagation exponent 3.7-3.9.
Improved resuscitation minimizes respiratory dysfunction and blunts interleukin-6 and nuclear factor-&kgr;B activation after traumatic hemorrhage*

ObjectiveWe hypothesized that modifying resuscitation would alter hemorrhagic shock-induced respiratory dysfunction and correlate with nuclear factor-&kgr;B and cytokine expression. DesignRandomized, controlled, prospective study. SettingUniversity hospital trauma research laboratory. SubjectsFemale, Swiss Webster mice, 8–12 wks old. InterventionsHemorrhagic shock was induced by removing 0.025 mL of blood/g of body weight via a carotid catheter. Animals were resuscitated 30 mins later. Mice were randomized into four groups: group I was cannulated but not bled (sham); group II received normal saline to three times their shed blood volume; group III received their shed blood; and group IV received shed blood + normal saline at two times shed blood volume. Measurements and Main ResultsWe measured the following: serum lactates at the end of shock and after resuscitation, pulmonary function before any instrumentation and after 24 hrs, cytokine concentrations by enzyme-linked immunosorbent assay, and nuclear factor-&kgr;B activity by electrophoretic mobility shift assay. Groups that were hemorrhaged had significant hypotension and a significant increase in serum lactates over 30 mins. Resuscitation returned the blood pressure to baseline in all groups, and lactates improved in all groups except group II. Group II also demonstrated a significant decrease in pulmonary function characterized by increased airway resistance and decreases in minute volume, lung compliance, and alveolar function. Bronchoalveolar fluid and serum interleukin-6 and whole lung nuclear factor-&kgr;B activity also were elevated significantly in group II. ConclusionsGroup II demonstrated the least improvement in serum lactate after resuscitation, the most significant acute lung injury, and the greatest interleukin-6 and nuclear factor-&kgr;B response. Group IV mice had the least acute lung injury, with no detectable interleukin-6 response. Improved resuscitation with crystalloid and shed blood minimized acute lung injury. The reduction in pulmonary dysfunction after improved resuscitation may be attributable to a blunting of the nuclear factor-&kgr;B and interleukin-6 responses to hemorrhage.
Arctic Ice Dynamics Joint Experiment (AIDJEX) assumptions revisited and found inadequate

[1] This paper revisits the Arctic Ice Dynamics Joint Experiment (AIDJEX) assumptions about pack ice behavior with an eye to modeling sea ice dynamics. The AIDJEX assumptions were that (1) enough leads were present in a 100 km by 100 km region to make the ice isotropic on that scale; (2) the ice had no tensile strength; and (3) the ice behavior could be approximated by an isotropic yield surface. These assumptions were made during the development of the AIDJEX model in the 1970s, and are now found inadequate. The assumptions were made in part because of insufficient large-scale (10 km) deformation and stress data, and in part because of computer capability limitations. Upon reviewing deformation and stress data, it is clear that a model including deformation on discontinuities and an anisotropic failure surface with tension would better describe the behavior of pack ice. A model based on these assumptions is needed to represent the deformation and stress in pack ice on scales from 10 to 100 km, and would need to explicitly resolve discontinuities. Such a model would require a different class of metrics to validate discontinuities against observations.
Suppression of ischemia in arterial occlusive disease by JNK-promoted native collateral artery development

Arterial occlusive diseases are major causes of morbidity and mortality. Blood flow to the affected tissue must be restored quickly if viability and function are to be preserved. We report that disruption of the mixed-lineage protein kinase (MLK) - cJun NH2-terminal kinase (JNK) signaling pathway in endothelial cells causes severe blockade of blood flow and failure to recover in the murine femoral artery ligation model of hindlimb ischemia. We show that the MLK-JNK pathway is required for the formation of native collateral arteries that can restore circulation following arterial occlusion. Disruption of the MLK-JNK pathway causes decreased Dll4/Notch signaling, excessive sprouting angiogenesis, and defects in developmental vascular morphogenesis. Our analysis demonstrates that the MLK-JNK signaling pathway is a key regulatory mechanism that protects against ischemia in arterial occlusive disease. DOI: http://dx.doi. org/10.7554/eLife.18414. 001
E3 ubiquitin ligases and abscisic acid signaling

The ubiquitin proteasome system is involved in the regulation of nearly every aspect of plant growth and development. Protein ubiquitination involves the covalent attachment of ubiquitin to target proteins through a cascade catalyzed by three enzymes known as E1, E2 and E3. E3s, which are of particular interest as they confer substrate specificity during ubiquitination through their diverse substrate recognition domains. Recently, a number of E3s have been identified that actively participate in abscisic acid hormone biology, including regulation of biosynthesis, de-repression or activation of abscisic acid response and degradation of signaling components. In this review, we summarize recent exciting studies of the different type of E3s that target specific mediators of abscisic acid signaling or affect the plants response to the hormone.
Advanced Topics In Types And Programming Languages

The study of type systems for programming languages now touches many areas of computer science, from language design and implementation to software engineering, network security, databases, and analysis of concurrent and distributed systems. This book offers accessible introductions to key ideas in the field, with contributions by experts on each topic. The topics covered include precise type analyses, which extend simple type systems to give them a better grip on the run time behavior of systems; type systems for low-level languages; applications of types to reasoning about computer programs; type theory as a framework for the design of sophisticated module systems; and advanced techniques in ML-style type inference. Advanced Topics in Types and Programming Languages builds on Benjamin Pierce's Types and Programming Languages (MIT Press, 2002); most of the chapters should be accessible to readers familiar with basic notations and techniques of operational semantics and type systems -- the material covered in the first half of the earlier book. Advanced Topics in Types and Programming Languages can be used in the classroom and as a resource for professionals. Most chapters include exercises, ranging in difficulty from quick comprehension checks to challenging extensions, many with solutions.
TIARA genome database: update 2013

The Total Integrated Archive of short-Read and Array (TIARA; http://tiara.gmi.ac.kr) database stores and integrates human genome data generated from multiple technologies including next-generation sequencing and high-resolution comparative genomic hybridization array. The TIARA genome browser is a powerful tool for the analysis of personal genomic information by exploring genomic variants such as SNPs, indels and structural variants simultaneously. As of September 2012, the TIARA database provides raw data and variant information for 13 sequenced whole genomes, 16 sequenced transcriptomes and 33 high resolution array assays. Sequencing reads are available at a depth of ∼30× for whole genomes and 50× for transcriptomes. Information on genomic variants includes a total of ∼9.56 million SNPs, 23 025 of which are non-synonymous SNPs, and ∼1.19 million indels. In this update, by adding high coverage sequencing of additional human individuals, the TIARA genome database now provides an extensive record of rare variants in humans. Following TIARA’s fundamentally integrative approach, new transcriptome sequencing data are matched with whole-genome sequencing data in the genome browser. Users can here observe, for example, the expression levels of human genes with allele-specific quantification. Improvements to the TIARA genome browser include the intuitive display of new complex and large-scale data sets.
Derecho : Group Communication at the Speed of Light

Today’s platforms provide surprisingly little help to developers of high-performance scalable services. To address this, Derecho automates the creation of complex application structures in which each member plays a distinct role. Derecho’s data plane runs a novel RDMAbased multicast protocol that scales exceptionally well. The Derecho control plane introduces an asynchronous monotonic logic programming model, which is used to implement strong guarantees while providing a substantial performance improvement over today’s fastest multicast and Paxos platforms. A novel subgrouping feature allows any single group to be structured into a set of subgroups, or sharded in a regular pattern. These features yield a highly flexible and expressive new programming option for the cloud.
Non-intrusive on-the-fly data race detection using execution replay

This paper presents a practical solution for detecting data races in parallel programs. The solution consists of a combination of execution replay (RecPlay) with automatic on-the-fly data race detection. This combination enables us to perform the data race detection on an unaltered execution (almost no probe effect). Furthermore, the usage of multilevel bitmaps and snooped matrix clocks limits the amount of memory used. As the record phase of RecPlay is highly efficient, there is no need to switch it off, hereby eliminating the possibility of Heisenbugs because tracing can be left on all the time.
Improving outcomes and preventing relapse in cognitive-behavioral therapy

McCabe, Antony, Panic Disorder and Agoraphobia. Ledley, Heimberg, Social Anxiety Disorder. Waters, Craske, Generalized Anxiety Disorder. Franklin, Riggs, Pai, Obsessive-Compulsive Disorder. Feeny, Foa, Posttraumatic Stress Disorder. Rowa, Bieling, Segal, Depression. Lam, Mansell, Bipolar Disorder. McFarlane, Carter, Olmsted, Eating Disorders. Tarrier, Schizophrenia. Rotgers, Sharp, Alcohol Use Disorders. Whisman, McKelvie, Chatav, Couple Distress.
AN ECONOMIC THEORY OF ATTITUDES

This paper examines the role of a person’s attitude, or mental position with regard to an object, in explaining economic behavior. Observations drawn from research and “real-life” examples form the basis for a utility function that incorporates attitudes. Employing the utility function in a model of decision-making, I use comparative static analysis to examine the effect on economic outcomes of price-driven, and other exogenous, attitude changes. The model’s analysis is then applied to investigate the implications of attitudes for motivating people, fighting terrorism, and fighting the spread of AIDS. In each of these cases, incorporating attitudes substantially improves the ability of economic analysis to explain observed outcomes and provides the basis for developing more effective private strategies and public policies.
Caspases signal not only apoptosis but also antigen-induced activation in cells of the immune system.

Members of the caspase family of aspartate-specific cysteine proteases are best known for their involvement in apoptosis (human caspases 2, 3, 6, 7, 8, 9, 10; mouse caspases 2, 3, 6, 7, 8, 9, 12) and the maturation of cytokines such as IL-1 and IL-18 (human caspases 1, 4, 5; mouse caspases 1, 11; Thornberry and Lazebnik 1998; Shi 2002) . Recently, however, there have been a number of reports suggesting that caspases, in particular caspase 8, may have an additional role in the immune system promoting lymphocyte activation and proliferation (Chun et al. 2002; Salmena et al. 2003). The seemingly paradoxical observations that caspase 8 is critical for both activation and death of cells of the immune system are the focus of this review.
Identification of a new catenin: the tyrosine kinase substrate p120cas associates with E-cadherin complexes

p120cas is a tyrosine kinase substrate implicated in ligand-induced receptor signaling through the epidermal growth factor, platelet-derived growth factor, and colony-stimulating factor receptors and in cell transformation by Src. Here we report that p120 associates with a complex containing E-cadherin, alpha-catenin, beta-catenin, and plakoglobin. Furthermore, p120 precisely colocalizes with E-cadherin and catenins in vivo in both normal and Src-transformed MDCK cells. Unlike beta-catenin and plakoglobin, p120 has at least four isoforms which are differentially expressed in a variety of cell types, suggesting novel means of modulating cadherin activities in cells. In Src-transformed MDCK cells, p120, beta-catenin, and plakoglobin were heavily phosphorylated on tyrosine, but the physical associations between these proteins were not disrupted. Association of p120 with the cadherin machinery indicates that both Src and receptor tyrosine kinases cross talk with proteins important for cadherin-mediated cell adhesion. These results also strongly suggest a role for p120 in cell adhesion.
Racism in Soccer? Perception of Challenges of Black and White Players by White Referees, Soccer Players, and Fans

This experiment investigated challenge evaluations in soccer and their relation to prejudice: more precisely, whether skin colour may influence judgments of soccer tackles. Three groups of participants (soccer players, referees, and soccer fans) were asked to evaluate challenges, featuring Black and White players as aggressors and victims in a mixed-design study. Results showed that participants made some differentiations between Black and White players in a challenge evaluation task. Participants were more likely to consider within-group challenges as fouls and were faster to consider challenges made by Black players as fouls. On the other hand, fouls made by White players were seen as more severe. There were no major differences between the participating groups, suggesting that the observed effects were independent of how good players were or whether the participants were referees or not.