Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the IBD 5 locus and potential gene-gene interactions in Crohn ’ s disease

Background and aims: Genetic variation in the chromosome 5q31 cytokine cluster (IBD5 risk haplotype) has been associated with Crohn’s disease (CD) in a Canadian population. We studied the IBD5 risk haplotype in both British and Japanese cohorts. Disease associations have also been reported for CARD15/NOD2 and TNF variants. Complex interactions between susceptibility loci have been shown in animal models, and we tested for potential gene-gene interactions between the three CD associated loci. Methods: Family based association analyses were performed in 457 British families (252 ulcerative colitis, 282 CD trios) genotyped for the IBD5 haplotype, common CARD15, and TNF−857 variants. To test for possible epistatic interactions between variants, transmission disequilibrium test analyses were further stratified by genotype at other loci, and novel log linear analyses were performed using the haplotype relative risk model. Case control association analyses were performed in 178 Japanese CD patients and 156 healthy controls genotyped for the IBD5 haplotype. Results: The IBD5 haplotype was associated with CD (p=0.007), but not with UC, in the British Caucasian population. The CARD15 variants and IBD5 haplotype showed additive main effects, and in particular no evidence for epistatic interactions was found. Variants from the IBD5 haplotype were extremely rare in the Japanese. Conclusions: The IBD5 risk haplotype is associated with British CD. Genetic variants predisposing to CD show heterogeneity and population specific differences.
The Macrolide-Lincosamide-Streptogramin B Resistance Determinant from Clostridium difficile 630 Contains Two erm(B) Genes

ABSTRACT The ErmB macrolide-lincosamide-streptogramin B (MLS) resistance determinant from Clostridium difficile 630 contains two copies of an erm(B) gene, separated by a 1.34-kb direct repeat also found in an Erm(B) determinant from Clostridium perfringens. In addition, both erm(B) genes are flanked by variants of the direct repeat sequence. This genetic arrangement is novel for an ErmB MLS resistance determinant.
Depiction and imagination

Abstract Depiction and imagination are intimately linked. In this article, I discuss the role imagination (as well as inference and knowledge/belief) plays in depiction, with a focus on photographic depiction. I partly embrace a broadly Waltonian view, but not always, and not always for Walton’s own reasons. In Walton’s view, imagination plays a crucial role in depiction. I consider the objection to his view that not all cases of depiction involve imagination – for instance, documentary photographs. From this discussion, two points will emerge: first, we will see that it is an unnecessary mistake to insist too heavily on the fact that photographs are produced in a mechanical way (as opposed to, say, paintings), and second, we will see that the notion of “imagining-seeing”, as it is articulated by Walton, is perhaps too strong and does not entirely do justice to the external character of the role imagination plays here. Focusing mainly on photographs, I then illustrate the view I want to advocate by a series of different cases, where the nature of the role that imagination, knowledge/belief, and inference play in depiction will become apparent.
Evaluation of a Dynamic Bayesian Belief Network to Predict Osteoarthritic Knee Pain Using Data from the Osteoarthritis Initiative

The most common cause of disability in older adults in the United States is osteoarthritis. To address the problem of early disease prediction, we have constructed a Bayesian belief network (BBN) composed of knee OA-related symptoms to support prognostic queries. The purpose of this study is to evaluate a static and dynamic BBN--based on the NIH Osteoarthritis Initiative (OAI) data--in predicting the likelihood of a patient being diagnosed with knee OA. Initial validation results are promising: our model outperforms a logistic regression model in several designed studies. We can conclude that our model can effectively predict the symptoms that are commonly associated with the presence of knee OA.
Susceptibility testing of Dientamoeba fragilis ATCC 30948 with iodoquinol, paromomycin, tetracycline, and metronidazole

Susceptibility testing was performed on Dientamoeba fragilis ATCC 30948 in a dixenic culture with Klebsiella pneumoniae and Bacteroides vulgatus. D. fragilis was cocultured with the bacteria in TYGM-9 medium (ATCC medium 1171). The activities of antiparasitic drugs were assessed by counting viable D. fragilis trophozoites with a hemacytometer by trypan blue exclusion. The minimal amebicidal concentrations of the following four drugs were determined: iodoquinol at 128 micrograms/ml, paromomycin at 16 micrograms/ml, tetracycline (questionably) at 32 micrograms/ml, and metronidazole at 32 micrograms/ml.
Structural Insight into the Binding Diversity between the Tyr-phosphorylated Human EphrinBs and Nck2 SH2 Domain*

The binding interaction between the Nck2 SH2 domain and the phosphorylated ephrinB initiates a critical pathway for the reverse signaling network mediated by Eph receptor-ephrinB. Previously, the NMR structure and Tyr phosphorylations of the human ephrinB cytoplasmic domain have been studied. To obtain a complete story, it would be of significant interest to determine the structure of the Nck2 SH2 domain that shows a low sequence identity to other SH2 domains with known structures. Here, we report the determination of the solution structure of the human Nck2 SH2 domain and investigate its interactions with three phosphorylated ephrinB fragments by NMR spectroscopy. The results indicate that: 1) although the human Nck2 SH2 domain adopts a core tertiary fold common to all SH2 domains, it owns some unique properties such as a shorter C-terminal helix and unusual electrostatic potential surface. However, the most striking finding is that the C-terminal tail of the human Nck2 SH2 domain adopts a short antiparallel β-sheet that, to the best of our knowledge, has never been identified in other SH2 domains. The truncation study suggests that one function of the C-terminal tail is to control the folding/solubility of the SH2 domain. 2) In addition to [Tyr(P)304]ephrinB2301–322 and [Tyr(P)316]ephrinB2301–322, here we identified [Tyr(P)330]ephrinB2324–333 also capable of binding to the SH2 domain. The detailed NMR study indicated that the binding mechanisms for the three ephrinB fragments might be different. The binding with [Tyr(P)304]-ephrinB2301–322 and [Tyr(P)316]ephrinB2301–322 might be mostly involved in the residues over the N-half of the SH2 domain and provoked a significant increase in the backbone and side chain dynamics of the SH2 domain on the microsecond-millisecond time scale. In contrast, binding with [Tyr(P)330]ephrinB2324–333 might have most residues over both halves engaged but induced less profound conformational dynamics on the μs-ms time scale.
Epidemiology, risk factors, and prognosis of capillary leak syndrome in pediatric recipients of stem cell transplants: a retrospective single‐center cohort study

CLS involves sudden loss of intravascular fluids into the interstitial spaces. CLS was described as a possible complication after SCT. Few studies report the incidence of CLS in pediatric populations. We aimed to assess CLS incidence, its risk factors, and impact on the survival. The clinical charts of patients <18 years of age transplanted at our institution between 2002 and 2012 were reviewed. CLS was defined by weight gain >3% in 24 hours and positive intake balance despite furosemide administration. In total, 234 patients underwent 275 allogeneic SCT procedures in the analyzed time frame. Fifteen patients developed CLS (5.4%). The probability of developing CLS was significantly increased in patients suffering from sepsis (14.3% vs 0.6%, P<.001). Patients with CLS exhibited an increased risk of acute GvHD in the first 30 days after SCT (10.8% vs 1.8%, P=.002). Ten of the patients with CLS required intensive care. CLS strongly impacts OS at day +100 after SCT and is a predictive factor of TRM at the same date (42.9% vs 5%, P<.0001). The biological relation among sepsis, GvHD, and CLS development in terms of cytokine release and endothelial damage warrants further studies.
Lack of genetic susceptibility of KCNJ11 E23K polymorphism with risk of type 2 diabetes in an Iranian population

Abstract Aims: The KCNJ11 gene has a strong effect on glucose-stimulated insulin secretion. Common polymorphism KCNJ11 E23K has been reported to be associated with type 2 diabetes in various European-descent populations. However, there were inconsistent results in previous studies in Asian populations, and no study has been carried out in the Iranian population. We examined the contribution of KCNJ11 E23K variant in the susceptibility to type 2 diabetes in the Iranian population. Methods: We undertook a population-based association study between type 2 diabetes and E23K mutation using 400 people with type 2 diabetes and 420 controls. Genotyping was performed using TaqMan technology on an ABI7300 system. Results: No significant difference was observed in either genotype distribution (p = 0.71) or allele frequency (p = 0.88) between individuals with and without type 2 diabetes. After adjusting for the confounding effects of age, gender and body mass index (BMI), no significant effect of genotypes on type 2 diabetes was found regarding any genetic models tested (recessive, dominant or co-dominant models). Following subgroup analysis of individuals with and without diabetes based on BMI, a nominal significant association was observed between type 2 diabetes in the presence of obesity and E23K genotype in the recessive model (p = 0.03). Conclusion: The KCNJ11 E23K polymorphism is not associated with genetic susceptibility to type 2 diabetes in the Iranian population; however, it may play a role in disease progression in the presence of obesity.
Phase-field simulations of nuclei and early stage solidification microstructures

To investigate the local properties of heterogeneous nuclei on substrates, a phase-field model is extended to incorporate volume constraints and a third order line tension in the gradient free energy density formulation. The new model is applied to sessile drop simulations of Cu nuclei on Ni substrates to precisely analyse 3D equilibrium shapes and diffusion processes across the phase boundaries. In particular, the formalism with higher order potentials is used to investigate the length-scale dependent effect of the line tension on Young’s force balance at triple lines in 3D. The employment of parallel and adaptive simulation techniques is essential for three-dimensional numerical computations. Early stage solidification microstructures of cubic Ni crystals are simulated by scale-bridging molecular dynamics (MD) and phase-field (PF) simulations. The domain of the PF computations is initialized by transferring MD data of the atomic positions and of the shape of the nuclei. The combined approach can be used to study the responses of microstructures upon nucleation.
Autonomous induction of proliferation, JNK and NF‐κB activation in primary resting T cells by mobilized CD28

Induction of proliferation in primary resting T cells requires engagement of both the antigen‐specific TCR and the co‐stimulatory receptor CD28. Here we report that CD28 functions as an autonomous mitogenic receptor which is mobilized by TCR signaling through cytoskeletal rearrangement. Shortcutting of TCR‐dependent CD28 recruitment by stimulation with monoclonal antibodies specific for mobilized CD28 results in maximum proliferation and IL‐2 secretion in primary resting T cells without activation of ZAP‐70, a central component of the TCR's signal transduction machinery. Engagement of mobilized CD28 fully activates the c‐Jun N‐terminal kinase cascade and translocation of NF‐κB, two key targets of signal integration in co‐stimulation. We propose a two‐step activation model for co‐stimulation in primary resting T cells in which antigen recognition recruits co‐stimulatory receptors which then autonomously transduce signals promoting T cell proliferation.
Positive Technology as a Driver for Health Engagement

Despite the fact that older adults are healthier than in the past, the current trend of an ageing population implies an increased risk and severity of chronic diseases. Low-resource healthcare systems face increased organizational healthcare costs, which is likely to result in an allocation of limited health resources. Healthcare organizations themselves must deal with patients' increasing need for a more active role in all the steps of the care & cure process. Technological advances may play a crucial role in sustaining people's health management in daily life, but only if it is "ecologically" designed and well-attuned to people's health needs and expectations. Healthcare is more and more called to orient innovative research approaches that recognize the crucial role of a person's engagement in health and well-being. This will enable patients to reach a higher quality of life and achieve a general psychophysical well-being. Thus, positive technological innovation can sustain people's engagement in health and invoke community empowerment, as we shall discuss in this document.
Factors Influencing Planning for Retirement

This research identified four different aspects of decisions to retire. Firstly, it describes the planned retirement age decision of the sample in terms of an ogive; secondly, it identifies the factors influencing the decisions to retire by retirees and contrasts them with factors important to non-retirees. Thirdly, it reports a model of the probability of working full time because those who find fulltime employment are in a better position not only to plan for their retirement but also to have a secure income at retirement; and finally, it analyses the planned retirement age of non-retired Australians and investigates further the determinants of planned retirement ages.
Microfluidique 3D et actionneurs magnétiques : de leur intégration à la préparation d'échantillons biologiques

Les puces microfluidiques sont des elements cles pour la manipulation et l'analyse de solutions et d'echantillons biologiques. Elles facilitent les etudes aux echelles microscopiques et sont le fondement du concept de laboratoire sur puce, a la pointe des diagnostics medicaux. L'objectif de ces travaux de these a ete d'explorer les possibilites fonctionnelles offertes par les architectures microfluidiques 3D, dans le cadre du developpement d'outils diagnostiques reposant sur le tri, le marquage et la manipulation de cellules. Ces fonctions ont ete validees sur des sous-populations de monocytes, qui sont des marqueurs de maladies inflammatoires. Afin de couvrir une chaine coherente d'etapes necessaires au pretraitement des echantillons biologiques complexes, trois fonctions complementaires ont ete etudiees : le tri par taille par filtration hydrodynamique, le tri immunologique par separation magnetique et le marquage sur puce par microparticules magnetiques. En vue d'effectuer des reactions de marquage (sondes fluorescentes ou microbilles magnetiques), un micro-melangeur reposant sur la separation et recombinaison de flux (transformation du boulanger) a ete fabrique et caracterise. Des experiences de test des dispositifs pour les melanges fluoresceine/eau et cellules/microbilles sont proposees, ainsi que les modeles analytiques et numeriques associes. De nouvelles approches de tri par taille par filtration hydrodynamique ont ete etudiees, en realisant des structures 3D en "bypass", qui rendent possible une strategie de melange adaptee aux cellules et particules. Un modele analytique des ecoulements et de l'efficacite de tri et de melange est propose, ainsi qu'une caracterisation des dispositifs. Il a ete de plus demontre que cette approche permettait egalement de realiser la separation d'especes sub-micrometriques comme les microparticules sanguines. Tous les systemes microfluidiques 3D ont ete obtenus par une technique originale d'empilement (laminage) de films secs photosensibles, reduisant nettement le temps de micro-fabrication et compatibles avec les procedes standards. Cette technique de fabrication permet egalement l'integration de micro-sources magnetiques dans les laboratoires sur puce par la realisation de micro-bobines planaires sous des canaux microfluidiques. En couplant les effets des micro-bobines integrees aux champs generes par des aimants exterieurs, nous apportons la preuve de concept de systemes pour la separation, la deviation et le piegeage de microbilles magnetiques. Les modeles (champs et force magnetiques) et la caracterisation des dispositifs seront presentes. Nous aborderons egalement la realisation d'instrumentation specifique (source de courant) pour l'actionnement des bobines, permettant le controle (temporel et en intensite) des champs magnetiques appliques.
Factor analysis of household factors: are they associated with respiratory conditions in Chinese children?

BACKGROUND We explored methods to develop uncorrelated variables for epidemiological analysis models. They were used to examine associations between respiratory health outcomes and multiple household risk factors. METHODS We analysed data collected in the Four Chinese Cities Study (FCCS) to examine health effects on prevalence rates of respiratory symptoms and illnesses in 7058 school children living in the four Chinese cities: Lanzhou, Chongqing, Wuhan, and Guangzhou. We used factor analysis approaches to reduce the number of the children's lifestyle/household variables and to develop new uncorrelated 'factor' variables. We used unconditional logistic regression models to examine associations between the factor variables and the respiratory health outcomes, while controlling for other covariates. RESULTS Five factor variables were derived from 21 original variables: heating coal smoke, cooking coal smoke, socioeconomic status, ventilation, and environmental tobacco smoke (ETS) and parental asthma. We found that higher exposure to heating coal smoke was associated with higher reporting of cough with phlegm, wheeze, and asthma. Cooking coal smoke was not associated with any of the outcomes. Lower socioeconomic status was associated with lower reporting of persistent cough and bronchitis. Higher household ventilation was associated with lower reporting of persistent cough, persistent phlegm, cough with phlegm, bronchitis, and wheeze. Higher exposure to ETS and the presence of parental asthma were associated with higher reporting of persistent cough, persistent phlegm, cough with phlegm, bronchitis, wheeze, and asthma. CONCLUSIONS Our study suggests that independent respiratory effects of exposure to indoor air pollution, heating coal smoke, and ETS may exist for the studied children.
Tandem‐base mutations occur in mouse liver and adipose tissue preferentially as G:C to T:A transversions and accumulate with age

Tandem‐base mutations (TBM) are associated with ultraviolet light and other mutagens. Herein, we report an age‐ and tissue‐specific difference in the frequency of spontaneous TBM in Big Blue® transgenic mice. A total of 390 mutants from liver and adipose tissue contained 17 and 4 TBM, respectively, while no TBM were detected in 683 mutants from six other tissues. There was a proportional increase in the frequency of TBM in liver with age (29 days postconception to 25 months of age). Nine TBM (43%) were GG to TT transversions that preferentially occurred at specific sites. The remaining 12 mutants contained at least one transversion mutation each. We speculate that the increase of TBM in liver and adipose tissue with age is due to chronic mutagen exposure, perhaps derived from fat in the diet. Environ. Mol. Mutagen. 33:320–324, 1999 © 1999 Wiley‐Liss, Inc.
Spatial variability of liquid water path in marine low cloud : Part II . Geographic distribution and dependence upon large-scale parameters

In part I of this study we focused upon models to describe the mesoscale spatial variability of cloud liquid water path LWP in low cloud. Here, we construct simple, exploratory, climatologies of the spatial variability characteristics of marine low clouds for one season and two regions of the East Pacific. The climatologies show interesting and important geographical variability. Large scale meteorological conditions are assessed for each MODIS scene using NCEP/NCAR reanalysis data, and regression analysis is used to assess relationships between large-scale forcings and mesoscale variability. Cloud fraction and LWP homogeneity are both strongly correlated with lower tropospheric stability LTS on timescales of days to weeks. While marine boundary layer (MBL) depth zi is itself strongly correlated with LTS , cloud fraction is not found to correlate particularly well with zi, suggesting that it is LTS itself, rather than zi that is the primary determinant of low cloud fraction. However, MBL thermodynamic and cloud mesoscale variability does appear to be influenced by zi. This result reflects the findings that mesoscale variability is an increasing function of the characteristic lengthscale of the mesoscale cellular convection (MCC), and that the characteristic lengthscale scales with zi. The observed changes in cloud mesoscale variability from shallow stratus-topped MBLs through to trade cumulus can be accounted for using a physical framework that links MBL thermodynamic variability and cloud liquid water path variability using a pdf formulation. The pdf width is strongly tied to the MBL depth, and it is suggested that this framework, with scalings constrained by observations, is suitable for the parameterization of low cloud subgrid spatial variability in large-scale numerical models.
A new strategy for bridging the semantic gap in image retrieval

Content-based image retrieval CBIR research is currently faced with the so called the 'semantic gap' problem. CBIR researchers work at the near end of the gap, applying computer science methods to bridge the gap. Cognitive psychology researchers work at the far end of the gap, studying how humans perceive things in their environment. This article looks at the literature from a new perspective, and presents a structured analysis of what CBIR researchers have done, in their efforts to bridge the gap. This analysis suggests that more emphasis should be placed on studying the far end of the gap. The second part of this article discusses a study conducted at the far end of the gap, to begin the process of developing and testing techniques for externalising and analysing the visual concepts that are evoked by images. This more disciplined approach has the potential to guide researchers in their efforts to bridge the gap.
A New Algorithm for Minimum Cost Binary Trees

A new algorithm for constructing minimum cost binary trees in $O(n \log n)$ time is presented. The algorithm is similar to the well-known Hu-Tucker algorithm. Our proof of validity is based on finite variational methods and is therefore quite different and somewhat simpler than the proof for the Hu-Tucker algorithm. Our proof also yields some additional information about the structure of minimum cost binary trees. This permits a linear time implementation of our algorithm in a special case.