Miracle-dz/UniFAR-FTUs huggingface dataset:
A20 inactivation in ocular adnexal MALT lymphoma

Recent studies showed A20 inactivation by deletion, mutation and promoter methylation in ocular adnexal mucosa-associated lymphoid tissue lymphoma. However, the incidences of A20 abnormalities and their clinical impact remain for the most part unknown. It is also unknown whether ABIN-1 and ABIN-2, the components of the A20 NF-κB inhibitor complex, are inactivated by genetic changes in ocular adnexal mucosa-associated lymphoid tissue lymphoma. A total of 105 cases were investigated for A20 mutation/deletion, ABIN-1/2 mutation, MALT1 and IGH involved translocation. Somatic mutation was seen frequently in A20 (28.6%) but rarely in ABIN-1 (1%) and ABIN-2 (1%). A20 mutations were significantly associated with A20 heterozygous deletion, and both were mutually exclusive from the MALT1 or IGH involved translocations. A20 mutation/deletion was also significantly associated with increased expression of the NF-κB target genes CCR2, TLR6 and BCL2. The cases with A20 mutation/deletion required significantly higher radiation dosages to achieve complete remission than those without these abnormalities.
Pregnancy incidence and associated factors among HIV-infected female adolescents in HIV care in urban Côte d'Ivoire, 2009–2013

Objective Adolescents living with HIV are sexually active and engaged in risky sexual behaviors. Knowledge on how and to what extent adolescents in HIV care are affected by pregnancy is needed so as to adopt better preventive services. We estimated 4-year pregnancy incidence and correlates among HIV-infected female adolescents in HIV care in urban Côte d'Ivoire. Design We conducted retrospective analysis of a pediatric prospective cohort of the International epidemiological Databases to Evaluate AIDS (IeDEA) West Africa Collaboration. Female patients with confirmed HIV infection aged 10–19 years, having at least one clinical visit in 2009 to health facilities participating in the pediatric IeDEA West African cohort in Abidjan, Côte d'Ivoire, were included. Data on incident pregnancies were obtained through medical records and interviews with health professionals. Pregnancy incidence rate was estimated per 100 person-years (PY). Poisson regression models were used to identify factors associated with the first pregnancy and provided incidence rate ratios (IRR) with 95% confidence intervals (CI). Results In 2009, 266 female adolescents were included, with a median age of 12.8 years (interquartile range, IQR: 10.0–15.0), CD4 cell counts of 506 cells/mm3 (IQR: 302–737), and 80% on antiretroviral treatment. At the 48th month, 17 new pregnancies were reported after 938 PY of follow-up: 13 girls had one pregnancy while 2 had two pregnancies. Overall incidence rate of pregnancy was 1.8/100 PY (95% CI: 1.1–2.9). High incidence was observed among those aged 15–19 years: 3.6/100 PY (95% CI: 2.2–5.9). Role of maternal death in the risk of pregnancy was at the limit of statistical significance (adjusted IRR: 3.1, 95% CI: 0.9–11.0; ref. non-maternal orphans). Conclusions Incidence of pregnancy among HIV-infected adolescents in care aged 15–19 years reached a level observed in adult cohorts in Sub-Saharan Africa. Health personnel in pediatric care have to intensify their efforts to provide more realistic and age-adapted reproductive health services to meet the needs of adolescent patients already confronting issues of sexuality. Vulnerability of maternal orphans merits further investigation.
The Matrix Template Library: generic components for high-performance scientific computing

The paper discusses the Matrix Template Library, a generic component library for scientific computing. Although MTL consists of a relatively small number of software components, its power and utility arise from the composability of the components and the generic nature of the algorithms. That is, the components can be composed arbitrarily to produce an extremely wide variety of matrix formats. Similarly, each algorithm can operate on any matrix type defined in this fashion.
Towards Optimization of Building Energy and Occupant Comfort Using Multi-Agent Simulation

The primary consumers of building energy are heating, cooling, ventilation, and lighting systems, which maintain occupant comfort, and electronics and appliances that enable occupant functionality. The optimization of building energy is therefore a complex problem highly dependent on unique building and environmental conditions as well as on time dependent operational factors. To provide computational support for this optimization, this paper presents and implements a multi-agent comfort and energy simulation (MACES) to model alternative management and control of building systems and occupants. Human and device agents are used to explore current trends in energy consumption and management of a university test bed building. Reactive and predictive control strategies are then imposed on device agents in an attempt to reduce building energy consumption while maintaining occupant comfort. Finally, occupant agents are motivated by simulation feedback to accept more energy conscious scheduling through multi-agent negotiations. Initial results of the MACES demonstrate potential energy savings of 17% while maintaining a high level of occupant comfort. This work is intended to demonstrate a simulation tool, which is implementable in the actual test bed site and compatible with real-world input to instigate and motivate more energy conscious control and occupant behaviors.
Type I interferon pathway activation across the antiphospholipid syndrome spectrum: associations with disease subsets and systemic antiphospholipid syndrome presentation

Introduction While the type I interferon (IFN-I) pathway is crucial in autoimmunity, its role in antiphospholipid antibody (aPL)-positive subjects, including aPL carriers and antiphospholipid syndrome (APS) patients, is poorly understood. This study aims at characterizing IFN-I pathway activation within the spectrum of aPL-positive subsets. Methods A total of 112 patients [29 aPL carriers, 31 primary APS (PAPS), 25 secondary APS (SAPS), 27 systemic lupus erythematosus (SLE) patients without aPL, and 44 healthy controls (HCs)] were recruited. IFI6, IFI44, IFI44L, MX1, IFI27, OAS1, and RSAD2 gene expression was evaluated in whole blood, and a composite index (IFN score) was calculated. Results An overall activation of the IFN-I pathway was observed across the entire APS spectrum, with differences among genes based on the specific disease subset. The composite score revealed quantitative differences across subsets, being elevated in aPL carriers and PAPS patients compared to HCs (both p < 0.050) and increasing in SAPS (p < 0.010) and SLE patients (p < 0.001). An unsupervised cluster analysis identified three clusters, and correspondence analyses revealed differences in clusters usage across APS subsets (p < 0.001). A network analysis revealed different patterns characterizing different subsets. The associations between IFN-I pathway activation and clinical outcomes differed across APS subsets. Although no differences in gene expression were observed in systemic APS, the network analyses revealed specific gene–gene patterns, and a distinct distribution of the clusters previously identified was noted (p = 0.002). Conclusion IFN-I pathway activation is a common hallmark among aPL-positive individuals. Qualitative and quantitative differences across the APS spectrum can be identified, leading to the identification of distinct IFN-I signatures with different clinical values beyond traditional categorization.
Adherence as a Predictor of the Development of Class-Specific Resistance Mutations: The Swiss HIV Cohort Study

Background Non-adherence is one of the strongest predictors of therapeutic failure in HIV-positive patients. Virologic failure with subsequent emergence of resistance reduces future treatment options and long-term clinical success. Methods Prospective observational cohort study including patients starting new class of antiretroviral therapy (ART) between 2003 and 2010. Participants were naïve to ART class and completed ≥1 adherence questionnaire prior to resistance testing. Outcomes were development of any IAS-USA, class-specific, or M184V mutations. Associations between adherence and resistance were estimated using logistic regression models stratified by ART class. Results Of 314 included individuals, 162 started NNRTI and 152 a PI/r regimen. Adherence was similar between groups with 85% reporting adherence ≥95%. Number of new mutations increased with increasing non-adherence. In NNRTI group, multivariable models indicated a significant linear association in odds of developing IAS-USA (odds ratio (OR) 1.66, 95% confidence interval (CI): 1.04-2.67) or class-specific (OR 1.65, 95% CI: 1.00-2.70) mutations. Levels of drug resistance were considerably lower in PI/r group and adherence was only significantly associated with M184V mutations (OR 8.38, 95% CI: 1.26-55.70). Adherence was significantly associated with HIV RNA in PI/r but not NNRTI regimens. Conclusion Therapies containing PI/r appear more forgiving to incomplete adherence compared with NNRTI regimens, which allow higher levels of resistance, even with adherence above 95%. However, in failing PI/r regimens good adherence may prevent accumulation of further resistance mutations and therefore help to preserve future drug options. In contrast, adherence levels have little impact on NNRTI treatments once the first mutations have emerged.
Innovative and Emerging Technologies in GI Physiology and Disease Colonic myofibroblast cell line stimulates colonoid formation

Hirokawa Y, Yip KHY, Tan CW, Burgess AW. Colonic myofibroblast cell line stimulates colonoid formation. Am J Physiol Gastrointest Liver Physiol 306: G547–G556, 2014. First published January 30, 2014; doi:10.1152/ajpgi.00267. 2013. —A stable and efficient system for the culture of murine colon epithelial cells or crypts is required to facilitate studies of the dynamics and factors affecting colon stem cell niche and crypt formation. Survival of colonic epithelial cells or crypts in vitro was not established until recently, when it was found that exogenous Wnt3A and R-spondin could promote cell survival and formation of spheroids (colonospheres) or some advanced organoids with well-developed crypts (colonoids). However, after 6–8 days in these culture conditions, only small numbers of colonospheres form organoids with crypt-like structures (colonoids). This study describes the use of a myofibroblast cell line and a coculture system that increases the efficiency of colonoid formation from isolated crypts. The enhanced coculture system has significantly improved colonoid-forming efficiency compared with results from previous systems. Crypt formation can be detected as early as day 2. The coculture system will facilitate the characterization of the colon stem cell niche and the changes that occur as a result of perturbations or mutations in colon stem or epithelial cells, such as those that favor precancerous adenoma or cancer.
A Lattice Interpretation Of The Chinese Wall Policy

The Chinese Wall policy was identi ed and so named by Brewer and Nash [2]. This policy arises in the segment of the commercial sector which provides consulting services to other companies. Consultants naturally have to deal with con dential company information for their clients. The objective of the Chinese Wall policy is to prevent information ows which cause con ict of interest for individual consultants. Brewer and Nash develop a mathematical model of the Chinese Wall policy, on the basis of which they claim that this policy \cannot be correctly represented by a Bell-LaPadula model. " In this paper we demonstrate that the Brewer-Nash model is too restrictive to be employed in a practical system. This is due to their treatment of users and subjects as synonymous concepts, with the consequence that they do not distinguish security policy as applied to human users versus security policy as applied to computer subjects. By maintaining a careful distinction between users, principals and subjects, we show that the Chinese Wall policy is just another lattice-based information policy which can be easily represented within the Bell-LaPadula framework.
Porcine complement regulators protect aortic smooth muscle cells poorly against human complement‐induced lysis and proliferation: consequences for xenotransplantation

Abstract: Background: Accelerated atherosclerosis after transplantation has been observed and is characterized by smooth muscle cell proliferation in the graft. Porcine cells are frequently used in models of atherosclerosis and porcine organs are considered for use in transplantation. Complement (C) activation is known to play a major role in rejection of xenografts and is also considered to play a role in the development of atherosclerosis. The aim of this study was to investigate the expression and function of membrane bound regulators of complement (CReg) on porcine aortic smooth muscle cells (PASMC).
Cartilaginous Epiphyses in Extant Archosaurs and Their Implications for Reconstructing Limb Function in Dinosaurs

Extinct archosaurs, including many non-avian dinosaurs, exhibit relatively simply shaped condylar regions in their appendicular bones, suggesting potentially large amounts of unpreserved epiphyseal (articular) cartilage. This “lost anatomy” is often underappreciated such that the ends of bones are typically considered to be the joint surfaces, potentially having a major impact on functional interpretation. Extant alligators and birds were used to establish an objective basis for inferences about cartilaginous articular structures in such extinct archosaur clades as non-avian dinosaurs. Limb elements of alligators, ostriches, and other birds were dissected, disarticulated, and defleshed. Lengths and condylar shapes of elements with intact epiphyses were measured. Limbs were subsequently completely skeletonized and the measurements repeated. Removal of cartilaginous condylar regions resulted in statistically significant changes in element length and condylar breadth. Moreover, there was marked loss of those cartilaginous structures responsible for joint architecture and congruence. Compared to alligators, birds showed less dramatic, but still significant changes. Condylar morphologies of dinosaur limb bones suggest that most non-coelurosaurian clades possessed large cartilaginous epiphyses that relied on the maintenance of vascular channels that are otherwise eliminated early in ontogeny in smaller-bodied tetrapods. A sensitivity analysis using cartilage correction factors (CCFs) obtained from extant taxa indicates that whereas the presence of cartilaginous epiphyses only moderately increases estimates of dinosaur height and speed, it has important implications for our ability to infer joint morphology, posture, and the complicated functional movements in the limbs of many extinct archosaurs. Evidence suggests that the sizes of sauropod epiphyseal cartilages surpassed those of alligators, which account for at least 10% of hindlimb length. These data suggest that large cartilaginous epiphyses were widely distributed among non-avian archosaurs and must be considered when making inferences about locomotor functional morphology in fossil taxa.
Tele-operation of a 6-DOF serial robot using a new 6-DOF haptic interface

This paper presents the kinematic analysis of a new 6-DOF haptic interface and control system analysis for the tele-operation of 6-DOF serial robot. The haptic interface consists of two 3-DOF parallel structures connected with a steering handle. The design satisfies requirements of low mass moment of inertia, quick motion, big rotation, and large applied torques. Kinematics for position and differential motion are developed for the 6-DOF haptic interface. Tele-operation of a 6-DOF serial manipulator using this haptic interface is demonstrated. Experiment results provide comparison of trajectories and forces/torques between 6-DOF haptic interface and 6-DOF serial robot on the Cartesian space.
In vitro studies on the signal transduction of thyroidal uptake of 18F-FDG and 131I-Iodide.

UNLABELLED Glucose metabolism in radioiodine-negative metastases of differentiated thyroid carcinomas (DTC) may still be increased by thyroid-stimulating hormone (TSH) as demonstrated by PET with 18F-FDG. The mechanisms of signal transduction involved in that process are as yet not completely understood. Therefore, the aim of this study was to investigate the effects of TSH, of an analog of cyclic adenosine monophosphate (dibutyryl cyclic AMP (Bu)2cAMP), and of inhibitors of the phosphatidylinositol 3-kinase (PI3-kinase) and of the protein kinase A (PKA) on 18F-FDG and radioiodide uptake in the thyroid cell line FRTL-5. METHODS FRTL-5 cells were cultured in the presence of hormones with or without 1 mU/ mL TSH. Glucose carrier (GLUT-1) was determined by Western blot analysis. Cells were incubated with 0.5-1.0 MBq/mL 18F-FDG for 1 h or 18-37 kBq/mL 131I for 45 min, respectively, and tracer uptake was related to protein concentration. (Bu)2cAMP (1 mmol/L) was used as cAMP enhancer, H89 (0.25-25 micromol/L) as selective PKA inhibitor, and wortmannin (1 micromol/L) as inhibitor of PI3-kinase. RESULTS TSH induced a 2.6-fold +/- 0.5 increase of radioiodide uptake in FRTL-5 cells (P < 0.001, n = 8). The use of wortmannin inhibited TSH-induced uptake of 131I only moderately by 21.1% +/- 3.5% (P < 0.05, n = 8), whereas H89 markedly blocked the effect of TSH by 53.8% +/- 16.7% (P < 0.001, n = 8). TSH enhanced GLUT-1 concentration of FRTL-5 cell membrane preparations by a factor of 1.6 (n = 3). TSH-treated cells showed a 2.6-fold increased uptake of 18F-FDG (P < 0.001, n = 20). Stimulation by (Bu)2cAMP analogously increased 18F-FDG uptake (P < 0.001, n = 20). Wortmannin, but not H89, significantly inhibited TSH- and (Bu)2cAMP-stimulation of 18F-FDG uptake by 42% +/- 25% (P < 0.001, n = 20) and 42% +/- 31% (P < 0.001, n = 20), respectively. CONCLUSION The effect of TSH and cAMP on 18F-FDG uptake by FRTL-5 cells is mediated by PI3-kinase and not by PKA, thus differing from the mechanism of radioiodide accumulation of this cell line. This observation is one possible explanation for the persistence of TSH-dependent 18F-FDG uptake in radioiodine-negative metastases of DTC.
Approaches to supporting lactation and breastfeeding for very preterm infants in the NICU: a qualitative study in three European regions

Objectives To explore differences in approaches to supporting lactation and breastfeeding for very preterm infants in neonatal intensive care units (NICU) in 3 European regions. Design Qualitative cross-sectional study carried out by means of face-to-face semistructured interviews. Verbatim transcripts were coded using a theoretical framework derived from the literature and supplemented by data-driven concepts and codes. Setting 4 purposively selected NICUs in each of 3 European regions in 2010 (Ile-de-France in France, Lazio in Italy, and the former Trent region in the UK). Participants NICU staff members (n=22). Results Policies and practices for managing mother's own milk for very preterm babies differed between regions, and were much more complex in Ile-de-France than in the Trent or Lazio regions. Staff approaches to mothers to initiate lactation differed by region, with an emphasis on the nutritional and immunological value of human milk in the Trent region and on the ‘normalising’ effect of breastfeeding on the mother-child relationship in Lazio. French and English staff expressed conflicting opinions about the use of bottles, which was routine in Italy. Italian informants stressed the importance of early maternal milk expression and feeding, but also mentioned discharging infants home before feeding at the breast was established. In Ile-de-France and Trent, successful feeding from the breast was achieved before discharge, although this was seen as a factor that could prolong hospitalisation and discourage continued breastfeeding for some women. Conclusions Targeted health promotion policies in the NICU are necessary to increase the number of infants receiving their mother's milk and to support mothers with transfer of the infant to the breast. Integrating knowledge about the different approaches to lactation and breastfeeding in European NICUs could improve the relevance of recommendations in multiple cultural settings.
The Research on Causes of Megacity Problem Based on Spatial Disequilibrium

By using spatial models with lag and error and through many experiments, this paper uses distance threshold which can maximize spatial autocorrelation, instead of setting spatial weight matrix by adjacent boundaries, making measurement better suit the features of our country’s cities distribution to explore the reasons for big city disease empirically. It finds that distribution of public service distribution and spatial non-equilibrium are factors for excessive population agglomeration and therefore big city disease, and provides solutions for the factors mentioned above.
Domain adaptation for semantic role labeling in the biomedical domain

MOTIVATION Semantic role labeling (SRL) is a natural language processing (NLP) task that extracts a shallow meaning representation from free text sentences. Several efforts to create SRL systems for the biomedical domain have been made during the last few years. However, state-of-the-art SRL relies on manually annotated training instances, which are rare and expensive to prepare. In this article, we address SRL for the biomedical domain as a domain adaptation problem to leverage existing SRL resources from the newswire domain. RESULTS We evaluate the performance of three recently proposed domain adaptation algorithms for SRL. Our results show that by using domain adaptation, the cost of developing an SRL system for the biomedical domain can be reduced significantly. Using domain adaptation, our system can achieve 97% of the performance with as little as 60 annotated target domain abstracts. AVAILABILITY Our BioKIT system that performs SRL in the biomedical domain as described in this article is implemented in Python and C and operates under the Linux operating system. BioKIT can be downloaded at http://nlp.comp.nus.edu. sg/software. The domain adaptation software is available for download at http://www.mysmu. edu/faculty/jingjiang/software/DALR.html. The BioProp corpus is available from the Linguistic Data Consortium http://www.ldc. upenn.edu.