Miracle-dz/UniFAR-FTUs huggingface dataset:
Morphometric analysis of the porcine gastrointestinal tract in a 10-day high-dose indomethacin administration with or without probiotic bacteria Escherichia coli Nissle 1917

Background: Nonsteroidal anti-inflammatory drugs may cause severe injury to all parts of the gastrointestinal tract. It has been hypothesised that probiotic bacteria might reduce this adverse effect. The aim of this study was to perform a morphometric evaluation of the gastrointestinal tract in experimental pigs treated using a 10-day high-dose of indomethacin with or without Escherichia coli Nissle 1917 (EcN). Methods: Twenty-four healthy mature pigs were included: Group A (controls; 6 animals), Group B (EcN; n = 6), Group C (indomethacin; n = 6) and Group D (EcN & indomethacin; n = 6). EcN (3.5 × 1010 live bacteria/day for 14 days) and/or indomethacin (15 mg/kg/day for 10 days) were administered. Specimens of the stomach, small and large bowel were routinely processed for microscopic examination. The height of glandular mucosa, height and width of interfoveolar spaces and villi and basement size of epithelial cells were evaluated. Results: Different effects of indomethacin and EcN on particular parts of the gastrointestinal tract were shown. The indomethacin and probiotics group demonstrated a significantly lower height of cryptal mucosa and colonocytes and widening of the basement size of colonocytes compared to controls (p = 0.004; p < 0.001; p = 0.025). The height of cryptal mucosa was significantly higher in the EcN group compared to controls (p = 0.001). Conclusions: Indomethacin alone induced marked adaptation of the gastric mucosa. EcN alone provided a significant favourable trophic effect on the colonic mucosa. However, indomethacin and probiotics administered together comprise the worst impact on all porcine stomach, small and large bowel.
Ventilator-associated pneumonia: Bacteremia and death after traumatic injury

BACKGROUND: The implications of bacteremia in critically ill patients are uncertain. Some reports suggest bacteremia is linked to higher mortality whereas others do not. These differences may, in part, be because of differences in patient cohorts. To address the potential independent relationship between bacteremia and outcome, we focused on critically ill trauma patients with ventilator-associated pneumonia (VAP), of whom a significant proportion had concomitant bacteremia. We tested the hypothesis that bacteremia was associated with death in trauma patients who developed VAP. METHODS: In this retrospective cohort study, we measured the incidence of bacteremia associated with VAP and compared the case-fatality rates between patients with and without bacteremia. We adjusted for other mortality risk factors and possible confounders in two ways. First, using forward conditional logistic regression and second, we calculated propensity scores and then adjusted for this score in a regression model. RESULTS: There were 554 with VAP. Patients with bacteremia had a 26% case-fatality rate (19 of 74 patients). Patients with VAP alone had a case-fatality rate of 12% (56 of 480 patients). The unadjusted relative risk (RR) for death associated with bacteremia was 2.2 (95% confidence interval = 1.4–3.5). After adjusting for age, acute physiology score, and severity of injury, patients with bacteremia had an increased risk of death compared with patients with VAP alone (adjusted odds ratio = 2.65, 95% confidence interval = 1.36–5.17). Our propensity score analysis resulted in a similar association between bacteremia and mortality. CONCLUSIONS: VAP with bacteremia is associated with an increased mortality in comparison with VAP alone after severe traumatic injury.
Triplex-Induced DNA Damage Response

Cellular DNA damage response is critical to preserving genomic integrity following exposure to genotoxic stress. A complex series of networks and signaling pathways become activated after DNA damage and trigger the appropriate cellular response, including cell cycle arrest, DNA repair, and apoptosis. The response elicited is dependent upon the type and extent of damage sustained, with the ultimate goal of preventing propagation of the damaged DNA. A major focus of our studies is to determine the cellular pathways involved in processing damage induced by altered helical structures, specifically triplexes. Our lab has demonstrated that the TFIIH factor XPD occupies a central role in triggering apoptosis in response to triplex-induced DNA strand breaks. We have shown that XPD co-localizes with γH2AX, and its presence is required for the phosphorylation of H2AX tyrosine142, which stimulates the signaling pathway to recruit pro-apoptotic factors to the damage site. Herein, we examine the cellular pathways activated in response to triplex formation and discuss our finding that suggests that XPD-dependent apoptosis plays a role in preserving genomic integrity in the presence of excessive structurally induced DNA damage.
Full diversity binary message-passing decoders for block fading channels

Binary message-passing (BMP) decoders for root-low-density parity-check (LDPC) codes over block fading channels (BFC) are studied using density evolution (DE) and outage boundary analysis. A-priori channel estimation techniques suitable for root-LDPC code are proposed based on DE. The results show that BMP decoders can achieve full diversity performance if soft decisions from the channel are available.
A tangibility approach to affective interaction

People use their cognitive, perceptual-motor and affective skills to interact with electronic products. In normal language we could say that interacting with products requires not only knowing and doing, but also feeling. Lately, researchers on human-computer and human-product interaction realized that a one sided cognitive approach will not solve all the complexity of human product interaction. New approaches focus on the aspects of the perceptual motor skills or on the affective skills and are called respectively tangible interaction and affective interaction. Instead of focussing on one type of skill, design has always been about integrating. Therefore this design research thesis integrates the cognitive, perceptual-motor and affective aspects of product interaction. It advocates a tangibility approach to affective interaction to answer the research question. âHow can we design for human product interaction, so that the product gets information aboutâ¦ what we âknowâ and how we âfeelâ from the way we âdoâ this interaction, in order to adapt to this information? â This thesis follows a âResearch through Designâ approach which generates new knowledge through the act of designing. The design process is used as a form of research where the results contribute to the design for emotionally intelligent products. The context of the design case for this thesis is a typical every day experience, yet filled with a diversity of emotions, i.e., the experience of waking up. The current accompanying product, the alarm clock, is a perfect example of a product that is completely unaware of, and inappropriate for the many different emotional experiences of the user. The design process is structured along the lines of three design questions: 1. What are relevant emotional aspects for a context for experience? 2. How can a product recognize and express these aspects? 3. How can the product adapt to the person on the basis of this information?
Vertebral compression fractures: a review of current management and multimodal therapy

Vertebral compression fractures are a prevalent disease affecting osteoporotic patients. When symptomatic, they cause significant pain and loss of function and have a high public health impact. In this paper we outline the diagnosis and management of these patients, with evidence-based review of treatment outcomes for the various therapeutic options. Diagnosis involves a clinical history focusing on the nature of the patient’s pain as well as various imaging studies. Management is multimodal in nature and starts with conservative therapy consisting of analgesic medication, medication for osteoporosis, physical therapy, and bracing. Patients who are refractory to conservative management may be candidates for vertebral augmentation through either vertebroplasty or kyphoplasty.
Physiological State, Growth Mode, and Oxidative Stress Play a Role in Cd(II)-Mediated Inhibition of Nitrosomonas europaea 19718

ABSTRACT The goal of this study was to determine the impact of physiological growth states (batch exponential and batch stationary growth) and growth modes (substrate-limited chemostat, substrate-sufficient exponential batch, and substrate-depleted stationary batch growth) on several measures of growth and responses to Cd(II)-mediated inhibition of Nitrosomonas europaea strain 19718. The specific oxygen uptake rate (sOUR) was the most sensitive indicator of inhibition among the different responses analyzed, including total cell abundance, membrane integrity, intracellular 16S rRNA/DNA ratio, and amoA expression. This observation remained true irrespective of the physiological state, the growth mode, or the mode of Cd(II) exposure. Based on the sOUR, a strong time-dependent exacerbation of inhibition (in terms of an inhibition coefficient [Ki]) in exponential batch cultures was observed. Long-term inhibition levels (based on Ki estimates) in metabolically active chemostat and exponential batch cultures were also especially severe and comparable. In contrast, the inhibition level in stationary-phase cultures was 10-fold lower and invariable with exposure time. Different strategies for surviving substrate limitation (a 10-fold increase in amoA expression) and starvation (the retention of 16S rRNA levels) in N. europaea cultures were observed. amoA expression was most negatively impacted by Cd(II) exposure in the chemostat cultures, was less impacted in exponential batch cultures, and was least impacted in stationary batch cultures. Although the amoA response was consistent with that of the sOUR, the amoA response was not as strong. The intracellular 16S rRNA/DNA ratio, as determined by fluorescence in situ hybridization, also did not uniformly correlate with the sOUR under conditions of inhibition or no inhibition. Finally, Cd(II)-mediated inhibition of N. europaea was attributed partially to oxidative stress.
Hybrid analog and digital beamforming for OFDM-based large-scale MIMO systems

Hybrid analog and digital beamforming is a promising technique for large-scale MIMO systems since it can achieve a performance close to the performance of the conventional fully-digital beamforming schemes, but with much lower hardware implementation complexity and power consumption. One of the major challenges in hybrid beamforming is to design the hybrid beamformers for broadband systems with frequency-selective channels. This is because in broadband systems, it is desirable to design the same analog beamformers for the entire band while adapting digital beamformers in each frequency tone. In this paper, we consider the hybrid beamforming design for large-scale MIMO systems with orthogonal frequency division multiplexing (OFDM) modulation. Specifically, we propose a unified heuristic design for two different hybrid beamforming structures, the fully-connected and partially-connected structures, to maximize the overall spectral efficiency of a broadband system. Numerical results show that the proposed algorithm outperforms the existing hybrid beamforming designs and further the proposed algorithm for the fully-connected structure can achieve spectral efficiency close to that of the optimal fully-digital solution with much less number of RF chains.
The Impact of Brainstorming Strategies Iranian EFL Learners' Writing Skill Regarding their Social Class Status

The present study aimed at investigating the effect of brainstorming strategy on EFL learners' writing performance. To this end, eighty four Iranian EFL intermediate learners were invited in this study. Their performance on the pretest and posttest in both experimental and control groups has been taken into account. As data analysis indicated, the experimental group's performance on the post test was considerably higher than that of their performance on the pre-test. The results of the Analysis of Covariance revealed that the instruction of brainstorm strategy had a positive effect on EFL learners’ writing achievements. It also made them more active, which might make them responsible for their own learning and likely to learn better.
Behçet's disease in Lebanon: report of 100 cases.

PURPOSE To present clinical features of Behçet's disease in Lebanon and to evaluate the efficacy of treatment. PATIENTS AND METHODS The 100 patients are seen at Hotel-Dieu de France Hospital of Beirut between 1980 and 1992. Diagnostic criteria are those of the Behçet Syndrome Research Committee of Japan. RESULTS Recurrent oral ulcers are present in 95% of cases, genital ulcers in 78%, ocular manifestations are more frequent than those of several studies whereas skin lesions and vascular signs are less frequent. Joint involvement are recorded in 65% of cases and neurological one in 14%. The effectiveness of colchicine therapy is confirmed for mucocutaneous lesions and arthritis. Immunosuppressive agents are more beneficial than steroids alone on serious uveitis. An aggressive treatment with corticosteroids and immunosuppressive drugs improve the prognosis of meningoencephalitis. CONCLUSION Behçet's disease doesn't have any specific characteristics in Lebanon despite some variation in the frequency of lesions.
A Study of CNVs As Trait-Associated Polymorphisms and As Expression Quantitative Trait Loci

We conducted a comprehensive study of copy number variants (CNVs) well-tagged by SNPs (r2≥0.8) by analyzing their effect on gene expression and their association with disease susceptibility and other complex human traits. We tested whether these CNVs were more likely to be functional than frequency-matched SNPs as trait-associated loci or as expression quantitative trait loci (eQTLs) influencing phenotype by altering gene regulation. Our study found that CNV–tagging SNPs are significantly enriched for cis eQTLs; furthermore, we observed that trait associations from the NHGRI catalog show an overrepresentation of SNPs tagging CNVs relative to frequency-matched SNPs. We found that these SNPs tagging CNVs are more likely to affect multiple expression traits than frequency-matched variants. Given these findings on the functional relevance of CNVs, we created an online resource of expression-associated CNVs (eCNVs) using the most comprehensive population-based map of CNVs to inform future studies of complex traits. Although previous studies of common CNVs that can be typed on existing platforms and/or interrogated by SNPs in genome-wide association studies concluded that such CNVs appear unlikely to have a major role in the genetic basis of several complex diseases examined, our findings indicate that it would be premature to dismiss the possibility that even common CNVs may contribute to complex phenotypes and at least some common diseases.
Semantic Adaptation for Models of Computation

In the context of Model Driven Engineering, models are the primary artifacts of the system development cycle. In order to manage the complexity of systems, models are decomposed into models of simpler subsystems. A major difficulty is to handle the heterogeneity of the different models of computation used for modeling the subsystems. Through the example of a power window system, this article presents an approach to the specification of the semantic adaptation of data, time and control between models of computation. The approach is supported by ModHel'X, a heterogeneous modeling and simulation environment. The example is simple enough to be completely described in the article, but rich enough to illustrate the matters of (a) defining models of computation, and (b) specifying the semantic adaptation between models of computation.
Evaluating Social and Ecological Vulnerability of Coral Reef Fisheries to Climate Change

There is an increasing need to evaluate the links between the social and ecological dimensions of human vulnerability to climate change. We use an empirical case study of 12 coastal communities and associated coral reefs in Kenya to assess and compare five key ecological and social components of the vulnerability of coastal social-ecological systems to temperature induced coral mortality [specifically: 1) environmental exposure; 2) ecological sensitivity; 3) ecological recovery potential; 4) social sensitivity; and 5) social adaptive capacity]. We examined whether ecological components of vulnerability varied between government operated no-take marine reserves, community-based reserves, and openly fished areas. Overall, fished sites were marginally more vulnerable than community-based and government marine reserves. Social sensitivity was indicated by the occupational composition of each community, including the importance of fishing relative to other occupations, as well as the susceptibility of different fishing gears to the effects of coral bleaching on target fish species. Key components of social adaptive capacity varied considerably between the communities. Together, these results show that different communities have relative strengths and weaknesses in terms of social-ecological vulnerability to climate change.
Linking Image and Text with 2-Way Nets

Linking two data sources is a basic building block in numerous computer vision problems. Canonical Correlation Analysis (CCA) achieves this by utilizing a linear optimizer in order to maximize the correlation between the two views. Recent work makes use of non-linear models, including deep learning techniques, that optimize the CCA loss in some feature space. In this paper, we introduce a novel, bi-directional neural network architecture for the task of matching vectors from two data sources. Our approach employs two tied neural network channels that project the two views into a common, maximally correlated space using the Euclidean loss. We show a direct link between the correlation-based loss and Euclidean loss, enabling the use of Euclidean loss for correlation maximization. To overcome common Euclidean regression optimization problems, we modify well-known techniques to our problem, including batch normalization and dropout. We show state of the art results on a number of computer vision matching tasks including MNIST image matching and sentence-image matching on the Flickr8k, Flickr30k and COCO datasets.
Through the Eyes of Parents: A Singaporean Perspective of the Importance of Cognitive and Non-Cognitive Skills for Six-Year-Old Children

THIS STUDY REPORTS THE importance 244 parents of six-year-old children living in Singapore placed on cognitive (problem-solving and creativity) and non-cognitive (practical school skills and conforming) behaviours. Our research team hypothesised that, as the age of the parent increased, the importance placed on each covariant skill (problem solving, creativity, practical, conformity) would differ. It was further hypothesised that the importance placed on cognitive skills compared with non-cognitive skills for six-year-old children would decrease. Our results indicate that, when controlling for demographics, as parents aged they did place different levels of importance on each of the cognitive skills but not the non-cognitive skills. Furthermore, older parents placed less importance on cognitive compared with non-cognitive skills. The gap between average cognitive rating and average non-cognitive scores decreased as parents' age increased. This gap was found to be smaller for Chinese than non-Chinese parents. It decreased with age when controlling for child gender and parent ethnicity, gender and occupation.
Interaction of child maltreatment and 5-HTT polymorphisms: suicidal ideation among children from low-SES backgrounds.

OBJECTIVE To investigate whether genotypic variation of the serotonin transporter gene-linked promoter region (5-HTTLPR) moderates the effect of maltreatment on suicidal ideation in school-aged children. METHODS Eight hundred and fifty low-income children (478 maltreated; 372 non-maltreated) provided DNA samples and self-reported depressive and suicidal symptoms. Genotypes of 5-HTTLPR (s/s or s/l vs. l/l) were determined by fragment analyses. RESULTS Higher suicidal ideation was found among maltreated than non-maltreated children; the groups did not differ in 5-HTTLPR genotype frequencies. Children with one to two maltreatment subtypes and s/s or s/l genotypes had higher suicidal ideation than those with the l/l genotype; suicidal ideation did not differ in non-maltreated children or children with three to four maltreatment subtypes based on 5-HTTLPR variation. The results were applicable to emotionally maltreated/neglected and to physically/sexually abused children. Gene-environment interaction was not found for depressive symptoms. CONCLUSION The protective effect of the 5-HTTLPR l/l genotype on suicidal ideation was limited to maltreated children experiencing fewer subtypes.
Effect of therapeutic HIV recombinant poxvirus vaccines on the size of the resting CD4+ T-cell latent HIV reservoir

Objectives:Therapeutic HIV vaccinations may alter the size of the resting memory CD4+ T-cell latent HIV reservoir as HIV establishes latency when memory responses are formed, including those toward HIV. Alternatively, latently infected CD4+ T cells maybe killed, while exiting the reservoir upon activation. Methods:The effect of therapeutic immunization with modified vaccinia Ankara and Fowlpox-based HIV vaccines on the latent reservoir was examined in 19 young adults who were receiving effective antiretroviral therapy. Correlations between size of the reservoir [measured in infectious units per million (IUPM)] resting CD4+ T cells and HIV-specific immune responses, including immune activation were examined. Decay of the reservoir was assessed using random-effects model. Results:A modest transient decrease in the size of the reservoir was observed at week 40 [mean −0.31 log10 IUPM (95% confidence interval: −0.60 to −0.03; P = 0.03] following HIV vaccinations. The estimated half-life (T1/2) of the reservoir during the 40 weeks following vaccination was 9.8 months and statistically different from zero (P = 0.02), but 35.3 months and not different from zero (P = 0.21) over 72 weeks of study. Latent reservoir size at baseline was not correlated with HIV-specific CD4+, CD8+ responses or immune activation, but became correlated with CD4+ IFN&ggr; (r = 0.54, P = 0.02) and IL-2 responses at 6 weeks after immunization (r = 0.48, P = 0.04). Conclusion:Therapeutic HIV vaccinations led to a transient increase in decay of latently infected CD4+ T cells. Further studies of therapeutic HIV vaccines may provide important insights into facilitating decay of the latent reservoir.