Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between proton pump inhibitor use and spontaneous bacterial peritonitis in cirrhotic patients with ascites.

BACKGROUND There are data suggesting a link between proton pump inhibitor (PPI) use and the development of spontaneous bacterial peritonitis (SBP) in cirrhotic patients with ascites; however, these data are controversial. OBJECTIVE To assess whether the use of PPIs in cirrhotic patients with ascites is associated with an increased risk for SBP. METHODS A retrospective case-control study (June 2004 to June 2010) was conducted at the Centre Hospitalier de l'Université de Montréal in Montreal, Quebec. Fifty-one cirrhotic patients admitted with paracentesis-proven SBP (≥250 neutrophils/mm3), occurring within seven days of hospital admission, met the inclusion criteria. These patients were matched 1:2 (for age, Child-Pugh class and year of admission) with 102 comparable cirrhotic patients with ascites who were admitted for conditions other than SBP. RESULTS Patients with SBP had a significantly higher rate of pre-hospital PPI use (60.8%) compared with cirrhotic patients without SBP (42.2%; P=0.03). On multivariate analysis, PPI use was the only factor independently associated with SBP (OR 2.09 [95% CI 1.04 to 4.23]; P=0.04). Thirty-five (35%) patients in both groups had no documented indication for PPI use in their charts. Forty-five percent of the remaining cirrhotic patients with SBP had an inappropriate indication, as defined in the protocol, for PPI use compared with 25% of controls. CONCLUSIONS Cirrhotic patients with SBP were twice as likely to have taken PPIs than patients without SBP. These findings reinforce the association between PPI use and SBP observed in other studies. A high percentage of cirrhotic patients were taking a PPI without any documented indication.
The GDOF of 3-user MIMO Gaussian interference channel

The paper establishes the optimal generalized degrees of freedom (GDOF) of 3-user M × N multiple-input multiple-output (MIMO) Gaussian interference channel (GIC) in which each transmitter has M antennas and each receiver has N antennas. A constraint of 2M ≤ N is imposed so that random coding with message-splitting achieves the optimal GDOF. Unlike symmetric case, two cross channels to unintended receivers from each transmitter can have different strengths, and hence, well known Han-Kobayashi common-private message splitting would not achieve the optimal GDOF. Instead, splitting each user's message into three parts is shown to achieve the optimal GDOF as well as O(1) capacity approximation.
Cognitive biases for trauma stimuli in people with schizophrenia.

OBJECTIVES This study investigates whether cognitive biases related to trauma (physical and sexual trauma) are present in a sample of participants with a diagnosis of schizophrenia. METHOD Fifty-three participants, with a DSM-IV diagnosis of schizophrenia, completed tasks of attentional and memory bias, followed by several trauma report questionnaires. Those who reported a history of sexual and/or physical trauma were compared with a 'non-specific/no-trauma' subgroup. The reliability of trauma reports was determined by comparing current data on the Trauma History Questionnaire to that gathered one year previously, for a subsample of participants. Concordance rates and kappa coefficients suggested moderate to high reliability for reports of sexual and physical trauma. Attentional bias was assessed by comparing colour-naming times on modified Stroops, of either a sexual or physical nature, with control Stroops with negative, positive and neutral emotionally valenced stimuli. A subsequent incidental recall memory task was then employed. RESULTS High rates of sexual and/or physical trauma were found. Those who reported a history of sexual trauma evidenced a statistically significant increase in colour-naming times for sexual trauma stimuli, compared to both the 'physical trauma only' and the 'non-specific/no trauma' control groups. They also showed greater incidental recall of sexual trauma words in comparison to the other groups. Such a pattern was not, however, discerned for those reporting histories of physical trauma. CONCLUSIONS Findings suggest cognitive schemata related to sexual trauma remains 'active' in those people with schizophrenia who report a related history.
A social and ecological assessment of tropical land uses at multiple scales: the Sustainable Amazon Network

Science has a critical role to play in guiding more sustainable development trajectories. Here, we present the Sustainable Amazon Network (Rede Amazônia Sustentável, RAS): a multidisciplinary research initiative involving more than 30 partner organizations working to assess both social and ecological dimensions of land-use sustainability in eastern Brazilian Amazonia. The research approach adopted by RAS offers three advantages for addressing land-use sustainability problems: (i) the collection of synchronized and co-located ecological and socioeconomic data across broad gradients of past and present human use; (ii) a nested sampling design to aid comparison of ecological and socioeconomic conditions associated with different land uses across local, landscape and regional scales; and (iii) a strong engagement with a wide variety of actors and non-research institutions. Here, we elaborate on these key features, and identify the ways in which RAS can help in highlighting those problems in most urgent need of attention, and in guiding improvements in land-use sustainability in Amazonia and elsewhere in the tropics. We also discuss some of the practical lessons, limitations and realities faced during the development of the RAS initiative so far.
Graspables revisited: multi-touch vs. tangible input for tabletop displays in acquisition and manipulation tasks

We present an experimental comparison of multi-touch and tangible user interfaces for basic interface actions. Twelve participants completed manipulation and acquisition tasks on an interactive surface in each of three conditions: tangible user interface; multi-touch; and mouse and puck. We found that interface control objects in the tangible condition were easiest to acquire and, once acquired, were easier/more accurate to manipulate. Further qualitative analysis suggested that in the evaluated tasks tangibles offer greater adaptability of control and specifically highlighted a problem of exit error that can undermine fine-grained control in multi-touch interactions. We discuss the implications of these findings for interface design.
Combining Genome-Wide Information with a Functional Structural Plant Model to Simulate 1-Year-Old Apple Tree Architecture

In crops, optimizing target traits in breeding programs can be fostered by selecting appropriate combinations of architectural traits which determine light interception and carbon acquisition. In apple tree, architectural traits were observed to be under genetic control. However, architectural traits also result from many organogenetic and morphological processes interacting with the environment. The present study aimed at combining a FSPM built for apple tree, MAppleT, with genetic determinisms of architectural traits, previously described in a bi-parental population. We focused on parameters related to organogenesis (phyllochron and immediate branching) and morphogenesis processes (internode length and leaf area) during the first year of tree growth. Two independent datasets collected in 2004 and 2007 on 116 genotypes, issued from a ‘Starkrimson’ × ‘Granny Smith’ cross, were used. The phyllochron was estimated as a function of thermal time and sylleptic branching was modeled subsequently depending on phyllochron. From a genetic map built with SNPs, marker effects were estimated on four MAppleT parameters with rrBLUP, using 2007 data. These effects were then considered in MAppleT to simulate tree development in the two climatic conditions. The genome wide prediction model gave consistent estimations of parameter values with correlation coefficients between observed values and estimated values from SNP markers ranging from 0.79 to 0.96. However, the accuracy of the prediction model following cross validation schemas was lower. Three integrative traits (the number of leaves, trunk length, and number of sylleptic laterals) were considered for validating MAppleT simulations. In 2007 climatic conditions, simulated values were close to observations, highlighting the correct simulation of genetic variability. However, in 2004 conditions which were not used for model calibration, the simulations differed from observations. This study demonstrates the possibility of integrating genome-based information in a FSPM for a perennial fruit tree. It also showed that further improvements are required for improving the prediction ability. Especially temperature effect should be extended and other factors taken into account for modeling GxE interactions. Improvements could also be expected by considering larger populations and by testing other genome wide prediction models. Despite these limitations, this study opens new possibilities for supporting plant breeding by in silico evaluations of the impact of genotypic polymorphisms on plant integrative phenotypes.
Expression of Notch1 Correlates with Breast Cancer Progression and Prognosis

Various studies have evaluated the significance of Notch1 expression in breast cancer, but the results have ever been disputed. By using 21 studies involving 3867 patients, this meta-analysis revealed that the expression of Notch1 was significantly higher in breast cancer than in normal tissues (OR=7.21; 95%CI, 4.7-11.07) and that higher Notch1 expression was associated with transition from ductal carcinoma in situ (DCIS) to invasive cancer (OR=3.75; 95% CI, 1.8-7.78). Higher Notch1 activity was observed in the basal subtype of breast cancer (OR=2.53; 95% CI, 1.18-5.43). Moreover, patients with Notch1 overexpression exhibited significantly worse overall and recurrence-free survival. Our meta-analysis suggests that Notch inhibitors may be useful in blocking the early progression of DCIS and that the outcomes of clinical trials for Notch1-targeting therapeutics could be improved by the molecular stratification of breast cancer patients.
Surface roughness properties of polyester woven fabrics after abrasion

Effect of abrasion on surface roughness properties of textured polyester woven fabrics has been investigated. The effects of weft density, weft yarn filament number, fiber fineness, and weave pattern on surface roughness after abrasion were studied. Surface roughness values of control fabric (not abraded) and abraded fabrics after four different abrasion cycles were discussed according to different constructional parameters. Surface roughness values of fabrics changed according to abrasion cycles and the changes were related to yarn float lengths, yarn densities, yarn fiber fineness, and initial fabric surface roughness. A general overview of the results showed that abrasion eliminated the effect of texture especially at the fabric samples with initially high surface roughness. The surface roughness of fabrics with initially high surface roughness decreased at a greater extent than the ones with low surface roughness after abrasion. Fabrics with high surface roughness were affected more by abrasion and the effect of abrasion on rough surfaces depended on different manners regarding the compactness of woven structures.
A palindromic regulatory site within vertebrate GATA-1 promoters requires both zinc fingers of the GATA-1 DNA-binding domain for high-affinity interaction

GATA-1, a transcription factor essential for the development of the erythroid lineage, contains two adjacent highly conserved zinc finger motifs. The carboxy-terminal finger is necessary and sufficient for specific binding to the consensus GATA recognition sequence: mutant proteins containing only the amino-terminal finger do not bind. Here we identify a DNA sequence (GATApal) for which the GATA-1 amino-terminal finger makes a critical contribution to the strength of binding. The site occurs in the GATA-1 gene promoters of chickens, mice, and humans but occurs very infrequently in other vertebrate genes known to be regulated by GATA proteins. GATApal is a palindromic site composed of one complete [(A/T)GATA(A/G)] and one partial (GAT) canonical motif. Deletion of the partial motif changes the site to a normal GATA site and also reduces by as much as eightfold the activity of the GATA-1 promoter in an erythroid precursor cell. We propose that GATApal is important for positive regulation of GATA-1 expression in erythroid cells.
Chemically synthesized CdSe quantum dots inhibit growth of human lung carcinoma cells via ROS generation

Quantum dots (QDs), semiconducting materials have potential applications in the field of electronic and biomedical applications including cancer therapy. In present study, cadmium selenide (CdSe) QDs were synthesized by chemical method. Octadecene was used as non-coordinating solvent which facilitated the formation of colloidal solutions of nanoparticles. CdSe QDs were characterized by UV-vis spectrometer and transmission electron microscope (TEM). The size measured by TEM was varied between 2-5 nm depending upon temperature. The cytotoxic activity of QDs was monitored by MTT assay, nuclear condensation, ROS activity and DNA fragmentation assay on human lung epithelial A549 cell line. Cells were treated with different concentrations of varying size of CdSe QDs for 24 h. CdSe QDs induced significant (p < 0.05) dose dependent cytotoxicity and this was comparable to the sizes of particles. Smaller particles were more cytotoxic to the large particles. Fluorescence microscopic analysis revealed that QDs induced oxidative stress generating significant ROS level and consequently, induced nuclear condensation and DNA fragmentation. Study suggested the cytotoxicity of CdSe QDs via ROS generation and DNA fragmentation depending upon particles size.
A screen for neurotransmitter transporters expressed in the visual system of Drosophila melanogaster identifies three novel genes

The fly eye provides an attractive substrate for genetic studies, and critical transport activities for synaptic transmission and pigment biogenesis in the insect visual system remain unknown. We therefore screened for transporters in Drosophila melanogaster that are down‐regulated by genetically ablating the eye. Using a large panel of transporter specific probes on Northern blots, we identified three transcripts that are down‐regulated in flies lacking eye tissue. Two of these, CG13794 and CG13795, are part of a previously unknown subfamily of putative solute carriers within the neurotransmitter transporter family. The third, CG4476, is a member of a related subfamily that includes characterized nutrient transporters expressed in the insect gut. Using imprecise excision of a nearby transposable P element, we have generated a series of deletions in the CG4476 gene. In fast phototaxis assays, CG4476 mutants show a decreased behavioral response to light, and the most severe mutant behaves as if it were blind. These data suggest an unforeseen role for the “nutrient amino acid transporter” subfamily in the nervous system, and suggest new models to study transport function using the fly eye. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007
Antibacterial Activity of Spirulina (Arthospira platensis Geitler) against Bacterial Pathogens in Aquaculture

The antibacterial activity of seven crude extracts of a cyanobacterium, Arthospira platensis (previously called Spirulina platensis), was evaluated against seven bacterial fish pathogens. The antibacterial activity of the acetone soluble fraction of the A. platensis was considerable against all seven pathogens and equaled the antibacterial activity of the positive control (chloramphenicol) against Aeromonas hydrophila. Edwardsiella tarda was the most susceptible pathogen to this fraction. The minimum inhibitory and minimum bactericidal concentrations were lowest for the acetone soluble fraction. Atomic force microscopy of A. hydrophila cells showed that cell walls were considerably damaged after one hour of exposure to the acetone soluble fraction, i.e., pores, holes, and grooves had formed on the cell envelope. After two hours of exposure, the cells had became permeabilized and collapsed due to disintegration of the cell wall.
The Immune Response in Inflammatory Bowel Disease

Ulcerative colitis (UC) and Crohn's disease (CD), collectively referred to as inflammatory bowel disease (IBD), present with differing histologic and cytokine profiles. While the precise mechanisms underlying the development of IBD are not known, sufficient data have been collected to suggest that it results from a complex interplay of genetic, environmental, and immunologic factors. Animal models of colitis, along with a more detailed understanding of the immune response in the normal bowel, have led to unifying hypotheses regarding the pathogenesis. An inappropriate mucosal immune response to normal intestinal constituents is a key feature, leading to an imbalance in local pro- and anti-inflammatory cytokines. Neutrophil and monocyte influx occurs with subsequent secretion of oxygen radicals and enzymes, leading to tissue damage. Therapy of IBD has improved and expanded as the understanding of disease mechanisms has evolved. Pharmacologic agents such as aminosalicylates, azathioprine/6-mercaptopurine, or steroids are the mainstays of therapy. Newer agents including monoclonal antibodies targeted to specific proinflammatory cytokines, such as tumor necrosis factor-α (TNF-α), have emerged and provide great clinical benefit, but unknown long-term toxicity and immunogenicity may limit their use.
Molecular characterization of a puromycin‐insensitive leucyl‐specific aminopeptidase, PILS‐AP

The family M1 of Zn‐dependent aminopeptidases comprises members of closely related enzymes which are known to be involved in a variety of physiologically important processes. On the basis of two highly conserved peptide motifs, we have identified a new member of this family by PCR amplification and cDNA‐library screening. The longest ORF encodes a protein of 930 residues. It contains the HEXXH(X)18E Zn‐binding motif and displays high homology to the other M1 family members except for its N‐terminus for which a signal sequence of 20 residues can be predicted. This interpretation was supported by expressing fusion proteins formed with green fluorescent protein which localized to intracellular vesicles in COS‐7 and BHK cells. Northern‐blot analysis revealed ubiquitous expression of a major 3.1‐kb transcript. For enzymatic studies, the complete protein was expressed in Sf 9 insect cells. When aminoacyl β‐naphthylamides were used as substrates, efficient hydrolysis was only observed for Leu (and to a lesser extent Met). The activity was inhibited by chelators of bivalent cations and by other known aminopeptidase inhibitors, but surprisingly puromycin was without effect. This newly identified puromycin‐insensitive leucyl‐specific aminopeptidase is a signal‐sequence‐bearing member of family M1 and may be another example of the small subset of substrate‐specific peptidases.
Zymogenic and enzymatic properties of the 70–80 loop mutants of factor X/Xa

The Ca2+ binding 70–80 loop of factor X (fX) contains one basic (Arg71) and three acidic (Glu74, Glu76, and Glu77) residues whose contributions to the zymogenic and enzymatic properties of the protein have not been evaluated. We prepared four Ala substitution mutants of fX (R71A, E74A, E76A, and E77A) and characterized their activation kinetics by the factor VIIa and factor IXa in both the absence and presence of cofactors. Factor VIIa exhibited normal activity toward E74A and E76A and less than a twofold impaired activity toward R71A and E77A in both the absence and presence of tissue factor. Similarly, factor IXa in the absence of factor VIIIa exhibited normal activity toward both E74A and E76A; however, its activity toward R71A and E77A was impaired approximately two‐ to threefold. In the presence of factor VIIIa, factor IX activated all mutants with approximately two‐ to fivefold impaired catalytic efficiency. In contrast to changes in their zymogenic properties, all mutant enzymes exhibited normal affinities for factor Va, and catalyzed the conversion of prothrombin to thrombin with normal catalytic efficiencies. However, further studies revealed that the affinity of mutant enzymes for interaction with metal ions Na+ and Ca2+ was impaired. These results suggest that although charged residues of the 70–80 loop play an insignificant role in fX recognition by the factor VIIa‐tissue factor complex, they are critical for the substrate recognition by factor IXa in the intrinsic Xase complex. The results further suggest that mutant residues do not play a specific role in the catalytic function of fXa in the prothrombinase complex.
Change in Renal Function among HIV-Infected Koreans Receiving Tenofovir Disoproxil Fumarate-Backbone Antiretroviral Therapy: A 3-Year Follow-Up Study

Purpose Tenofovir disoproxil fumarate (TDF) is commonly prescribed as a fixed-dose, co-formulated antiretroviral drug for HIV-1 infection. The major concern of long-term TDF use is renal dysfunction. However, little is known about the long-term patterns of changes in renal function in HIV-infected Koreans receiving TDF. Materials and Methods We prospectively followed 50 HIV-infected Koreans, performing laboratory tests every 3 months during the first year and every 6 months for the next 2 years. Urine N-acetyl-β-D-glucosaminidase (NAG) and plasma cystatin-C were measured using samples collected in the first year. Data on renal function were retrospectively collected on HIV-infected patients receiving first-line TDF (n=40) and in antiretroviral therapy (ART)-naïve patients (n=24) for 3 years. Renal function was evaluated as estimated glomerular filtration rate (eGFR) from serum creatinine [Modification of Diet in Renal Disease (MDRD)] and cystatin-C. Results The eGFR (cystatin-C) showed significant changes from 0 to 48 wks (p=0.002), with the lowest levels at 24 wks (84.3±18.8 mL/min vs. 90.3±22.5 mL/min, p=0.021 by post hoc test). Urine NAG levels did not differ at 0, 12, 24, and 48 wks, although eGFR (MDRD) significantly decreased from 0 (98.7±18.9 mL/min/1.73 m2) to 144 wks (89.0±14.7 mL/min/1.73 m2) (p=0.010). The first-line TDF group had significantly lower eGFR (MDRD) than the ART-naïve group at 144 wks (89.7 mL/min/1.73 m2 vs. 98.4 mL/min/1.73 m2, p=0.036). Thirteen (26%) participants experienced a decrease in renal impairment of 10 mL/min/1.73 m2 in eGFR (MDRD) at 144 wks. Conclusion These data suggest that clinically meaningful renal injury can develop in HIV-infected Koreans receiving long-term TDF.
Dynamic Pricing and Energy Consumption Scheduling With Reinforcement Learning

In this paper, we study a dynamic pricing and energy consumption scheduling problem in the microgrid where the service provider acts as a broker between the utility company and customers by purchasing electric energy from the utility company and selling it to the customers. For the service provider, even though dynamic pricing is an efficient tool to manage the microgrid, the implementation of dynamic pricing is highly challenging due to the lack of the customer-side information and the various types of uncertainties in the microgrid. Similarly, the customers also face challenges in scheduling their energy consumption due to the uncertainty of the retail electricity price. In order to overcome the challenges of implementing dynamic pricing and energy consumption scheduling, we develop reinforcement learning algorithms that allow each of the service provider and the customers to learn its strategy without a priori information about the microgrid. Through numerical results, we show that the proposed reinforcement learning-based dynamic pricing algorithm can effectively work without a priori information about the system dynamics and the proposed energy consumption scheduling algorithm further reduces the system cost thanks to the learning capability of each customer.