Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting signals of drug-drug interactions in a spontaneous reports database.

AIMS The spontaneous reports database is widely used for detecting signals of ADRs. We have extended the methodology to include the detection of signals of ADRs that are associated with drug-drug interactions (DDI). In particular, we have investigated two different statistical assumptions for detecting signals of DDI. METHODS Using the FDA's spontaneous reports database, we investigated two models, a multiplicative and an additive model, to detect signals of DDI. We applied the models to four known DDIs (methotrexate-diclofenac and bone marrow depression, simvastatin-ciclosporin and myopathy, ketoconazole-terfenadine and torsades de pointes, and cisapride-erythromycin and torsades de pointes) and to four drug-event combinations where there is currently no evidence of a DDI (fexofenadine-ketoconazole and torsades de pointes, methotrexade-rofecoxib and bone marrow depression, fluvastatin-ciclosporin and myopathy, and cisapride-azithromycine and torsade de pointes) and estimated the measure of interaction on the two scales. RESULTS The additive model correctly identified all four known DDIs by giving a statistically significant (P < 0.05) positive measure of interaction. The multiplicative model identified the first two of the known DDIs as having a statistically significant or borderline significant (P < 0.1) positive measure of interaction term, gave a nonsignificant positive trend for the third interaction (P = 0.27), and a negative trend for the last interaction. Both models correctly identified the four known non interactions by estimating a negative measure of interaction. CONCLUSIONS The spontaneous reports database is a valuable resource for detecting signals of DDIs. In particular, the additive model is more sensitive in detecting such signals. The multiplicative model may further help qualify the strength of the signal detected by the additive model.
Calcium metabolism in lactating ewes

1. A combination of balance and isotope techniques has been used to study calcium metabolism at different stages of lactation in six sheep and the results have been compared with those obtained from four of the sheep 1 month after the end of lactation. 2. At first the animals were in negative Ca balance but, as milk yields decreased, so the animals moved progressively into positive balance. 3. Ca absorption from the gut was significantly increased throughout the whole of lactation but not sufficiently to meet the initial high demands for Ca. 4. Most of the extra Ca was supplied by bone resorption which was high in early lactation and decreased to a very low value at the end. 5. The rate of bone accretion remained constant throughout the period and was 1.5 times as high as in the non-lactating animals. 6. In the later stages, a combination of factors, but in particular a low rate of resorption of bone, enabled the animals to replenish some of the Ca lost from the skeleton in early lactation. 7. A month after the end of lactation replenishment of skeletal stores of Ca was still continuing as shown by the excess of bone accretion over bone resorption.
MCPIP1 attenuates the innate immune response to influenza A virus by suppressing RIG‐I expression in lung epithelial cells

The pattern recognition receptor retinoic acid‐inducible gene I (RIG‐I) reportedly plays a key role in sensing influenza A virus (IAV) infection and activating type I interferon (IFN) response. MCP‐1‐induced protein 1 (MCPIP1) can directly degrade cytokine mRNAs, such as IL‐6, IL‐12, IL‐1β, and IL‐2, by functioning as an RNase. Here, we initially observed that MCPIP1 exhibited virus supportive functions later in the course of IAV infection in A549 cells, and negatively regulated IAV‐induced RIG‐I‐dependent innate antiviral response. Exogenous overexpression of MCPIP1 suppressed the expression of RIG‐I, whereas shRNA‐mediated inhibition of endogenous MCPIP1 enhanced RIG‐I expression. The results of experiments with actinomycin D and luciferase assay demonstrated that MCPIP1 reduced RIG‐I expression through destabilizing its mRNA. Various mutants of functional domains of MCPIP1 further confirmed that the inhibitory effect of MCPIP1 on RIG‐I expression required RNase activity but not deubiquitinase activity. Finally, the overexpression of several IAV proteins, which have the ability to inhibit the host IFN response at different levels, induced MCPIP1 expression, especially non‐structural protein 1 (NS1). Conclusively, these data demonstrate the MCPIP1 contributes to attenuate IAV‐induced host antiviral response by suppressing RIG‐I expression.
Detection of basepair substitution mutation at a frequency of 1 × 10−7 by combining two genotypic selection methods, MutEx enrichment and allele‐specific competitive blocker PCR

The detection of rare mutations has many important applications, including risk assessment of drugs and chemicals, measuring environmental exposures to genotoxins, and cancer cell detection. A sensitive genotypic selection method has been developed that combines two different mutant allele selection techniques, MutEx enrichment and allele‐specific competitive blocker PCR (ACB‐PCR). This method was developed and evaluated for the detection of a CAA → AAA mutation at codon 61 of the mouse H‐ras gene. The MutEx enrichment is based on MutS binding to a mismatched basepair in heteroduplex DNA. The bound MutS protects the mutant allele from degradation during subsequent exonuclease treatment. ACB‐PCR preferentially amplifies a mutant allele in a PCR reaction using a primer that has more mismatches to the wild‐type allele than the mutant allele. By combining these two approaches, the codon 61 mutation was detected at mutant fractions as low as 1 in 107. This sensitivity was achieved with the thermostable Thermus aquaticus MutS protein but not the Escherichia coli MutS protein. Using the combined approach, the average Pfu DNA polymerase error rate ± the standard error of the mean for this particular basepair was estimated to be 8 ± 3 × 10−7 errors per duplication. The results indicate that MutEx/ACB‐PCR is among the most sensitive genotypic selection methods for the detection of mutation. Environ. Mol. Mutagen. 32:200–211, 1998 © 1998 Wiley‐Liss, Inc.
An association based approach to discovering ordering rules

The work presented in this paper focuses on discovering ordering rules between ordinal attributes. Generally speaking, rough set theory is the foundation of many algorithms of mining ordering rules. We provide a new approach using algorithm of mining association rules to solve this problem. The key to the problem is to transform information tables into transaction database. The comparison results demonstrate that our method can find more interesting ordering rules.
Differential expression of carboxyl terminal derivatives of amyloid precursor protein among cell lines

Understanding the pathway for amyloid precursor protein (APP) catabolism has become an important line of investigation. APP is a ubiquitous membrane bound protein that is rapidly cleaved at the membrane, yielding a secreted protein identical to protease nexin II and an internalized 11.5 kDa 100 residue C terminal derivative (CTD). The levels of CTDs in a variety of cell lines have been examined and were found to differ. Cell types associated with the pathology of Alzheimer's disease (AD), such as olfactory neuroblasts (ON) and cortical vascular endothelial cells, have higher levels of CTDs than lymphoblasts and melanoma cells. The mechanism of CTD catabolism appears to involve the lysosome because blockade of lysosomal but not endosomal or mitochondrial function results in increased levels of CTDs. Under these conditions, production of larger, amyloidogenic CTDs is also seen. In cells possessing higher levels of CTDs we find that the mechanism for production of amyloidogenic CTDs may involve the internalization of intact full‐length APP. Thus, inhibition of the lysosomal system appears capable of generating amyloidogenic peptides. The amount of amyloidogenic peptides appears to vary among cell lines. Such variation may shed light on why amyloid accumulates around specific cell types such as vascular endothelial cells, neurons, and glia. Finally, disfunction of the lysosomal system may play a role in the pathogenesis of Alzheimer's disease. © 1992 Wiley‐Liss, Inc.
Effect of risks on earnings and the US bank share valuation

The financial crisis of 2008 had a great impact on the banking industry of the United States. This paper looks at the impact of the financial risks on the share revaluation of commercial banks in United States. It is expected that the earnings announcements will affect investors' decisions to trade in bank shares. The Earnings Response Coefficients (ERCs) are applied in this paper to ascertain whether the estimated financial risks have incremental information content beyond the reported earnings. The findings support the notion that investors in the United States do look beyond the reported numbers and look for credit, market and price risk significantly in the earnings response valuation among other financial risks variables.
Crumpling of PIFA Textile Antenna

The performance of a PIFA textile antenna under different crumpling conditions is presented. The PIFA was designed for integration into clothing and other textile applications and the bending and crumpling conditions studied are typical of those found under normal use conditions both on and off body. Input impedance, efficiency and radiation patterns are investigated based on numerical and experimental methods at 2.4 GHz. Crumpling can have a serious effect on the resonant frequency, bandwidth and radiation from textile antennas.
Drosophila hnRNP A1 homologs Hrp36/Hrp38 enhance U2-type versus U12-type splicing to regulate alternative splicing of the prospero twintron

During Drosophila embryogenesis, the transcription factor Prospero is critical for neuronal differentiation and axonal outgrowth. The prospero pre-mRNA undergoes alternative splicing, but is unique in that it harbors a rare twintron whereby one intron lies embedded within another. The innermost intron is excised by the major U2-type spliceosome and the outermost is excised by the minor U12-type spliceosome. Previously, an intronic purine-rich element (PRE) was identified as an enhancer of both U2- and U12-type splicing, with a greater effect on the U2-type pathway. We find that the PRE binds Drosophila homologs of heterogeneous nuclear ribonucleoprotein (hnRNP) A1, Hrp38 and Hrp36. RNAi-mediated knockdown of these proteins in S2 cells specifically decreases U2-type splicing of the twintron, which is surprising because hnRNPs usually are repressive. Conversely, tethering Hrp38 to the twintron increases U2-type splicing. Thus, developmentally regulated alternative splicing of the prospero twintron can be explained by documented changes in the abundance of these hnRNP A1-like proteins during embryogenesis.
Beyond Forward Shortcuts: Fully Convolutional Master-Slave Networks (MSNets) with Backward Skip Connections for Semantic Segmentation

Recent deep CNNs contain forward shortcut connections; i.e. skip connections from low to high layers. Reusing features from lower layers that have higher resolution (location information) benefit higher layers to recover lost details and mitigate information degradation. However, during inference the lower layers do not know about high layer features, although they contain contextual high semantics that benefit low layers to adaptively extract informative features for later layers. In this paper, we study the influence of backward skip connections which are in the opposite direction to forward shortcuts, i.e. paths from high layers to low layers. To achieve this -- which indeed runs counter to the nature of feed-forward networks -- we propose a new fully convolutional model that consists of a pair of networks. A `Slave' network is dedicated to provide the backward connections from its top layers to the `Master' network's bottom layers. The Master network is used to produce the final label predictions. In our experiments we validate the proposed FCN model on ADE20K (ImageNet scene parsing), PASCAL-Context, and PASCAL VOC 2011 datasets.
New asymmetrical commutation cell for multilevel inverters with reduced number of components

This paper proposes a new topology of multilevel inverters with asymmetrical commutation cell that consists of three sources and six switches to synthesize asymmetrical output voltage level. This category of topologies is typically used in voltage AC generation. The structure provides multilevel waveform utilizing reduced number of components as compared to the conventional topologies. The performance and operation of the proposed inverter is introduced in two modes: 1) six level asymmetrical, 2) eleven level symmetrical output voltage. A comparison between the proposed and conventional structures is established. The proposed inverter is simulated in MATLAB/Simulink software. To validate proper operation of the proposed circuit, experimental setups are implemented in the laboratory in two modes.
Ultraviolet Radiation‐Induced Downregulation of SERCA2 Mediates Activation of NLRP3 Inflammasome in Basal Cell Carcinoma

Basal cell carcinomas (BCCs) account for majority of skin malignancies in the United States. The incidence of BCCs is strongly associated with exposure of ultraviolet (UV) radiation. Nucleotide‐binding domain, leucine‐rich‐repeat‐containing family, pyrin domain‐containing 3 (NLRP3) inflammasome plays an important role in innate immune responses. Different stimuli such as toxins, microorganisms and particles released from injured cells activate the NLRP3 inflammasome. Activated NLRP3 results in activation of caspase‐1, which cleaves pro‐IL‐1β to active IL‐1β. In this study, we have shown that NLRP3 is expressed in human basal cell carcinomas. The proximal steps in activation of NLRP3 inflammasome are not well understood. Here, we have attempted to elucidate a critical role for Ca2+ mobilization in activation of the NLRP3 inflammasome by UVB exposure using HaCaT keratinocytes. We have demonstrated that UVB exposure blocks Ca2+ mobilization by downregulating the expression of sarco/endoplasmic reticulum Ca2+‐ATPase (SERCA2), a component of store‐operated Ca2+ entry that leads to activation of the NLRP3 inflammasome.
Modeling and Design Considerations for ZVS Asymmetrical Half-Bridge Converter

Practical point of view in modeling and design considerations for a zero-voltage-switched (ZVS) asymmetrical half-bridge (ASY-HB) converter is proposed. Six dynamic conversion states for describing the converter characteristics are explored and modeled, including two power-delivery states, two resonant states, and two energy-transition states etc. Design considerations are examined thoroughly. A design of 300 W ZVS ASY-HB converter is examined and a high efficiency up to 92% at full load is achieved. All performances verified by experiment are quite well and close to the theoretical predictions.
Robust Tuning Datasets for Statistical Machine Translation

We explore the idea of automatically crafting a tuning dataset for Statistical Machine Translation (SMT) that makes the hyper-parameters of the SMT system more robust with respect to some specific deficiencies of the parameter tuning algorithms. This is an under-explored research direction, which can allow better parameter tuning. In this paper, we achieve this goal by selecting a subset of the available sentence pairs, which are more suitable for specific combinations of optimizers, objective functions, and evaluation measures. We demonstrate the potential of the idea with the pairwise ranking optimization (PRO) optimizer, which is known to yield too short translations. We show that the learning problem can be alleviated by tuning on a subset of the development set, selected based on sentence length. In particular, using the longest 50% of the tuning sentences, we achieve two-fold tuning speedup, and improvements in BLEU score that rival those of alternatives, which fix BLEU+1’s smoothing instead.
Phylogenetic Measures of Biodiversity

We developed a theoretical framework based on phylogenetic comparative methods to integrate phylogeny into three measures of biodiversity: species variability, richness, and evenness. These metrics can be used in conjunction with permutation procedures to test for phylogenetic community structure. As an illustration, we analyzed data on the composition of 58 lake fish communities in Wisconsin. The fish communities showed phylogenetic underdispersion, with communities more likely to contain closely related species. Using information about differences in environmental characteristics among lakes, we demonstrated that phylogenetic underdispersion in fish communities was associated with environmental factors. For example, lakes with low pH were more likely to contain species in the same clade of acid‐tolerant species. Our metrics differ from existing metrics used to calculate phylogenetic community structure, such as net relatedness index and Faith’s phylogenetic diversity. Our metrics have the advantage of providing an integrated and easy‐to‐understand package of phylogenetic measures of species variability, richness, and evenness with well‐defined statistical properties. Furthermore, they allow the easy evaluation of contributions of individual species to different aspects of the phylogenetic organization of communities. Therefore, these metrics should aid with the incorporation of phylogenetic information into strategies for understanding biodiversity and its conservation.
oL-1,6-Glucan-Binding Protein from Streptococcus sobrinus

Glucan-binding protein 1 (GBP1), the most abundant glucan-binding protein isolated from culture supernatants of Streptococcus sobrinus 6715-49, has been purified by affinity chromatography on Sephadex G-50 followed by gel permeation chromatography with Bio-Gel P-10. The specificity and affinity of GBP1 for glucans were assessed by affinity electrophoresis. GBP1 did not detectably bind to glucans lacking linear arrays of a-1,6 linkages. The association constant for the linear ca-1,6-glucan Dextran T2000 was 3 x 10 M. Providing small isomaltosaccharide ligands to compete with this dextran indicated that the binding site maximally accommodated isomaltosaccharides with a degree of polymerization of 8. When glucans produced by purified S. sobrinus glucosyltransferases were tested, GBP1 displayed the highest affinity for the glucan from the soluble-product, primer-independent glucosyltransferase.
Indexes of power and aerobic capacity obtained in cycle ergometry and treadmill running: comparisons between sedentary, runners, cyclists and triathletes

The objectives of this study were: a) to determine, in a cross-sectional manner, the effect of aerobic training on the peak oxygen uptake (VO2peak), the intensity at VO2peak (IVO 2peak ) and the anaerobic threshold ( AnT) during running and cycling; and b) to verify if the transference of the training effects are dependent on the analized type of exercise or physiological index. Eleven untrained males ( UN), nine endurance cyclists (EC), seven endurance runners (ER), and nine triathletes ( TR) were submitted, on separate days, to incremental tests until voluntary exhaustion on a mechanical braked cycle ergometer and on a treadmill. The values of VO 2peak (ml.kg -1 .min -1 ) obtained in running and cycle ergometer (ER = 68.8 ± 6.3 and 62.0 ± 5.0; EC = 60.5 ± 8.0 and 67.6 ± 7.6; TR = 64.5 ± 4.8 and 61.0 ± 4.1; UN = 43.5 ± 7.0 and 36.7 ± 5.6; respectively) were higher in the group that presented specific training in the modality. The UN group presented the lower values of VO2peak, regardless of the type of exercise. This same behavior was observed for the AnT (ml.kg -1 .min -1 ) determined in running and cycle ergometer (ER = 56.8 ± 6.9 and 44.8 ± 5.7; EC = 51.2 ± 5.2 and 57.6 ± 7.1; TR = 56.5 ± 5.1 and 49.0 ± 4.8; UN = 33.2 ± 4.2 and 22.6 ± 3.7; respectively). It can be concluded that the transference of the training effects seems to be only partial, independently of the index ( VO 2peak , IVO 2peak or AnT)
Grounding Software Domain Ontologies in the Unified Foundational Ontology (UFO): The case of the ODE Software Process Ontology

Foundational Ontologies are theoretically well-founded domainindependent systems of categories that have been successfully used to improve the quality of conceptual modeling languages and models. In this paper, we present the latest developments in the UFO ontology. Moreover, we elaborate on the relevance of these foundational ontologies in the development of domain ontologies by showing a case study in the software process domain.
Thrombotic complications and tip position of transjugular chronic dialysis catheter scheduled into superior vena cava

Background: Catheter-related thrombotic complications(TCs) can occur during the long term use of a chronic dialysis catheter (CDC), including fibrin sheath (FS), mural thrombosis (MT), venous thrombosis (VT), and intraluminal clots (IC), which has not been reported with MRI. The aim of our study was to evaluate the determination of catheter tip position (TP) and resolution of TCs in patients with transjugular CDC scheduled into the superior vena cava using high resolution magnetic resonance cholangiopancreatography (HR-MRCP) and T2-weighted imaging (HR-T2WI). Methods: The study protocol was approved by the local Research Ethics Committee. Informed consent was obtained from all patients. In total, 41 consecutively enrolled transjugular CDC patients with suspected catheter dysfunction were scanned with HRMRCP and HR-T2WI. The distance from the top to the tip of the catheter and the presence and nature of catheter TCs were assessed by 2 experienced radiologists. Chest x-ray was taken within 1 to 2 days and CDC was withdrawn within 3 to 10 days from those patients with TCs identified by HR-MRI. Results: A total of 38 subjects successfully underwent HR-MRI, including 13 normal and 25 with TCs (fibrin sheath [FS]: n = 21, mural thrombosis [MT]: n = 7, venous thrombosis [VT]: n = 3, intraluminal clots [IC]: n = 4). There was no significant difference between HR-MRCP and chest x-ray in catheter TP determination (P = .124). Normal catheter appeared as “double eyes” on HR-T2WI and “double tracks” on HR-MRCP. TCs appeared as follows: FS displayed as a “thin ring” (<1mm) around the catheter, MT as patchy hyperintensity and VT as a “thick ring” (>5mm) on HR-T2WI. Unilateral IC appeared as a “single eye” on HR-T2WI and a “single track” on HR-MRCP (n = 3). Bilateral IC appeared as neither “eye” nor “track” (n = 1). Catheter withdrawal confirmed FS (n = 16), MT (n = 6), VT (n = 1), and IC (n = 4). Conclusion: HR-MRCP and HR-T2WI are promising methods for visualizing TP and TCs in CDC patients, and are helpful in adjusting the treatment plan and avoiding the risk of pulmonary embolism.
An Enhancement Algorithm for Video Surveillance Image Based on Multi-scale Retinex

Aiming at the similarity of adjacent frame image's background and light in video surveillance, it legitimately uses of the information between frames and builds an enhancement algorithm for video surveillance image based on multi-scale Retinex. This algorithm uses different scales and parameters Gauss low pass filter to filter each frame image, takes Minimum operation for filter results, extracts each frame background's information, By taking the maximum operation, fuses multi frames of image's background, obtains the video image's accurate background for that moment, Using Retinex algorithm enhances the background. The experimental results show that after the image enhancement, the image detail information is richer and obtains more comfortable visual effect.