Miracle-dz/UniFAR-FTUs huggingface dataset:
Baculovirus-mediated expression and characterization of rat CYP2A3 and human CYP2a6: role in metabolic activation of nasal toxicants.

Cytochrome P450 2A3 (CYP2A3) was previously identified in rat lung by cDNA cloning and recently found to be expressed at a high level in the olfactory mucosa. In the current study, CYP2A3 was expressed in insect cells lacking endogenous cytochrome P450 (P450) activity, and the substrate specificity of the recombinant cytochrome was characterized and compared with that of CYP2A6, a human ortholog of rat CYP2A3, which has been detected in human olfactory mucosa as well as in liver. The CYP2A3 and CYP2A6 cDNAs were cloned into baculovirus, and recombinant viruses were used to produce active enzymes in Spodoptera frugiperta (SF9) cells. The metabolic activities of S. frugiperta cell microsomal fractions containing CYP2A3 or CYP2A6 were studied in a reconstituted system with purified rabbit NADPH-P450 reductase. CYP2A3 was found to be active toward testosterone, producing 15 alpha-hydroxytestosterone and several other metabolites, but it had only low activity toward coumarin. On the other hand, CYP2A6 was active toward coumarin but not toward testosterone. However, both enzymes were active in the metabolic activation of hexamethylphosphoramide, a nasal procarcinogen, and 2,6-dichlorobenzonitrile (DCBN), a herbicide known to cause tissue-specific toxicity in the olfactory mucosa of rodents at very low doses. In addition, both enzymes were active toward 4-nitrophenol, a preferred substrate for CYP2E1. Consistent with CYP2A3 being a major catalyst in microsomal metabolism of DCBN, the activities of both CYP2A3 and rat olfactory microsomes in DCBN metabolism were inhibited strongly by metyrapone and methoxsalen (ID50 < 1 microM, with DCBN at 30 microM), but only marginally by 4-methylpyrazole, an inhibitor of CYP2E1. In contrast, the activity of CYP2A6 was only weakly inhibited by metyrapone or methoxsalen (ID50 > 50 microM). Thus, rat CYP2A3 and human CYP2A6 have differences in substrate specificity as well as tissue distributor. These findings should be taken into account when assessing the risk of exposure to potential nasal toxicants in humans.
Momentum broadening in an anisotropic plasma

The rates governing momentum broadening in a quark-gluon plasma with a momentum anisotropy are calculated to leading-log order for a heavy quark using kinetic theory. It is shown how the problematic singularity for these rates at leading order is lifted by next-to-leading-order gluon self-energy corrections to give a finite contribution to the leading-log result. The resulting rates are shown to lead to larger momentum broadening along the beam axis than in the transverse plane, which is consistent with recent STAR results. This might indicate that the quark-gluon-plasma at RHIC is not in equilibrium.
Enabling a genetically informed approach to cancer medicine: a retrospective evaluation of the impact of comprehensive tumor profiling using a targeted next-generation sequencing panel.

BACKGROUND Oncogenic genetic alterations "drive" neoplastic cell proliferation. Small molecule inhibitors and antibodies are being developed that target an increasing number of these altered gene products. Next-generation sequencing (NGS) is a powerful tool to identify tumor-specific genetic changes. To determine the clinical impact of extensive genetic analysis, we reviewed our experience using a targeted NGS platform (FoundationOne) in advanced cancer patients. PATIENTS AND METHODS We retrospectively assessed demographics, NGS results, and therapies received for patients undergoing targeted NGS (exonic sequencing of 236 genes and selective intronic sequencing from 19 genes) between April 2012 and August 2013. Coprimary endpoints were the percentage of patients with targeted therapy options uncovered by mutational profiling and the percentage who received genotype-directed therapy. RESULTS Samples from 103 patients were tested, most frequently breast carcinoma (26%), head and neck cancers (23%), and melanoma (10%). Most patients (83%) were found to harbor potentially actionable genetic alterations, involving cell-cycle regulation (44%), phosphatidylinositol 3-kinase-AKT (31%), and mitogen-activated protein kinase (19%) pathways. With median follow-up of 4.1 months, 21% received genotype-directed treatments, most in clinical trials (61%), leading to significant benefit in several cases. The most common reasons for not receiving genotype-directed therapy were selection of standard therapy (35%) and clinical deterioration (13%). CONCLUSION Mutational profiling using a targeted NGS panel identified potentially actionable alterations in a majority of advanced cancer patients. The assay identified additional therapeutic options and facilitated clinical trial enrollment. As time progresses, NGS results will be used to guide therapy in an increasing proportion of patients.
Malware detection in android based on dynamic analysis

Android is the most preferable target for malware attacks due to its increased popularity amongst other operating systems for Smartphone devices. Owing to its open architecture and large user base, it provides the developers with an open access to its code base and a large surface area to launch their malicious activities. This paper presents an approach to perform dynamic analysis of android applications to classify the applications as malicious or non malicious. To this end we have developed a syscall-capture system which collects and extracts the system call traces of all the applications during their run-time interactions with the phone platform. Subsequently all the collected system call data is aggregated and analysed to detect and classify the behaviour of Android applications. We have used our system to analyse the behaviour of 50 malicious applications obtained from the Android Malware Genome Project and 50 benign applications obtained from the Google Play Store. With the aim to classify the behaviour of these applications, we have considered the frequency of system calls made by each application as the prime feature set. To this effect we have achieved an acceptable levels of accuracy in correctly classifying the application as malicious or benign using the J48 Decision Tree algorithm and the Random Forest algorithm.
CocaRank: A Collaboration Caliber-based Method for Finding Academic Rising Stars

Evaluating the scientific impact of scholars has been studied by researchers from various disciplines for a long time. However, very few efforts have been devoted to evaluate the future potential of researchers based on their performance at the initial stage of scientific careers. Academic rising stars represent junior researchers who may not be very outstanding among the peers at the initial stage of their careers, but tend to become influential scholars in the future. In this paper, we propose a novel method named CocaRank, which integrates our proposed new indicator called the collaboration caliber, the typical indicator citation counts and hybrid calculation results on heterogeneous academic networks, to find academic rising stars. In addition, we investigate the appropriate time interval for the prediction of rising stars. The experimental results on real datasets demonstrate that our method can find more top ranked rising stars with higher average citation counts than other state-of-art methods.
Ahmed glaucoma valves in refractory glaucoma: a 7-year audit

Purpose To present the long-term results of Ahmed glaucoma valve (AGV) implantation. Methods Consecutive case series of 94 eyes with AGV implantation over 7 years. Temporary tube ligation with C3F8 gas fill was used in high-risk eyes (group G&L) and compared with standard implantation in both phakic (group A) and pseudophakic/aphakic eyes (group B). Success was intraocular pressure (IOP) of 6 mm Hg or greater and 21 mm Hg or less and/or IOP reduction of 20% or greater. Results Average follow-up was 28.9±20.3 months. The mean preoperative IOP changed from 30.8±8.2 to 19.7±7.6 mm Hg and mean preoperative medications changed from 3.3±1.2 to 1.2±1.1 at the final visit. Cumulative probability of survival at 1 and 4 years was 89.1% and 72.9%. There was no statistically significant difference in success between the three groups, but complications due to postoperative hypotony (six eyes) only occurred in group B. Other complications were corneal decompensation (three eyes), tube erosion (six eyes) and aqueous misdirection (four eyes). Conclusions AGV implantation offered good long-term IOP control with a success rate of 78.7%. The authors recommend C3F8 gas fill and temporary tube ligation in eyes at high risk of postoperative hypotony and the use of donor sclera or human pericardial patch to prevent tube erosion.
Role of Endosomes in Simian Virus 40 Entry and Infection

ABSTRACT After binding to its cell surface receptor ganglioside GM1, simian virus 40 (SV40) is endocytosed by lipid raft-mediated endocytosis and slowly transported to the endoplasmic reticulum, where partial uncoating occurs. We analyzed the intracellular pathway taken by the virus in HeLa and CV-1 cells by using a targeted small interfering RNA (siRNA) silencing screen, electron microscopy, and live-cell imaging as well as by testing a variety of cellular inhibitors and other perturbants. We found that the virus entered early endosomes, late endosomes, and probably endolysosomes before reaching the endoplasmic reticulum and that this pathway was part of the infectious route. The virus was especially sensitive to a variety of perturbations that inhibited endosome acidification and maturation. Contrary to our previous models, which postulated the passage of the virus through caveolin-rich organelles that we called caveosomes, we conclude that SV40 depends on the classical endocytic pathway for infectious entry.
Evaluation of Nanofiber-Based Polyglycolic Acid Scaffolds for Improved Chondrocyte Retention and In Vivo Bioengineered Cartilage Regeneration

Background: In conventional studies on the regeneration of auricle-shaped cartilage in autogenous models using large animals, there were problems with the cartilage regeneration induction capacity and long-term retention of geometric shape. In this study, the authors sought to improve on outcome in these regards: a nonwoven fabric of polyglycolic acid was developed through nanotechnology, and the effect of nanofiber diameter on in vitro cell-seeding efficiency and the in vivo response after implantation in an autogenous large-animal model were evaluated. Methods: Canine chondrocytes were isolated and seeded onto polyglycolic acid fabric ranging from 0.5 to 20 &mgr;m in average diameter. Cell seeding efficiency was highest for mid-range polyglycolic acid fibers (average diameter, 0.8, 3.0, and 7.0 &mgr;m). Flat and auricle-shaped scaffolds were constructed using polypropylene structural support, sandwiching a nonwoven polyglycolic acid fabric that contained autogenous chondrocytes together with basic fibroblast growth factor–laden particles and an exterior fibrin sealant. Scaffolds were then implanted autogenously and evaluated at 5 and 20 weeks. Results: Biomechanical strength was optimal for polyglycolic acid fiber diameters of 0.8 to 3.0 &mgr;m. Optimal cell maintenance and neocartilage response were seen with polyglycolic acid fiber diameters in the same mid-range for nanofiber constructs. Conclusion: These findings demonstrate the potential for nanoscale modulation of auricle-shaped cartilage regeneration in a large-animal model.
Vibration energy harvesters for wireless sensor networks for aircraft health monitoring

This paper reports a self-powered WSN system based on piezoelectric energy harvesting and used for aircraft health monitoring. The system consists of three main subsystems, energy harvesting unit, MCU & wireless transceiver unit, and sensors unit. The prototype has dimension of 138 mm (L) × 41 mm (W) × 23 mm (H) with a weight of only 40 grams, making it easily integrated and implemented in an aircraft environment. Simulation results showed that with an excitation of 40 Hz frequency and 0.5 g acceleration on the harvester, the system takes about 3.4 secs to power the system with a selected voltage and another 23 secs to perform the initialization operations of the system. After the initialization, data are measured and transmitted wirelessly with a total energy consumption of 0.65 mJ in one cycle every one second. In addition, a new power management strategy for the applications using capacitors to store harvested energy was proposed. The mechanism relies on the analysis of how much energy has been stored on capacitor to determine the executions of the operations in the system. A novel energy saving interface (ESI) is designed to minimize the power consumption during the voltage measurement and an intelligent algorithm was developed to implement the strategy. Initial experiments show that the adapted Z-Stack and the proposed algorithm can be implemented on the system designed in this paper.
Improvements in the ultrasonic contrast of targeted perfluorocarbon nanoparticles using an acoustic transmission line model

Targeted acoustic contrast agents offer the potential for sensitive ultrasonic detection of pathologic tissues. We have previously reported the development of a ligand-targeted, lipid-encapsulated, liquid perfluorodichlorooctane ultrasonic contrast system with a small nominal particle size (approximately 250-nm diameter)Perfluorocarbon nanoparticles substantially increase reflectivity when bound to targeted surfaces, and we propose that this system can be approximated physically as a simple, thin layer, acoustic transmission line. In this study, we evaluate this model and compare the ultrasonic reflectivity of different perfluorocarbon formulations with widely varying acoustic impedances targeted to either nitrocellulose membranes or plasma thrombi in vitro. Five perfluorocarbons were investigated: perfluorohexane (PFH), perfluorooctane (PFO), perfluorooctyl bromide (PFOB), perfluorodichlorooctane (PFDCO), and perfluorodecalin (PFD). Ultrasonic reflection was measured by acoustic microscopy (17 to 35 MHz). Acoustic reflectivity was increased (P < 0.05) by all targeted perfluorocarbon formulations, and the magnitude of the contrast effect was inversely correlated with the perfluorocarbon acoustic impedance. PFH nanoparticles exhibited the greatest enhancement, and PFD nanoparticles showed the least. The acoustic transmission line model predicted well the relative differences in acoustic reflectivity and frequency dependence among the perfluorocarbon formulations. For future clinical applications, PFO nanoparticles may provide the best combination of acoustic enhancement, in vivo physical stability, and safety.
Utility of Aminotransferase/Platelet Ratio Index to Predict Liver Fibrosis in Intestinal Failure–Associated Liver Disease in Pediatric Patients

Background: Intestinal failure–associated liver disease (IFALD) is a frequent indication for intestinal transplantation. Liver biopsy (LBX) is the gold standard test for its diagnosis. Identifying noninvasive markers of fibrosis progression would be of considerable clinical use. Aspartate aminotransferase/platelet ratio index (APRI) has a good correlation in adult patients with chronic liver disease; few studies have been performed in children with IFALD. Aim: To evaluate APRI in a cohort of children with IFALD. Materials and Methods: Retrospective analysis of a prospective database of patients <18 years with severe intestinal failure and at least 1 LBX, registered in our unit from March 2006 to December 2014. Results: Forty-nine LBX were done on 36 patients: 20 were male, and 31 had short gut. Fibrosis was found in 71% of LBX. Biopsies were grouped according to the fibrosis stage (METAVIR [M]): (1) group 1 (G1) LBX with M 0, 1, 2 (n = 33) and (2) group 2 (G2) LBX with M 3, 4 (n = 16). The median APRI score was 0.92 (interquartile range [IQR] 0.63–1.50) for G1 and 2.50 (IQR 1.81–5.82) for G2 (P = .001) The c statistic of the receiving operating characteristic curve was 0.79 (95% CI 0.64–0.94; P < .001). The analyses allowed identifying a cutoff value for APRI of 1.6 as the point with the best sensitivity (81%) and specificity (76%) to predict advanced fibrosis. Conclusions: APRI in this cohort of patients shows that a score >1.6 correlates with advanced fibrosis.
Interruption of nocturnal pineal melatonin synthesis in spontaneous recrudescent Djungarian hamsters (Phodopus sungorus)

Abstract: The duration of nighttime synthesis of the pineal hormone melatonin is believed to determine the breeding season in many mammalian species. Hamsters exposed to short days undergo gonadal involution followed by a return to normal function, suggesting a developed insensitivity to regressive photoperiods. This recrudescence may be due to either exhaustion of the pineal or to target‐desensitization. Both theories have been tested previously but failed to explain this phenomenon. We performed an experiment in the Djungarian hamster (Phodopus sungorus), a well‐characterized photosensitive species with a type C melatonin pattern (prolonged peak during majority of dark phase), in an attempt to resolve this issue. Among age‐matched male hamsters exposed to short days for either 16 weeks (involuted) or 38 weeks (spontaneous recrudescent), marked phase differences in diurnal pineal melatonin rhythms were observed. Furthermore, in recrudescent hamsters the melatonin pattern was divided into two parts, possibly no longer recognizable as a typical short‐day rhythm.
Weak Gravitational Lensing Systematics from Image Combination

Extremely accurate shape measurements of galaxy images are needed to probe dark energy properties with weak gravitational lensing surveys. To increase survey area with a fixed observing time and pixel count, images from surveys such as the Wide Field Infrared Survey Telescope (WFIRST) or Euclid will necessarily be undersampled and therefore distorted by aliasing. Oversampled, unaliased images can be obtained by combining multiple, dithered exposures of the same source with a suitable reconstruction algorithm. Any such reconstruction must minimally distort the reconstructed images for weak lensing analyses to be unbiased. In this paper, we use the image combination (IMCOM) algorithm of Rowe, Hirata, and Rhodes to investigate the effect of image combination on shape measurements (size and ellipticity). We simulate dithered images of sources with varying amounts of ellipticity and undersampling, reconstruct oversampled output images from them using IMCOM, and measure shape distortions in the output. Our simulations show that IMCOM creates no significant distortions when the relative offsets between dithered images are precisely known. Distortions increase with the uncertainty in those offsets, but become problematic only with relatively poor astrometric precision; e.g., for images similar to those from the Astrophysics Focused Telescope Asset (AFTA) implementation of WFIRST, combining eight undersampled images (sampling ratio Q = 1) with highly pessimistic uncertainty in astrometric registration (σd ∼ 10-3 pixels) yields an rms shear error of O(10-4). Our analysis pipeline is adapted from that of the Precision Projector Laboratory—a joint project between NASA Jet Propulsion Laboratory and Caltech that characterizes image sensors using laboratory emulations of astronomical data.
Visualization of irregular multivariate data

The authors discuss effective techniques for representing scalar and vector valued functions that interpolate to irregularly located data. Special attention is given to the situations where the sampling domain is a two-dimensional plane, 3-D volume, or a closed 3-D surface. The authors first discuss the multiquadric and thin-plate spline methods for interpolating scalar data sampled at arbitrary locations in a plane. Straightforward generalizations are then made to data sampled in 3-D volumetric regions as well as in higher dimensional spaces. The globally defined interpolants can be evaluated on a fine regular grid and they can then be visualized using conventional techniques. Triangular and tetrahedral based visualization techniques are also presented. <<ETX>>
Antimicrobial peptides from amphibians

Abstract Increased prevalence of multi-drug resistance in pathogens has encouraged researchers to focus on finding novel forms of anti-infective agents. Antimicrobial peptides (AMPs) found in animal secretions are components of host innate immune response and have survived eons of pathogen evolution. Thus, they are likely to be active against pathogens and even those that are resistant to conventional drugs. Many peptides have been isolated and shown to be effective against multi-drug resistant pathogens. More than 500 AMPs have been identified from amphibians. The abundance of AMPs in frog skin is remarkable and constitutes a rich source for design of novel pharmaceutical molecules. Expression and post-translational modifications, discovery, activities and probable therapeutic application prospects of amphibian AMPs will be discussed in this article.
VALIDAÇÃO DO TAPETE DE CONTATO NA MENSURAÇÃO DA ALTURA DO SALTO EM JOGADORES DE BASQUETE DE ELITE VALIDITY OF CONTACT MAT FOR MEASURING JUMP HEIGHT IN ELITE BASKETBALL PLAYERS

O tapete de contato tem sido utilizado em diversos estudos e possui grande aplicacao pratica no treinamento e no controle esportivo. Embora a plataforma de forca seja considerada o “padrao ouro” na avaliacao da certas variaveis dos saltos verticais, ela requer um ambiente de laboratorio, assim como um alto custo para aquisicao e manutencao. Consequentemente, os testes realizados no tapete de contato constituem uma boa alternativa para a avaliacao de atletas na condicao esportiva, quando, muitas vezes, o acesso a um laboratorio se torna impossivel e inacessivel. Desta forma, o objetivo do presente estudo foi mensurar os criterios de validade do tapete de contato (Ergojump Jump Pro 2.0-Brazil), comparando-se tais calculos com os resultados do “padrao ouro” na plataforma de forca. Quinze atletas de basquetebol de elite, categoria sub-21, foram submetidos a tres tentativas do SCM no tapete de salto (Ergojump Jump Pro 2.0) e na plataforma de forca (OR6-1000, AMTI). A altura do salto vertical foi calculada utilizando-se ambos os equipamentos. Os valores de media (±1DP) para a altura do SCM, medidos pela plataforma de forca, foram 32.3±5.1cm e, para o tapete de contato, foram 32.44. 5cm. O teste t de Student pareado nao apresentou diferencas significantes entre ambas as formas de mensuracao (p = 0.90). O grafico de Bland-Altman foi construido para fornecer uma interpretacao visual aos dados. Portanto, o presente estudo sugere que os SCMs avaliados no tapete de contato apresentam confiaveis e consistentes medidas para a definicao da altura de salto comparadas as obtidas por meio de plataformas de forca, e que seu uso pode apresentar menor custo e praticidade.