Miracle-dz/UniFAR-FTUs huggingface dataset:
A Multispecificity Syntaxin Homologue, Vam3p, Essential for Autophagic and Biosynthetic Protein Transport to the Vacuole

Protein transport in eukaryotic cells requires the selective docking and fusion of transport intermediates with the appropriate target membrane. t-SNARE molecules that are associated with distinct intracellular compartments may serve as receptors for transport vesicle docking and membrane fusion through interactions with specific v-SNARE molecules on vesicle membranes, providing the inherent specificity of these reactions. VAM3 encodes a 283–amino acid protein that shares homology with the syntaxin family of t-SNARE molecules. Polyclonal antiserum raised against Vam3p recognized a 35-kD protein that was associated with vacuolar membranes by subcellular fractionation. Null mutants of vam3 exhibited defects in the maturation of multiple vacuolar proteins and contained numerous aberrant membrane-enclosed compartments. To study the primary function of Vam3p, a temperature-sensitive allele of vam3 was generated (vam3tsf). Upon shifting the vam3tsf mutant cells to nonpermissive temperature, an immediate block in protein transport through two distinct biosynthetic routes to the vacuole was observed: transport via both the carboxypeptidase Y pathway and the alkaline phosphatase pathway was inhibited. In addition, vam3tsf cells also exhibited defects in autophagy. Both the delivery of aminopeptidase I and the docking/ fusion of autophagosomes with the vacuole were defective at high temperature. Upon temperature shift, vam3tsf cells accumulated novel membrane compartments, including multivesicular bodies, which may represent blocked transport intermediates. Genetic interactions between VAM3 and a SEC1 family member, VPS33, suggest the two proteins may act together to direct the docking and/or fusion of multiple transport intermediates with the vacuole. Thus, Vam3p appears to function as a multispecificity receptor in heterotypic membrane docking and fusion reactions with the vacuole. Surprisingly, we also found that overexpression of the endosomal t-SNARE, Pep12p, suppressed vam3Δ mutant phenotypes and, likewise, overexpression of Vam3p suppressed the pep12Δ mutant phenotypes. This result indicated that SNAREs alone do not define the specificity of vesicle docking reactions.
Blunted autonomic reactivity to pharmacological panic challenge under long-term escitalopram treatment in healthy men

Background: Central serotonergic pathways influence brain areas involved in vagal cardiovascular regulation and, thereby, influence sympathetic efferent activity. Selective serotonin reuptake inhibitors (SSRIs) affect multiple serotonergic pathways, including central autonomic pathways. However, only a few studies have assessed SSRI-mediated effects on autonomic reactivity in healthy individuals using heart rate variability (HRV). Methods: The present study assessed the influence of long-term treatment with escitalopram (ESC) on autonomic reactivity to an intravenous application of 50 µg cholecystokinin tetrapeptide (CCK-4) in 30 healthy young men using a double-blind, placebo (PLA)-controlled, randomized, within-subject cross-over design. Main outcome measures were time- and frequency-domain HRV parameters, assessed at both baseline and immediately after CCK-4 application. Results: Results showed substantial effects for the treatment × CCK-4 challenge interaction with respect to heart rate (p < 0.001; pη2 = 0.499), SDNN (p < 0.001; pη2 = 576), RMSSD (p = 0.015; pη2 = 194), NN50% (p = 0.008; pη2 = 0.224), and LF% (p = 0.014; pη2 = 0.196), and moderate effects with respect HF% (p = 0.099; pη2 = 0.094), with PLA subjects showing a higher increase in HR and SDNN and a higher decrease in RMSSD, NN50, LF and HF than subjects in the ESC condition. Thus, ESC treatment significantly blunted the autonomic reactivity to CCK-4. Secondary analysis indicated no effect of the 5-HTTLPR polymorphism on CCK-4-induced autonomic response. Conclusions: Our results support findings suggesting an effect of SSRI treatment on autonomic regulation and provide evidence that ESC treatment is associated with blunted autonomic reactivity in healthy men.
Integrating the Concept of Synthesis in the Software Architecture Design Process

Synthesis is a widely applied problem-solving approach of mature engineering disciplines including the sub-processes of technical problem analysis, identification and composition of solution domain concepts, and alternative-space analysis. Current software development processes do not adopt an explicit synthesis process and as such may fall short in identifying, composing and evaluating the relevant concerns. In order to advance ad hoc software development process to a mature engineering discipline it is necessary to integrate the concept of synthesis in current software engineering processes. In software engineering, software architecture design forms a key artifact including the early design decisions, which embodies the overall structure that impacts the quality of the overall system. For ensuring the quality of software architecture, it is necessary to identify and compose the relevant concerns. For this, we integrate the concept of synthesis in the software architecture design process and present the synthesis-based software architecture design process. This approach differs from existing software architecture design approaches since it explicitly includes the synthesis sub-processes of technical problem analysis, solution domain analysis and alternative space analysis, integrating these in a common process.
Reproductive toxicology. Methyl salicylate.

Although many of the regulators of actin assembly are known, we do not understand how these components act together to organize cell shape and movement. To address this question, we analyzed the spatial dynamics of a key actin regulator–the Scar/WAVE complex–which plays an important role in regulating cell shape in both metazoans and plants. We have recently discovered that the Hem‐1/Nap1 component of the Scar/WAVE complex localizes to propagating waves that appear to organize the leading edge of a motile immune cell, the human neutrophil. Actin is both an output and input to the Scar/WAVE complex: the complex stimulates actin assembly, and actin polymer is also required to remove the complex from the membrane. These reciprocal interactions appear to generate propagated waves of actin nucleation that exhibit many of the properties of morphogenesis in motile cells, such as the ability of cells to flow around barriers and the intricate spatial organization of protrusion at the leading edge. We propose that cell motility results from the collective behavior of multiple self‐organizing waves.
Automated malaria parasite detection in thin blood films:- A hybrid illumination and color constancy insensitive, morphological approach

This paper illustrates the automated diagnosis of malaria parasite (Plasmodium species) in microscopic images of Giemsa stained thin blood films. The procedure adapts a morphological approach for blood cell identification and uses the image features such as intensity, histogram, relative size and geometry for further analysis. Two methods of object classification have been described for parasite detection; one based on relative size and morphology and the other based on intensity variation. Furthermore, an analytical study on both methods has been performed in order to validate the accuracy of the methods.
Précipitation dans les alliages de structure -suivre les atomes pour construire des avions

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Précipitation dans les alliages de structure -suivre les atomes pour construire des avions Frédéric de Geuser, Laurent Couturier, Alexis Deschamps
Motion and force control of cooperative robotic manipulators with passive joints

In this paper, robotic systems when two or more underactuated manipulators are working in a cooperative way are studied. The underactuation effects on object to be controlled and on load capacity of the cooperative arms are analyzed. A hybrid control of motion and squeeze force is proposed. For the motion control, a Jacobian matrix that relates the torques in the actuated joints to the resulting force in the load is obtained. In addition, a method to compute the dynamic load-carrying capacity of cooperative manipulators with passive joints is presented. Results of the control system are verified in simulations and in an actual system formed by two cooperative arms.
Elevation of the serum Fas ligand in patients with hemophagocytic syndrome and Diamond-Blackfan anemia.

Fas ligand (FasL) is a membrane protein that is expressed in activated T cells and natural killer cells. FasL binds to Fas on target cells and induces apoptosis. There exists a soluble form of FasL (sFasL), and sFasL also induces apoptosis of Fas-bearing cells. The serum sFasL concentrations were reported to be elevated in patients with large granular lymphocytic leukemia and natural killer cell lymphoma. In this study, we have measured serum sFasL concentrations in other hematological disorders, including severe aplastic anemia (SAA), hemophagocytic lymphohistiocytosis (HLH), and Diamond-Blackfan anemia (DBA). The serum sFasL concentration of age-matched healthy controls was 0.16 +/- 0.11 ng/mL (mean +/- SD, n = 22). The serum sFasL levels in the patients with HLH and DBA were 3.75 +/- 3.82 (n = 19; P < .0001, HLH v control) and 2.76 +/- 2.43 ng/mL (n = 6; P = .012, DBA v control), respectively. Serum interferon-gamma concentration was elevated in the patients with HLH (1.61 +/- 2.62 ng/mL) but not in those with DBA (below the detectable level). These results suggest that the Fas-FasL system plays a role, at least in part, in the pathophysiology of HLH and DBA.
Fuel consumption minimization of a microgrid

A cost optimization scheme for a microgrid is presented. Prior to the optimization of the microgrid itself, several schemes for sharing power between two generators are compared. The minimization of fuel use in a microgrid with a variety of power sources is then discussed. The optimization of a small power system has important differences from the case of a large system and its traditional economic dispatch problem. Among the most important differences is the presence of a local heat demand which adds another dimension to the optimization problem. The microgrid considered in this paper consists of two reciprocating gas engines, a combined heat and power plant, a photovoltaic array and a wind generator. The optimization is aimed at reducing the fuel consumption rate of the system while constraining it to fulfil the local energy demand (both electrical and thermal) and provide a certain minimum reserve power. A penalty is applied for any heat produced in excess of demand. The solution of the optimization problem strongly supports the idea of having a communication infrastructure operating between the power sources.
In Vitro Investigations into the Roles of Drug Transporters and Metabolizing Enzymes in the Disposition and Drug Interactions of Dolutegravir, a HIV Integrase Inhibitor

Dolutegravir (DTG; S/GSK1349572) is a potent HIV-1 integrase inhibitor with a distinct resistance profile and a once-daily dose regimen that does not require pharmacokinetic boosting. This work investigated the in vitro drug transport and metabolism of DTG and assessed the potential for clinical drug-drug interactions. DTG is a substrate for the efflux transporters P-glycoprotein (Pgp) and human breast cancer resistance protein (BCRP). Its high intrinsic membrane permeability limits the impact these transporters have on DTG’s intestinal absorption. UDP-glucuronosyltransferase (UGT) 1A1 is the main enzyme responsible for the metabolism of DTG in vivo, with cytochrome P450 (P450) 3A4 being a notable pathway and UGT1A3 and UGT1A9 being only minor pathways. DTG demonstrated little or no inhibition (IC50 values > 30 μM) in vitro of the transporters Pgp, BCRP, multidrug resistance protein 2, organic anion transporting polypeptide 1B1/3, organic cation transporter (OCT) 1, or the drug metabolizing enzymes CYP1A2, 2A6, 2B6, 2C8, 2C9, 2C19, 2D6, 3A4, UGT1A1, or 2B7. Further, DTG did not induce CYP1A2, 2B6, or 3A4 mRNA in vitro using human hepatocytes. DTG does inhibit the renal OCT2 (IC50 = 1.9 μM) transporter, which provides a mechanistic basis for the mild increases in serum creatinine observed in clinical studies. These in vitro studies demonstrate a low propensity for DTG to be a perpetrator of clinical drug interactions and provide a basis for predicting when other drugs could result in a drug interaction with DTG.
A Safe, Quick and Scalable Solution to Data Flow Transfer in Wide Area Network of Sensors

One of the challenges facing us in a wide area sensor network (WASN) is how to transfer real-time data produced by sensors quickly and safely to authentic users. In this paper, we propose a solution which is based on both sensor agent which is used to dividing WASN and random number ID encryption. By setting a sensor agent node, we group the sensors according to their geographical condition, and we also grant the agent node some administration privilege to manage the sensors. By selecting a random number for a sensor's ID, we encrypt the data to be transferred. Experiment results shows that our approach is timesaving and has a better locating performance
Computational Analysis of Lifespan Experiment Reproducibility

Independent reproducibility is essential to the generation of scientific knowledge. Optimizing experimental protocols to ensure reproducibility is an important aspect of scientific work. Genetic or pharmacological lifespan extensions are generally small compared to the inherent variability in mean lifespan even in isogenic populations housed under identical conditions. This variability makes reproducible detection of small but real effects experimentally challenging. In this study, we aimed to determine the reproducibility of C. elegans lifespan measurements under ideal conditions, in the absence of methodological errors or environmental or genetic background influences. To accomplish this, we generated a parametric model of C. elegans lifespan based on data collected from 5,026 wild-type N2 animals. We use this model to predict how different experimental practices, effect sizes, number of animals, and how different ‘shapes’ of survival curves affect the ability to reproduce real longevity effects. We find that the chances of reproducing real but small effects are exceedingly low and would require substantially more animals than are commonly used. Our results indicate that many lifespan studies are underpowered to detect reported changes and that, as a consequence, stochastic variation alone can account for many failures to reproduce longevity results. As a remedy, we provide power of detection tables that can be used as guidelines to plan experiments with statistical power to reliably detect real changes in lifespan and limit spurious false positive results. These considerations will improve best-practices in designing lifespan experiment to increase reproducibility.
The geometry of confocal curves for passing through a door

This paper presents a geometric approach to the problem of steering a robot subject to nonholonomic constraints through a door by using only visual measurements coming from a single fixed on-board monocular camera. The door is represented by two landmarks located on its vertical supports. After exploring the geometric structure that naturally emerges from the problem statement, e.g., bundle of hyperbolae, ellipses, and circles, we exploit this planar geometry to provide stabilizing feedback control laws to drive the vehicle through the middle of the door. Using visual servoing, we prove that this geometry can be directly measured in the camera image plane. Hence, we provide an image-based control scheme, avoiding the use of a state observer. Simulations in a realistic scenario and experiments are provided to show the effectiveness of the feedback control laws.
Exposing splicing forgeries in digital images through dichromatic plane histogram discrepancies

One of the common image forgery techniques is the splicing, where parts from different images are copied and pasted onto a single image. This paper proposes a new forensics method for detecting splicing forgeries in images containing human faces. Our approach is based on extracting an illumination-signature from the faces of people present in an image using the dichromatic reflection model (DRM). The dichromatic plane histogram (DPH), which is calculated by applying the 2D Hough Transform on the face images, is used as the illumination-signature. The correlation measure is employed to compute the similarity between the DPHs obtained from different faces present in an image. Finally, a simple threshold on this similarity measure exposes splicing forgeries in the image. Experimental results show the efficacy of the proposed method.
An Interactive Visualization Framework for Time-Series of Web Graphs in a 3D Environment

We propose an interactive framework for the 3D visualization of the time-series of Web graphs. The purpose of our framework is to enable users to examine the evolution of Web graphs by comparing multiple graphs that have different timings and topics. To achieve this, we provide TimeSlices that are 2D planes to visualize Web graphs in a 3D environment. Users can interactively add new TimeSlices along the timeline, and they can manipulate them to animate Web graphs. Visualized Web graphs on TimeSlices are snapshots of different timings. Moreover, we provide mechanisms to generate and manipulate overlay views and parallel views in the 3D environment to enable Web graphs to be compared. Users can seamlessly change these viewing modes. Our system can also visualize two Web graphs created from different keywords to display the evolutional correlation between them. This system enables us to observe structural and temporal changes in multiple Web graphs such as shifts in influential blogs or power shifts in the diffusion of blogs between topics.
Purple Sweet Potato Color Ameliorates Cognition Deficits and Attenuates Oxidative Damage and Inflammation in Aging Mouse Brain Induced by D-Galactose

Purple sweet potato color (PSPC), a naturally occurring anthocyanin, has a powerful antioxidant activity in vitro and in vivo. This study explores whether PSPC has the neuroprotective effect on the aging mouse brain induced by D-galactose (D-gal). The mice administrated with PSPC (100 mg/kg.day, 4 weeks, from 9th week) via oral gavage showed significantly improved behavior performance in the open field and passive avoidance test compared with D-gal-treated mice (500 mg/kg.day, 8 weeks). We further investigate the mechanism involved in neuroprotective effects of PSPC on mouse brain. Interestingly, we found, PSPC decreased the expression level of glial fibrillary acidic protein (GFAP), inducible nitric oxide synthase (iNOS), and cyclooxygenase-2 (COX-2), inhibited nuclear translocation of nuclear factor-kappaB (NF-κB), increased the activity of copper/zinc superoxide dismutase (Cu/Zn-SOD) and catalase (CAT), and reduced the content of malondialdehyde (MDA), respectively. Our data suggested that PSPC attenuated D-gal-induced cognitive impairment partly via enhancing the antioxidant and anti-inflammatory capacity.
Pre-calculated protein structure alignments at the RCSB PDB website

Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user. Availability and Implementation: A web user interface is available at http://www.rcsb. org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava. org. A source bundle, prepared for local execution, is available from http://source.rcsb. org Contact: andreas@sdsc.edu; pbourne@ucsd.edu
Cross-scale Drivers of Natural Disturbances Prone to Anthropogenic Amplification: The Dynamics of Bark Beetle Eruptions

ABSTRACT Biome-scale disturbances by eruptive herbivores provide valuable insights into species interactions, ecosystem function, and impacts of global change. We present a conceptual framework using one system as a model, emphasizing interactions across levels of biological hierarchy and spatiotemporal scales. Bark beetles are major natural disturbance agents in western North American forests. However, recent bark beetle population eruptions have exceeded the frequencies, impacts, and ranges documented during the previous 125 years. Extensive host abundance and susceptibility, concentrated beetle density, favorable weather, optimal symbiotic associations, and escape from natural enemies must occur jointly for beetles to surpass a series of thresholds and exert widespread disturbance. Opposing feedbacks determine qualitatively distinct outcomes at junctures at the biochemical through landscape levels. Eruptions occur when key thresholds are surpassed, prior constraints cease to exert influence, and positive feedbacks amplify across scales. These dynamics are bidirectional, as landscape features influence how lower-scale processes are amplified or buffered. Climate change and reduced habitat heterogeneity increase the likelihood that key thresholds will be exceeded, and may cause fundamental regime shifts. Systems in which endogenous feedbacks can dominate after external forces foster the initial breach of thresholds appear particularly sensitive to anthropogenic perturbations.