Miracle-dz/UniFAR-FTUs huggingface dataset:
SNARE interactions in membrane trafficking: A perspective from mammalian central synapses

SNAREs (soluble N‐ethylmaleimide‐sensitive factor attachment protein receptors) are a large family of proteins that are present on all organelles involved in intracellular vesicle trafficking and secretion. The interaction of complementary SNAREs found on opposing membranes presents an attractive lock‐and‐key mechanism, which may underlie the specificity of vesicle trafficking. Moreover, formation of the tight complex between a vesicle membrane SNARE and corresponding target membrane SNAREs could drive membrane fusion. In synapses, this tight complex, also referred to as the synaptic core complex, is essential for neurotransmitter release. However, recent observations in knockout mice lacking major synaptic SNAREs challenge the prevailing notion on the executive role of these proteins in fusion and open up several questions about their exact role(s) in neurotransmitter release. Persistence of a form of regulated neurotransmitter release in these mutant mice also raises the possibility that other cognate or non‐cognate SNAREs may partially compensate for the loss of a particular SNARE. Future analysis of SNARE function in central synapses will also have implications for the role of these molecules in other vesicle trafficking events such as endocytosis and vesicle replenishment. Such analysis can provide a molecular basis for synaptic processes including certain forms of short‐term synaptic plasticity. BioEssays 24:926–936, 2002. © 2002 Wiley Periodicals, Inc.
Graph annotations in modeling complex network topologies

The coarsest approximation of the structure of a complex network, such as the Internet, is a simple undirected unweighted graph. This approximation, however, loses too much detail. In reality, objects represented by vertices and edges in such a graph possess some nontrivial internal structure that varies across and differentiates among distinct types of links or nodes. In this work, we abstract such additional information as network annotations. We introduce a network topology modeling framework that treats annotations as an extended correlation profile of a network. Assuming we have this profile measured for a given network, we present an algorithm to rescale it in order to construct networks of varying size that still reproduce the original measured annotation profile. Using this methodology, we accurately capture the network properties essential for realistic simulations of network applications and protocols, or any other simulations involving complex network topologies, including modeling and simulation of network evolution. We apply our approach to the Autonomous System (AS) topology of the Internet annotated with business relationships between ASs. This topology captures the large-scale structure of the Internet. In depth understanding of this structure and tools to model it are cornerstones of research on future Internet architectures and designs. We find that our techniques are able to accurately capture the structure of annotation correlations within this topology, thus reproducing a number of its important properties in synthetically-generated random graphs.
Stormy geomorphology: geomorphic contributions in an age of climate extremes

The increasing frequency and/or severity of extreme climate events are becoming increasingly apparent over multi‐decadal timescales at the global scale, albeit with relatively low scientific confidence. At the regional scale, scientific confidence in the future trends of extreme event likelihood is stronger, although the trends are spatially variable. Confidence in these extreme climate risks is muddied by the confounding effects of internal landscape system dynamics and external forcing factors such as changes in land use and river and coastal engineering. Geomorphology is a critical discipline in disentangling climate change impacts from other controlling factors, thereby contributing to debates over societal adaptation to extreme events. We review four main geomorphic contributions to flood and storm science. First, we show how palaeogeomorphological and current process studies can extend the historical flood record while also unraveling the complex interactions between internal geomorphic dynamics, human impacts and changes in climate regimes. A key outcome will be improved quantification of flood probabilities and the hazard dimension of flood risk. Second, we present evidence showing how antecedent geomorphological and climate parameters can alter the risk and magnitude of landscape change caused by extreme events. Third, we show that geomorphic processes can both mediate and increase the geomorphological impacts of extreme events, influencing societal risk. Fourthly, we show the potential of managing flood and storm risk through the geomorphic system, both near‐term (next 50 years) and longer‐term. We recommend that key methods of managing flooding and erosion will be more effective if risk assessments include palaeodata, if geomorphological science is used to underpin nature‐based management approaches, and if land‐use management addresses changes in geomorphic process regimes that extreme events can trigger. We argue that adopting geomorphologically‐grounded adaptation strategies will enable society to develop more resilient, less vulnerable socio‐geomorphological systems fit for an age of climate extremes. © 2016 The Authors. Earth Surface Processes and Landforms published by John Wiley & Sons Ltd.
Filling and intensity changes in hurricanes over land

The change in central pressure after landfall of 13 selected hurricanes is analyzed. A formula that fits the average filling curve is given. The average change in pressure gradient after landfall is also evaluated. One of several incidental findings pertains to the consistent values obtained when applying an objec tive definition for the pressure at the periphery of a hurricane.
Natural weathering of Scots pine (Pinus sylvestris L.) boards modified with functionalised commercial silicone emulsions

A quat-silicone micro-emulsion (particle size <40 nm), an amino-silicone macro-emulsion (110 nm), and an alkyl modified silicone macro-emulsion (740 nm) were used to modify Scots pine (Pinus sylvestris L.) sapwood. Treated and uncoated boards were exposed to natural weathering for one year along with water treated controls according to EN 927-3. The treatment with silicone emulsions did not enhance the color stability, which was assessed at three months intervals using a spectrophotometer and classified according to the CIE-Lab system. Treatment with amino-silicone emulsions gave a more yellowish appearance of the wood surface before weathering than the other silicones and the control. Boards treated with quat- and amino-silicone were less overgrown by staining fungi and displayed reduced surface roughness than those treated with alkyl-modified silicone and the control samples.
The Leiden Thrombophilia Study (LETS)

Study Design (5) LETS was designed to assess the importance at the population level of various risk factors for thrombosis, many of which had been identified by family studies. Generally, two approaches are possible: cohort studies and case-control studies. In the former, patients with and without a risk factor are followed over time, and absolute risks (probability of disease, incidence) and relative risks (incidence rate ratio) can be calculated. In a case-control study, patients with thrombosis and healthy controls are included, and relative risks (odds ratios) can be calculated. Due to the rarity of the genetic risk factors for thrombosis, a follow-up study of a truly unselected sample from the
Combinatorial Multi-Armed Bandit with General Reward Functions

In this paper, we study the stochastic combinatorial multi-armed bandit (CMAB) framework that allows a general nonlinear reward function, whose expected value may not depend only on the means of the input random variables but possibly on the entire distributions of these variables. Our framework enables a much larger class of reward functions such as the max() function and nonlinear utility functions. Existing techniques relying on accurate estimations of the means of random variables, such as the upper confidence bound (UCB) technique, do not work directly on these functions. We propose a new algorithm called stochastically dominant confidence bound (SDCB), which estimates the distributions of underlying random variables and their stochastically dominant confidence bounds. We prove that SDCB can achieve O(log T) distribution-dependent regret and O(√T) distribution-independent regret, where T is the time horizon. We apply our results to the K-MAX problem and expected utility maximization problems. In particular, for K-MAX, we provide the first polynomial-time approximation scheme (PTAS) for its offline problem, and give the first O(√T) bound on the (1 — e)-approximation regret of its online problem, for any e > 0.
Targeting ofAdenovirus via Genetic Modification of the Viral Capsid Combined with aProteinBridge

ABSTRACT A potential barrier to the development of genetically targeted adenovirus (Ad) vectors for cell-specific delivery of gene therapeutics lies in the fact that several types of targeting protein ligands require posttranslational modifications, such as the formation of disulfide bonds, which are not available to Ad capsid proteins due to their nuclear localization during assembly of the virion. To overcome this problem, we developed a new targeting strategy, which combines genetic modifications of the Ad capsid with a protein bridge approach, resulting in a vector-ligand targeting complex. The components of the complex associate by virtue of genetic modifications to both the Ad capsid and the targeting ligand. One component of this mechanism of association, the Fc-binding domain of Staphylococcus aureus protein A, is genetically incorporated into the Ad fiber protein. The ligand is comprised of a targeting component fused with the Fc domain of immunoglobulin, which serves as a docking moiety to bind to these genetically modified fibers during the formation of the Ad-ligand complex. The modular design of the ligand solves the problem of structural and biosynthetic compatibility with the Ad and thus facilitates targeting of the vector to a variety of cellular receptors. Our study shows that targeting ligands incorporating the Fc domain and either an anti-CD40 single-chain antibody or CD40L form stable complexes with protein A-modified Ad vectors, resulting in significant augmentation of gene delivery to CD40-positive target cells. Since this gene transfer is independent of the expression of the native Ad5 receptor by the target cells, this strategy results in the derivation of truly targeted Ad vectors suitable for tissue-specific gene therapy.
Regional dendritic and spine variation in human cerebral cortex: a quantitative golgi study.

The present study explored differences in dendritic/spine extent across several human cortical regions. Specifically, the basilar dendrites/spines of supragranular pyramidal cells were examined in eight Brodmann's areas (BA) arranged according to Benson's (1993, Behav Neurol 6:75-81) functional hierarchy: primary cortex (somatosensory, BA3-1-2; motor, BA4), unimodal cortex (Wernicke's area, BA22; Broca's area, BA44), heteromodal cortex (supple- mentary motor area, BA6beta; angular gyrus, BA39) and supramodal cortex (superior frontopolar zone, BA10; inferior frontopolar zone, BA11). To capture more general aspects of regional variability, primary and unimodal areas were designated as low integrative regions; heteromodal and supramodal areas were designated as high integrative regions. Tissue was obtained from the left hemisphere of 10 neurologically normal individuals (M(age) = 30 +/- 17 years; five males, five females) and stained with a modified rapid Golgi technique. Ten neurons were sampled from each cortical region (n = 800) and evaluated according to total dendritic length, mean segment length, dendritic segment count, dendritic spine number and dendritic spine density. Despite considerable inter-individual variation, there were significant differences across the eight Brodmann's areas and between the high and low integrative regions for all dendritic and spine measures. Dendritic systems in primary and unimodal regions were consistently less complex than in heteromodal and supramodal areas. The range within these rankings was substantial, with total dendritic length in BA10 being 31% greater than that in BA3-1-2, and dendritic spine number being 69% greater. These findings demonstrate that cortical regions involved in the early stages of processing (e.g. primary sensory areas) generally exhibit less complex dendritic/spine systems than those regions involved in the later stages of information processing (e.g. prefrontal cortex). This dendritic progression appears to reflect significant differences in the nature of cortical processing, with spine-dense neurons at hierarchically higher association levels integrating a broader range of synaptic input than those at lower cortical levels.
A Robust and Efficient Three-Layered Dialogue Component for a Speech-to-Speech Translation System

We present the dialogue component of the speech-to-speech translation system VERBMOBIL. In contrast to conventional dialogue systems it mediates the dialogue while processing maximally 50% of the dialogue in depth. Special requirements (robustness and efficiency) lead to a 3-layered hybrid architecture for the dialogue module, using statistics, an automaton and a planner. A dialogue memory is constructed incrementally.
Title In vitro effects of artesunate on the survival of worm pairs and eggproduction of Schistosoma mansoni

The effect of artesunate (ART) on the survival time of adult worm pairs of Schistosoma mansoni and on their egg output during in vitro culture was assessed. ART significantly decreased the survival time of both paired male and female worms at concentrations of 5, 10, 20 and 40 mg l during in vitro cultivation. An inhibitory effect of ART on the daily egg output of paired female worms during in vitro cultivation was also observed.
Coffee, tea and caffeine intake and the risk of severe depression in middle-aged Finnish men: the Kuopio Ischaemic Heart Disease Risk Factor Study

Abstract Objective Only a few cross-sectional studies have assessed the association between coffee, tea and caffeine and the risk of depression. Our aim was to determine the association in a population-based cohort study. Design The population-based Kuopio Ischaemic Heart Disease Risk Factor Study cohort was recruited between 1984 and 1989 and followed until the end of 2006. We investigated the association between the intake of coffee, tea and caffeine and depression. Setting Eastern Finland. Subjects Middle-aged men (n 2232). Results Altogether, forty-nine men received a discharge diagnosis of depression. We classified subjects into quartiles according to their mean daily coffee intake: non-drinkers (n 82), light drinkers (<375 ml/d, n 517), moderate drinkers (375–813 ml/d, n 1243) and heavy drinkers (>813 ml/d, n 390). Heavy drinkers had a decreased risk (RR = 0·28, 95 % CI 0·08, 0·98) for depression when compared with non-drinkers, after adjustment for age and examination years. Further adjustment for socio-economic status, alcohol consumption, smoking, maximal oxygen uptake, BMI and the energy-adjusted daily intakes of folate and PUFA did not attenuate this association (relative risk (RR) = 0·23, 95 % CI 0·06, 0·83). No associations were observed between depression and intake of tea (drinkers v. non-drinkers; RR = 1·19, 95 % CI 0·54, 2·23) or caffeine (highest quartile v. lowest quartile; RR = 0·99, 95 % CI 0·40, 2·45). Conclusions Coffee consumption may decrease the risk of depression, whereas no association was found for tea and caffeine intake.
Surveillance and Screening of Primary Sclerosing Cholangitis

Primary sclerosing cholangitis (PSC) represents an idiopathic chronic cholestatic liver disease due to inflammatory destruction of the biliary tree. Clinically, the progressive disease leads to biliary cirrhosis in association with cholangiocarcinoma in 6–20% of the patients. Currently, liver transplantation remains the only life-extending treatment option in end-stage disease. However, due to the high risk of carcinoma development, PSC patients should be tightly screened and evaluated including newer technologies like endoscopic ultrasound-guided fine-needle aspiration biopsy and cholangioscopy including cytology and direct biopsy of the biliary mucosal lesions.
STOCHASTIC “BEADS ON A STRING” IN THE ACCRETION TAIL OF ARP 285

We present Spitzer infrared, Galaxy Evolution Explorer UV, and Sloan Digitized Sky Survey and Southeastern Association for Research in Astronomy optical images of the peculiar interacting galaxy pair Arp 285 (NGC 2856/4), and compare with a new numerical model of the interaction. We estimate the ages of clumps of star formation in these galaxies using population synthesis models, carefully considering the uncertainties on these ages. This system contains a striking example of “beads on a string”: a series of star-formation complexes ∼1 kpc apart. These “beads” are found in a tail-like feature that is perpendicular to the disk of NGC 2856, which implies that it was formed from material accreted from the companion NGC 2854. The extreme blueness of the optical/UV colors and redness of the mid-infrared colors implies very young stellar ages (∼4–20 Myr) for these star-forming regions. Spectral decomposition of these “beads” shows excess emission above the modeled stellar continuum in the 3.6 μm and 4.5 μm bands, indicating either contributions from interstellar matter to these fluxes or a second older stellar population. These clumps have −12.0 < MB< −10.6, thus they are less luminous than most dwarf galaxies. Our model suggests that bridge material falling into the potential of the companion overshoots the companion. The gas then piles up at apogalacticon before falling back onto the companion, and star formation occurs in the pile-up. There was a time delay of ∼500 Myr between the point of closest approach between the two galaxies and the initiation of star formation in this feature. A luminous (MB ∼ −13.6) extended (FWHM ∼ 1.3 kpc) “bright spot” is visible at the northwestern edge of the NGC 2856 disk, with an intermediate stellar population (400–1500 Myr). Our model suggests that this feature is part of a expanding ripple-like “arc” created by an off-center ring-galaxy-like collision between the two disks.
Loss factorization, weakly supervised learning and label noise robustness

We prove that the empirical risk of most well-known loss functions factors into a linear term aggregating all labels with a term that is label free, and can further be expressed by sums of the loss. This holds true even for non-smooth, non-convex losses and in any RKHS. The first term is a (kernel) mean operator --the focal quantity of this work-- which we characterize as the sufficient statistic for the labels. The result tightens known generalization bounds and sheds new light on their interpretation. Factorization has a direct application on weakly supervised learning. In particular, we demonstrate that algorithms like SGD and proximal methods can be adapted with minimal effort to handle weak supervision, once the mean operator has been estimated. We apply this idea to learning with asymmetric noisy labels, connecting and extending prior work. Furthermore, we show that most losses enjoy a data-dependent (by the mean operator) form of noise robustness, in contrast with known negative results.
Dual-channel fiber ultrasonic sensor system based on fiber Bragg grating in an erbium-doped fiber ring laser

A novel method to realize two point fiber-optic ultrasonic sensor system has been demonstrated, which is based on fiber Bragg grating (FBG) in an erbium-doped fiber (EDF) ring laser (EFRL). There are two pairs of FBGs with different Bragg wavelength in this system. Each pair of FBGs has a long FBG (LFBG) and a short FBG (SFBG), which have an appropriate matching operating point and determine one potential lasing line. Two pairs of FBGs are used as both the comb filter and the ultrasonic sensors. Due to the different spectral response of the LFBG and SFBG to ultrasound, the cavity loss will change regularly by the ultrasound, and the intensity of the laser output will be modulated by the cavity loss. Meanwhile, an adjustable attenuator is added to the fiber ring cavity. By adjusting the attenuator, the gain and loss of the two specific wavelengths can be balanced, and the laser oscillation at two specific wavelengths is stabled. With the modulation of the adjustable attenuator, multiplexing ultrasonic EFRL sensors can be achieved within a single cavity fiber laser. The proposed method has been experimentally demonstrated by using a dual-channel laser system with a single section of gain medium, EDF.
Image Analysis Workflow for 2-D Electrophoresis Gels Based on ImageJ

A number of commercial software packages are currently available to perform digital two-dimensional electrophoresis (2D-GE) gel analysis. However, both the high cost of the commercial packages and the unavailability of a standard data analysis workflow, have prompted several groups to develop freeware systems to perform certain steps of gel analysis. Unfortunately, to the best of our knowledge none of them offer a package that performs all the steps envisaged in a 2D-GE gel analysis. Here we describe an ImageJ-based procedure, able to manage all the steps of a 2D-GE gel analysis. ImageJ is a free available image processing and analysis application developed by National Institutes of Health (NIH) and widely used in different life sciences fields as medical imaging, microscopy, western blotting and PAGE. Nevertheless no one has yet developed a procedure enabled to compare spots on 2D-GE gels. We collected all used ImageJ tools in a plug-in that allows us to perform the whole 2D-GE analysis. To test it, we performed a set of 2D-GE experiments on plasma samples from 9 patients victims of acute myocardial infarction and 8 controls, and we compared the results obtained by our procedure to those obtained using a widely diffuse commercial package, finding similar performances.
DESIGN OF A MICROCHANNEL BASED SOLAR RECEIVER / REACTOR FOR BIOFUEL PROCESSING

This study investigates use of solar thermochemical processing of clean fuels using biomass products (CH4, CO2, H2O). To address technological feasibility of a microchannel-based solar receiver/reactor a combined numerical and experimental study of methane-steam reforming is carried out on a single microchannel with Palladium-deposited channel walls and heat input to facilitate endothermic heterogeneous reactions producing hydrogen. A simple one-dimensional model solving steady state species mass fraction, energy, and overall conservation of mass equations is developed and verified against the full, threedimensional direct numerical simulation studies as well as experimental data by Eilers and co-workers [1,2]. Methane-steam reforming is modeled by three reduced-order reactions occurring on the reactor walls. The effects of the total heat input, heat flux profile, and inlet flow rate on production of hydrogen are investigated in detail to assess the effectiveness of the microchannel configuration for production of hydrogen. A shape-optimization procedure is developed and applied to design the solar receiver shape that can yield a desired heat flux distribution along the microchannel walls. This constrained nonlinear optimization problem was solved in Matlab using SNOPT. A coupled optimization and Monte-Carlo radiative heat transfer model is developed to design the receiver shape.
Complete Genome Sequence of Escherichia Phage ADB-2 Isolated from a Fecal Sample of Poultry

ABSTRACT Escherichia phage ADB-2 was isolated from a chicken fecal sample. It is a virulent phage and shows effective inhibition of Escherichia coli strains. Here we announce the completely sequenced genome of Escherichia phage ADB-2, and major findings from its annotation are described.