Miracle-dz/UniFAR-FTUs huggingface dataset:
Caching XML Web Services for Mobility

Web services are emerging as the dominant application on the Internet. The Web is no longer just a repository of information but has evolved into an active medium for providers and consumers of services: Individuals provide peer-to-peer services to access personal contact information or photo albums for other individuals; individuals provide services to businesses for accessing personal preferences or tax information; Web-based businesses provide consumer services such as travel arrangement (Orbitz), shopping (eBay), and e-mail (Hotmail); and several business-to-business (B2B) services such as supply chain management form important applications of the Internet.
Green Tea, Intermittent Sprinting Exercise, and Fat Oxidation

Fat oxidation has been shown to increase after short term green tea extract (GTE) ingestion and after one bout of intermittent sprinting exercise (ISE). Whether combining the two will result in greater fat oxidation after ISE is undetermined. The aim of the current study was to investigate the combined effect of short term GTE and a single session of ISE upon post-exercise fat oxidation. Fourteen women consumed three GTE or placebo capsules the day before and one capsule 90 min before a 20-min ISE cycling protocol followed by 1 h of resting recovery. Fat oxidation was calculated using indirect calorimetry. There was a significant increase in fat oxidation post-exercise compared to at rest in the placebo condition (p < 0.01). After GTE ingestion, however, at rest and post-exercise, fat oxidation was significantly greater (p < 0.05) than that after placebo. Plasma glycerol levels at rest and 15 min during post-exercise were significantly higher (p < 0.05) after GTE consumption compared to placebo. Compared to placebo, plasma catecholamines increased significantly after GTE consumption and 20 min after ISE (p < 0.05). Acute GTE ingestion significantly increased fat oxidation under resting and post-exercise conditions when compared to placebo.
Multidirectional Scanning Model, MUSCLE, to Vectorize Raster Images with Straight Lines

This paper presents a new model, MUSCLE (Multidirectional Scanning for Line Extraction), for automatic vectorization of raster images with straight lines. The algorithm of the model implements the line thinning and the simple neighborhood methods to perform vectorization. The model allows users to define specified criteria which are crucial for acquiring the vectorization process. In this model, various raster images can be vectorized such as township plans, maps, architectural drawings, and machine plans. The algorithm of the model was developed by implementing an appropriate computer programming and tested on a basic application. Results, verified by using two well known vectorization programs (WinTopo and Scan2CAD), indicated that the model can successfully vectorize the specified raster data quickly and accurately.
Evolution of ozone, particulates, and aerosol direct radiative forcing in the vicinity of Houston using a fully coupled meteorology‐chemistry‐aerosol model

[1] A new fully coupled meteorology-chemistry-aerosol model is used to simulate the urban- to regional-scale variations in trace gases, particulates, and aerosol direct radiative forcing in the vicinity of Houston over a 5 day summer period. Model performance is evaluated using a wide range of meteorological, chemistry, and particulate measurements obtained during the 2000 Texas Air Quality Study. The predicted trace gas and particulate distributions were qualitatively similar to the surface and aircraft measurements with considerable spatial variations resulting from urban, power plant, and industrial sources of primary pollutants. Sulfate, organic carbon, and other inorganics were the largest constituents of the predicted particulates. The predicted shortwave radiation was 30 to 40 W m−2 closer to the observations when the aerosol optical properties were incorporated into the shortwave radiation scheme; however, the predicted hourly aerosol radiative forcing was still underestimated by 10 to 50 W m−2. The predicted aerosol radiative forcing was larger over Houston and the industrial ship channel than over the rural areas, consistent with surface measurements. The differences between the observed and simulated aerosol radiative forcing resulted from transport errors, relative humidity errors in the upper convective boundary layer that affect aerosol water content, secondary organic aerosols that were not yet included in the model, and uncertainties in the primary particulate emission rates. The current model was run in a predictive mode and demonstrates the challenges of accurately simulating all of the meteorological, chemical, and aerosol parameters over urban to regional scales that can affect aerosol radiative forcing.
Two types of dacitic pumices from the caldera-forming eruption of Numazawa Volcano, NE Japan

The 3400 BC caldera-forming eruption of Numazawa Volcano in NE Japan started with a cataclysmic pyroclastic flow eruption (∼ 2 km3 dense rock equivalent), which accounted for more than 90% of the total volume of the eruption products. This was followed by a Plinian eruption, phreatomagmatic eruptions, and a second Plinian eruption. The juvenile pyroclasts produced during the first two eruption phases are mostly dacitic, whereas those in the two subsequent phases are essentially andesitic. We recognized two distinct types of dacitic pumices: white and gray pumices. The two pumices are virtually identical in terms of both whole-rock composition (∼ 64.8-66.1 wt% SiO2) and crystal content (∼ 40-46 vol%), but are very different in terms of texture. The white pumice, which typically contains abundant euhedral phenocrysts, is the dominant variety and occurs throughout the pyroclastic flow deposits and in the overlying Plinian fall deposit. The gray pumice, which typically has bread-crusted surfaces and contains ubiquitous crystal fragments and xenoliths, occurs in the upper flow units of the pyroclastic flow deposits. We suggest that the textural differences between the two types of pumices reflect the difference in local stress conditions within the volcanic conduit below the magma fragmentation level. The abundance of euhedral phenocrysts in the white pumice suggests that it is the vesicular equivalent of the dacite that chamber ascended through the central part of the conduit that suffered low shear stress. In contrast, the magma that generated the gray pumice is thought to have originated from similar dacitic magma; the gray pumice magma was probably produced by the mechanical breakage of phenocrysts during magma ascent along the region of high shear stress near the conduit walls. The limited accumulation of the gray pumice in the upper units of the pyroclastic flow deposits suggests that crystal size reduction mainly occurred during the late stage of the pyroclastic flow eruption prior to the first Plinian eruption. It is likely that an abrupt conduit blockage caused by the waning of the eruption activity and the resulting temporal high shear stress at the conduit walls promoted crystal fragmentation, thus forming the gray-pumice magma and resulting in the subsequent eruption being a Plinian eruption.
Proteomics-Based Identification of Anchorless Cell Wall Proteins as Vaccine Candidates against Staphylococcus aureus

ABSTRACT Staphylococcus aureus is an important human pathogen with increasing clinical impact due to the extensive spread of antibiotic-resistant strains. Therefore, development of a protective polyvalent vaccine is of great clinical interest. We employed an intravenous immunoglobulin (IVIG) preparation as a source of antibodies directed against anchorless S. aureus surface proteins for identification of novel vaccine candidates. In order to identify such proteins, subtractive proteome analysis (SUPRA) of S. aureus anchorless cell wall proteins was performed. Proteins reacting with IVIG but not with IVIG depleted of S. aureus-specific opsonizing antibodies were considered vaccine candidates. Nearly 40 proteins were identified by this preselection method using matrix-assisted laser desorption ionization—time of flight analysis. Three of these candidate proteins, enolase (Eno), oxoacyl reductase (Oxo), and hypothetical protein hp2160, were expressed as glutathione S-transferase fusion proteins, purified, and used for enrichment of corresponding immunoglobulin Gs from IVIG by affinity chromatography. Use of affinity-purified anti-Eno, anti-Oxo, and anti-hp2160 antibodies resulted in opsonization, phagocytosis, and killing of S. aureus by human neutrophils. High specific antibody titers were detected in mice immunized with recombinant antigens. In mice challenged with bioluminescent S. aureus, reduced staphylococcal spread was measured by in vivo imaging. The recovery of S. aureus CFU from organs of immunized mice was diminished 10- to 100-fold. Finally, mice immunized with hp2160 displayed statistically significant higher survival rates after lethal challenge with clinically relevant S. aureus strains. Taken together, our data suggest that anchorless cell wall proteins might be promising vaccine candidates and that SUPRA is a valuable tool for their identification.
Inference and uncertainty of snow depth spatial distribution at the kilometre scale in the Colorado Rocky Mountains: the effects of sample size, random sampling, predictor quality, and validation procedures

Historically, observing snow depth over large areas has been difficult. When snow depth observations are sparse, regression models can be used to infer the snow depth over a given area. Data sparsity has also left many important questions about such inference unexamined. Improved inference, or estimation, of snow depth and its spatial distribution from a given set of observations can benefit a wide range of applications from water resource management, to ecological studies, to validation of satellite estimates of snow pack. The development of Light Detection and Ranging (LiDAR) technology has provided non‐sparse snow depth measurements, which we use in this study, to address fundamental questions about snow depth inference using both sparse and non‐sparse observations. For example, when are more data needed and when are data redundant? Results apply to both traditional and manual snow depth measurements and to LiDAR observations.
Detection of genome-edited mutant clones by a simple competition-based PCR method

Genome editing by the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats / CRISPR-associated protein 9) system is a revolutionary strategy to study gene functions. Since the efficiency of gene disruption in cell culture does not reach 100% typically, cloning of mutant cells is often performed to obtain fully mutated cells. Therefore, a method to discriminate accurately mutated clones easily and quickly is crucial to accelerate the research using CRISPR/Cas9. Here, we show that knockout cells can be discriminated by a competition-based PCR, using a mixture of three primers, among which one primer overlaps with the Cas9 cleavage site. Together, we show how to optimize primer design in order to improve the effectiveness of the discrimination. Finally, we applied this method to show that mutations conferring drug resistance can be detected with high accuracy. The provided method is easy to perform and requires only basic laboratory equipment, making it suitable for almost all laboratories.
Multi-scale segmentation of carotid artery wall in MRI images

The segmentation of carotid artery wall is essential for subsequent plaque analysis. Involving with attempt of different techniques, this work will focus on obtaining the boundaries of lumen and external wall based on a comparatively accurate and efficient approach. In particular, a method described as prior-constrained carotid artery segmentation in DOG scale-space (multi-scale PCS) is proposed. Moreover, due to the significance, lumen segmentation is testified through several feasible algorithms in order to find a better option, by means of self-defined computing method to assess the quality.
Two Round MPC from LWE via Multi-Key FHE

We construct a general multiparty computation (MPC) protocol in the common random string (CRS) model with only two rounds of interaction, which is known to be optimal. In the honest-but-curious setting we only rely on the learning with errors (LWE) assumption, and in the fully malicious setting we additionally assume the existence of non-interactive zero knowledge arguments (NIZKs). Previously, Asharov et al. (EUROCRYPT ’12) showed how to achieve three rounds based on LWE and NIZKs, while Garg et al. (TCC ’14) showed how to achieve the optimal two rounds based on indistinguishability obfuscation, but it was unknown if two rounds were possible under simpler assumptions without obfuscation. Our approach relies on multi-key fully homomorphic encryption (MFHE), introduced by Lopez-Alt et al. (STOC ’12), which enables homomorphic computation over data encrypted under different keys. We simplify a recent construction of MFHE based on LWE by Clear and McGoldrick (ePrint ’14), and give a stand-alone exposition of that scheme. We then extend this construction to allow for a one-round distributed decryption of a multi-key ciphertext. Our entire MPC protocol consists of the following two rounds: 1. Each party individually encrypts its input under its own key and broadcasts the ciphertext. All parties can then homomorphically compute a multi-key encryption of the output. 2. Each party broadcasts a partial decryption of the output using its secret key. The partial decryptions can be combined to recover the output in plaintext. ∗Aarhus University. E-mail: pratyay85@gmail.com †Northeastern University. E-mail: danwichs@gmail.com.
Inference of Population Structure using Dense Haplotype Data

The advent of genome-wide dense variation data provides an opportunity to investigate ancestry in unprecedented detail, but presents new statistical challenges. We propose a novel inference framework that aims to efficiently capture information on population structure provided by patterns of haplotype similarity. Each individual in a sample is considered in turn as a recipient, whose chromosomes are reconstructed using chunks of DNA donated by the other individuals. Results of this “chromosome painting” can be summarized as a “coancestry matrix,” which directly reveals key information about ancestral relationships among individuals. If markers are viewed as independent, we show that this matrix almost completely captures the information used by both standard Principal Components Analysis (PCA) and model-based approaches such as STRUCTURE in a unified manner. Furthermore, when markers are in linkage disequilibrium, the matrix combines information across successive markers to increase the ability to discern fine-scale population structure using PCA. In parallel, we have developed an efficient model-based approach to identify discrete populations using this matrix, which offers advantages over PCA in terms of interpretability and over existing clustering algorithms in terms of speed, number of separable populations, and sensitivity to subtle population structure. We analyse Human Genome Diversity Panel data for 938 individuals and 641,000 markers, and we identify 226 populations reflecting differences on continental, regional, local, and family scales. We present multiple lines of evidence that, while many methods capture similar information among strongly differentiated groups, more subtle population structure in human populations is consistently present at a much finer level than currently available geographic labels and is only captured by the haplotype-based approach. The software used for this article, ChromoPainter and fineSTRUCTURE, is available from http://www.paintmychromosomes. com/.
Stimulus Design for Model Selection and Validation in Cell Signaling

Mechanism-based chemical kinetic models are increasingly being used to describe biological signaling. Such models serve to encapsulate current understanding of pathways and to enable insight into complex biological processes. One challenge in model development is that, with limited experimental data, multiple models can be consistent with known mechanisms and existing data. Here, we address the problem of model ambiguity by providing a method for designing dynamic stimuli that, in stimulus–response experiments, distinguish among parameterized models with different topologies, i.e., reaction mechanisms, in which only some of the species can be measured. We develop the approach by presenting two formulations of a model-based controller that is used to design the dynamic stimulus. In both formulations, an input signal is designed for each candidate model and parameterization so as to drive the model outputs through a target trajectory. The quality of a model is then assessed by the ability of the corresponding controller, informed by that model, to drive the experimental system. We evaluated our method on models of antibody–ligand binding, mitogen-activated protein kinase (MAPK) phosphorylation and de-phosphorylation, and larger models of the epidermal growth factor receptor (EGFR) pathway. For each of these systems, the controller informed by the correct model is the most successful at designing a stimulus to produce the desired behavior. Using these stimuli we were able to distinguish between models with subtle mechanistic differences or where input and outputs were multiple reactions removed from the model differences. An advantage of this method of model discrimination is that it does not require novel reagents, or altered measurement techniques; the only change to the experiment is the time course of stimulation. Taken together, these results provide a strong basis for using designed input stimuli as a tool for the development of cell signaling models.
Hydrographic and transient tracer response on atmospheric changes over the Nordic Seas

Knowledge of the timing and intensity of convec-tion in the Nordic Seas is important for our understand-ing of the global thermohaline circulation because it gen-erates waters that flow over the sills between Greenlandand Scotland and contribute to the ventilation of thelower branch of the North Atlantic Deep Water. Atpresent most of the overflowing waters are generatedby rather shallow convection in the Norwegian and Ice-land seas (Hansen and Osterhus, 2000). However, deepwater ventilation in the region is also important as itmaintains the interior overturning of the Nordic Seas/Arctic Ocean system. A key region for direct deep waterventilation is the central Greenland Sea. It is the regionwith the lowest stratification and the densest outcrop inwinter and, although never directly observed, it is hy-pothesized that ventilation of the deep waters down tothe bottom occurs in the centre of the gyre. Water massformation and hence ventilation rely on the forcing atthe air/sea interface. Model studies have shown that inthe Nordic Seas changes in the freshwater flux (includ-ing sea ice) may inhibit convection and in turn have majorimpact on the patterns and strength of the thermohalinecirculation (e.g. Broecker et al., 1990; Marotzke andWillebrand, 1991). As part of repeat hydrographic cruises by the In-stitute of Marine Research in Bergen, transient tracermeasurements have been carried out in the Nordic Seasbetween 1991 and 2000 on an annual basis. Although thestation spacing was not following an exact pattern(Fig. 1), the cruises followed quasi-standard lines. Oneof those lines, at about 75
The Effects of Recombination on Phenotypic Exploration and Robustness in Evolution

Recombination is a commonly used genetic operator in artificial and computational evolutionary systems. It has been empirically shown to be essential for evolutionary processes. However, little has been done to analyze the effects of recombination on quantitative genotypic and phenotypic properties. The majority of studies only consider mutation, mainly due to the more serious consequences of recombination in reorganizing entire genomes. Here we adopt methods from evolutionary biology to analyze a simple, yet representative, genetic programming method, linear genetic programming. We demonstrate that recombination has less disruptive effects on phenotype than mutation, that it accelerates novel phenotypic exploration, and that it particularly promotes robust phenotypes and evolves genotypic robustness and synergistic epistasis. Our results corroborate an explanation for the prevalence of recombination in complex living organisms, and helps elucidate a better understanding of the evolutionary mechanisms involved in the design of complex artificial evolutionary systems and intelligent algorithms.
Current balance control in a multilevel current source inverter

Multilevel converters constitute a high performance and high reliability option for industrial applications such as motor control, transmission and distribution electrical systems, and interface with alternative energy sources and non-conventional storage systems. The biggest challenge about multilevel topologies is the balance of dividing reactive components (capacitors in voltage converters, and inductors in current converters). In this paper, two methods to force current balance in a Multilevel Current Source Inverter (MCSI) are presented. Both require minimum computing power with excellent closed loop dynamic response.
Inhibitory Effects of Anti-VEGF Antibody on the Growth and Angiogenesis of Estrogen-induced Pituitary Prolactinoma in Fischer 344 Rats: Animal Model of VEGF-targeted Therapy for Human Endocrine Tumors

Estrogen-induced pituitary prolactin-producing tumors (PRLoma) in F344 rats express a high level of vascular endothelial growth factor (VEGF) associated with marked angiogenesis and angiectasis. To investigate whether tumor development in E2-induced PRLoma is inhibited by anti-VEGF monoclonal antibody (G6-31), we evaluated tumor growth and observed the vascular structures. With simultaneous treatment with G6-31 for the latter three weeks of the 13-week period of E2 stimulation (E2+G6-31 group), the following inhibitory effects on the PRLoma were observed in the E2+G6-31 group as compared with the E2-only group. In the E2+G6-31 group, a tendency to reduction in pituitary weight was observed and significant differences were observed as (1) reductions in the Ki-67-positive anterior cells, (2) increases in TUNEL-positive anterior cells, and (3) repair of the microvessel count by CD34-immunohistochemistry. The characteristic “blood lakes” in PRLomas were improved and replaced by repaired microvascular structures on 3D observation using confocal laser scanning microscope. These inhibitory effects due to anti-VEGF antibody might be related to the autocrine/paracrine action of VEGF on the tumor cells, because VEGF and its receptor are co-expressed on the tumor cells. Thus, our results demonstrate that anti-VEGF antibody exerted inhibitory effects on pituitary tumorigenesis in well-established E2 induced PRLomas.