Miracle-dz/UniFAR-FTUs huggingface dataset:
Coupling efficiency and transmission through hollow-core photonic bandgap fibers

We study the transmission of light through different lengths of Hollow-core bandgap fiber. We demonstrate 95% transmission of 5 picosecond pulses at 1064nm through fiber lengths of 1m, but only 77% transmission through longer lengths of 10m. This variation is not consistent with the measured attenuation of the "fundamental" low-loss mode of the fiber as being below 20dB/km in this spectral range, because the light transmitted through the short fiber not exclusively in the fundamental fiber mode. We conclude that great care is required to understand coupling efficiencies using short fiber lengths.
Analysis of PC and SGA models for an ultra wide-band ad-hoc network with multiple pulses

The performance of six different shapes of pulses is compared for Packet Collision (PC) and Standard Gaussian Approximation (SGA) communication systems, based on the requirements of the Federal Communications Commission (FCC) emission mask. The shapes are a second derivative sinusoid Gaussian pulse, a second order Gaussian pulse and the first four orders of modified Hermite pulses. For the SGA model, the performance of time-hopping (TH) pulse position modulation (PPM) and pulse amplitude modulation (PAM) are compared, in terms of Bit Error Rate (BER). For the PC model, we investigated pulse position modulation (PPM) to analysis the performance from the energy attenuation issue. Results show that the zero order modified Hermite pulse outperforms other pulses in terms of BER in the PC model. It is also found that the performance of both the PC and SGA models will get worse as the number of users increases. The results can be applied to deal with interference issues in wireless body area networks (WBAN) in field of remote health monitoring and telemedicine systems design.
Frequent Subgraph Retrieval in Geometric Graph Databases

Discovery of knowledge from geometric graph databases is of particular importance in chemistry and biology, because chemical compounds and proteins are represented as graphs with 3D geometric coordinates. In such applications, scientists are not interested in the statistics of the whole database. Instead they need information about a novel drug candidate or protein at hand, represented as a query graph. We propose a polynomial-delay algorithm for geometric frequent subgraph retrieval. It enumerates all subgraphs of a single given query graph which are frequent geometric epsi-subgraphs under the entire class of rigid geometric transformations in a database. By using geometric epsi-subgraphs, we achieve tolerance against variations in geometry. We compare the proposed algorithm to gSpan on chemical compound data, and we show that for a given minimum support the total number of frequent patterns is substantially limited by requiring geometric matching. Although the computation time per pattern is larger than for non-geometric graph mining, the total time is within a reasonable level even for small minimum support.
Essential Role for Sphingosine Kinases in Neural and Vascular Development

ABSTRACT Sphingosine-1-phosphate (S1P), an important sphingolipid metabolite, regulates diverse cellular processes, including cell survival, growth, and differentiation. Here we show that S1P signaling is critical for neural and vascular development. Sphingosine kinase-null mice exhibited a deficiency of S1P which severely disturbed neurogenesis, including neural tube closure, and angiogenesis and caused embryonic lethality. A dramatic increase in apoptosis and a decrease in mitosis were seen in the developing nervous system. S1P1 receptor-null mice also showed severe defects in neurogenesis, indicating that the mechanism by which S1P promotes neurogenesis is, in part, signaling from the S1P1 receptor. Thus, S1P joins a growing list of signaling molecules, such as vascular endothelial growth factor, which regulate the functionally intertwined pathways of angiogenesis and neurogenesis. Our findings also suggest that exploitation of this potent neuronal survival pathway could lead to the development of novel therapeutic approaches for neurological diseases.
The Chemistry of Deformation: How Solutes Soften Pure Metals

Solutes have been added to strengthen elemental metals, generating usable materials for millennia; in the 1960s, solutes were found to also soften metals. Despite the empirical correlation between the “electron number” of the solute and the change in strength of the material to which it is added, the mechanism responsible for softening is poorly understood. Using state-of-the-art quantum-mechanical methods, we studied the direct interaction of transition-metal solutes with dislocations in molybdenum. The interaction increases dramatically with increasing electron number and strongly influences the mechanisms responsible for plasticity in these materials. Our quantitative model explains solution softening of metals by using changes in energy and stress scales of plasticity from solutes.
Reducing sedentary behavior in minority girls via a theory-based, tailored classroom media intervention.

OBJECTIVE To develop, implement and test an innovative, theory-based classroom media intervention known as Get Moving! to increase physical activity and decrease sedentary behaviors in predominantly Latina middle school girls. RESEARCH METHODS AND PROCEDURES School-based intervention on five to seven consecutive school days in seven schools (four intervention and three control) with high Latino populations (above 60%). Intervention schools were matched to control schools by ethnic makeup and socioeconomic status (SES). Measures conducted 3 months before and 3 months after intervention included height, weight, percentage body fat (bioimpedance analysis), physical activity and psychosocial aspects of activity by questionnaire. Subjects were middle school girls, mean age 12.5 years old, 73% Latina (N=459 girls). RESULTS Get Moving! significantly reduced time spent on sedentary behavior (beta+/- standard error, SE=-0.27+/-0.14, p<0.05) and significantly increased intrinsic motivation (beta+/-SE=0.11+/-0.05, p<0.05). There was a trend for mediation effects of intrinsic motivation, but this did not reach significance. DISCUSSION Get Moving! is a promising school-based approach that specifically targets physical activity and sedentary behavior in Latina girls, a population at high risk for obesity and related diseases.
White Sharks (Carcharodon carcharias) Scavenging on Whales and Its Potential Role in Further Shaping the Ecology of an Apex Predator

Scavenging, a result of a temporary pulse of resources, occurs in virtually all ecosystems containing carnivores, and is an important energy transfer pathway that can impact ecosystem structure and function, and this ecological significance has largely been considered from a terrestrial standpoint; however, little is known about the role of scavenging in shaping the behavioral ecology of marine species, specifically apex predators. Here we present findings from multiple opportunistic observations of white sharks scavenging on whale carcasses in False Bay, South Africa. Observations of white sharks scavenging over successive days provided evidence of strategic and selective scavenging by this species. Moreover, extended daily observations permitted recordings of unique social, aggregative, and feeding behaviors. We further compare these data against observations of natural predation by sharks on seals in the study area. We discuss these data in relation to environmental conditions, shark social interactions, migration patterns, whale biology, and behaviorally-mediated trophic cascades. While the appearance of a whale carcass is largely a stochastic event, we propose that white shark scavenging on whales may represent an underestimated, yet significant component to the overall foraging ecology of this species, especially as individuals attain sexual maturity.
Medium factor optimization and fermentation kinetics for phenazine‐1‐carboxylic acid production by Pseudomonas sp. M18G

We investigated the production of biofungicide phenazine‐1‐carboxlic (PCA) by Pseudomonas sp. M18G, a gacA‐deficient mutant of M18 for PCA high‐production. Glucose was chosen as the optimal carbon source and soy peptone as the nitrogen source. A Plackett–Burman design revealed that glucose, soy peptone and NaCl were the most significant factors in PCA fermentation. Response surface methodology (RSM) and artificial neural network (ANN) models involving the significant factors were developed using common data. The prediction accuracy of ANN was slightly higher compared to RSM. The genetic algorithm (GA) was used to search the optimal input space of the trained ANN model and find the corresponding PCA yield. The optimum composition was found to be: glucose 34.3 g L−1, soy peptone 43.2 g L−1, NaCl 5.7 g L−1, and the predictive maximum PCA yield reached 980.1 µg mL−1. The optimized medium allowed PCA yield to be increased from 673.3 to 966.7 µg mL−1 after verification experiment tests. Additionally, PCA fermentation kinetics was investigated. Kinetic models based on the modified Logistic and Luedeking–Piret equations were developed, providing a good description of temporal variations of biomass (X), product (P), and substrate (S) in PCA fermentation. Biotechnol. Bioeng. 2008;100: 250–259. © 2007 Wiley Periodicals, Inc.
Detection and quantification of the human IgG4 half‐molecule, HL, from unpurified cell‐culture supernatants

The presence and absence of inter‐heavy‐chain disulphide linkages contribute to the existence of the tetrameric (H2L2) and half (HL) human IgG molecules, respectively [Schuurman, Perdok, Gorter and Aalberse (2001) Mol. Immunol. 38, 1–8]. Reduced effector response in the human IgG4 subclass presents an alternative therapeutic platform in a monoclonal‐antibody (mAb) development program. During the initial cell‐selection stage, titres of the recombinant human antibody present in crude cell‐culture supernatants are determined by ELISA, a technique requiring nanogram quantities of mAb. In the case of an IgG4 antibody, this material is represented mainly by the combination of the tetrameric (H2L2) and dimeric (HL) forms of the antibody. The determination of concentrations or ratios of tetramer and dimer usually requires at least one chromatographic purification step, and thus frequently this is evaluated later in the mAb development process when the number of potential clones has been reduced. In the present paper we describe a Western‐blot‐based method that detects and quantifies IgG4 half‐molecules, HL, from crude cell‐culture supernatants without purification so that H2L2/HL ratios can be included as a part of early clonal evaluation along with the screening of mAb titres. This method was demonstrated (1) to have a linear HL detection range of 0.5–10 ng, (2) to require microlitre volumes of culture and (3) to react specifically with human IgG4 produced from hybridoma and Chinese‐hamster ovary cell cultures. Moreover, this protocol is applicable to evaluate and monitor potential H2L2/HL variations as a result of changes during the process‐development stage of a mAb development program.
Color-based texture image segmentation for vehicle detection

This paper describes a novel method for detecting vehicles on a highway using two visual features: color and texture. Our method consists of a segmentation process computed on the L*u*v* color space and a texture feature extraction procedure based on Dual-Tree Complex Wavelet Transform. We also apply a denoising process using morphological operations to build a background model and make possible the detection of the vehicles in the scene.
Characterizations of trajectory structure of fitness landscapes based on pairwise transition probabilities of solutions

Characterization of trajectory structure of fitness landscapes is a major problem of evolutionary computation theory. In this paper a hardness measure of fitness landscapes is introduced which is based on statistical properties of trajectories. These properties are approximated with the help of a heuristic based on the transition probabilities between the elements of the search space. This makes it possible to compute the measure for some well-known functions: a ridge function, a long path function, a fully deceptive function and a combinatorial problem: the subset sum problem. Using the same transition probabilities the expected number of evaluations needed to reach the global optimum from any point in the space are approximated and examined for the above problems.
Smoking motivations and quitting motivations among HIV-infected smokers

Background The aim of this study was to examine smoking motivation and motivation to quit, and determinants of these motivations among HIV-infected cigarette smokers. Methods We conducted a 1-day cross-sectional survey on cigarette smoking in a representative sample of HIV-infected outpatients of French hospitals. A cluster analysis was used to characterize respondents’ smoking motivation. A logistic regression was performed to study the factors associated with motivation to quit, including the clusters describing smoking motives. Results We found four clusters of smoking motivation. These included intellectual/emotional support (22% of respondents), automatic/stress relief (22%; characterized by heavy smoking and strong dependency); weight control (29%; characterized by frequent symptoms of fat accumulation because of antiretroviral therapy) and pleasure/conviviality (27%; corresponding to ‘lighter’ smokers). In the logistic regression model, among other significant covariates (cigarette consumption level, tobacco dependence and perceived risk of developing a smoking-related disease), the automatic/stress relief cluster was negatively correlated to the motivation to quit (odds ratio 0.39), whereas the weight control cluster was strongly associated to this motivation (odds ratio 2.87). Conclusions The diversity of HIV-infected smokers’ profiles suggests that different types of anti-tobacco measures should be implemented in this population, such as information campaigns on specific risks incurred by HIV-infected smokers, non-specific and comprehensive measures for those for whom smoking is combined with other difficulties, and alternative therapeutic solutions for those who smoke to deal with lipodystrophy.
Effects of Sepiapterin Infusion on Renal Oxygenation and Early Acute Renal Injury After Suprarenal Aortic Clamping in Rats

Acute kidney injury (AKI) can occur after aortic clamping due to microvascular dysfunction leading to renal hypoxia. In this rat study, we have tested the hypothesis that the administration of the precursor of the nitric oxide synthase essential cofactor tetrahydrobiopterin (BH4) could restore renal oxygenation after ischemia reperfusion (I/R) and prevent AKI. We randomly distributed rats into 4 groups: sham group; ischemia-reperfusion group; I/R + sepiapterin, the precursor of BH4; and I/R + sepiapterin + methotrexate, an inhibitor of the pathway generating BH4 from sepiapterin. Cortical and outer medullary microvascular oxygen pressure, renal oxygen delivery, renal oxygen consumption were measured using dual-wavelength oxygen-dependent quenching phosphorescence techniques during ischemia and throughout 3 hours of reperfusion. Kidney injury was assessed using myeloperoxidase staining for leukocyte infiltration and urine neutrophil gelatinase-associated lipocalin levels. Ischemia reperfusion induced a drop in microvascular PO2 (P < 0.01 vs. Sham, both), which was prevented by the infusion of sepiapterin. Sepiapterin partially prevented the rise in renal oxygen extraction (P < 0.001 vs. I/R). Finally, treatment with sepiapterin prevented renal infiltration by inflammatory cells and decreased urine neutrophil gelatinase-associated lipocalin levels indicating a decrease of renal injury. These effects were blunted when adding methotrexate, except for myeloperoxidase. In conclusion, the administration of sepiapterin can prevent renal hypoxia and AKI after suprarenal aortic clamping in rats.
Gamma Interferon Production Is Critical for Protective Immunity to Infection with Blood-Stage Plasmodium berghei XAT but Neither NO Production nor NK Cell Activation Is Critical

ABSTRACT We have examined the roles of gamma interferon (IFN-γ), nitric oxide (NO), and natural killer (NK) cells in the host resistance to infection with the blood-stage malarial parasite Plasmodium berghei XAT, an irradiation-induced attenuated variant of the lethal strain P. berghei NK65. Although the infection withP. berghei XAT enhanced NK cell lytic activity of splenocytes, depletion of NK1.1+ cells caused by the treatment of mice with anti-NK1.1 antibody affected neither parasitemia nor IFN-γ production by their splenocytes. The P. bergheiXAT infection induced a large amount of NO production by splenocytes during the first peak of parasitemia, while P. berghei NK65 infection induced a small amount. Unexpectedly, however, mice deficient in inducible nitric oxide synthase (iNOS−/−) clearedP. berghei XAT after two peaks of parasitemia were observed, as occurred for wild-type control mice. Although the infected iNOS−/− mouse splenocytes did not produce a detectable level of NO, they produced an amount of IFN-γ comparable to that produced by wild-type control mouse splenocytes, and treatment of these mice with neutralizing anti-IFN-γ antibody led to the progression of parasitemia and fatal outcome. CD4−/− mice infected withP. berghei XAT could not clear the parasite, and all these mice died with apparently reduced IFN-γ production. Furthermore, treatment with carrageenan increased the susceptibility of mice toP. berghei XAT infection. These results suggest that neither NO production nor NK cell activation is critical for the resistance to P. berghei XAT infection and that IFN-γ plays an important role in the elimination of malarial parasites, possibly by the enhancement of phagocytic activity of macrophages.
Multiple protein structure alignment

A method was developed to compare protein structures and to combine them into a multiple structure consensus. Previous methods of multiple structure comparison have only concatenated pairwise alignments or produced a consensus structure by averaging coordinate sets. The current method is a fusion of the fast structure comparison program SSAP and the multiple sequence alignment program MULTAL. As in MULTAL, structures are progressively combined, producing intermediate consensus structures that are compared directly to each other and all remaining single structures. This leads to a hierarchic “condensation,” continually evaluated in the light of the emerging conserved core regions.
Service Oriented Framework for Mining Software Repository

Mining software repository is one of important topic in empirical software engineering. A wide variety of mining tools are published on the Web and we can easily apply individual mining approaches. However, there is no supporting system for sharing the mining techniques, procedures, knowledge and know-how. This sharing problem also poses great difficulties for independent validation and experimental replication from mining researchers. The goal of this paper is to provide a framework that supports sharing the repository mining techniques for reducing mining effort and external validation of analysis results. This paper proposes Service Oriented Framework for Mining Software Repository (SO-MSR) which applied Service Oriented Architecture (SOA) to the repository mining. Following the SO-MSR, we also develop Metrics Web API which is a prototype system for metrics measurement. Metrics Web API can measure a variety of source code metrics without relying on any types of repositories and programming languages. The proposed system is designed and implemented as a Web service and demonstrated using actual software repository.
Two Anaplasma phagocytophilum Strains in Ixodes scapularis Ticks, Canada

We developed PCR-based assays to distinguish a human pathogenic strain of Anaplasma phagocytophilum, Ap-ha, from Ap-variant 1, a strain not associated with human infection. The assays were validated on A. phagocytophilum-infected blacklegged ticks (Ixodes scapularis) collected in Canada. The relative prevalence of these 2 strains in I. scapularis ticks differed among geographic regions.
Securing Relay Networks with Artificial Noise: An Error Performance-Based Approach

We apply the concept of artificial and controlled interference in a two-hop relay network with an untrusted relay, aiming at enhancing the wireless communication secrecy between the source and the destination node. In order to shield the square quadrature amplitude-modulated (QAM) signals transmitted from the source node to the relay, the destination node designs and transmits artificial noise (AN) symbols to jam the relay reception. The objective of our considered AN design is to degrade the error probability performance at the untrusted relay, for different types of channel state information (CSI) at the destination. By considering perfect knowledge of the instantaneous CSI of the source-to-relay and relay-to-destination links, we first present an analytical expression for the symbol error rate (SER) performance at the relay. Based on the assumption of an average power constraint at the destination node, we then derive the optimal phase and power distribution of the AN that maximizes the SER at the relay. Furthermore, we obtain the optimal AN design for the case where only statistical CSI is available at the destination node. For both cases, our study reveals that the Gaussian distribution is generally not optimal to generate AN symbols. The presented AN design takes into account practical parameters for the communication links, such as QAM signaling and maximum likelihood decoding.
Crop water stress maps for an entire growing season from visible and thermal UAV imagery

Abstract. This study investigates whether a water deficit index (WDI) based on imagery from unmanned aerial vehicles (UAVs) can provide accurate crop water stress maps at different growth stages of barley and in differing weather situations. Data from both the early and late growing season are included to investigate whether the WDI has the unique potential to be applicable both when the land surface is partly composed of bare soil and when crops on the land surface are senescing. The WDI differs from the more commonly applied crop water stress index (CWSI) in that it uses both a spectral vegetation index (VI), to determine the degree of surface greenness, and the composite land surface temperature (LST) (not solely canopy temperature). Lightweight thermal and RGB (red–green–blue) cameras were mounted on a UAV on three occasions during the growing season 2014, and provided composite LST and color images, respectively. From the LST, maps of surface-air temperature differences were computed. From the color images, the normalized green–red difference index (NGRDI), constituting the indicator of surface greenness, was computed. Advantages of the WDI as an irrigation map, as compared with simpler maps of the surface-air temperature difference, are discussed, and the suitability of the NGRDI is assessed. Final WDI maps had a spatial resolution of 0.25 m. It was found that the UAV-based WDI is in agreement with measured stress values from an eddy covariance system. Further, the WDI is especially valuable in the late growing season because at this stage the remote sensing data represent crop water availability to a greater extent than they do in the early growing season, and because the WDI accounts for areas of ripe crops that no longer have the same need for irrigation. WDI maps can potentially serve as water stress maps, showing the farmer where irrigation is needed to ensure healthy growing plants, during entire growing season.