Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Prioritization of Resistant Rice Gene against Xanthomas oryzae pv. oryzae by Using Text Mining Technologies

To effectively assess the possibility of the unknown rice protein resistant to Xanthomonas oryzae pv. oryzae, a hybrid strategy is proposed to enhance gene prioritization by combining text mining technologies with a sequence-based approach. The text mining technique of term frequency inverse document frequency is used to measure the importance of distinguished terms which reflect biomedical activity in rice before candidate genes are screened and vital terms are produced. Afterwards, a built-in classifier under the chaos games representation algorithm is used to sieve the best possible candidate gene. Our experiment results show that the combination of these two methods achieves enhanced gene prioritization.
Vision-Based Tactile Sensing and Shape Estimation Using a Fluid-Type Touchpad

In this paper, we propose a new method to estimate the shape and irregularity of objects by a vision-based tactile sensor, which consists of a CCD camera, LED lights, transparent acrylic plate, and a touchpad which consists of an elastic membrane filled with translucent red water. Intensities of red, green and blue bands of the traveling light in the touchpad are analyzed in this study to estimate the shape/irregularity of the object. The LED light traveling in the touchpad is scattered and absorbed by the red pigment in the fluid. The depth of the touchpad is estimated by using the intensity of the light obtained from the red-green-blue (RGB) values of the image, in consideration of the scattering and reflection effects. The reflection coefficient that depends on the shape of the membrane, was decoupled in the proposed formulation. The intensity of the traveling light is represented with the geometrical parameters of the touchpad surface. In order to reduce the approximation error caused by unmodeled factors, we compensate the error by using a function of the deformation of the membrane. The validation of the proposed method is confirmed through experimental results.
Nonlinear metal–dielectric nanoantennas for light switching and routing

We introduce a novel hybrid metal–dielectric nanoantenna composed of dielectric (crystalline silicon) and metal (silver) nanoparticles. In such a nanoantenna, the phase shift between the dipole moments of the nanoparticles, caused by differences in the polarizabilities, allows for directional light scattering; while the nonlinearity of the metal nanoparticle helps to control the radiation direction. We show that the radiation pattern of this nanoantenna can be switched between the forward and backward directions by varying only the light intensity around the level of 6 MW cm−2, with a characteristic switching time of 40 fs.
High-speed policy-based packet forwarding using efficient multi-dimensional range matching

The ability to provide differentiated services to users with widely varying requirements is becoming increasingly important, and Internet Service Providers would like to provide these differentiated services using the same shared network infrastructure. The key mechanism, that enables differentiation in a connectionless network, is the packet classification function that parses the headers of the packets, and after determining their context, classifies them based on administrative policies or real-time reservation decisions. Packet classification, however, is a complex operation that can become the bottleneck in routers that try to support gigabit link capacities. Hence, many proposals for differentiated services only require classification at lower speed edge routers and also avoid classification based on multiple fields in the packet header even if it might be advantageous to service providers. In this paper, we present new packet classification schemes that, with a worst-case and traffic-independent performance metric, can classify packets, by checking amongst a few thousand filtering rules, at rates of a million packets per second using range matches on more than 4 packet header fields. For a special case of classification in two dimensions, we present an algorithm that can handle more than 128K rules at these speeds in a traffic independent manner. We emphasize worst-case performance over average case performance because providing differentiated services requires intelligent queueing and scheduling of packets that precludes any significant queueing before the differentiating step (i.e., before packet classification). The presented filtering or classification schemes can be used to classify packets for security policy enforcement, applying resource management decisions, flow identification for RSVP reservations, multicast look-ups, and for source-destination and policy based routing. The scalability and performance of the algorithms have been demonstrated by implementation and testing in a prototype system.
Methodological Lessons Learned from the Process Evaluation of the Comprehensive Strategy for Serious, Violent, and Chronic Juvenile Offenders

Five important methodological lessons learned from the national process evaluation of the Comprehensive Strategy for Serious, Violent, and Chronic Juvenile Offenders, conducted in the United States, are discussed. The Comprehensive Strategy is an example of a comprehensive community initiative (CCI), which is an initiative targeted at an entire community and intended to provide holistic, multifaceted responses to complex social problems. The five lessons learned for future evaluations of CCIs are: (1) the need for explicating theories of change; (2) a process of clarifying stakeholder roles; (3) the importance of mechanisms for engagement of evaluator with sites; (4) the need to develop a stakeholderdriven anticipated timeline of change within communities; and (5) the value of empirically testing pathways of change in CCIs.
The Effect of Aerobic Exercise Training on Plasma Apelin Levels and Pain Threshold in T1DM Rats

Background Diabetes mellitus (types 1 and 2) leads to secondary complications such as neuropathy, which reduce a patient’s quality of life. Apelin and its receptor, APJ, have been shown to have antinociceptive effects and to decrease blood glucose levels. Objectives The present experimental study was conducted in Iran and investigated the role of apelin, which is used to manage type 1 diabetes mellitus, during exercise training. Materials and Methods Male Wistar rats (n = 36) were assigned by simple random allocation to six groups (n = 6): non-diabetic (ND), diabetic (D), sedentary non-diabetic (SND), sedentary diabetic (SD), exercise non-diabetic (END), and exercise diabetic (ED). Diabetes was induced by a single subcutaneous injection of streptozotocin (50 mg/kg). Exercise training consisted of treadmill running 60 minutes/day × 5 days/week for 10 weeks. The tail-flick test was used to assess the thermal pain threshold, and an apelin enzyme immunoassay kit was utilized to assess plasma apelin levels. Results Plasma apelin level was higher (0.3 vs. 0.1, P < 0.0001) and the tail-flick latency was lower (2.2 vs. 3.8, P < 0.0001) in the D group than in the ND group. After the training program, plasma apelin levels decreased in the exercise groups, and the tail-flick latency increased in the ED group. No correlation was found between apelin blood concentrations and tail-flick latency following the training program in the ED group. Conclusions These findings suggest that apelin does not play any significant role in regulating the pain threshold in type 1 diabetes mellitus during exercise training.
Spacetime Foam: From Entropy and Holography to Infinite Statistics and Nonlocality

Due to quantum fluctuations, spacetime is foamy on small scales. The degree of foaminess is found to be consistent with holography, a principle prefigured in the physics of black hole entropy. It has bearing on the ultimate accuracies of clocks and measurements and the physics of quantum computation. Consistent with existing archived data on active galactic nuclei from the Hubble Space Telescope, the application of the holographic spacetime foam model to cosmology requires the existence of dark energy which, we argue, is composed of an enormous number of inert "particles" of extremely long wavelength. We suggest that these "particles" obey infinite statistics in which all representations of the particle permutation group can occur, and that the nonlocality present in systems obeying infinite statistics may be related to the nonlocality present in holographic theories. We also propose to detect spacetime foam by looking for halos in the images of distant quasars, and argue that it does not modify the GZK cutoff in the ultra-high energy cosmic ray spectrum and its contributions to time-of-flight differences of high energy gamma rays from distant GRB are too small to be detectable.
Rapid Convergence to Feature Layer Correspondences

We describe a neural network able to rapidly establish correspondence between neural feature layers. Each of the network's two layers consists of interconnected cortical columns, and each column consists of inhibitorily coupled subpopulations of excitatory neurons. The dynamics of the system builds on a dynamic model of a single column, which is consistent with recent experimental findings. The network realizes dynamic links between its layers with the help of specialized columns that evaluate similarities between the activity distributions of local feature cell populations, are subject to a topology constraint, and can gate the transfer of feature information between the neural layers. The system can robustly be applied to natural images, and correspondences are found in time intervals estimated to be smaller than 100 ms in physiological terms.
Sparse Fault-Tolerant BFS Structures

A fault-tolerant structure for a network is required for continued functioning following the failure of some of the network’s edges or vertices. This article considers breadth-first search (BFS) spanning trees and addresses the problem of designing a sparse fault-tolerant BFS structure (FT-BFS structure), namely, a sparse subgraph T of the given network G such that subsequent to the failure of a single edge or vertex, the surviving part T′ of T still contains a BFS spanning tree for (the surviving part of) G. For a source node s, a target node t, and an edge e ∈ G, the shortest s − t path Ps, t, e that does not go through e is known as a replacement path. Thus, our FT-BFS structure contains the collection of all replacement paths Ps, t, e for every t ∈ V(G) and every failed edge e ∈ E(G). Our main results are as follows. We present an algorithm that for every n-vertex graph G and source node s constructs a (single edge failure) FT-BFS structure rooted at s with O(n ċ min {Depth(s), √n{) edges, where Depth(s) is the depth of the BFS tree rooted at s. This result is complemented by a matching lower bound, showing that there exist n-vertex graphs with a source node s for which any edge (or vertex) FT-BFS structure rooted at s has Ω(n3/2) edges. We then consider fault-tolerant multi-source BFS structures (FT-MBFS structures), aiming to provide (following a failure) a BFS tree rooted at each source s ∈ S for some subset of sources S⊆V. Again, tight bounds are provided, showing that there exists a poly-time algorithm that for every n-vertex graph and source set S⊆V of size σ constructs a (single failure) FT-MBFS structure T*(S) from each source si ∈ S, with O(√σ ċ n3/2) edges, and, on the other hand, there exist n-vertex graphs with source sets S⊆V of cardinality σ, on which any FT-MBFS structure from S has Ω(√σ ċ n3/2) edges. Finally, we propose an O(log n) approximation algorithm for constructing FT-BFS and FT-MBFS structures. The latter is complemented by a hardness result stating that there exists no Ω(log n) approximation algorithm for these problems under standard complexity assumptions. In comparison with previous constructions, our algorithm is deterministic and may improve the number of edges by a factor of up to √n for some instances. All our algorithms can be extended to deal with one vertex failure as well, with the same performance.
Genomic Characterization of Haemophilus parasuis SH0165, a Highly Virulent Strain of Serovar 5 Prevalent in China

Haemophilus parasuis can be either a commensal bacterium of the porcine respiratory tract or an opportunistic pathogen causing Glässer's disease, a severe systemic disease that has led to significant economical losses in the pig industry worldwide. We determined the complete genomic sequence of H. parasuis SH0165, a highly virulent strain of serovar 5, which was isolated from a hog pen in North China. The single circular chromosome was 2,269,156 base pairs in length and contained 2,031 protein-coding genes. Together with the full spectrum of genes detected by the analysis of metabolic pathways, we confirmed that H. parasuis generates ATP via both fermentation and respiration, and possesses an intact TCA cycle for anabolism. In addition to possessing the complete pathway essential for the biosynthesis of heme, this pathogen was also found to be well-equipped with different iron acquisition systems, such as the TonB system and ABC-type transport complexes, to overcome iron limitation during infection and persistence. We identified a number of genes encoding potential virulence factors, such as type IV fimbriae and surface polysaccharides. Analysis of the genome confirmed that H. parasuis is naturally competent, as genes related to DNA uptake are present. A nine-mer DNA uptake signal sequence (ACAAGCGGT), identical to that found in Actinobacillus pleuropneumoniae and Mannheimia haemolytica, followed by similar downstream motifs, was identified in the SH0165 genome. Genomic and phylogenetic comparisons with other Pasteurellaceae species further indicated that H. parasuis was closely related to another swine pathogenic bacteria A. pleuropneumoniae. The comprehensive genetic analysis presented here provides a foundation for future research on the metabolism, natural competence and virulence of H. parasuis.
Extensible Authentication Protocol (EAP) Key Management Framework

The Extensible Authentication Protocol (EAP), defined in [RFC3748], enables extensible network access authentication. This document specifies the EAP key hierarchy and provides a framework for the transport and usage of keying material generated by EAP authentication algorithms, known as "methods". It also provides a system-level security analysis.
Heart Rate Variability Is Associated With Polymorphic Variation in the Choline Transporter Gene

Objective: The objective of this study was to determine whether interindividual variation in parasympathetic (cholinergic) and sympathetic (adrenergic) regulation of heart rate (as estimated by frequency components of heart rate variability [HRV]) may be accounted for, in part, by genetic variation in the choline transporter, a component of acetylcholine neurotransmission. Methods: Resting HRV estimates of high- (HF) and low-frequency (LF) power and LF/HF ratio were determined from electrocardiogram recordings collected continuously over 5 minutes in 413 white individuals of European ancestry (49% men; aged 30–54 years [mean, 44 years]). Subjects were genotyped for a single nucleotide polymorphism (SNP) located in the 3′ untranslated region of the choline transporter gene (CHT1). Frequencies of the alternate CHT1 alleles, labeled G and T, were 76% and 24%. Results: Compared with GG homozygotes, participants having any T allele had greater HF power (p <.02), lower LF power (p <.02), and lower LF/HF ratios (p <.005). Relative to men, women had lower LF power (p <.001) and lower LF/HF ratios (p <.005). Conclusions: These findings show that polymorphic variation in the CHT1 gene is associated significantly with interindividual variability in HRV indices related to parasympathetic (cholinergic) activity. ACh = acetylcholine; CHT1 = choline transporter gene; UTR = untranslated region; HRV = heart rate variability; HF = high frequency; LF = low frequency; nu = normalized units; ln = natural log; BMI = body mass index.
LIMIT CYCLES AND THE DISTRIBUTION OF ZEROS OF FAMILIES OF ANALYTIC FUNCTIONS

We estimate the expected number of limit cycles situated in a neighbourhood of the origin of a planar polynomial vector field. Our main tool is a distributional inequality for the number of zeros of some families of univariate holomorphic functions depending analytically on a parameter. We obtain this inequality by methods of Pluripotential Theory. This inequality also implies versions of a strong law of large numbers and the central limit theorem for a probabilistic scheme associated with the distribution of zeros.
Pitch detection using the short-term phase spectrum

A new frequency domain method for determining the fundamental frequency of speech is presented in this paper. This method uses the information contained in the short-term phase spectral whereas the previous methods were limited to the amplitude spectrum. The short-term spectrum is computed by DFT and it is interpreted as the output of a bank of band-pass overlapping filters. Harmonic components are detected by searching for sets of three contiguous filters having the same instantaneous frequency. The frequency of a detected harmonic is given by the instantaneous frequency itself. A conventional harmonic numbering algorithm is used to convert the set of detected harmonics to a value of the fundamental frequency. Preliminary results show the validity of the method.
A Monte Carlo Method for Pricing American Options

This paper presents an algorithm for pricing American options using Monte Carlo simulation. The method is based on using a parametric representation of the exercise boundary. Error bounds are constructed using two di erent estimates, one which is biased low, and one which is biased high. I show that both are consistent and asymptotically unbiased estimators of the true option value. Results for high-dimensional American options con rm the viability of the numerical procedure. The convergence results of the paper shed light into the biases present in other algorithms proposed in the literature. JEL classi cation: C15, C63, G13.
MASARU TANIGUCHI AND TOMIO TADA 125 body synthesis . II . Effect of antigen dose and suppression by passive antibody on the affinity of antibody synthesized

The role of the thymus in the immune response oi the rabbit is still uncertain. This is probably because neonatal as well as adult thymectomy has much less effect on the subsequent immune response of rabbits than rodents (1-3). Furthermore, Richter and his co-workers have reported that antigenreactive cells, comparable to thymus-derived lymphocytes (T cells) of rodents, were found in the bone marrow but not in other lymphoid tissues of rabbits (4-6). Nevertheless, the multicellular model for humoral antibody response is applicable to that of rabbits, as shown by three different lines of evidence: (a) cooperation between different antigenic determinants on the same molecule occurs in the secondary antibody response of the rabbit, as revealed by both in vivo and in vitro studies (7-10); (b) preimmunization with carrier antigen enhances the primary antibody response to a hapten-carrier conjugate (10); (c) at least two different cell types provided by the thymus, bone marrow, and appendix are required to reconstitute the early antibody response of lethally X-irradiated rabbits to sheep erythrocytes (11, 12). Although there is no clear indication that the thymus-derived lymphocytes actually act as helper cells in the rabbit, it may be predicted from these studies that the thvmus is endowed with an important role in the immune response of the rabbit. Another important indicator of maturation of the immune response, demonstrated mainly in the rabbit, is the time-dependent increase of antibody affinity that reflects the differentiation of antibody-forming cells (13-17). The increase in antibody affinity appears to result from selection of antibodyforming cell precursors by antigen and is thus primarily determined by the effective concentration of antigen available to such precursor cells (18-20). However, Gershon and Paul (21) have recently shown that the affinity of antibody produced by mice is also influenced by the quantity of T cells present in the immunized animals. They found that mice relatively deficient in T cells could produce only low affinity antibodies upon immunization with small amounts of a hapten-carrier conjugate. The present studies were undertaken to learn the regulatory role of the thymus in the immune response of the rabbit with respect to the amount and
Claudin family members exhibit unique temporal and spatial expression boundaries in the chick embryo

The claudin family of proteins are integral components of tight junctions and are responsible for determining the ion specificity and permeability of paracellular transport within epithelial and endothelial cell layers. Several members of the claudin family have been shown to be important during embryonic development and morphogenesis. However, detailed embryonic expression patterns have been described for only a few claudins. Here, we provide a phylogenetic analysis of the chicken claudins and a comprehensive analysis of their mRNA expression profiles. We found that claudin family members exhibit both overlapping and unique expression patterns throughout development. Especially striking were the distinct expression boundaries observed between neural and non-neural ectoderm, as well as within ectodermal derivatives. Claudins were also expressed in endodermally-derived tissues, including the anterior intestinal portal, pharynx, lung and pancreas and in mesodermally derived tissues such as the kidney, gonad and heart. The overlapping zones of claudin expression observed in the chick embryo may confer distinct domains of ion permeability within the early epiblast and in epithelial, mesodermal and endothelial derivatives that may ultimately influence embryonic patterning and morphogenesis during development.
Using Spot Instance SLAs for Reliable Cloud Federation UCSB Technical Report Number 2015-02

Spot instances are a commonly offered by IaaS cloud providers to opportunistically utilize spare capacity and meet temporary user demand for additional resources at low cost. Although the availability of service SLAs is a core paradigm of cloud computing, spot instances typically come without any service quality guarantees. We aim to extend the spot instance service to provide SLAs for eviction probability, based on the user estimate of the maximum expected instance lifetime. In addition to providing users with better usability and ahead-of-time quality of service guarantees, this statistical certainty also opens the door to cloud-to-cloud federation of workloads. For this federation to be possible, however, the statistical guarantees must be adhered to strictly, for a wide range of real-world workloads, at cloud scale. To this end, we propose a new approach to providing SLAs on the time-until-eviction for spot instances. We employ Monte-Carlo simulation to compute the quantiles of the conditional distributions of future spot instances for different available capacity levels. An IaaS cloud scheduler then uses these quantiles to determine when to provision federated requests in order to maintain an SLA at a specific target eviction probability for spot instances. We investigate the reliability of such SLA enforcement using synthetic and realworld traces, test its viability for cloud-to-cloud workload federation, and provide an in-depth analysis of trade-offs and cost factors of such federation.