Miracle-dz/UniFAR-FTUs huggingface dataset:
Epstein–Barr Virus Genetic Variation in Lymphoblastoid Cell Lines Derived from Kenyan Pediatric Population

Epstein-Barr virus (EBV) is associated with Burkitt’s lymphoma (BL), and in regions of sub-Saharan Africa where endemic BL is common, both the EBV Type 1 (EBV-1) and EBV Type 2 strains (EBV-2) are found. Little is known about genetic variation of EBV strains in areas of sub-Saharan Africa. In the present study, spontaneous lymphoblastoid cell lines (LCLs) were generated from samples obtained from Kenya. Polymerase chain reaction (PCR) amplification of the EBV genome was done using multiple primers and sequenced by next-generation sequencing (NGS). Phylogenetic analyses against the published EBV-1 and EBV-2 strains indicated that one sample, LCL10 was closely related to EBV-2, while the remaining 3 LCL samples were more closely related to EBV-1. Moreover, single nucleotide polymorphism (SNP) analyses showed clustering of LCL variants. We further show by analysis of EBNA-1, BLLF1, BPLF1, and BRRF2 that latent genes are less conserved than lytic genes in these LCLs from a single geographic region. In this study we have shown that NGS is highly useful for deciphering detailed inter and intra-variations in EBV genomes and that within a geographic region different EBV genetic variations can co-exist, the implications of which warrant further investigation. The findings will enhance our understanding of potential pathogenic variants critical to the development and maintenance of EBV-associated malignancies.
Chicken Anti-Campylobacter Vaccine – Comparison of Various Carriers and Routes of Immunization

Campylobacter spp, especially the species Campylobacter jejuni, are important human enteropathogens responsible for millions of cases of gastro-intestinal disease worldwide every year. C. jejuni is a zoonotic pathogen, and poultry meat that has been contaminated by microorganisms is recognized as a key source of human infections. Although numerous strategies have been developed and experimentally checked to generate chicken vaccines, the results have so far had limited success. In this study, we explored the potential use of non-live carriers of Campylobacter antigen to combat Campylobacter in poultry. First, we assessed the effectiveness of immunization with orally or subcutaneously delivered Gram-positive Enhancer Matrix (GEM) particles carrying two Campylobacter antigens: CjaA and CjaD. These two immunization routes using GEMs as the vector did not protect against Campylobacter colonization. Thus, we next assessed the efficacy of in ovo immunization using various delivery systems: GEM particles and liposomes. The hybrid protein rCjaAD, which is CjaA presenting CjaD epitopes on its surface, was employed as a model antigen. We found that rCjaAD administered in ovo at embryonic development day 18 by both delivery systems resulted in significant levels of protection after challenge with a heterologous C. jejuni strain. In practice, in ovo chicken vaccination is used by the poultry industry to protect birds against several viral diseases. Our work showed that this means of delivery is also efficacious with respect to commensal bacteria such as Campylobacter. In this study, we evaluated the protection after one dose of vaccine given in ovo. We speculate that the level of protection may be increased by a post-hatch booster of orally delivered antigens.
A Dietary Supplement Containing Standardized Phaseolus vulgaris Extract Influences Body Composition of Overweight Men and Women

Background: More than one billion human adults worldwide are overweight and, therefore, are at higher risk of developing cardiovascular diseases, diabetes, and a variety of other chronic perturbations. Many believe that use of natural dietary supplements could aid in the struggle against obesity. So-called "starch blockers" are listed among natural weight loss supplements. Theoretically, they may promote weight loss by interfering with the breakdown of complex carbohydrates thereby reducing, or at least slowing, the digestive availability of carbohydrate-derived calories and/or by providing resistant starches to the lower gastrointestinal tract. Aims: The present research study examines a dietary supplement containing 445 mg of Phaseolus vulgaris extract derived from the white kidney bean, previously shown to inhibit the activity of the digestive enzyme alpha amylase, on body composition of overweight human subjects. Methods: A randomized, double-blinded, placebo-controlled study was conducted on 60 pre-selected, slightly overweight volunteers, whose weight had been essentially stable for at least six months. The volunteers were divided into two groups, homogeneous for age, gender, and body weight. The test product containing Phaseolus vulgaris extract and the placebo were taken one tablet per day for 30 consecutive days before a main meal rich in carbohydrates. Each subject's body weight, fat and non-fat mass, skin fold thickness, and waist/hip/thigh circumferences were measured. Results: After 30 days, subjects receiving Phaseolus vulgaris extract with a carbohydrate-rich, 2000- to 2200-calorie diet had significantly (p<0.001) greater reduction of body weight, BMI, fat mass, adipose tissue thickness, and waist,/hip/ thigh circumferences while maintaining lean body mass compared to subjects receiving placebo. Conclusion: The results indicate that Phaseolus vulgaris extract produces significant decrements in body weight and suggest decrements in fat mass in the face of maintained lean body mass.
Two-sample scale rank procedures optimal for the generalized secant hyperbolic distribution

There are many linear rank tests for the two-sample dispersion problem presented in literature. However just a few of them, the simplest ones, are commonly used. These common tests are not efficient for many practical distributions and thus other simple tests need to be developed to serve a wider range of distributions. The generalized secant hyperbolic distribution, proposed by Vaughan in [9], includes a large family of symmetric heavyand light-tailed distributions, from Cauchy to uniform. Kravchuk in [7] discussed location rank procedures optimal for this family. In the current paper, we introduce two-sample scale linear rank tests locally optimal for the generalized secant hyperbolic distribution. We discuss the asymptotic and exact properties of the new test statistics and illustrate the corresponding tests and rank estimators with numerical examples.
Building intrusion pattern miner for snort network intrusion detection system

We propose a framework for Snort network-based intrusion detection system to make it have the ability of not only catching new attack patterns automatically, but also detecting sequential attack behaviors. To do that, we first build an intrusion pattern discovery module to find single intrusion patterns and sequential intrusion patterns from a collection of attack packets in offline training phase. The module applies data mining technique to extract descriptive attack signatures from large stores of packets, and then it converts the signatures to Snort detection rules for online detection. In order to detect sequential intrusion behavior, the Snort detection engine is accompanied with our intrusion behavior detection engine. When a series of incoming packets match the signatures representing sequential intrusion scenarios, intrusion behavior detection engine make an alert.
A sparse VLIW instruction encoding scheme compatible with generic binaries

Very Long Instruction Word (VLIW) processors are commonplace in embedded systems due to their inherent lowpower consumption as the instruction scheduling is performed by the compiler instead by sophisticated and power-hungry hardware instruction schedulers used in their RISC counterparts. This is achieved by maximizing resource utilization by only targeting a certain application domain. However, when the inherent application ILP (instruction-level parallelism) is low, resources are under-utilized/wasted and the encoding of NOPs results in large code sizes and consequently additional pressure on the memory subsystem to store these NOPs. To address the resource-utilization issue, we proposed a dynamic VLIW processor design that can merge unused resources to form additional cores to execute more threads. Therefore, the formation of cores can result in issue widths of 2, 4, and 8. Without sacrificing the possibility of code interruptability and resumption, we proposed a generic binary scheme that allows a single binary to be executed on these different issue-width cores. However, the code size issue remains as the generic binary scheme even slightly further increases the number NOPS. Therefore, in this paper, we propose to apply a well-known stop-bit code compression technique to the generic binaries that, most importantly, maintains its code compatibility characteristic allowing it to be executed on different cores. In addition, we present the hardware designs to support this technique in our dynamic core. For prototyping purposes, we implemented our design on a Xilinx Virtex-6 FPGA device and executed 14 embedded benchmarks. For comparison, we selected a nondynamic/ static VLIW core that incorporates a similar stop-bit technique for its code compression. We demonstrate, while maintaining code compatibility on top of a flexible dynamic VLIW processor, that the code size can be significantly reduced (up to 80%) resulting in energy savings, and that the performance can be increased (up to a factor of three). Finally, our experimental results show that we can use smaller caches (2 to 4 times as small), which will further help in decreasing energy consumption.
Concentration-Dependent Requirement for Local Protein Synthesis in Motor Neuron Subtype-Specific Response to Axon Guidance Cues

Formation of functional motor circuits relies on the ability of distinct spinal motor neuron subtypes to project their axons with high precision to appropriate muscle targets. While guidance cues contributing to motor axon pathfinding have been identified, the intracellular pathways underlying subtype-specific responses to these cues remain poorly understood. In particular, it remains controversial whether responses to axon guidance cues depend on axonal protein synthesis. Using a growth cone collapse assay, we demonstrate that mouse embryonic stem cell-derived spinal motor neurons (ES-MNs) respond to ephrin-A5, Sema3f, and Sema3a in a concentration-dependent manner. At low doses, ES-MNs exhibit segmental or subtype-specific responses, while this selectivity is lost at higher concentrations. Response to high doses of semaphorins and to all doses of ephrin-A5 is protein synthesis independent. In contrast, using microfluidic devices and stripe assays, we show that growth cone collapse and guidance at low concentrations of semaphorins rely on local protein synthesis in the axonal compartment. Similar bimodal response to low and high concentrations of guidance cues is observed in human ES-MNs, pointing to a general mechanism by which neurons increase their repertoire of responses to the limited set of guidance cues involved in neural circuit formation.
Brief Subthreshold Events Can Act as Hebbian Signals for Long-Term Plasticity

Background Action potentials are thought to be determinant for the induction of long-term synaptic plasticity, the cellular basis of learning and memory. However, neuronal activity does not lead systematically to an action potential but also, in many cases, to synaptic depolarizing subthreshold events. This is particularly exemplified in corticostriatal information processing. Indeed, the striatum integrates information from the whole cerebral cortex and, due to the membrane properties of striatal medium spiny neurons, cortical inputs do not systematically trigger an action potential but a wide range of subthreshold postsynaptic depolarizations. Accordingly, we have addressed the following question: does a brief subthreshold event act as a Hebbian signal and induce long-term synaptic efficacy changes? Methodology/Principal Findings Here, using perforated patch-clamp recordings on rat brain corticostriatal slices, we demonstrate, that brief (30 ms) subthreshold depolarizing events in quasi-coincidence with presynaptic activity can act as Hebbian signals and are sufficient to induce long-term synaptic plasticity at corticostriatal synapses. This “subthreshold-depolarization dependent plasticity” (SDDP) induces strong, significant and bidirectional long-term synaptic efficacy changes at a very high occurrence (81%) for time intervals between pre- and postsynaptic stimulations (Δt) of −110<Δt<+110 ms. Such subthreshold depolarizations are able to induce robust long-term depression (cannabinoid type-1 receptor-activation dependent) as well as long-term potentiation (NMDA receptor-activation dependent). Conclusion/Significance Our data show the existence of a robust, reliable and timing-dependent bidirectional long-term plasticity induced by brief subthreshold events paired with presynaptic activity. The existence of a subthreshold-depolarization dependent plasticity extends considerably, beyond the action potential, the neuron's capabilities to express long-term synaptic efficacy changes.
Correlation between DPOAE I/O functions and pure-tone thresholds

Abstract Different studies have been carried out in order to correlate audiometric thresholds and distortion product otoacoustic emissions measurements (DPOAE). However, high variability and external interferences make hearing thresholds estimates by means of the DPOAE very little sensitive. The aim of this study was to check the correspondence between the pure tone thresholds and the cochlear response thresholds by DPOAE Input/output functions, considering the influence of the following variables: gender, past of acute otitis media, and ear side. Method Prospective study comprehending 69 normal hearing individuals. Multiple mix regression models were applied to evaluate the correspondence between the two measurements studied. Results Statistically significant positive correlation was observed among all the frequencies compared (2000, 3000, 4000 e 6000 Hz). Conclusions The 1dB HL resolution pure tone thresholds and the above-mentioned variables had a direct impact on the high correlation between the measures studied, and it also reduced response variability. Nevertheless, response variability was still high, limiting the use of DPOAE I/O functions for hearing threshold estimates. We suggest that these variables should be considered for future studies with pure tone thresholds estimations by DPOAE I/O functions.
Sensor fusion based ambulatory system for indoor localization

Indoor localization for pedestrian is the key technology for caring the elderly, the visually impaired and the handicapped in health care districts. It also becomes essential for the emergency responders where the GPS signal is not available. This paper presents newly developed pedestrian localization system using the gyro sensors, the magnetic compass and pressure sensors. Instead of using the accelerometer, the pedestrian gait is estimated from the gyro sensor measurements and the travel distance is estimated based on the gait kinematics. Fusing the gyro information and the magnetic compass information for heading angle estimation is presented with the error covariance analysis. A pressure sensor is used to identify the floor the pedestrian is walking on. A complete ambulatory system is implemented which estimates the pedestrian`s 3D position and the heading.
A distinction among O-features : The role of gender and number in the retrieval of pronoun antecedents

We investigated the use of two O-features, gender and number, in pronoun antecedent identification in six experiments in Italian. In a previous work (Di Domenico & De Vincenzi 1996) we found that 1000 msec after the presentation of a pronoun only number information is used to restrict the set of possible antecedents for the pronoun, whereas gender information is not. Here we add two experiments with onset of the target word at 500 msec, which show that neither number nor gender are used. The conclusion is thus that while number information is used within 500 and 1000 msec to restrict the reactivation of pronoun antecedents, gender is not. The results are compared to previous experiments conducted in English by Nicol (1988). The author found an immediate use of number information but a less clear result for gender, possibly due to the fact that in English gender is not marked on the same way as number is. Our study in Italian, with nouns where gender and number are equally overtly and regularly marked, suggests that the different use of gender and number is not specific to English nor has to do with the surface markedness of features, but, on the contrary, is to be attributed to an intrinsic difference between the two features. This difference is characterized in terms of a different syntactic representation of the two features, as assumed in recent proposals in linguistic theory, and of the parser's modular use of linguistic information. *
The spatially resolved refractometer.

PURPOSE To investigate factors controlling the aberrations of the eye, including accommodation, wavelength, and the apodization of the optics of the eye by cone directional selectivity. METHODS We constructed a new implementation of the Spatially Resolved Refractometer (SRR). This is an instrument, based on the Scheiner principle, that allows the rapid psychophysical measurement of the complete wavefront aberrations of the eye. We have investigated both the reproducibility of the measurements, and the effect of static accommodation and wavelength on the wavefront aberrations of the eye. In addition we combined the wave front aberrations with cone photoreceptor directionality to compute the modulation transfer function of the eye, at the retinal level. RESULTS The SRR measurements were rapid (4 minutes per measurements, 12 minutes per patient) and reproducible. There are significant changes in wavefront quality with accommodation, with optimal image quality near the resting point of accommodation. Image quality for polychromatic (white) light is strongly affected by both longitudinal and transverse chromatic aberration. Finally, we find that incorporating the effects of cone directionality into the calculation of image quality can increase image quality by up to 50%. CONCLUSION Calculation of a simple "optimal surgical shape" for wave-front guided refractive surgery will depend on improved understanding of the interplay between the biological and physical properties of the eye.
Visual information and redundancy conveyed by internal articulator dynamics in synthetic audiovisual speech

This paper reports results of a study investigating the visual information conveyed by the dynamics of internal articulators. Intelligibility of synthetic audiovisual speech with and without visualization of the internal articulator movements was compared. Additionally speech recognition scores were contrasted before and after a short learning lesson in which articulator trajectories were explained, once with and once without motion of internal articulators. Results show that the motion information of internal articulator dynamics did not lead to significant different recognition scores at first, and that only in case of this additional visual information the training lesson was able to significantly increase visual and audiovisual speech intelligibility. After the learning lesson with all internal articulatory movements the visual recognition could be enhanced to a higher degree than the audiovisual recognition. The absolute increase of visual recognition could not be integrated completely into audiovisual recognition. It could be shown that this was due to redundant information conveyed by auditory and visual sources of information.
Association of Serum Phytoestrogen Concentration and Dietary Habits in a Sample Set of the JACC Study

BACKGROUND: Phytoestrogens may be associated with a reduced risk of hormone dependent neoplasms such as prostate and breast cancers. We tried to determine the validity of the association between serum phytoestrogen concentrations and dietary habits obtained from a food frequency questionnaire used in the Japan Collaborative Cohort Study (JACC Study) for Evaluation of Cancer Risk sponsored by the Ministry of Education, Science, Sports and Culture of Japan (Monbusho). METHODS: The subjects were 151 male controls who were selected for a nested case-control study for evaluating prostate cancer risk as part of the JACC Study. Dietary habits were determined using a food frequency questionnaire at baseline, and the concentrations of genistein, daidzein, and equol in frozen-stored serum samples assayed in 2002 were compared. RESULTS: Tofu intake showed a significant association with the serum concentrations of genistein and daidzein (Spearman’s correlation coefficients (rs) =0.30 and 0.27, respectively), and miso soup showed a slight association with serum concentrations of these phytoestrogens. In contrast, serum concentrations of equol were not associated with dietary intake of tofu and miso soup. After adjustment for serum daidzein concentration, serum equol concentration was associated with the intake of foods containing fat, meat, and coffee, but not green tea. CONCLUSIONS: Serum genistein and daidzein concentrations were significantly associated with dietary intake of tofu, and slightly with intake of miso soup. Consumption of fat, meat, and coffee may be associated with equol production by intestinal microflora in this sample set.
β-Amyloid Precursor Protein Does Not Possess Ferroxidase Activity but Does Stabilize the Cell Surface Ferrous Iron Exporter Ferroportin

Ceruloplasmin is a ferroxidase that interacts with ferroportin to export cellular iron, but is not expressed in neurons. We recently reported that the amyloid precursor protein (APP) is the analogous iron-exporting chaperone for neurons and other cells. The ferroxidase activity of APP has since been called into question. Using a triplex Fe2+ oxidation assay, we analyzed the activity of a soluble form of APP (sAPPα) within a buffer of physiological pH and anionic charge, and determined that iron oxidation originated from phosphate. Using various techniques such as flow-cytometry to measure surface presented proteins, we confirmed that endogenous APP is essential for ferroportin persistence on the neuronal surface. Therefore, despite lacking ferroxidase activity, APP still supports iron export from neurons.