Miracle-dz/UniFAR-FTUs huggingface dataset:
A packet marking algorithm for congestion pricing

In the resource pricing concept, developed by Kelly et al. [1], the network marks packets with appropriate price signals to direct the users’ actions. The theoretically correct congestion dependent prices, however, are not all known at the time when the marking occurs at a network resource. In this paper, we propose a packet marking algorithm which maximally utilises the information available at the time of marking. The known prices are marked directly on the packets, while the unknown ones are replaced by their expected values. Calculation of the expected values depends on a suitable system model. We derive these prices for a simple M/M/1/K resource model and generalise the result for GI/GI/1/K models using an approximate diffusion approach.
Muscarinic acetylcholine receptor 3 is dominant in myopia progression.

PURPOSE Numerous studies have proven that the nonselective muscarinic acetylcholine receptor (mAChR) antagonist atropine prevents the axial elongation that leads to myopia. Five distinct receptor genes (CHRM1-CHRM5), each encoding a muscarinic receptor protein (M[1]-M[5]), have been cloned. Copy number variations (CNVs), which constitute a substantial portion of genetic variability and structural genetic variants, are increasingly being recognized as modulators of human diseases. In this study, CNVs of CHRMs were detected to determine the genes associated with myopia. METHODS Participants were divided into three groups: high myopia group (myopia of 6-10 diopters [D]), severe high myopia group (myopia ≥ 10 D), and control group (myopia ≤ 0.5 D). The CNVs were detected, and the relative copy number was estimated using the comparative 2(-ΔΔCt) METHOD Syrian hamsters with form-deprivation myopia (FDM) were used as animal models of myopia. RESULTS The CNVs of CHRM2, CHRM3, and CHRM4 were significantly different among the groups, and the variations were most dominant in the CHRM3. The CNVs of CHRM3 showed significant differences among all 3 groups (P = 0.005). A replication cohort was collected to further confirm the association of CHRM3 CNV with myopia (P = 0.011). The expression of M(3) on the sclera of the FDM Syrian hamsters was upregulated and then downregulated after atropine administration. CONCLUSIONS CHRM3 and M(3) were suggested to play important roles in the pathogenesis of myopia and in the arrested progression of myopia by atropine.
Cokriging-Based Sequential Design Strategies Using Fast Cross-Validation Techniques for Multi-Fidelity Computer Codes

Cokriging-based surrogate models have become popular in recent decades to approximate a computer code output from a few simulations using both coarse and more complex versions of the code. In practical applications, it is common to sequentially add new simulations to obtain more accurate approximations. We propose a method of cokriging-based sequential design, which combines both the error evaluation provided by the cokriging model and the observed errors of a leave-one-out cross-validation procedure. This method is proposed in two versions, the first one selects points one at a time. The second one allows us to parallelize the simulations and to add several design points at a time. The main advantage of the suggested strategies is that at a new design point they choose which code versions should be simulated (i.e., the complex code or one of its fast approximations). A multifidelity application is used to illustrate the efficiency of the proposed approaches. In this example, the accurate code is a two-dimensional finite element model and the less accurate one is a one-dimensional approximation of the system. This article has supplementary material online.
Interaction of polyomavirus internal protein VP2 with the major capsid protein VP1 and implications for participation of VP2 in viral entry

A complex of the polyomavirus internal protein VP2/VP3 with the pentameric major capsid protein VP1 has been prepared by co‐expression in Escherichia coli. A C‐terminal segment of VP2/VP3 is required for tight association, and a crystal structure of this segment, complexed with a VP1 pentamer, has been determined at 2.2 Å resolution. The structure shows specific contacts between a single copy of the internal protein and a pentamer of VP1. These interactions were not detected in the previously described structure of the virion, but the location of VP2 in the recombinant complex is consistent with features in the virion electron‐density map. The C‐terminus of VP2/VP3 inserts in an unusual, hairpin‐like manner into the axial cavity of the VP1 pentamer, where it is anchored strongly by hydrophobic interactions. The remainder of the internal protein appears to have significant flexibility. This structure restricts possible models for exposure of the internal proteins during viral entry.
Evaluation of speech processing for telephone use by elderly listeners with hearing loss

Communicating over the telephone is a daily struggle for many older adults with hearing loss. Hearing aids and assistive listening devices improve the situation, but the vast majority of hearing-impaired elderly do not own such devices. In response to this problem, a Telephone Speech Enhancement Algorithm (TSEA) was designed through a collaborative effort of The Ohio State University Department of Speech and Hearing Science and the Department of Electrical and Computer Engineering. The TSEA uses an algorithm that preprocesses speech, such that the signal is enhanced on the talker’s end before being sent across the telephone line to the listener with hearing loss. Previous research examined the effectiveness of the TSEA at improving speech intelligibility for three levels of speech perception (phoneme, word, and sentence) (Poling, 2004; Harhager, 2007), but ceiling effects in recognition were noted, possibly biasing the results. Twelve older adults with a mild to severe sensorineural hearing loss consistent with presbycusis participated in this study. The objective of this study was to equate the level of difficulty of the three speech perception tests used to measure speech intelligibility first, before measuring the effectiveness of the TSEA at improving speech intelligibility over the telephone. Specifically, the MRT (phoneme-based test), the SPIN (word-based test), and the QSIN (sentence-
Effect of Regular Exercise on the Histochemical Changes of d-Galactose-Induced Oxidative Renal Injury in High-Fat Diet-Fed Rats

Renal lipid accumulation exhibits slowly developing chronic kidney disease and is associated with increased oxidative stress. The impact of exercise on the obese- and oxidative stress-related renal disease is not well understood. The purpose of this study was to investigate whether a high-fat diet (HFD) would accelerate d-galactose-induced aging process in rat kidney and to examine the preventive effect of regular exercise on the obese- and oxidative stress-related renal disease. Oxidative stress was induced by an administration of d-galactose (100 mg/kg intraperitoneally injected) for 9 weeks, and d-galactose-treated rats were also fed with a high-fat diet (60% kcal as fat) for 9 weeks to induce obesity. We investigated the efficacy of regular exercise in reducing renal injury by analyzing Nε-carboxymethyllysine (CML), 8-hydroxygluanine (8-OHdG) and apoptosis. When rats were fed with a HFD for 9 weeks in d-galactose-treated rats, an increased CML accumulation, oxidative DNA damage and renal podocyte loss were observed in renal glomerular cells and tubular epithelial cells. However, the regular exercise restored all these renal changes in HFD plus d-galactose-treated rats. Our data suggested that long-term HFD may accelerate the deposition of lipoxidation adducts and oxidative renal injury in d-galactose-treated rats. The regular exercise protects against obese- and oxidative stress-related renal injury by inhibiting this lipoxidation burden.
Multivoltage Floorplan Design

Energy efficiency has become a very important issue to be addressed in today's system-on-a-chip (SoC) designs. One way to lower power consumption is to reduce the supply voltage. Multisupply voltage (MSV) is thus introduced to provide flexibility in controlling the power and performance tradeoff. In region-based MSV, circuits are partitioned into ¿voltage islands¿ where each island occupies a contiguous physical space and operates at one voltage level. These tasks of island partitioning and voltage level assignment should be done simultaneously in the floorplanning process in order to take those important physical information into consideration. In this paper, we consider this core-based voltage island driven floorplanning problem including islands with power down mode, and propose a method to solve it. Given a candidate floorplan solution represented by a normalized Polish expression, we are able to obtain optimal voltage assignment and island partitioning (including islands with power down mode) simultaneously to minimize the total power consumption. Simulated annealing is used as the basic searching engine. By using this approach, we can achieve significant power saving (up to 50%) for all datasets, without any significant increase in area and wire length. We compared our approach with the most updated previous work on the same problem, and results show that our approach is much more efficient and is able to save more power in most cases. We have also studied two other approaches to solve the same problem, a simple dynamic programming approach and a lowest possible power consumption approach. Experimental results show that ours can perform the best among these three approaches. Our floorplanner can also be extended to minimize the number of level shifters, to address a minVdd version of the problem and to simplify the power routing step by placing islands close to their corresponding power pins.
Rationing scarce cadaver organs: a medical responsibility?

Transplantation is a specialty that raises the prickliest questions because it saves lives, prolongs good-quality life in the terminally ill, is extremely costly, and invokes ethical and social issues of administering the public resource of donated organs. Worldwide, there is a sorrowful state of organ shortage, with the result that patients are suffering while waiting for unavailable new kidneys, livers, pancreases, hearts and lungs. The paper by Mor et al. in this issue [1] reports on the efforts made by the Israel Transplant Center to shorten the inordinately long time that patients in end-stage renal failure have to wait to receive a transplant (the mean time is 3 years 8 months). The Spanish model for organ donation and the use of marginal donors were applied to expand the national donor pool. Spain currently has 139 hospital coordinating teams, one in each hospital. These transplant coordinators are involved in donation and organ procurement processes and are accountable for performance [2]. This policy led to a shift, in Israel, toward elderly donors (40% over 50 years old) with cerebrovascular accident (47%). Kidneys from donors over 50 years were at significant increased risk for delayed function and for primary non-function (38%) as compared with donors under 50 (19%). Age-matching policy (i.e., the allocation of an old kidney to an old patient) was an additional factor for poor outcome. The authors suggest that the cold ischemia delay be shortened and that stable first-graft recipients be selected. Donor age and delayed graft function in rejection-free patients are indeed risk factors for allograft failure. The senescent kidney is more vulnerable to ischemic and reperfusion injuries since nephron mass is reduced in the elderly. Therefore, every effort should be made to reduce ischemia stress. Also, following the dilemma to exclude organs, the use of two marginal kidneys in a single recipient might be an option [3].
Non-Standard Genetic Codes Define New Concepts for Protein Engineering

The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally designated as immutable and universal due to its conservation in most organisms, but sequencing of genes from the human mitochondrial genomes revealed deviations in codon assignments. Since then, alternative codes have been reported in both nuclear and mitochondrial genomes and genetic code engineering has become an important research field. Here, we review the most recent concepts arising from the study of natural non-standard genetic codes with special emphasis on codon re-assignment strategies that are relevant to engineering genetic code in the laboratory. Recent tools for synthetic biology and current attempts to engineer new codes for incorporation of non-standard amino acids are also reviewed in this article.
Discriminative category matching: efficient text classification for huge document collections

With the rapid growth of textual information available on the Internet, having a good model for classifying and managing documents automatically is undoubtedly important. When more documents are archived, new terms, new concepts and concept-drift will frequently appear Without a doubt, updating the classification model frequently, rather than using the old model for a very long period is absolutely essential. Here, the challenges are: a) obtain a high accuracy classification model; b) consume low computational time for both model training and operation; and c) occupy low storage space. However, none of the existing classification approaches could achieve all of these requirements. In this paper, we propose a novel text classification approach, called discriminative category matching, which could achieve all of the stated characteristics. Extensive experiments using two benchmarks and a large real-life collection are conducted. The encouraging results indicated that our approach is highly feasible.
Serovars of Salmonella from captive reptiles

The distribution on serovars of 60 Salmonella isolates from reptiles kept in captivity in Denmark during the period 1995–2006 was investigated. The isolates were all recovered from clinical specimens submitted to the National Veterinary Institute. A majority of the samples were from reptiles in zoological gardens or similar, while a minor number was from reptiles kept in private homes. A total of 43 serovars were detected, most of them being what is usually called exotic serotypes, and many not having a trivial name, while a few isolates belonged to well‐known human pathogenic serovars, such as S. Enteritidis, S. Typhimurium, S. Bovismorbificans. One isolate was rough and two were non‐typeable. Isolates from turtles belonged to the subspecies enterica, while many isolates from both sauria and snakes belonged to other subspecies. The findings underline the potential zoonotic risk by handling reptiles in zoological garden or other public settings, or keeping pet reptiles in private homes.
Effects of oxygen breathing on the heart rate, blood pressure, and cardiac index of normal men--resting, with reactive hyperemia, and after atropine.

Oxygen breathing has been used extensively to treat a wide variety of clinical disorders. An understanding of its effects on the normal circulation, at rest and under conditions of increased cardiac output, is fundamental to the understanding of the efficacy of oxygen therapy in clinical situations. Furthermore, interpretation of physiologic data concerning the effects of hyperoxia on the regional circulations requires definition of any changes in cardiac output or over-all peripheral circulation that occur during oxygen breathing. This investigation was undertaken for two purposes: 1) to evaluate the effects of oxygen breathing on the heart rate, systemic blood pressure, and cardiac index of normal men, resting, after atropine, and subjected to the circulatory stress of reactive hyperemia; and 2) to study the higher ranges of oxygen-sensitive chemoreceptor activity in man.
The non-coding landscape of head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is an aggressive disease marked by frequent recurrence and metastasis and stagnant survival rates. To enhance molecular knowledge of HNSCC and define a non-coding RNA (ncRNA) landscape of the disease, we profiled the transcriptome-wide dysregulation of long non-coding RNA (lncRNA), microRNA (miRNA), and PIWI-interacting RNA (piRNA) using RNA-sequencing data from 422 HNSCC patients in The Cancer Genome Atlas (TCGA). 307 non-coding transcripts differentially expressed in HNSCC were significantly correlated with patient survival, and associated with mutations in TP53, CDKN2A, CASP8, PRDM9, and FBXW7 and copy number variations in chromosomes 3, 5, 7, and 18. We also observed widespread ncRNA correlation to concurrent TP53 and chromosome 3p loss, a compelling predictor of poor prognosis in HNSCCs. Three selected ncRNAs were additionally associated with tumor stage, HPV status, and other clinical characteristics, and modulation of their expression in vitro reveals differential regulation of genes involved in epithelial-mesenchymal transition and apoptotic response. This comprehensive characterization of the HNSCC non-coding transcriptome introduces new layers of understanding for the disease, and nominates a novel panel of transcripts with potential utility as prognostic markers or therapeutic targets.
A slow component of intramembranous charge movement during sarcoplasmic reticulum calcium release in frog cut muscle fibers

Cut muscle fibers from Rana temporaria were mounted in a double Vaseline-gap chamber and equilibrated with an end-pool solution that contained 20 mM EGTA and 1.76 mM Ca (sarcomere length, 3.3-3.8 microns; temperature, 14-16 degrees C). Sarcoplasmic reticulum (SR) Ca release, delta[CaT], was estimated from changes in myoplasmic pH (Pape, P.C., D.- S. Jong, and W.K. Chandler. 1995. J. Gen. Physiol. 106:259-336). The maximal value of delta[CaT] obtained during a depleting depolarization was assumed to equal the SR Ca content before stimulation, [CaSR]R (expressed as myoplasmic concentration). After a depolarization to -55 to -40 mV in fibers with [CaSR]R = 1,000-3,000 microM, currents from intramembranous charge movement, Icm, showed an early I beta component. This was followed by an I gamma hump, which decayed within 50 ms to a small current that was maintained for as long as 500 ms. This slow current was probably a component of Icm because the amount of OFF charge, measured after depolarizations of different durations, increased according to the amount of ON charge. Icm was also measured after the SR had been depleted of most of its Ca, either by a depleting conditioning depolarization or by Ca removal from the end pools followed by a series of depleting depolarizations. The early I beta component was essentially unchanged by Ca depletion, the I gamma hump was increased (for [CaSR]R > 200 microM), the slow component was eliminated, and the total amount of OFF charge was essentially unchanged. These results suggest that the slow component of ON Icm is not movement of a new species of charge but is probably movement of Q gamma that is slowed by SR Ca release or some associated event such as the accompanying increase in myoplasmic free [Ca] that is expected to occur near the Ca release sites. The peak value of the apparent rate constant associated with this current, 2-4%/ms at pulse potentials between -48 and -40 mV, is decreased by half when [CaSR]R approximately equal to 500-1,000 microM, which gives a peak rate of SR Ca release of approximately 5-10 microM/ms.
Modified Local Discriminant Bases and Its Application in Audio Feature Extraction

One of the major challenges in classification problems based on signal decomposition approach is to identify the right basis function and its derivatives that can provide optimal features to distinguish the classes. Local Discriminant Bases (LDB) algorithm is one such algorithm, which efficiently selects a set of significant basis functions from the library of orthonormal bases based on certain defined dissimilarity measure. In this paper, we modified the LDB algorithm and used the fisher criterion for feature selection. Finally, support vector machines is used as a classifier to identify music, pure speech and speech with music.
Modeling and control of Transverse Flux Reluctance Machines

This paper presents a lumped parameter model describing the electromagnetic behavior of Transverse Flux Reluctance Machines. Current dynamics and torque generation are obtained utilizing varying magnetic conductivities of the air gap along the rotor perimeter. The model parameters are identified experimentally using a high accuracy current control for sinusoidal reference currents. A low torque ripple mode of operation is proposed.
On the Approximation of Finding A(nother) Hamiltonian Cycle in Cubic Hamiltonian Graphs

It is a simple fact that cubic Hamiltonian graphs have at least two Hamiltonian cycles. Finding such a cycle isNP-hard in general, and no polynomial-time algorithm is known for the problem of finding a second Hamiltonian cycle when one such cycle is given as part of the input. We investigate the complexity of approximating this problem where by a feasible solution we mean a(nother) cycle in the graph, and the quality of the solution is measured by cycle length. First we prove a negative result showing that the Longest Path problem is not constant approximable in cubic Hamiltonian graphs unlessP=NP. No such negative result was previously known for this problem in Hamiltonian graphs. In strong opposition with this result we show that there is a polynomial-time approximation scheme for finding a second cycle in cubic Hamiltonian graphs if a Hamiltonian cycle is given in the input.
Development of a passive MEG stimulus for measurement of the binaural masking level difference

The ability to hear a target signal over background noise is an important aspect of efficient hearing in everyday situations. This mechanism depends on binaural hearing whenever there are differences in the inter-aural timing of inputs from the noise and the signal. Impairments in binaural hearing may underlie some auditory processing disorders, for example temporal-lobe epilepsies. The binaural masking level difference (BMLD) measures the advantage in detecting a tone whose inter-aural phase differs from that of the masking noise. BMLD’s are typically estimated psychophysically, but this is challenging in children or those with cognitive impairments. The aim of this doctorate is to design a passive measure of BMLD using magnetoencephalography (MEG) and test this in adults, children and patients with different types of epilepsy. The stimulus consists of Gaussian background noise with 500-Hz tones presented binaurally either in-phase or 180° out-of-phase between the ears. Source modelling provides the N1m amplitude for the in-phase and out-of-phase tones, representing the extent of signal perception over background noise. The passive BMLD stimulus is successfully used as a measure of binaural hearing capabilities in participants who would otherwise be unable to undertake a psychophysical task.