Miracle-dz/UniFAR-FTUs huggingface dataset:
Minimizing Contradictions on Circular Order of Phylogenic Trees

Distance-based approaches to phylogeny use estimations of the evolutionary distance between sequences to reconstruct an evolution tree. If the evolution can be represented by an X-tree, the different sequences can be ordered so that the distance matrix Yi, jn, representing the distance from a leaf n to the path (i, j), is perfectly ordered meaning that Yi, jn ≥ Yi, kn and Yk, jn ≥ Yk, in for i ≤ j ≤ k. After ordering of the sequences, the distance matrix Yi, jn permits to visualize phylogenetic relationships between taxa and to localize deviations from perfect order. The effect of perturbations resulting from lateral gene transfer or crossover can be modeled probabilistically. The order is shown to be quite robust against many perturbations. We have developed algorithms to minimize the level of contradiction in the order of the sequences. These algorithms are tested on the SSU rRNA data for Archaea. The degree of contradiction after optimization is for most taxa quite low. Regions in the taxa space with deviations from perfect order were identified.
A gradient adaptive population importance sampler

Monte Carlo (MC) methods are widely used in signal processing and machine learning. A well-known class of MC methods is composed of importance sampling and its adaptive extensions (e.g., population Monte Carlo). In this paper, we introduce an adaptive importance sampler using a population of proposal densities. The novel algorithm dynamically optimizes the cloud of proposals, adapting them using information about the gradient and Hessian matrix of the target distribution. Moreover, a new kind of interaction in the adaptation of the proposal densities is introduced, establishing a trade-off between attaining a good performance in terms of mean square error and robustness to initialization.
Relapsing peripheral facial palsy: An unusual early sign of Friedreich ataxia

Abstract A 4-year-old child presented with peripheral left facial palsy. Neurological examination was normal except for deep tendon areflexia in the lower limbs. Serologic evaluation and cerebral magnetic resonance imaging to rule out post-infectious causes were normal. Electroneurography (ENG) showed absent sensory action potentials. After 15 days, the patient experienced a relapse of peripheral left facial palsy; ENG was unchanged, and somatosensory evoked potentials showed posterior column involvement. Genetic analysis demonstrated GAA repeat expansion on both alleles (860 and 900 GAA triplets) of the frataxin gene, and the child was diagnosed with Friedreich ataxia. Neurological findings at the last examination, performed at 7 years of age, were unchanged except for mild bilateral pes cavus. Peripheral seventh cranial nerve palsy could be an early and unusual sign of central nervous system degeneration and axonal sensory neuropathy. Its occurrence in this patient provides further evidence that Friedreich ataxia may have a varied clinical presentation at onset. In accordance with other studies, we believe that the size of both GAA expansions affect the age at onset of the disease, despite atypical phenotype.
TRAVELERS WHO ARE DEAFBLIND: A CORRELATIONAL STUDY OF INFLUENCES ON ASSISTANCE-GAINING FOR STREET CROSSINGS

This research investigated how some travelers who are deafblind can effectively solicit assistance to cross the street, addressing how leaders, mobility specialists, and municipal planners can encourage interventions for safer street crossings. The researcher conducted a quantitative study of 200 street crossings by travelers who are deafblind to determine whether there were relationships among soliciting assistance (assistance-gaining, the dependent variable), the size of a communication card asking for help (an independent variable), and the genders of the traveler and helper (independent variables). The study, supported by the psychology, sociology, and rehabilitation literature, examined the predictive capacity of the independent variables, card size and gender. The experiment was conducted in a typical urban setting, predetermined and defined by the researcher, with the expectation that the findings could be generalizable to similar environments. Predicated on standard techniques in the field of orientation and mobility, collaborators followed a precise alternate protocol for travelers who are deafblind. One male and one female traveler performed 100 street crossings each, alternately using assistance cards of different dimensions: the traditional card with a dimension of three by five inches and another four by eight inches. Correlation coefficients examined the one-to-one relationships among the independent and dependent variables, and a step-wise multiple regression reported on the strength of beta coefficients. The researcher concluded that the card size and the gender of the traveler influenced assistance-gaining; the larger communication card required fewer passersby to obtain assistance, as did the male traveler. However, these variables explained only 10% of the variation in assistancegaining. Further research is necessary to examine other possible influences such as race, ethnicity, environmental features, and alternate approaches for improving attentional capture.
Fumaric Acid and its Esters: An Emerging Treatment for Multiple Sclerosis

Fumaric acid is an intermediate product of the citric acid cycle that is a source of intracellular energy in the form of adenosine triphosphate (ATP). It is generated by oxidation of adenylsuccinate by the enzyme succinate dehydrogenase and is then converted to maleate by the enzyme fumarase. At present, fumaric acid esters (FAE) are licensed for the treatment of psoriasis. Several lines of evidence have demonstrated immunomodulatory effects for FAE. Clinical studies in psoriasis showed a reduction of peripheral CD4+- and CD8+-T-lymphocytes due to the ability of FAE to induce apoptosis. In vitro studies with the ester dimethyl fumarate (DMF) described an inhibitory effect on nuclear factor kappa B (NF-κB)-dependent transcription of tumor necrosis factor-alpha (TNF-α) induced genes in human endothelial cells. Animal studies using a model of central nervous system demyelination, MOG-induced experimental autoimmune encephalomyelitis (EAE), revealed a reduction of microglia and macrophages in inflamed lesions. A phase II clinical study in relapsing-remitting multiple sclerosis (RRMS) patients with a modified fumaric acid ester, BG-12, showed as "proof of principle" a significant reduction in the number of gadolinium enhancing lesions after 24 weeks of treatment as compared to placebo. Further phase III studies have now started to explore the long-term efficacy of FAE.
Probabilistic interpolative decomposition

Interpolative decomposition (ID) is a low-rank matrix decomposition where the data matrix is expressed via a sub-set of its own columns. In this work, we propose a novel probabilistic method for ID where it is expressed as a statistical model within a Bayesian framework. The proposed method considerably differs from other ID methods in the literature: It handles the model selection automatically and enables the construction of problem-specific interpolative decompositions. We derive the analytical solution for the normal distribution and we provide a numerical solution for the generic case. Simulation results on synthetic data are provided to illustrate that the method converges to the true decomposition, independent of the initialization; and it can successfully handle noise. In addition, we apply probabilistic ID to the problem of automatic polyphonic music transcription to extract important information from a huge dictionary of spectrum instances. We supply comparative results with the other proposed techniques in the literature and show that it performs better. Probabilistic interpolative decomposition serves as a promising feature selection and de-noising tool to be exploited in big data problems.
The development trend of a next-generation car and the its propulsion motor

From deterrence and the energy problem of global warming, application of the electric motor is progressing as a motor of a automobiles. Technical evolution of the electric motor for automobiles is remarkable by acceleration of EV, HEV, and FCV development. This paper introduces the latest example about technical evolution of the electric motor for them.
Fomepizole for the treatment of methanol poisoning.

BACKGROUND Methanol poisoning may result in metabolic acidosis, blindness, and death. The inhibition of alcohol dehydrogenase is fundamental to the treatment of methanol poisoning. We performed a multicenter study to evaluate fomepizole, an inhibitor of alcohol dehydrogenase, in the treatment of patients with methanol poisoning. METHODS We administered intravenous fomepizole to 11 consecutive patients who presented with methanol poisoning at a participating center. Serial clinical and laboratory studies, including measurements of plasma formic acid and fomepizole, were performed. The outcomes measured were the preservation of visual acuity, the resolution of metabolic acidosis, the inhibition of formic acid production, the achievment of therapeutic plasma concentrations of fomepizole with the dosing regimen, residual illness or disability, and death. RESULTS Plasma formic acid concentrations were detectable in eight patients, and these concentrations were closely correlated with the initial arterial pH values (r=0.92, P<0.001). In response to fomepizole, plasma formic acid concentrations fell and metabolic abnormalities resolved in all patients. Nine patients survived. Seven patients initially had visual abnormalities, but at the end of the trial no surviving patient had any detectable visual deficits related to methanol poisoning. Fomepizole had few adverse effects. The two patients who died had anoxic brain injury that was present at the time of enrollment. During treatment, methanol had an elimination half-life of 54 hours. CONCLUSIONS Fomepizole appears to be safe and effective in the treatment of methanol poisoning.
Learning for joint attention helped by functional development

Cognitive scientists and developmental psychologists have suggested that development in perceptual, motor and memory functions of human infants as well as adaptive evaluation by caregivers facilitate learning for cognitive tasks by infants. This article presents a robotic approach to understanding the mechanism of how learning for joint attention can be helped by such functional development. A robot learns visuomotor mapping needed to achieve joint attention based on evaluations from a caregiver. The caregiver adjusts the criterion for evaluating the robot's performance from easy to difficult as the performance improves. At the same time, the robot also gradually develops its visual function by sharpening input images. Experiments reveal that the adaptive evaluation by the caregiver accelerates the robot's learning and that the visual development in the robot improves the accuracy of joint attention tasks due to its well-structured visuomotor mapping. These results constructively explain what roles synchronized functional development in infants and caregivers play in task learning by infants.
Human cerebral cortex Cajal-Retzius neuron: development, structure and function. A Golgi study

The development, morphology and possible functional activity of the Cajal-Retzius cell of the developing human cerebral cortex are explored herein. The C-RC, of extracortical origin, is the essential neuron of the neocortex first lamina. It receives inputs from afferent fibers that reach the first lamina early in development. Although the origin and function of these original afferent fibers remain unknown, their target is the first lamina sole neuron: the C-RC. This neuron orchestrates the arrival, size and stratification of all pyramidal neurons (of ependymal origin) of the neocortex gray matter. Its axonic terminals spread radially and horizontally throughout the entirety of the first lamina establishing contacts with the dendritic terminals of all gray matter pyramidal cells regardless of size, location and/or eventual functional roles. While the neuron axonic terminals spread radially and horizontally throughout the first lamina, the neuronal’ body undergoes progressive developmental dilution and locating any of them in the adult brain become quite difficult. The neuron bodies are probably retained in the older regions of the neocortex while their axonic collaterals will spread throughout its more recent ones and eventually will extend to great majority of the cortical surface. The neocortex first lamina evolution and composition and that of the C-RC are intertwined and mutually interdependent. It is not possible to understand the C-RC evolving morphology without understanding that of the first lamina. The first lamina composition and its structural and functional organizations obtained with different staining methods may be utterly different. These differences have added unnecessary confusion about its nature. The essential emptiness observed in hematoxylin and eosin preparations (most commonly used) contrast sharply with the concentration of dendrites (the cortex’ largest) obtained using special (MAP-2) stain for dendrites. Only Golgi preparations demonstrate the numerous dendritic and axonic terminals that compose the first lamina basic structure. High power microscopic views of Golgi preparations demonstrate the intimate anatomical and functional interrelationships among dendritic and axonic terminals as well as synaptic contacts between them. The C-RC’ essential morphology does not changes but it is progressively modified by the first lamina increase in thickness and in number of terminal dendrites and their subsequent maturation. This neuron variable morphologic appearance has been the source of controversy. Its morphology depends on the first lamina thickness that may be quite variable among different mammals. In rodents (most commonly used experimental mammal), the first lamina thickness, number and horizontal expansion of dendrites is but a fraction of those in humans. This differences are reflected in the C-RC’ morphology among mammals (including humans) and should not be thought as representing new types of neurons.
Concurrent Indicators of Gait Velocity and Variability Are Associated with 25-Year Cognitive Change: A Retrospective Longitudinal Investigation

Background/Objectives: Physical function indicators, including gait velocity, stride time and step length, are linked to neural and cognitive function, morbidity and mortality. Whereas cross-sectional associations are well documented, far less is known about long-term patterns of cognitive change as related to objective indicators of mobility-related physical function. Methods: Using data from the Victoria Longitudinal Study, a long-term investigation of biological and health aspects of aging and cognition, we examined three aspects of cognition-physical function linkages in 121 older adults. First, we examined a simple marker of physical function (3 m timed-walk) as a predictor of cross-sectional differences and up to 25-year change for four indicators of cognitive function. Second, we tested associations between two markers of gait function derived from the GAITRite system (velocity and stride-time variability) and differences and change in cognition. Finally, we evaluated how increasing cognitive load during GAITRite assessment influenced the associations between gait and cognition. Results: The simple timed-walk measure, commonly used in clinical and research settings, was a minor predictor of change in cognitive function. In contrast, the objectively measured indicator of walking speed significantly moderated long-term cognitive change. Under increasing cognitive load, the moderating influence of velocity on cognitive change increased, with increasing variability in stride time also emerging as a predictor of age-related cognitive decline. Conclusion: These findings: (a) underscore the utility of gait as a proxy for biological vitality and for indexing long-term cognitive change; and (b) inform potential mechanisms underlying age-related linkages in physical and cognitive function.
Elaboration de techniques d’analyse adaptees a la construction d’une base de connaissances

Le probl6me de l 'acquisition de connaissances pour constituer une base de connaissances ou moddliser le comportement d'un expert n6cessite souvent le traitement de donndes verbales. Les techniques courantes en linguistique computationnelte ne semblent pas adaptdes: il est irr6aliste d'6crire un analyseur spdcialisd pour chaque sous-domaine considdrd (chaque syst~me expert) (cf SAGER et al. 87). Ces donndes verbales sont souvent incorrectes (retranscriptions de conversations). Les approches statistiques (ZERNIK et al.90) sont inadaptdes. Notre objectif est d'accdl6rer le ddchiffrage du domaine en procurant, sur une station de travail dddi6e a la moddlisation, les outils n6cessaires au traitement de la langue m6me, afin d'assister le cogniticien dans la premiere phase d'analyse d'un domaine. Comme d'autres chercheurs (WROBEL 90) (GRUBER 90), nous pensons qu' i l faut d6velopper un processus coopdratff entre l 'utilisateur et le systbme qui doit prendre en charge le plus possible la vdrification de la coh6rence des entr6es, qui doit aider "~ poser de bonnes questions h l'expert, qui doit suggdrer des choix d'interpr6tation, proposer des concepts. A la diff6rence de ces auteurs, nous envisageons cette coopdration dbs l'dtape d'analyse des donndes textuelles, sans pr6voir un prdtraitement manuel de la langue comme (MOLLER 88) et (KERSTEN 86), sans nous restreindre a un domaine particulier comme (SCHMIDT et al 91) (JANSEN-WINKEL 88). Nous basant sur les rdgularitds du langage scientifique dans la situation de recueil d'expertise, nous dlaborons des outils gdndraux, c 'est h dire inddpendant du domaine et d 'un type de probl~me particulier. Nous dtudions surtout des domaines o/a moddliser des actions est important: planification, conception, conception de plans, conception d'expdriences (JELTSCH et al. 89), mais aussi des probl~mes de type diagnostic. Cette recherche s'inscrit dans le eontexte de la moddlisation de connaissances (KEITH et al. 90), nous n'aborderons ici que raspect traitemerit de la langue. Ce processus consiste ici aussi en la cr6ation d'une certaine reprdsentation du texte. CeUe-ci doit 6tre adaptde a son utilisation future: la compr6hension d 'un domaine et de certains problames h rdsoudre dans ce domaine. Newell, (NEWELL 82) parle de trois abstractions h extraire des doundes, ce sont: les buts de l 'agent intelligent, les actions dont il est capable, et les connaissances qui lui pennettent de rdaliser ces buts. Les expressions d'actions rencontrdes dans les donndes linguistiques sont donc d6terminantes pour ranalyse de rexpertise. La repr6sentation doit avoir une certaine addquation psychologique (CARD et al. 83)(VALLACHER 87) (KLAUS et al. 72), opdratoire (MAHLING 90) cf GOMS (CARD et al. 80) et linguistique
1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is N-demethylated by cytochromes P450 2D6, 1A2 and 3A4--implications for susceptibility to Parkinson's disease.

1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) induces a Parkinson-like syndrome through biotransformation by monoamine oxidase B to the neurotoxic metabolite 1-methyl-4-phenylpyridine. Neuroprotection may be provided by parallel N-demethylation and N-oxidation pathways mediated by the microsomal cytochrome P450 and flavin monooxygenase systems, respectively. The aims of this study were to characterise the N-demethylation of MPTP by human liver microsomes over a wide range of concentrations, and to identify the cytochrome P450 enzymes involved in this reaction. The kinetics of the N-demethylation of MPTP (1 microM - 3 mM) by microsomes from the liver of an extensive metabolizer with respect to cytochrome P4502D6 (CYP2D6) activity were biphasic (apparent Km1 and Km2 values = 48 and 2882 microM). The high affinity activity was abolished in the presence of quinidine (1 microM) and was absent in microsomes from a genotypically poor metabolizer with respect to CYP2D6. Yeast microsomes containing heterologously expressed CYP2D6 N-demethylated MPTP (Km = 39 microM), and there was a high correlation between the quinidine-inhibitable N-demethylation of MPTP (50 microM) (0.7-91%, mean 44%, of total activity) and the alpha-hydroxylation of metoprolol in microsomes from 11 human livers (rs = 0.92; P < .001). At 50 microM MPTP, N-demethylase activity in human liver microsomes was also inhibited by furafylline (10 microM) and ketoconazole (2 microM) (mean inhibition 39 and 13%, respectively; n = 11 livers). Yeast microsomes containing heterologously expressed human CYP1A2 N-demethylated MPTP with a Km of 2246 microM. These findings indicate that CYP2D6, CYP1A2 and, to a lesser extent CYP3A4, may have a role in protecting against Parkinson's disease induced by MPTP and other potential environmental neurotoxins. The data provide some biochemical support for the proposition that genotypically poor metabolizers with respect to CYP2D6 are overrepresented in some populations of Parkinson's patients, and that smokers (induced CYP1A2? ) are underrepresented.
High photothermal properties in silicon nanostructures

This research describes the p-type nanostalactites (p-type NS) with high photothermal conversion capability has been demonstrated by rapid INC process without extra heat treatment. In optical property, p-type NS has ultralow reflectance below 5 % and high light absorption due to rough structures in the broadband wavelength (350 nm-1100 nm). It looks like a black body. Silicon, an indirect band material, can release thermal energy during the recombination process of photo-generated electron-hole pairs. P-type NS converts photon energy into heat rapidly and then photothermal effect occurs. Then, the temperature change of p-type NS is faster in 10 second than bulk p-type silicon. These nanostructures can not only enhance thermal conversion efficiency but be regarded as a great heat absorber.
Authentic Assessment as “Best Practice” for Early Childhood Intervention

The early childhood professionals recognize the limitations of conventional testing with young children. This recognition has given rise to Authentic Assessment, now recognized officially as best practice by the major professional organizations. However, no national studies have been conducted to document the comparative qualities of either authentic or conventional approaches—according to meaningful external standards. Based on a national Internet survey of professionals, we report details of a social validity study of common measurement methods on eight operationally defined standards for developmentally appropriate assessment linked to professionally sanctioned practice standards and indicators. Approximately 1,500 professional responses reveal higher quality appraisals for authentic assessment over conventional testing methods for early childhood intervention purposes. Based on these results, we offer recommendations to advance valid, sensible, and contextually appropriate assessment for early childhood intervention.