Miracle-dz/UniFAR-FTUs huggingface dataset:
simuPOP: a forward-time population genetics simulation environment

SUMMARY simuPOP is a forward-time population genetics simulation environment. The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time. Using this R/Splus-like environment, users can create, manipulate and evolve populations interactively, or write a script and run it as a batch file. Owing to its flexible and extensible design, simuPOP can simulate large and complex evolutionary processes with ease. At a more user-friendly level, simuPOP provides an increasing number of built-in scripts that perform simulations ranging from implementation of basic population genetics models to generating datasets under complex evolutionary scenarios. AVAILABILITY simuPOP is freely available at http://simupop.sourceforge. net, distributed under GPL license.
-Induced Cerebellar Ataxia in Mice b IL-1Protective Effect of IL-18 on Kainate- and

The pathogenesis of sporadic cerebellar ataxia remains unknown. In this study, we demonstrate that proinﬂammatory cytokines, IL-18 and IL-1 (cid:1) , reciprocally regulate kainate-induced cerebellar ataxia in mice. We show that systemic administration of kainate activated IL-1 (cid:1) and IL-18 predominantly in the cerebellum of mice, which was accompanied with ataxia. Mice deﬁcient in caspase-1, IL-1R type I, or MyD88 were resistant to kainate-induced ataxia, while IL-18- or IL-18R (cid:2) -deﬁcient mice displayed signiﬁcant delay of recovery from ataxia. A direct intracerebellar injection of IL-1 (cid:1) -induced ataxia and intracerebellar coinjection of IL-18 counteracted the effect of IL-1 (cid:1) . Our data ﬁrstly show that IL-18 and IL-1 (cid:1) display differential direct regulation in kainate-induced ataxia in mice. Our results might contribute toward the development of a new therapeutic strategy for cerebellar ataxia in humans. The Journal of Immunology, 2008, 180: 2322–2328. -glutamate, three of Our results show may suggest / , and IL-18R (cid:1) / (cid:1) mice, but used a BALB/c background for caspase-I / mice. Regarding the differences in the development of inﬂammatory disease of the IL-1ra (cid:1) / (cid:1) mice, Horai et al. (47) showed that the IL-1ra-deﬁcient mice on a BALB/c background, but not those on a C57BL/6J background, spontaneously developed chronic inﬂammatory polyarthropathy. Their results suggested that genes other than IL-1ra are involved in the development of spontaneously developed arthritis. They also observed that IL-1ra (cid:1) / mice on the C57BL/6 background developed arthritis at a high incidence when these mice were immunized with type II collagen. Their result demonstrated that IL-1ra (cid:1) / mice on C57BL/6 background as well as BALB/c background showed the corresponding susceptibility to experimentally induced arthritis. In our study, we observed the effect of kainate on the acutely induced ataxia (induc-tion within 20 min after the kainate injection and the following subsidence within 60–120 min). Our data showed that the mice deﬁcient with IL-1RI, or MyD88 on the same C57BL/6 background were resistant to kainate-induced ataxia, while IL-18- or IL-18R (cid:1) -deﬁcient mice on the same C57BL/6 background displayed signiﬁcant delay of the recovery from ataxia. In these experiments, we had compared the responses with the wild-type mice on the same C57BL/6 background. We have also compared the locomotion time of normal BALB/c mice and C57BL/6 mice after systemic administration of kainate, and observed the similar responses in normal BALB/c mice and
Relative Time Compression for Slow-Motion Stimuli through Rapid Recalibration

A number of psychophysical studies have shown that moving stimuli appear to last longer than static stimuli. Here, we report that the perceived duration for slow moving stimuli can be shorter than for static stimuli under specific circumstances. Observers were tested using natural movies presented at various speeds (0.0× = static, 0.25× = slow, or 1.9× = fast, relative to original speed) and indicated whether test duration was perceived as longer or shorter than comparison movies presented at their original speed. While fast movies were perceived as longer than slow and static movies (in accordance with previous studies), we found that slow movies were perceived as shorter (i.e., time compressed) compared to static images. Similar results were obtained for artificial stimuli consisting of drifting gratings. However, time compression for slow stimuli disappeared if comparison stimuli were replaced by a white static disk that removed repetitive exposures to moving stimuli. Results suggest that duration estimation is modulated by contextual effects induced by the specific diet – or distribution – of prior visual stimuli to which observers are exposed. A simple model, which includes a rapid recalibration of human time estimation via adaptation to preceding stimuli, succeeds in reproducing our experimental data.
Do the GDS and the GDS-15 adequately capture the range of depressive symptoms among older residents in congregate housing?

ABSTRACT Background: In light of inconsistencies in cut points for identifying non-major depression, this study examined the classification efficiency of the Geriatric Depression Scale (GDS and GDS-15) total scores and individual items, and four additional depressive symptoms for identification of subthreshold, minor, or criterion depression among 166 vulnerable residents of congregate housing. Methods: Depression (combined categories of major depressive episode, minor, or subthreshold depression) was determined by the Mini-International Neuropsychiatric Interview (MINI) diagnostic interview depression module administered by telephone to 166 older residents of congregate housing facilities who also completed the 30-item GDS and four other yes/no potential indicators of geriatric depression. Classification agreement and ROC curve analysis for the full and 15-item GDS scale scores were calculated. Individual item hit rates for MINI criterion were calculated for GDS items and four new items. Results: GDS and GDS-15 at standard cut points had 70–75% agreement with MINI. Best sensitivity and specificity were obtained at lower than standard cut points. Some GDS Withdrawal, Apathy, lack of Vigor (WAV) and cognitive items obtained very low hit rates. New items “I just don't feel like myself” and “I feel I am a burden to others” better discriminated MINI depression than most GDS items and had good item-to-total correlations with the GDS. Conclusions: Diagnostic criteria and GDS screen had partial agreement. Some GDS items did not adequately represent depression among functionally impaired or oldest old older adults. Feeling one is a burden and the sense of feeling “different” from usual may be useful indicators of depression among vulnerable older adults.
Reconnaissance automatique des grapho-éléments temporels de l'électroencéphalogramme du sommeil

En neurophysiologie, l'electroencephalogramme (EEG) constitue un moyen d'etude important dans divers domaines parmi lesquels nous pouvons citer le diagnostic des troubles du sommeil et l'analyse de la vigilance. L'etude clinique de ce signal physiologique se base essentiellement sur la reconnaissance visuelle d'un ensemble d'informations particulieres de deux types : les ondes, caracterisees par leur spectre frequentiel, et les grapho-elements caracterises par leur morphologie temporelle. Dans cet article, nous presentons une approche de reconnaissance automatique des grapho-elements de l'EEG qui se base sur une mesure de similitude temporelle par rapport a des grapho-elements de reference. La mesure est effectuee par la Dynamic TimeWarping (DTW). L'objectif de cette reconnaissance est d'enrichir l'analyse spectrale que nous avons exploitee dans d'autres travaux affin d'etudier leur influence sur les performances de notre systeme d'analyse automatique de l'EEG.
The Role of Attention in a Spatial Memory Task in Alzheimer Disease Patients

Memory and attention are interrelated cognitive processes that most likely influence the functioning of each other, yet they are often difficult to distinguish in psychological experiments. Young, aged adults, and patients with Alzheimer disease (AD) were tested on a delay response task measuring spatial memory that also placed high demands on attentional resources. Aged adults performed as well as young, suggesting that neither attentional nor memory abilities were exceeded in either group. However, AD subjects were severely impaired on this task. Two further experiments with AD patients examined the relative contribution of attentional and memory deficits in the performance of this population. Both memory and attentional impairments were found; however, errors due to memory factors were more closely related to severity of disease as measured on the Folstein Mini-Mental State Examination than were errors of attentional origin. These studies demonstrate the necessity of accounting for attentional components in studies examining memory, especially in patients with AD.
Estabilidade de Classificadores de Decisão em Árvore Binária para Dados Imagem em Alta Dimensão

This paper deals with the problem of classifying high-dimensional image data image data using a multiple stage classifier structured as a binary tree. The aim here consists in finding the optimal structure for the binary tree in the sense of achieving a stable accuracy. The advantage presented by a multiple stage classifier lies on the fact that only a sub-set of classes is considered at each stage, allowing a better selection of the features to be used at each node. The binary tree is a particular case of a tree structured classifier, on which only two classes are considered at each node. This peculiarity makes possible the direct use of statistical distances for feature reduction (selection or extraction). In this study the criterion used for feature reduction at each node consists in optimizing the Bhattacharyya distance separating both classes in the node. The optimization of Bhattacharyya distance was based 1 Centro Estadual de Pesquisas em Sensoriamento Remoto e Metereologia UFRGS Caixa Postal 15044 CEP 91501-970 Porto Alegre – RS, Brasil {d_altieri@yahoo.com. br} {victor.haertel@ufrgs.br} Estabilidade de Classificadores de Decisão em Árvore Binária para Dados Imagem em Alta Dimensão 28 RITA • Volume XV • Número 2 • 2008 on the covariance matrices. Once the final set of features is obtained at each particular node, the classification is performed using the Gaussian Maximum Likelihood decision rule. Tests were performed using high-dimensional image data collected by the sensor system AVIRIS covering a test area. The criteria to evaluate the performance of the classifiers are: the final accuracy yielded by the classifier, its stability, and the required computer time. Palavras-chaves: reconhecimento de padrões, imagem hiper-espectral, árvores de decisão, distância de Bhattacharyya.
Unraveling the true complexity of costly color signaling

Conspicuous displays of color comprise an enormously diverse and functionally complex class of biological signals. Many of these displays are widely publicized as resulting from chemical colorants known as pigments, which act by selectively "absorbing" part of the light spectrum (Appendix 1). However, the full diversity of animal coloration is just as strongly influenced by optically active surface structures, which act by selectively "reflecting" light (i.e., scattering). In cases where light is scattered coherently, these structural colors produce displays that are often metallic, iridescent, or kaleidoscopic in appearance. In addition to structural coloration, mechanisms such as bioluminescence and fluorescence allow the actual creation of colored light, thereby transcending the simple reflectance of whatever ambient wavelengths are available. There is enormous variation among all of these classes of colorants, and most signals arise through the interaction of diverse suites of pigments and reflecting (structural) mechanisms. Despite this complexity, however, the field of behavioral ecology has been largely preoccupied with understanding how carotenoids—a single group of pigments—may broker the honest signaling of individual quality. This focus has proven highly productive in many respects, but it has also fostered a limited and overly simplistic view of how color signals really work. As we outline here, the complete emerging story of animal coloration is far more complex and interesting.
Language Development in Individuals With Fragile X Syndrome

Fragile X syndrome (FXS) is the leading inherited cause of intellectual disability. The syndrome is caused by a single gene mutation on the X chromosome. Although individual differences are large, most individuals with FXS display weaknesses across all language and literacy domains compared with peers of the same chronological age with typical cognitive and language development. Expressive, receptive, and pragmatic language abilities as well as literacy skills are similar to those of younger, typically developing peers at similar cognitive and language developmental levels, although there are areas in which impairments exceed developmental-level expectations. One area of special impairment is the higher occurrence of repetition in the language of individuals with FXS compared with developmentally matched peers. In this article, we review the behavioral, language, and literacy profiles of individuals with FXS and discuss potential clinical implications.
Light-triggered methylcellulose gold nanoparticle hydrogels for leptin release to inhibit fat stores in adipocytes

Leptin is released in response to increased triglyceride storage in adipocytes and impacts body weight, but has drawbacks such as poor therapeutic effect and side effects when delivered systemically. Leptin also modifies adipocyte sensitivity to insulin to inhibit lipid accumulation. Here, light-triggered degradation of hydrogels was used to improve accuracy and effectiveness for sustained and controllable release. In our approach, leptin was entrapped within methylcellulose (MC)-based hydrogels, with incorporation of gold nanoparticles (NP). The incorporation of gold NP into MC hydrogels led to a tunable light irradiation response that dictated the hydrogel release rate of leptin. This manuscript demonstrates feasibility in designing tunable thermosensitive hydrogels for loading multimodality therapeutic agents to enhance the bioactivity of leptin for obesity therapy.
Time and Position Spoofing with Open Source Projects

Time and position data of mobile devices are trusted without checking by most vendors and developers. We discover a method of GPS spoofing with low-cost SDR devices. The method can be used to alter the location status as well as the time of affected devices, which poses a security threat to location-based services. We also examine other positioning methods used by smart devices (e.g. WiFi) and how to spoof them. Advices on preventing such spoofing are given.
On the asymptotic convergence of B-spline wavelets to Gabor functions

A family of nonorthogonal polynomial spline wavelet transforms is considered. These transforms are fully reversible and can be implemented efficiently. The corresponding wavelet functions have a compact support. It is proven that these B-spline wavelets converge to Gabor functions (modulated Gaussian) pointwise and in all L/sub p/-norms with 1 >
Self-blame and adjustment to breast cancer.

PURPOSE To examine the relationship between self-blame and illness adjustment in women with breast cancer. DESIGN Descriptive, correlational design. SETTING Outpatient facilities of two metropolitan medical centers. SAMPLE 234 women diagnosed with stage I or II breast cancer. METHODS Structured and semistructured interviews using the Psychosocial Adjustment to Illness Scale (PAIS), the Global Adjustment to Illness Scale (GAIS), an attributions and blame interview, and several questions about control over the cause and course of the cancer. MAIN RESEARCH VARIABLES Self-blame, controllability, and adjustment to illness. FINDINGS 39% of the sample reported some self-blame. Analysis of variance indicated that subjects with high levels of self-blame had poorer scores on the PAIS and GAIS. CONCLUSIONS The findings indicate the need for further study of the self-blame/adjustment relationship. Researchers must clarify the characteristics that compromise adjustment in patients with breast cancer. IMPLICATIONS FOR NURSING PRACTICE The findings support the importance of assessing self-blame and providing information to discourage its use by patients with breast cancer.
Reducing industrial wastewater and recovery of gold by direct contact membrane distillation with electrolytic system

To recover gold, this work used a novel direct contact membrane distillation (DCMD) reactor with a hybrid electrolytic process. Analytical results demonstrate that permeate flux increased as feed -2 -1 temperature and feed flow rate increased. Permeate flux increased from 2.8 to 17.6 kg m h when -2 -1 temperature increased from 30 to 70 °C, and increased from 9.2 to 19.9 kg m h when the feed flow -1 rate increased from 10 to 50 L h . A strong negative correlation between feed conductivity and permeate flux existed. Flux decreased about 21% following an increase in Au wastewater concentra-1 tion in the feed from 5,600 to 55,000 iS cm . The gold and total organic carbon concentrations in-1 creased as the concentration ratio increased. The Au concentration reached around 165 mg L with a concentrating efficiency exceeding 17-fold. After the DCMD process, 90% of the concentrated gold solution was recovered by electrolysis. Performance recovery rate increased about 20 times from -1 -1 10.6 to 252 mg A h . These positive results show that the new hybrid process integrating a DCMD reactor with electrolysis methods can be applied effectively to treat low concentrations of gold in wastewater.
Voting with Endogenous Information Acquisition: Theory and Evidence

The standard model of jury or committee voting, with costless, exogenously given and noisy but informative signals regarding the true state of the world, predicts that the efficiency of group decision-making increases unambiguously with the group size. However, once signal acquisition is made a costly and endogenous decision, there are important free-riding considerations that counterbalance the information aggregation effect. If the cost of acquiring information is fixed, then rational voters have disincentives to purchase information as the group size becomes larger since the impact of their vote becomes smaller. In this paper we investigate the extent to which human subjects recognize this trade-off between information aggregation and free-riding in a laboratory experiment where we vary the group size, the cost of information acquisition and the precision of signals. We find that in most of the settings we study, free-riding incentives are weak as there is a pronounced tendency for subjects to over-acquire information relative to equilibrium predictions and we offer several possible explanations for this finding.
Claudin-4: a potential therapeutic target in chemotherapy-resistant ovarian cancer.

BACKGROUND Claudin-4, a component of the tight junction, plays an important role in tumorigenesis and metastasis of ovarian cancer, but its role in platinum resistance has not been elucidated. MATERIALS AND METHODS Claudin-4 expression in ovarian cancer cells was inhibited and the changes in cisplatin sensitivity were examined. Fluorescence-labeled cisplatin was used to examine whether inhibition of claudin-4 changed the cellular accumulation of cisplatin. Claudin-4 expression in ovarian cancer tissue resected from the patients surgically was evaluated immunohistochemically. RESULTS Suppression of claudin-4 resulted in a significant increase of cisplatin sensitivity and cellular accumulation of fluorescence-labeled cisplatin. Claudin-4 expression was significantly greater in ovarian cancer tissue from chemoresistant patients compared to chemosensitive patients. The overall survival was significantly shorter for claudin-4-positive than claudin-4-negative cases. CONCLUSION These data suggest that claudin-4 contributes to platinum resistance in ovarian cancer and may be a potential target in the treatment of platinum-resistant tumors.
Development and Application of a Reduced Order Model for the Control of Self-Sustained Instabilities in Cavity Flows

Flow around a cavity is characterized by a self-sustained mechanism in which the shear layer impinges on the downstream edge of the cavity resulting in a feedback mechanism. Direct numerical simulations of the flow at low Reynolds number has been carried out to get pressure and velocity fluctuations, for the case of un-actuated and multi frequency actuation. A reduced order model for the isentropic compressible equations based on themethod of proper orthogonal decomposition has been constructed. The model has been extended to include the effect of control. The reduced order dynamical system shows a divergence in time integration. A method of calibration based on theminimization of a linear functional of error, to the sensitivity of the modes, is proposed. The calibrated low order model is used to design a feedback control of cavity flows based on an observer design. For the experimental implementation of the controller, a state estimate based on the observed pressure measurements is obtained through a linear stochastic estimation. Finally the obtained control is introduced into the Direct Numerical Simulation to obtain a decrease in spectra of the cavity acoustic mode.
Crystal structures of Melanocarpus albomyces cellobiohydrolase Cel7B in complex with cello‐oligomers show high flexibility in the substrate binding

Cellobiohydrolase from Melanocarpus albomyces (Cel7B) is a thermostable, single‐module, cellulose‐degrading enzyme. It has relatively low catalytic activity under normal temperatures, which allows structural studies of the binding of unmodified substrates to the native enzyme. In this study, we have determined the crystal structure of native Ma Cel7B free and in complex with three different cello‐oligomers: cellobiose (Glc2), cellotriose (Glc3), and cellotetraose (Glc4), at high resolution (1.6–2.1 Å). In each case, four molecules were found in the asymmetric unit, which provided 12 different complex structures. The overall fold of the enzyme is characteristic of a glycoside hydrolase family 7 cellobiohydrolase, where the loops extending from the core β‐sandwich structure form a long tunnel composed of multiple subsites for the binding of the glycosyl units of a cellulose chain. The catalytic residues at the reducing end of the tunnel are conserved, and the mechanism is expected to be retaining similarly to the other family 7 members. The oligosaccharides in different complex structures occupied different subsite sets, which partly overlapped and ranged from −5 to +2. In four cellotriose and one cellotetraose complex structures, the cello‐oligosaccharide also spanned over the cleavage site (−1/+1). There were surprisingly large variations in the amino acid side chain conformations and in the positions of glycosyl units in the different cello‐oligomer complexes, particularly at subsites near the catalytic site. However, in each complex structure, all glycosyl residues were in the chair (4C1) conformation. Implications in relation to the complex structures with respect to the reaction mechanism are discussed.