Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward a Hybrid BCI: Self-Paced Operation of a P300-based Speller by Merging a Motor Imagery-Based “Brain Switch” into a P300 Spelling Approach

ABSTRACT This study presents the self-paced operation of a brain–computer interface (BCI) speller, which can be voluntarily turned on/off by merging a motor imagery (MI)-based brain switch into a P300-based BCI speller. From an off state (idle state), the users can generate a “control signal” by consciously changing the cognitive state differential from the idle state to turn on a P300-based spelling system when he or she wants to spell words. With the system turned on, the user can spell words, and then, the spelling system can be voluntarily turned off and switched to the initial state using a command. In this paradigm, the participants tried to perform the two different cognitive tasks sequentially, rather than simultaneously, and multiple EEG components were processed sequentially. The practicability and effectiveness of the proposed approach were validated by eleven participants, and all of them achieved a satisfactory performance. For the P300 speller, they achieved an average PITR of 42.61 bits/min. The preliminary results indicated that the proposed hybrid BCI system with different mental strategies operating sequentially is feasible and has potential applications for practical self-paced control.
Setting Practical Conservation Priorities for Birds in the Western Andes of Colombia

We aspired to set conservation priorities in ways that lead to direct conservation actions. Very large‐scale strategic mapping leads to familiar conservation priorities exemplified by biodiversity hotspots. In contrast, tactical conservation actions unfold on much smaller geographical extents and they need to reflect the habitat loss and fragmentation that have sharply restricted where species now live. Our aspirations for direct, practical actions were demanding. First, we identified the global, strategic conservation priorities and then downscaled to practical local actions within the selected priorities. In doing this, we recognized the limitations of incomplete information. We started such a process in Colombia and used the results presented here to implement reforestation of degraded land to prevent the isolation of a large area of cloud forest. We used existing range maps of 171 bird species to identify priority conservation areas that would conserve the greatest number of species at risk in Colombia. By at risk species, we mean those that are endemic and have small ranges. The Western Andes had the highest concentrations of such species—100 in total—but the lowest densities of national parks. We then adjusted the priorities for this region by refining these species ranges by selecting only areas of suitable elevation and remaining habitat. The estimated ranges of these species shrank by 18–100% after accounting for habitat and suitable elevation. Setting conservation priorities on the basis of currently available range maps excluded priority areas in the Western Andes and, by extension, likely elsewhere and for other taxa. By incorporating detailed maps of remaining natural habitats, we made practical recommendations for conservation actions. One recommendation was to restore forest connections to a patch of cloud forest about to become isolated from the main Andes.
Decrease in myostatin by ladder‐climbing training is associated with insulin resistance in diet‐induced obese rats

Background Suppression of myostatin (MSTN) has been associated with skeletal muscle atrophy and insulin resistance (IR). However, few studies link MSTN suppression by ladder‐climbing training (LCT) and IR. Therefore, we intended to identify the correlation with IR between LCT and to analyze the signaling pathways through which MSTN suppression by LCT regulates IR. Methods The rats were randomly assigned to two types of diet: normal pellet diet (NPD, n=8) and high‐fat diet (HFD, n=16). After 8 weeks, the HFD rats were randomly re‐assigned to two groups (n=8 for each group): HFD sedentary (HFD‐S) and high‐fat diet ladder‐climbing training (HFD‐LCT). HFD‐LCT rats were assigned to LCT for 8 weeks. Western blotting, immunohistochemistry and enzyme assays were used to measure expression levels and activities of MSTN, GLUT4, PI3K, Akt and Akt‐activated targets (mTOR, FoxO1 and GSK‐3&bgr;). Results The LCT significantly improved IR and whole‐body insulin sensitivity in HDF‐fed rats. MSTN protein levels decreased in matching serum (42%, P=0.007) and muscle samples (25%, P=0.035) and its receptor mRNA expression also decreased (16%, P=0.041) from obese rats after LCT. But the mRNA expression of insulin receptor had no obvious changes in LCT group compared with NPD and HFD‐S groups (P=0.074). The ladder‐climbing training significantly enhanced PI3K activity (1.7‐fold, P=0.024) and Akt phosphorylation (83.3%, P=0.022) in HFD‐fed rats, significantly increased GLUT4 protein expression (84.5%, P=0.036), enhanced phosphorylation of mTOR (4.8‐fold, P <0.001) and inhibited phosphorylation of FoxO1 (57.7%, P=0.020), but did not affect the phosphorylation of GSK‐3&bgr;. Conclusions The LCT significantly reduced IR in diet‐induced obese rats. MSTN may play an important role in regulating IR and fat accumulation by LCT via PI3K/Akt/mTOR and PI3K/Akt/FoxO1 signaling pathway in HFD‐fed rats.
Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast

MOTIVATION The intrinsic DNA sequence is an important determinant of nucleosome positioning. Some DNA sequence patterns can facilitate nucleosome formation, while others can inhibit nucleosome formation. Nucleosome positioning influences the overall rate of sequence evolution. However, its impacts on specific patterns of sequence evolution are still poorly understood. RESULTS Here, we examined whether nucleosomal DNA and nucleosome-depleted DNA show distinct polymorphism patterns to maintain adequate nucleosome architecture on a genome scale in yeast. We found that sequence polymorphisms in nucleosomal DNA tend to facilitate nucleosome formation, whereas polymorphisms in nucleosome-depleted DNA tend to inhibit nucleosome formation, which is especially evident at nucleosome-disfavored sequences in nucleosome-free regions at both ends of genes. Sequence polymorphisms facilitating nucleosome positioning correspond to stable nucleosome positioning. These results reveal that sequence polymorphisms are under selective constraints to maintain nucleosome positioning. CONTACT zhimdai@gmail.com; issdxh@mail.sysu. edu.cn
XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density.

Xfit is a model-building and map viewing program in XtalView that is used by the structural biology community including researchers in the fields of crystallography, molecular modeling, and electron microscopy. Among its distinguishing features are built-in fast Fourier transforms that allow users flexibility in map calculations including the creation of OMIT maps and the updating of structure factors to reflect model changes from within the program. Written in C and using the freely available XView toolkit, it is highly portable to almost any X-windows based workstation including Intel-based LINUX systems. Its user interface is designed to aid in facile model-building and contains a semiautomated fitting system that allows the user to interactively and rapidly build chain de novo into an electron density map. The program is highly optimized to allow such features as interactive contour levels and map calculations to be completed within a few seconds. Features in the latest version including phase-combination, solvent-flattening, automated water addition, and small-probe dot contact surfaces, as well as basic design features, are discussed.
Downward-looking 3D-SAR with dual-transmit and multiple-receive linear array antennas based on time and waveform diversity

The dual-transmit and multiple-receive (DTMR) configuration of linear array antennas (LAA) is firstly introduced in downward-looking 3D-SAR imaging in this paper. The geometrical model and the signal model based on the principle of time diversity and waveform diversity are analyzed. The three-dimensional imaging processing algorithm for downward-looking 3D-SAR with DTMR-LAA is given via a stepwise mathematical derivation and the analytic expression of 3D PSF after 3D imaging processing is presented. The simulation results confirm the feasibility of the downward-looking 3D-SAR with DTMR-LAA imaging concept.
Numerical simulations of bridging phenomena in contaminated transformer oil

Experiments were carried out on transformer oil contaminated by cellulose fibre. After the high voltage was applied to the electrodes, the pressboard particles accumulated in the highest electric field region and eventually formed a bridge. We have developed a mathematical model to simulate the bridging dynamics. The dielectrophoretic and drag forces are considered for simulation of the particles motion and accumulation. The predicted bridge formation rate and the conduction current between the electrodes showed similar trend to the experimental results. The model is a successful means of predicting bridge formation phenomenon compared with the experimental data.
Econometrie, theorie des tests et philosophie des sciences

Dans ce texte, nous revoyons certains developpements recents de l’econometrie qui peuvent etre interessants pour des chercheurs dans des domaines autres que l’economie et nous soulignons l’eclairage particulier que l’econometrie peut jeter sur certains themes generaux de methodologie et de philosophie des sciences, tels la falsifiabilite comme critere du caractere scientifique d’une theorie (Popper), la sous-determination des theories par les donnees (Quine) et l’instrumentalisme. En particulier, nous soulignons le contraste entre deux styles de modelisation - l’approche parcimonieuse et l’approche statistico-descriptive - et nous discutons les liens entre la theorie des tests statistiques et la philosophie des sciences.
A simple, flexible, and effective covariate‐adaptive treatment allocation procedure

We present a method for allocating treatment when subjects arrive in sequence. Based on the theory of propensity scores more commonly used in observational studies, the method balances both discrete and continuous covariates without assuming a model for the outcome. Although we allow for a number of possible specifications, we explore some specific instances in depth. The proposed method is compared with previously suggested sequential randomization and allocation procedures with relationships to some well‐known methods highlighted. Through simulations, the deterministic version is shown to achieve both covariate balance and near optimum efficiency with minimal assumptions. We also investigate the properties of selected randomized versions with respect to both optimality and selection bias. We conclude with an application to a pilot study on weight loss. The proposed method is shown to be robust to the number of covariates balanced and the marginal and joint distributions of those covariates. Copyright © 2013 John Wiley & Sons, Ltd.
Ex Vivo Examination of the Biocompatibility of Biodegradable Magnesium via Microdialysis in the Isolated Perfused Bovine Udder Model

Purpose Being biodegradable, magnesium is considered a promising future implant material but very little is known about the biocompatibility for the tissues in direct contact with it. In this study, the degradation of pure magnesium implants in the skin of an isolated bovine udder was examined over a period of five hours. Methods Microdialysis technique was used in order to investigate the reactions at the interface of implant and tissue. Pure titanium implants served as control. Degradation behavior and biocompatibility were evaluated via extracellular magnesium ion concentration and PGE2 and TNF alpha served as indicators of inflammation. Results Concentrations of 5.5 mmol/l Mg2+ were detected at the beginning, which decreased to a plateau of about 3.5 mmol/l after approximately two and a half hours. PGE2 and TNF alpha concentrations indicated no major inflammatory tissue response to the degradation. Conclusions These results give an idea of the ion burden at the implantation site of degrading magnesium and suggest good biocompatibility even at the tissue-implant interface.
Effect of mild hypothermia on focal cerebral ischemia. Review of experimental studies

Abstract The purposes of this review are to clarify the effect of hypothermia therapy on focal cerebral ischemia in rats, and to consider the relevancy of its application to human focal cerebral ischemia. Since 1990, 26 reports confirming the brain-protecting effect of hypothermia in rat focal cerebral ischemia models have been published. Seventy-four experimental groups in these 26 reports were classified as having transient middle cerebral arterial occlusion (MCAO) with mild hypothermia (group A; 43 groups), permanent MCAO with mild hypothermia (group B; 14 groups), permanent MCAO with deep hypothermia (group C; 8 groups) and transient or permanent MCAO with mild hyperthermia (group D; 9 groups). The results were evaluated as the % infarct volume change caused by hypothermia or hyperthermia compared with the infarct volume in normothermic animals. The effectiveness was confirmed in 36 (83%) of the 43 groups in group A, 10 (71%) of the 14 in group B, and six (75%) of the eight in group C. The infarct volume of eight of the nine groups in group D was markedly aggravated. The percent infarct volume change was 55.3% ± 27.1% in group A, 57.6% ± 24.7% in group B, 60.8% ± 45.5% in group C, and 189.7% ± 89.4% in group D. For effective reduction of the infarct volume, hypothermia should be started during ischemia or within 1 h, at latest, after the beginning of reperfusion in the rat transient MCAO model. However, it is not clear whether this neuroprotective effect of hypothermia can also be observed in the chronic stage, such as several months later. Keeping the body temperature normothermic in order to avoid mild hyperthermia seems to be rather important for not aggravating cerebral infarction. Clinical randomized studies on the efficacy of mild hypothermia for focal cerebral ischemia and sophisticated mild hypothermia therapy techniques are mandatory.
Exploring the Relationship Between Adverse Childhood Experiences and Hope

ABSTRACT To explore the relationship between adverse childhood experiences and hope, a convenience sample of caregivers bringing in children for medical investigation of child abuse at a regional child advocacy center were surveyed for adverse childhood experiences and dispositional hope. Hope in this sample had a significant negative correlation to the adverse childhood experiences subscale “abuse” (r = –.19; p < .05). The relationship between hope and the other adverse childhood experiences subscales “neglect” (r = –.14) and “dysfunctional family” (r = –.16) was not statistically significant. An analysis of variance was performed to determine if caregivers who have experienced both sexual and physical abuse (M = 29.67; SD = 15.96) have lower hope scores compared to those caregivers who have experienced neither physical nor sexual abuse (M = 42.64; SD = 18.44). This analysis (F (1, 84) = 5.28; p < 0.05) showed that caregivers who experienced both physical and sexual abuse scored significantly lower on hope compared to their counterparts who experienced no adverse events, with an estimated effect size of moderate strength (d = 0.70). Higher adverse childhood experiences scores are associated with lower hope. This result was especially true for those adult caregivers who reported experiencing both physical and sexual abuse when compared to adults who did not experience either form of child trauma. While the empirical literature continues to demonstrate the negative consequences of adverse childhood experiences across the life span, hope offers a compelling new line of inquiry in child maltreatment research especially for studies targeting prevention or intervention.
A platform for the fast interpretation of movements and localization of users in 3D applications driven by a range camera

Interactivity is one of the key challenges for immersive applications like gaming. Manufacturers have been working towards interfaces that are driven by a device (e.g. a Wiimote) or interfaces that are controlled by a camera with a subsequent computer vision module. Both approaches have unique advantages, but they do not permit to localize users in the scene with an appropriate accuracy. Therefore, we propose to use both a range camera and accurate range sensors to enable the interpretation of movements. This paper describes a platform that uses a range camera to acquire the silhouettes of users, regardless of illumination, and to improve the pose recovery with range information after some image processing steps. In addition, to circumvent the difficult process of calibration required to map range values to physical distances, we complete the system with several range laser sensors. These sensors are located in a horizontal plane, and measure distances up to a few centimeters. We combine all these measurements to obtain a localization map, used to locate users in the scene at a negligible computational cost. Our method fills a gap in 3D applications that require absolute positions.
Changes in apical dendritic structure correlate with sustained ERK1/2 phosphorylation in medial prefrontal cortex of a rat model of dopamine D1 receptor agonist sensitization

Rats lesioned with 6‐hydroxydopamine (6‐OHDA) as neonates exhibit behavioral and neurochemical abnormalities in adulthood that mimic Lesch–Nyhan disease, schizophrenia, and other developmental disorders of frontostriatal circuit dysfunction. In these animals a latent sensitivity to D1 agonists is maximally exposed by repeated administration of dopamine agonists in the postpubertal period (D1 priming). In neonate‐lesioned, adult rats primed with SKF‐38393, we found selective, persistent alterations in the morphology of pyramidal neuron apical dendrites in the prelimbic area of the medial prefrontal cortex (mPFC). In these animals, dendrite bundling patterns and the typically straight trajectories of primary dendritic shafts were disrupted, whereas the diameter of higher‐order oblique branches was increased. Although not present in neonate‐lesioned rats treated with saline, these morphological changes persisted at least 21 days after repeated dosing with SKF‐38393, and were not accompanied by markers of neurodegenerative change. A sustained increase in phospho‐ERK immunoreactivity in wavy dendritic shafts over the same period suggested a relationship between prolonged ERK phosphorylation and dendritic remodeling in D1‐primed rats. In support of this hypothesis, pretreatment with the MEK1/2‐ERK1/2 pathway inhibitors PD98059 or SL327, prior to each priming dose of SKF‐38393, prevented the morphological changes associated with D1 priming. Together, these findings demonstrate that repeated stimulation of D1 receptors in adulthood interacts with the developmental loss of dopamine to profoundly and persistently modify neuronal signaling and dendrite morphology in the mature prefrontal cortex. Furthermore, sustained elevation of ERK activity in mPFC pyramidal neurons may play a role in guiding these morphological changes in vivo. J. Comp. Neurol. 511:271–285, 2008. © 2008 Wiley‐Liss, Inc.
Development and Evaluation of a Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Enterovirus 71

ABSTRACT Human enterovirus 71 (EV71) is the major etiological agent of hand, foot, and mouth disease (HFMD), which is a common infectious disease in young children and infants. EV71 can cause various clinical manifestations and has been associated with severe neurological complications; it has resulted in fatalities during recent outbreaks in Asian-Pacific regions since 1997. The early and rapid detection is critical for prevention and control of EV71 infection, since no vaccine or antiviral drugs are currently available. In this study, a simple and sensitive reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed for rapid detection of EV71. The detection limit of the RT-LAMP assay was approximately 0.01 PFU per reaction mixture, and no cross-reactive amplification with other enteroviruses was observed. The assay was evaluated further with 40 clinical specimens and exhibited 92.9% sensitivity and 100% specificity. This RT-LAMP assay may become a useful alternative in clinical diagnosis of EV71, especially in resource-limited hospitals or rural clinics of China and other countries in the Asian-Pacific region.
La méthode des équations intégrales pour des analyses de sensitivité

Dans cette these, nous menons a l'aide de la methode des equations integrales des analyses de sensitivite de solutions ou de spectres de l'equation de conductivite par rapport aux variations geometriques ou de parametres de l'equation. En particulier, nous considerons le probleme de conductivite dans des milieux a forts contrastes, le probleme de perturbation du bord d'une inclusion de conductivite, le probleme de valeurs propres du Laplacien dans des domaines perturbes et le probleme d'ouverture de gap dans le spectre des cristaux photoniques.
Computational Insight into Small Molecule Inhibition of Cyclophilins

Cyclophilins (Cyp) are a family of cellular enzymes possessing peptidyl-prolyl isomerase activity, which catalyze the cis-trans interconversion of proline-containing peptide bonds. The two most abundant family members, CypA and CypB, have been identified as valid drug targets for a wide range of diseases, including HCV, HIV, and multiple cancers. However, the development of small molecule inhibitors that possess nM potency and high specificity for a particular Cyp is difficult given the complete conservation of all active site residues between the enzymes. Monte Carlo statistical sampling coupled to free energy perturbation theory (MC/FEP) calculations have been carried out to elucidate the origin of the experimentally observed nM inhibition of CypA by acylurea-based derivatives and the >200-fold in vitro selectivity between CypA and CypB from aryl 1-indanylketone-based μM inhibitors. The computed free-energies of binding were in close accord with those derived from experiments. Binding affinity values for the inhibitors were determined to be dependent upon the stabilization strength of the nonbonded interactions provided toward two catalytic residues: Arg55 and Asn102 in CypA and the analogous Arg63 and Asn110 residues in CypB. Fine-tuning of the hydrophobic interactions allowed for enhanced potency among derivatives. The aryl 1-indanylketones are predicted to differentiate between the cyclophilins by using distinct binding motifs that exploit subtle differences in the active site arrangements. Ideas for the development of new selective compounds with the potential for advancement to low-nanomolar inhibition are presented.
Predictability: definition, ananlysis and optimization

Predictability is the quantified from of accuracy. We propose a predictability driven design methodology. The novelty lies in defining and using the idea of predictability. In order to illustrate the basic concepts we focus on the low power binding problem. The binding problem for low power was solved in [3], [5], but in the presence of in-accuracies, their claims of optimality are imprecise. Our experiments show that these inaccuracies could be as high as 33%. Our methodology could improve this unpredictability to as low as 11% with minimal power penalty (7% on average).