Miracle-dz/UniFAR-FTUs huggingface dataset:
Telepresence based on remote real time control of a robot with brain waves

The term brain computer interface (BCI) is used to denote a direct communication pathway between the brain and an external device. In this poster we propose a BCI based on Steady State Visual Evoked Potentials (SSVEP). This BCI system attains the maximum theoretical transfer rates and an empirical transfer rate that surpass largely all the systems based on movement imagination. As additional features, the system false positive rate is negligible and with a minimal attention of the subject. This means that the subject can follow a conversation or divide visual attention without compromising the control of the external device. Expected to work for several classes, current version allow sending 4 different commands. Using this system we perform a telepresence experiment where one subject at our lab explored another lab several miles away by controlling in real time a robot through Internet.
I(kappa)B(gamma) inhibits DNA binding of NF-kappaB p50 homodimers by interacting with residues that contact DNA

NF-(kappa)B is an inducible transcription factor that activates many cellular genes involved in stress and immune response and whose DNA binding activity and cellular distribution are regulated by I(kappa)B inhibitor proteins. The interaction between NF-(kappa)B p50 and DNA was investigated by protein footprinting using chemical modification and partial proteolysis. Both methods confirmed lysine-DNA contacts already found in the crystal structure (K-147, K-149, K-244, K-275, and K-278) but also revealed an additional contact in the lysine cluster K-77-K-78-K-80 which was made on an extended DNA. Molecular modelling of such a DNA-protein complex revealed that lysine 80 is ideally placed to make phosphate backbone contacts in the extended DNA. Thus, it seems likely that the entire AB loop, containing lysines 77, 78, and 80, forms a C-shaped clamp that closes around the DNA recognition site. The same protein footprinting approaches were used to probe the interaction of p50 with the ankyrin repeat containing proteins I(kappa)B(gamma) and I(kappa)B(alpha). Lysine residues in p50 that were protected from modification by DNA were also protected from modification by I(kappa)B(gamma) but not I(kappa)B(alpha). Similarly, proteolytic cleavage at p50 residues which contact DNA was inhibited by bound I(kappa)B(gamma) but was enhanced by the presence of I(kappa)B(alpha). Thus, I(kappa)B(gamma) inhibits the DNA binding activity of p50 by direct interactions with residues contacting DNA, whereas the same residues remain exposed in the presence of I(kappa)B(alpha), which binds to p50 but does not block DNA binding.
Analysis of Sequence Diversity at the Highly Polymorphic Cpgp40/15 Locus among Cryptosporidium Isolates from Human Immunodeficiency Virus-Infected Children in South Africa

ABSTRACT Cryptosporidium sp. is a significant cause of diarrheal disease, particularly in human immunodeficiency virus (HIV)-infected patients in developing countries. We recently cloned and sequenced several alleles of the highly polymorphic single-copy Cryptosporidium parvum gene Cpgp40/15. This gene encodes a precursor protein that is proteolytically cleaved to yield mature cell surface glycoproteins gp40 and gp15, which are implicated in zoite attachment to and invasion of enterocytes. The most-striking feature of the Cpgp40/15 alleles and proteins is their unprecedented degree of sequence polymorphism, which is far greater than that observed for any other gene or protein studied in C. parvum to date. In this study we analyzed nucleic acid and amino acid sequence polymorphism at the Cpgp40/15 locus of 20 C. parvum isolates from HIV-infected South African children. Fifteen isolates exhibited one of four previously identified genotype I alleles at the Cpgp40/15 locus (Ia, Ib, Ic, and Id), while five displayed a novel set of polymorphisms that defined a new Cpgp40/15 genotype I allele, designated genotype Ie. Surprisingly, only 15 of these isolates exhibited concordant type I alleles at the thrombospondin-related adhesive protein of Cryptosporidium and Cryptosporidium oocyst wall protein loci, while five isolates (all of which displayed Cpgp40/15 genotype Ic alleles) displayed genotype II alleles at these loci. Furthermore, the last five isolates also manifested chimeric genotype Ic/Ib or Ic/II alleles at the Cpgp40/15 locus, raising the possibility of sexual recombination within and between prototypal parasite genotypes. Lastly, children infected with isolates having genotype Ic alleles were significantly older than those infected with isolates displaying other genotype I alleles.
Learning to select examples for program synthesis

Program synthesis is a class of regression problems where one seeks a solution, in the form of a source-code program, that maps the inputs to their corresponding outputs exactly. Due to its precise and combinatorial nature, it is commonly formulated as a constraint satisfaction problem, where input-output examples are expressed constraints, and solved with a constraint solver. A key challenge of this formulation is that of scalability: While constraint solvers work well with few well-chosen examples, constraining the entire set of example constitutes a significant overhead in both time and memory. In this paper we address this challenge by constructing a representative subset of examples that is both small and is able to constrain the solver sufficiently. We build the subset one example at a time, using a trained discriminator to predict the probability of unchosen input-output examples conditioned on the chosen input-output examples, adding the least probable example to the subset. Experiment on a diagram drawing domain shows our approach produces subset of examples that are small and representative for the constraint solver.
Towards Large Eddy Simulation in Internal-Combustion Engines: simulation of a compressed tumble flow.

The development of the Large Eddy Simulation (LES) 3D CFD code AVBP to yield a CFD tool able to predict cyclic variability in Internal Combustion (IC) engines is reported. In a first step the implementation of an Arbitrary Lagrangian Eulerian (ALE) method into AVBP is described, allowing to move solid boundaries. Then the principles and implementation of the Conditioned Temporal Interpolation (CTI) mesh management technique is described, and some specific adaptations for LES simulations are discussed. Finally a first validation of the so obtained LES IC engine code is presented by comparing predictions with findings on the square piston experiment.
Application of Hilbert-Huang Transform to Heart Rate Variability Analysis

The paper introduces a new methodology of heart rate variability(HRV) in time-frequency analysis, which is based on Hilbert-Huang transform. We adopt the empirical mode decompostition(EMD) technique to decompose the R-R interval series into several mono-component signals which become analytic signal by means of Hilbert transform. So a novel algorithm based on Hilbert-Huang transform is proposed to extract the features of HRV signals. The numerical simulation results presented herein show the method can be used to identify the low-frequency and high-frequency bands of HRV more sharply and effectively through Hilbert spectrum than using the Fourier spectrum.
Functional Differentiation of BMP7 Genes in Zebrafish: bmp7a for Dorsal-Ventral Pattern and bmp7b for Melanin Synthesis and Eye Development

Bone morphogenetic protein 7 (BMP7) belongs to the transforming growth factor β (TGF-β) family, which not only induces cartilage and bone formation, but also regulates eye development and melanoma tumorigenesis in mammals. In teleosts, BMP7 differentiates into two subtypes, bmp7a and bmp7b, which have clearly differentiated structures. To fully understand the functional differentiation of bmp7a and bmp7b in fish species, we successfully constructed bmp7a and bmp7b gene deletion mutants in zebrafish using CRISPR/Cas9-mediated gene editing technology. Our results showed that bmp7a mutation caused abnormal development of the embryo’s dorsal-ventral pattern that led to death; bmp7b mutation induced growth inhibition and increased melanin production in the skin and eye of mutants. Histological analysis revealed that melanin in the retina of the eyes in bmp7b mutants increased, and behavioral observation showed that the vision and sensitivity to food of the mutants were reduced. Transcriptome analysis of the skin and eye tissues showed that the expression changes of wnt7ba and gna14 in bmp7b mutants might promote the increase of melanin. Additionally, the eye transcriptome analysis indicated that changes in the structure of the eyes in bmp7b mutants led to defects in phototransduction, and seven DEGs (rgs9a, rgs9b, rcvrn2, guca1d, grk1b, opn1mw4, and gc2) were identified as key candidate genes that affected the photonic response of the eyes. The study revealed the functional differentiation of bmp7a and bmp7b in teleosts and the first report about the inhibitory effect of bmp7b on melanogenesis may provide useful information for the future research on human melanoma-related diseases.
Identification of a Functional Epitope in Plasminogen Activator Inhibitor-1, not Localized in the Reactive Center Loop

Summary Plasminogen activator inhibitor-1 (PAI-1) is unique among the ser-pins because of its conformational flexibility. Previously, we have characterized monoclonal antibodies that neutralize PAI-1 activity by switching the active, inhibitory pathway into the non-inhibitory substrate pathway (10). Here, we report the identification of the epitopes for two of these antibodies, i.e. MA-55F4C12 and MA-33H1 and apply this information to explain their functional effects. Using a random PAI-1 epitope library (11), phages displaying specific PAI-1 fragments were isolated after selective screening for binding onto the respective antibodies. Competition experiments with PAI-1 demonstrated that selected phages react with the antigen-binding site of the antibodies. Comparison of the sequences of the different overlapping inserts, encoding the PAI-1 epitope, with the PAI-1 cDNA sequence revealed that both epitopes, even though not identical, are located between amino acids Glu128 and Ala156 in the PAI-1 molecule. Analysis within the three-dimensional structure of PAI-1 showed that these residues completely cover helix F, which is localized close to the major β-sheet A. This localization provides a rational basis for explaining the mechanism of PAI-1 inactivation by both antibodies: upon binding of these antibodies to PAI-1, a stabilizing effect is induced on helix F resulting in a decrease of the kinetics of insertion of the reactive site loop into β-sheet A during interaction with the target proteinase. This forms the molecular basis for the observed functional effects of these antibodies and fully explains why PAI-1, in the presence of these antibodies, has lost its inhibitory properties but remains succeptible to cleavage by its target proteinases. The identification and localization of these functionally important epitopes opens new perspectives for the development of pharmacological agents with PAI-1 modulating properties.
Enhanced three-dimensional visualization of EEG signals

The analysis of EEG signals is a topic of significant interest to multiple scientific and medical branches. Since these signals lack any intrinsic visual data, their graphical representation presents multiple challenges, particularly for data spanning over frequency bands and extended durations. This paper presents several techniques for the representation of such signals, using a 3D model of a human head and multiple information visualization techniques, such as color scales, spots and glyphs. The proposed representation technique conveys an intuitive, efficient means to visually inspect EEG signals, while allowing the visualization of multiple relevant parameters without visually overloading the resulting images. Comprehensive descriptions of the aforementioned techniques are provided, as well as images containing the resulting representations. This approach intends to provide easy visual access to EEG data, for use in Brain-Computer Interface, medical or educational applications.
Prise en compte de critères acoustiques pour la synthèse de la parole

Cette these s'inscrit dans le domaine de la synthese vocale a partir du texte et traite plus articulierement de la synthese par corpus (SPC). Cette approche basee sur la concatenation de segments acoustiques contenus dans de grandes bases de donnees s'est peu a peu instauree comme un standard. En effet, moyennant la selection d'unites adaptees au contexte de synthese, elle permet d'aboutir a un signal de parole dont le naturel peut etre assez bien preserve. La qualite de la synthese obtenue par la methode par concatenation est etroitement liee d'une part au corpus de synthese et d'autre part a l'algorithme de selection des unites. Malgre le saut notable de qualite qu'a permis d'atteindre cette technologie, la SPC n'est pas capable de garantir une parole dont la qualite soit a peu pres constante sur l'ensemble d'un enonce. Ceci est en grande partie du au manque de controle acoustique des systemes de SPC actuels. L'objectif de cette these est donc d'introduire des mecanismes permettant un meilleur controle acoustique lors de la synthese. La methode proposee consiste a effectuer une selection sur la base d'une cible purement acoustique. Cette cible est deduite de modeles acoustiques - plus precisement des modeles de senones - estimes lors d'une phase d'apprentissage. Dans un premier temps, nous proposons un algorithme de selection base uniquement sur cette cible acoustique. Puis la methode de selection est modifiee de maniere a mieux controler l'information de frequence fondamentale. Le module de selection propose est egalement combine a un module de pre-selection des unites, ce qui conduit a une diminution sensible de la complexite algorithmique sans degradation perceptible des resultats. Des tests d'ecoutes formels revelent que la methode proposee permet de reduire significativement les discontinuites acoustiques lors de la concatenation. La methode proposee est egalement appliquee a la reduction de corpus acoustiques et conduit a une reduction de l'ordre de 60% de la base acoustique sans degradation de la qualite de la parole produite.
Body Cell Mass Measured by Total Body Potassium in Normal-Weight and Obese Men and Women

Objective: Total body potassium (TBK) concentration is linearly correlated with the size of the body cell mass (BCM). The aim of this study was to compare BCM in normal-weight and obese individuals. Methods: 271 individuals (207 males, 64 females), 20 to 67 years of age, participated in this study. Subjects were separated by body mass index (BMI): BMI < 25 kg/m2 (BMI-L) and BMI > 25 kg/m2 (BMI-H). 40K was assessed using a whole-body counter and BCM was calculated. Results: BCM and TBK were significantly greater in men, with a trend to be greater in women in BMI-H compared to men in BMI-L. TBK/body weight was significantly lower, while TBK/height was significantly greater for men and women in BMI-H compared to men and women in BMI-L. Fat-free mass (FFM) was significantly greater for men in BMI-H, with no significant differences in FFM between the two groups of women. Conclusions: The healthy obese subjects in the present study had a greater BCM than the non-obese subjects. These results indicate that it is important to assess BCM in obese individuals because it could influence the type of weight loss regimen that will be used in order to preserve BCM.
Description of Adults and Nymph, and Redescription of the Larva, of Ornithodoros marinkellei (Acari: Argasidae), with Data on Its Phylogenetic Position

Abstract The argasid tick Ornithodoros marinkellei Kohls, Clifford, and Jones, 1969 was described 4 decades ago based on larval specimens collected from bats (Pteronotus spp.) in Colombia and Panama. Thereafter, larval O. marinkellei parasitizing bats were reported from Venezuela, Guyana, and Brazil. Herein, we describe the adults and nymph, and redescribe the larva of O. marinkellei based on specimens recently collected in the western Brazilian Amazon region. In contrast to all other known adult argasids, the idiosoma of both males and females of O. marinkellei is covered with sclerotized plaques. The idiosoma of the nymph of O. marinkellei is entirely micromamillated, and differs from the adults by the absence of plaques. The larva of O. marinkellei is morphologically similar to the larvae of the 2 other species belonging to the subgenus Subparmatus, i.e., Ornithodoros viguerasi Cooley and Kohls, 1941 and Ornithodoros mormoops Kohls, Clifford, and Jones, 1969. Because of the long and narrow dorsal plate, the larva of O. marinkellei is readily distinguished from O. viguerasi and O. mormoops. Comparison of our larvae from Brazil with O. marinkellei paratype specimens from Colombia confirmed their taxonomic identification. However, a few morphological differences, particularly in the size of the gnathosoma, were observed. Further studies are necessary to clarify whether O. marinkellei is a complex of different species, or a single species represented by morphologically polymorphic, and geographically distinct populations. Partial mitochondrial 16S rDNA gene sequences were generated for O. marinkellei specimens from Brazil, and compared with available homologous sequences in GenBank. Phylogenetic analyses revealed O. marinkellei to be distinct from the remaining argasid species available in GenBank, including other bat-associated tick species that are found in sympatry with O. marinkellei in the Neotropical region.
Role of Tom5 in Maintaining the Structural Stability of the TOM Complex of Mitochondria*

Transport of nuclear encoded proteins into mitochondria is mediated by multisubunit translocation machineries in the outer and inner membranes of mitochondria. The TOM complex contains receptor and pore components that facilitate the recognition of preproteins and their transfer through the outer membrane. In addition, the complex contains a set of small proteins. Tom7 and Tom6 have been found in Neurospora and yeast, Tom5 has been found so far only in the latter organism. In the present study, we identified Neurospora Tom5 and analyzed its function in comparison to yeast Tom5, which has been proposed to play a role as a receptor-like component. Neurospora Tom5 crosses the outer membrane with its carboxyl terminus facing the intermembrane space like the other small Tom components. The temperature-sensitive growth phenotype of the yeast TOM5 deletion was rescued by overexpression of Neurospora Tom5. On the other hand, Neurospora cells deficient in tom5 did not exhibit any defect in growth. The structural stability of TOM complexes from cells devoid of Tom5 was significantly altered in yeast but not in Neurospora. The efficiency of protein import in Neurospora mitochondria was not affected by deletion of tom5, whereas in yeast it was reduced as compared with wild type. We conclude that the main role of Tom5, rather than being a receptor, is maintaining the structural integrity of the TOM complex.
Disease Management : Helping Patients ( Who Don ’ t ) Help Themselves ∗

Chronically ill patients currently consume a significant share of the U.S. health system’s resources and are a rapidly growing segment of the overall population. Disease Management (DM) programs identify high-risk patients among the chronically ill, encourage them to take better care of themselves, and help coordinate the care they receive from various providers. This paper examines the impact of a diabetes Disease Management program. We find that it led to increased compliance with clinical practice guidelines, improvements in patient health, and significant reductions in the total cost of care. The financial benefits are greater for patients lacking “self control” prior to enrollment, as indicated by their failure to comply with generally accepted clinical practice guidelines. These results are especially important for the Medicare program, which has the majority of the chronically ill as beneficiaries.
ON THE SUPPOSED DILEMMA OF CONCILIATIONISM

ABSTRACT My aim in this paper is to propose a way to resolve a supposed dilemma currently troubling the debate about rational belief formation in cases of peer disagreement. In section 1, I will introduce the general debate in question as well as the kind of view figuring in the supposed dilemma. In section 2, I will describe how the supposed dilemma arises. In section 3, I will consider the replies that have hitherto been offered and explain in how far these replies should be regarded as unsatisfying. Finally, in sections 4 and 5, I will propose and defend a new reply to the supposed dilemma. This reply consists in rejecting the intuitively appealing view that one should be conciliatory in the relevant kind of case, and in endorsing a more careful position, which respects the intuitions behind conciliationism and which, in contrast to the latter, does not give rise to the kind of dilemma in question.
Medicare cost containment strategy targets several oncology drugs.

At the same time that new targeted therapies are making their debuts in cancer clinics—at a cost set by their pharmaceutical manufacturers of often thousands of dollars a dose, and tens of thousands per treatment course—the federal government announced that it plans to slash Medicare reimbursement prices for some common chemotherapy drugs by as much as 81% below current levels. " It is at least as bad as we thought it could be, " said Deborah Kamin, senior director for policy and clinical affairs at the American Society of Clinical Oncology (ASCO). " The Congressional Budget Office had anticipated [cuts in reimbursement amounts] of $300 million, but this is $500 million. These are big, big cuts. " With the sampling of proposed reimbursement amounts in hand, private practice oncologists are now trying to " guestimate " how much they may lose starting Jan. 1, 2005, in reimbursements on cancer drugs they give to their Medicare patients. Although fees for chemotherapy services paid by Medi-care could balance any loss, the Centers for Medicare & Medicaid Services (CMS) warned that it will cut its 2004 drug administration reimbursements by 29%, said Kamin, although those figures will not be announced until much later this year. " Given all of this, the ability of community oncologists to even deliver services may be compromised, " she said. The proposed cuts, announced July 27 and open for comment until Septem-ber 24, are the first drug-specific numbers that CMS has attached to its 2003 Medicare Modernization Act (MMA), which provides a prescription drug benefit for senior citizens. To make such an entitlement (now estimated at $540 billion) affordable, the bill called for cutbacks in Medicare programs that Congress deemed to be bloated—one of which is the system that pays for chemotherapy drugs given by infusion in a doctor's office. Vast markups in the reimbursement of chemotherapy drugs had long been used by private oncologists to pay for services associated with delivering the therapy, which CMS either did not pay for or underfunded. But this imbalance caught the attention of the General Accounting Office in 2001 and subsequently provoked Congress to slash drug reimbursement fees last November when the MMA was narrowly approved. The bill called for an estimated $11.5 billion in drug reimbursements to be cut over the next decade, but practice expenses were also to be severely cut. Medicare had paid 95% of the average wholesale …