Miracle-dz/UniFAR-FTUs huggingface dataset:
ON IMPORTANCE RESAMPLING IN HIDDEN MARKOV MODELS

Given a sequence of observations from a discrete time, finite-state hidden Markov model, we would like to estimate the sampling distribution of a standardized statistic. The bootstrap method is employed to approximate the confidence regions of a multi-dimensional parameter. We proposed an importance resampling formula for efficient simulation in this context. Our approach consists of constructing a locally asymptotically normal (LAN) family of probability distributions around the default resampling rule and then minimizing the asymptotical variance within the LAN family. The solution of this minimization problem characterizes the asymptotically optimal resampling scheme, which is given by an optimal tilting formula. The implementation of the tilting formula is facilitated by solving a Poisson equation. A few numerical examples are given to demonstrate the efficiency of the proposed importance resampling scheme.
Assessment of School Functioning Among Israeli Arab Children with Hearing Loss in the Primary Grades

The study examined school functioning of Israeli Arab children with hearing impairment (HI) who were included in regular education classrooms, in comparison to their classmates with normal hearing (NH). Ninety-three children (60 NH and 33 HI), grades 1–6, participated. Teachers evaluated the children using the Arabic version of the Screening Instrument for Targeting Educational Risks (SIFTER; Anderson, 1989); they also reported children's achievement levels in Arabic and mathematics. Results demonstrated that the HI children's functioning was lower than that of the NH children. Children with unilateral and minimal hearing losses had lower functioning than those with more severe hearing loss. As grade level increased, functioning decreased among HI children. Use of the SIFTER was beneficial in detecting children with difficulties. Regular, ongoing SIFTER use and appropriate follow-up on the results may better enable each child to perform optimally in class.
Gamma Interferon Can Block Herpes Simplex Virus Type 1 Reactivation from Latency, Even in the Presence of Late Gene Expression

ABSTRACT Herpes simplex virus type 1 (HSV-1)-specific CD8+ T cells and the cytokine gamma interferon (IFN-γ) are persistently present in trigeminal ganglia (TG) harboring latent HSV-1. We define “latency” as the retention of functional viral genomes in sensory neurons without the production of infectious virions and “reactivation” as a multistep process leading from latency to virion assembly. CD8+ T cells can block HSV-1 reactivation in ex vivo mouse TG cultures and appear to be the sole source of IFN-γ in these cultures. Here we demonstrate that IFN-γ alone can block HSV-1 reactivation in some latently infected neurons, and we identify points of intervention in the life cycle of the reactivating virus. Cell suspensions of TG that were latently infected with recombinant RE HSV-1 expressing enhanced green fluorescent protein from the promoter for infected cell protein 0 (ICP0) or glycoprotein C (gC) were depleted of endogenous CD8+ or CD45+ cells and cultured in the presence or absence of IFN-γ. Our results demonstrate that IFN-γ acts on latently infected neurons to inhibit (i) HSV-1 reactivation, (ii) ICP0 promoter activity, (iii) gC promoter activity, and (iv) reactivation in neurons in which the ICP0 or gC promoter is active. Interestingly, we detected transcripts for ICP0, ICP4, and gH in neurons that expressed the ICP0 promoter but were prevented by IFN-γ from reactivation and virion formation. Thus, the IFN-γ blockade of HSV-1 reactivation from latency in neurons is associated with an inhibition of the expression of the ICP0 gene (required for reactivation) and a blockade of a step that occurs after the expression of at least some viral structural genes.
Screening for Lrrk2 G2019S and clinical comparison of Tunisian and North American Caucasian Parkinson's disease families

Mutations in the leucine‐rich repeat kinase‐2 gene (LRRK2) are responsible for some forms of familial as well as sporadic Parkinson's disease (PD). The purpose of this study was to examine the frequency of a single pathogenic mutation (6055G>A) in the kinase domain of this gene in United States and Tunisian familial PD and to compare clinical characteristics between patients with and without the mutation. Standardized case report forms were used for clinical and demographic data collection. We investigated the frequency of the most common substitution of LRRK2 (G2019S, 6055G>A) and its impact on epidemiological and phenotypic features. The frequency of mutations in Tunisian families was 42% (38/91) and in U.S. families 2.6% (1/39), with the unique opportunity to compare homozygous (n = 23) and heterozygous (n = 109) Tunisian carriers of G2019S substitutions. Individuals with G2019S substitutions had an older age at onset but few other differences compared with families negative for the substitution. Patients with LRRK2 mutations had typical clinical features of PD. Comparisons between individuals with heterozygous and homozygous LRRK2 mutations suggested that gene dosage was not correlated with phenotypic differences; however, the estimated penetrance was greater in homozygotes across all age groups. © 2006 Movement Disorder Society
Solar-generator-interfacing with a current-fed superbuck converter implemented by duality-transformation methods

Utilization of solar energy is one important action to decelerate the observed climate change and to ensure the availability of energy in the future. Reliable solar-energy systems composing of solar arrays and their interfacing converters are of prime importance but known to have certain operational constraints causing reliability problems. The paper investigates a real current-fed converter for the maximum-power-point (MPP) tracking purposes in solar-generator systems. The current-fed converter is implemented from the conventional voltage-fed converter by applying the duality transformation methods. The investigations show clearly that the input-voltage-controlled current-fed converter can operate without constraints in all the regions of solar generator I/U curve but the operation is limited to the voltages lower than the MPP voltage if any output control is used. The theoretical findings are verified with experimental current-fed superbuck converter sourced by a real solar array. Similar information cannot be found from the public literature.
Clinical manifestations and outcome of acute myocardial infarction in very young patients.

BACKGROUND Acute myocardial infarction is rare in people under the age of 30. OBJECTIVE To determine the clinical features and outcome in young patients presenting with AMI. METHODS All patients aged 30 years and younger hospitalized with AMI during a period of 8 years (1993-2000) were evaluated for clinical features and outcome. RESULTS Of the 3,758 patients with AMI, 15 were 30 years old or younger (0.4%). The mean age was 28 (range 21-30 years) and all were male. Eight had normal coronary arteries on angiogram; seven had obstructive coronary artery disease. Patients with OCA had more classical risk factors for coronary disease. A complete diagnostic workup was abnormal in four patients with NCA: thrombophilia in two patients, spasm due to alcohol withdrawal and hyperthyroidism in one patient each. All patients presented with typical new-onset chest pain. None had a previous history of angina. All patients with OCA received reperfusion therapy as compared to one patient with NCA. Peak creatine phosphokinase in NCA and OCA was 504 +/- 547 and 1,328 +/- 440 respectively (P < 0.01). All patients with NCA had good left ventricular function on follow-up echocardiography, compared to only three in the OCA group (P = 0.02). There was one death due to cardiogenic shock in a patient with OCA. Follow-up of 4 +/- 2 years demonstrated recurrent acute coronary syndromes in four of seven patients with OCA versus none in the NCA patients (P = 0.02). CONCLUSIONS AMI is rare in very young patients, and more than half NCA. A thrombophilic tendency or spasm should be considered. Young patients with NCA have an excellent prognosis.
Dynamics of dendritic cell‐derived vesicles: high‐resolution flow cytometric analysis of extracellular vesicle quantity and quality

Nano‐sized membrane vesicles are secreted by many cell types. These vesicles can serve as carriers of cellular information. DC‐derived vesicles can be targeted to other immune cells and modify their function. Accurate analysis of quantitative and qualitative changes in EV production by DC upon different activation stimuli is needed to further reveal the immune regulatory properties of DC‐derived EVs. However, methods for reliable quantification of individual EVs and for analysis of the heterogeneity of EV populations are limited. With our recently developed high‐resolution flow cytometry‐based method, we can perform a high‐throughput, multiparameter, and quantitative analysis of individual EVs. With the use of this novel technique, we show that despite previous assumptions, stimulation with bacterial LPS increases EV release by DC. Furthermore, we demonstrate heterogeneity in DC‐derived EVs regarding their buoyant density and MHC class II content. Finally, we show that cognate interaction between LPS‐stimulated DC and CD4+ T cells affects both the quantity and quality of LPS DC‐derived EVs present in the culture supernatant. These data indicate that flow cytometry‐based analysis of individual EVs is a valuable, novel tool to study the dynamics of EV secretion and composition, offering great opportunities to unveil the function of immune cell‐derived EVs.
Replantation of 400 avulsed permanent incisors. 4. Factors related to periodontal ligament healing.

400 avulsed and replanted permanent teeth were examined for periodontal ligament (PDL) healing, using standardized radiographic and clinical examination procedures (i.e. percussion test and mobility test). The effect of various clinical factors was examined, such as age and sex of the patient, type of tooth replanted, presence of crown fracture or bone fracture, stage of root development (including apical diameter and length of the pulp), type and length of extra-alveolar storage, clinical contamination of the root surface, type of root surface cleansing procedure, type and length of splinting period and antibiotic therapy. Surface resorption was generally diagnosed after 12 months; while inflammatory resorption and replacement resorption (ankylosis) were usually observed after 1 month and 1-2 months respectively. Most resorptive processes were diagnosed within the first 2-3 years. However, although rarely, even after 5 and 10 years new resorptive processes could be diagnosed. A univariate statistical analysis of 272 teeth revealed 9 factors significantly related to PDL healing. A subsequent multivariate analysis revealed that the following 4 factors had the strongest impact upon PDL healing, in descending order of significance: Stage of root development; length of the dry extra-alveolar storage period; immediate replantation and length of the wet period (saliva or saline storage). Nonphysiological storage, such as homemade saline and sterilizing solutions (chloramine and alcohol) always led to root resorption. Storage in tap water for more than 20 minutes usually led to root resorption. The common denominator for all these factors related to PDL healing appears to be survival of the PDL cells along the root surface. Based on these findings, immediate replantation is recommended irrespective of stage of root development.
Études d'épigraphie thasienne. II. Un poète thasien dans l'Anthologie grecque

L’epigramme funeraire Anth. Pal. VII, 167, pour la jeune Polyxene, est attribuee soit a Dioscoride, soit a un certain Hekataios de Thasos, inconnu par ailleurs. La defunte apparait sur une inscription honorifique de l’agora de Thasos (C. Dunant , J. Pouillou x, Recherches sur Thasos II, 237) que l’on peut placer a l’epoque d’Auguste environ. Le rapprochement des deux documents permet d’affirmer que le poete est bien Hekataios : il pourrait faire partie des auteurs reunis dans la Couronne de Philippe.
Iconographie des sociétés néolithiques : entre Atlantique et Méditerranée, les stèles décorées de l'Alentejo Central

Notre travail de recherche traite un corpus de steles decorees neolithiques localisees dans la region d'Alentejo Central, au Portugal. Sont presentes des releves actualises de ces steles, ainsi que la classification, description et analyse formelle des signes et elements de decor presents. Nous avons pu comprendre et detailler le processus qui mene le signe en tant que figure geometrique a la represention d'elements de decor utilises dans le corpus. Nous avons donc identifie ce que les signes representent de maniere explicite. Les choix iconiques, plastiques et d'implantation des steles ont ete detailles. De cette facon nous avons pu proposer des hypotheses concernant les significations implicites des elements de decor et deceler des recurrences et preferences dans les assemblages. Ces caracteristiques stylistiques nous ont aussi permis de trier l'ensemble et de former trois groupes au sein du corpus de depart. Chaque groupe se caracterise par des choix qui lui sont propres d'un point de vue iconique, plastique et d'implantation. De ces trois groupes de steles definis, deux thematiques principales se sont degagees: la thematique humanoide et la thematique narrative. La revision des donnees de fouille et l'etude comparative entre des elements de decor figures sur les steles etudiees et des objets reels et autres figurations archeologiques nous ont permis au final de proposer une integration chronologique et culturelle du corpus.
Purification, cloning, and primary structure of a new enantiomer-selective amidase from a Rhodococcus strain: structural evidence for a conserved genetic coupling with nitrile hydratase

A new enantiomer-selective amidase active on several 2-aryl propionamides was identified and purified from a newly isolated Rhodococcus strain. The characterized amidase is an apparent homodimer, each molecule of which has an Mr of 48,554; it has a specific activity of 16.5 mumol of S(+)-2-phenylpropionic acid formed per min per mg of enzyme from the racemic amide under our conditions. An oligonucleotide probe was deduced from limited peptide information and was used to clone the corresponding gene, named amdA. As expected, significant homologies were found between the amino acid sequences of the enantiomer-selective amidase of Rhodococcus sp. , the corresponding enzyme from Brevibacterium sp. strain R312, and several known amidases, thus confirming the existence of a structural class of amidase enzymes. Genes probably coding for the two subunits of a nitrile hydratase, albeit in an inverse order, were found 39 bp downstream of amdA, suggesting that such a genetic organization might be conserved in different microorganisms. Although we failed to express an active Rhodococcus amidase in Escherichia coli, even in conditions allowing the expression of an active R312 enzyme, the high-level expression of the active recombinant enzyme could be demonstrated in Brevibacterium lactofermentum by using a pSR1-derived shuttle vector.
Dynamic Scheduling of Receding Horizon Controllers with Application to Multiple Unmanned Hovercraft Systems

This paper develops a new algorithm for dynamic scheduling of multiple receding horizon control systems that accounts for bounded model uncertainty and bounded sensor noise. A cost function appropriate for control of multiple vehicle systems is proposed and an upper bound on the cost as a function of the execution horizon is developed. The upper bound is optimized to obtain an optimal schedule subject to the computational constraints. The algorithm is further improved using less conservative upper bounds. The new approach is illustrated through simulation of a two radio controlled hovercraft system.
Quatre essais sur les effets des rentes des ressources naturelles dans les pays en développement

Cette these presente un ensemble de travaux de recherche en economie politique qui s’inscrivent dans le champ contemporain de la litterature sur la malediction des ressources naturelles dans les pays en developpement. Elle s’interesse specifiquement aux liens entre les rentes des ressources naturelles et les institutions politiques et les conflits, puis entre les rentes et la pauvrete sous ses differentes formes. Son champ geographique se situe a plusieurs niveaux, international pour un groupe de pays en developpement, monographique et infranational pour le Tchad et ses regions. La premiere partie, en s’inspirant des theories des changements institutionnels, teste l’hypothese que les rentes issues de differentes ressources naturelles ont des effets differencies sur la qualite des institutions dans les pays en developpement. Par la suite, elle teste l’hypothese d’un « systeme de conflit regional » dans le Triangle Republique Centrafricaine, Tchad et Soudan. La deuxieme partie evalue le dispositif « original » de gestion des revenus petroliers sur differentes dimensions de la pauvrete au Tchad sur des donnees d’enquetes de terrain. Le premier chapitre de cette partie teste l’hypothese d’un biais urbain dans l’allocation de temps des enfants dans un contexte petrolier au Tchad. Alors que le second est dedie a l’evaluation de l’impact de l’exploitation petroliere sur le profil de la pauvrete dans la region productrice en utilisant les methodes quasi-experimentales d’evaluation d’impact.
An information theoretic approach to Sidorenko's conjecture

We investigate the famous conjecture by Erd\H os-Simonovits and Sidorenko using information theory. Our method gives a unified treatment for all known cases of the conjecture and it implies various new results as well. Our topological type conditions allow us to extend Sidorenko's conjecture to large families of $k$-uniform hypergraphs. This is somewhat unexpected since the conjecture fails for $k$ uniform hypergraphs in general.
Gene networks provide a high-resolution view of bacteriophage ecology

Bacteriophages are the most abundant and diverse biological entities on the planet, and new phage genomes are being discovered at a rapid pace from metagenomes. As more novel, uncultured phage genomes are published, new tools are needed for placing these genomes in an ecological and evolutionary context. Phages are difficult to study with phylogenetic methods, because they exchange genes regularly, and no single gene is conserved across all phages. Instead, genome-level networks have been used to group similar viruses into clusters for taxonomy. Here, we show that gene-level networks provide a high-resolution view of phage genetic diversity and offer a novel perspective on virus ecology. To that end, we developed a method that identifies informative associations between a phage’s annotated host and clusters of genes in the network. Given these associations, we were able to predict a phage’s host with 86% accuracy at the genus level, while also identifying genes that underlie these virus-host interactions. This approach, thus, provides one of the most accurate means of host prediction while also pointing to directions for future empirical work.
Epidemiology of research into interventions for the treatment of osteoarthritis of the knee joint

OBJECTIVE To assess the published research base for interventions for osteoarthritis of the knee, and to identify areas in need of further research. METHODS Literature searches were conducted on electronic databases (Medline, Embase, ISI, and Cochrane library), bibliographies of existing review articles were hand searched, and a postal questionnaire was sent to members of the Osteoarthritis Research Society International. All relevant articles were copied and searched for treatment type, study methodology, statistical results, conclusions, funding source, researcher affiliations, and year of publication, using a predetermined data extraction form. RESULTS There have been marked changes in the literature over the period studied (1950–98), with a recent rise in trials of physical therapy, educational interventions, and complementary treatments. However, overall, most research was either drug (59.1%) or surgically (25.6%) related. Most of the studies reported positive results (94%). Research on oral drugs was significantly more likely to provide a positive result than research on any other intervention (p<0.001 by χ2 test). Commercially funded studies were significantly more likely to produce a positive result than non-commercially funded research (p=0.0027 by χ2 test). CONCLUSIONS Analysis of time trends indicates that the research agenda does shadow changes in consumer demands. However, there are significant gaps in the research base that need to be considered.
BIOWASTE SEPARATION AT SOURCE AND ITS LIMITATIONS BASED ON SPATIAL CONDITIONS

The European regulation of biodegradable municipal waste (biowaste) treatment places a significant demand on local biowaste separation systems and consequent treatment (composting, anaerobic digestion). When implementing separate collection systems, there is a public demand for systems based on containers and bags. Based on a case study of the city Usti nad Labem in the Czech Republic, the authors illustrate the difficulties encountered in the implementation of this kind of system. A series of factors should be paramount in the organization of biowaste separate collection, including the location of containers, the amount of contaminants, and system parameters (e.g. volume of containers, frequency of collection). The results obtained confirm how a precision-targeted information campaign may contribute towards reducing contamination of biowaste container content. Lower amounts of contaminants imply a simplified biowaste treatment (composting) and increased system efficiency. Furthermore, it was observed that the relocation of biowaste containers, or placing of additional containers in the system, resulted in an increase in public involvement as a result of the added convenience of separate collection proximity of containers. The equipment of the chosen city district by additional 55 containers increases the number of address points covered by the system by approx. 149.20% and the number of inhabitants by about 38.14%. However, this added convenience of separate collection is not cost-neutral, with the increased proximity of containers contributing towards a rise in collection costs including transport, and containers. The increase of collection costs ranges between 105.5 and 156.78% in comparison with the current situation.
Spatial implications associated with using Euclidean distance measurements and geographic centroid imputation in health care research.

OBJECTIVE To determine the effect of using Euclidean measurements and zip-code centroid geo-imputation versus more precise spatial analytical techniques in health care research. DATA SOURCES Commercially insured members from a southeastern managed care organization. STUDY DESIGN Distance from admitting inpatient facility to member's home and zip-code centroid (geographic placement) was compared using Euclidean straight-line and shortest-path drive distances (measurement technique). DATA COLLECTION Administrative claims from October 2005 to September 2006. PRINCIPAL FINDINGS Measurement technique had a greater impact on distance values compared with geographic placement. Drive distance from the geocoded address was highly correlated (r=0.99) with the Euclidean distance from the zip-code centroid. CONCLUSIONS Actual differences were relatively small. Researchers without capabilities to produce drive distance measurements and/or address geocoding techniques could rely on simple linear regressions to estimate correction factors with a high degree of confidence.