Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning temporal evolution of probability distribution with Recurrent Neural Network

We propose to tackle a time series regression problem by computing temporal evolution of a probability density function to provide a probabilisitic forecast. A Recurrent Neural Network (RNN) based model is employed to learn a nonlinear operator for temporal evolution of a probability density function. We use a softmax layer for a numerical discretization of a smooth probability density functions, which transforms a function approximation problem to a classification task. Explicit and implicit regularization strategies are introduced to impose a smoothness condition on the estimated probability distribution. A Monte Carlo procedure to compute the temporal evolution of the distribution for a multiple-step forecast is presented. The evaluation of the proposed algorithm on two synthetic and two real data sets shows advantage over the compared baselines.
Kinesthetic and visual control of a bimanual task: specification of direction and amplitude

Kinesthetic information about a perturbation can quickly modify motor activity by producing reflexive compensation. The purpose of the present study was to determine how quickly kinesthetic information about target movement can modify motor activity. Visual information about target movement is known to guide motor activity both quickly and accurately. Therefore, we compared the speed and accuracy of responses to kinesthetically and visually presented targets. Human subjects produced changes in elbow torque as quickly and accurately as possible after the random presentation of 1 of 8 target torques. Information about the direction and amplitude of the target torque was provided either kinesthetically or visually. Responses to kinesthetic targets started at an average latency of 150 msec, and after an additional 159 msec, these responses became accurately graded according to target amplitude. Responses to visual targets started at an average latency of 250 msec, and after an additional 208 msec, these responses became accurately graded according to target amplitude. The accuracy of responses to kinesthetic targets was very similar to the accuracy of responses to visual targets. We conclude that the neural processing of kinesthetic information about target movement is sufficiently fast and accurate to guide typical motor activities.
On the use of hyperplane methods to compute the reachable set of controlled stochastic biochemical reaction networks

A fundamental question in the study of stochastic biochemical reaction networks is what values of mean and variance of the species present in the network are obtainable by perturbing the system with an external input. Here, we propose a computationally efficient technique to answer this question, for networks involving zero and first order reactions. Specifically, we adopt the hyperplane method to compute inner and outer approximations of the reachable set of the linear system describing the moments evolution. A remarkable feature of this approach is that it allows one to easily compute projections of the reachable set for pairs of species of interest, without requiring the computation of the full reachable set, which can be prohibitive for large networks. To illustrate the benefits of this method we consider a standard controlled gene expression model involving two species: the mRNA and the corresponding protein. We verify that the proposed approach leads to estimates of the reachable set, for the protein mean and variance, that are more accurate than those available in the literature and that are consistent with experimental data.
Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice

Significance Spatial structure is postulated to have a powerful influence on establishing and sustaining the signaling and metabolic exchanges that define relationships among members of the gut microbiota and host. However, information about gut community spatial structure is limited. Simultaneous imaging of components of a 15-member model human gut bacterial community over a range of spatial scales in gnotobiotic mice revealed that the colon is better conceptualized as an incompletely mixed bioreactor, rather than having sharply stratified luminal and mucosal compartments. Identifying host and microbial factors that constrain the ability of community members to establish sizeable single or oligotaxon agglomerations should yield new insights about how “micro”-scale mixing defines community function. Knowledge of the spatial organization of the gut microbiota is important for understanding the physical and molecular interactions among its members. These interactions are thought to influence microbial succession, community stability, syntrophic relationships, and resiliency in the face of perturbations. The complexity and dynamism of the gut microbiota pose considerable challenges for quantitative analysis of its spatial organization. Here, we illustrate an approach for addressing this challenge, using (i) a model, defined 15-member consortium of phylogenetically diverse, sequenced human gut bacterial strains introduced into adult gnotobiotic mice fed a polysaccharide-rich diet, and (ii) in situ hybridization and spectral imaging analysis methods that allow simultaneous detection of multiple bacterial strains at multiple spatial scales. Differences in the binding affinities of strains for substrates such as mucus or food particles, combined with more rapid replication in a preferred microhabitat, could, in principle, lead to localized clonally expanded aggregates composed of one or a few taxa. However, our results reveal a colonic community that is mixed at micrometer scales, with distinct spatial distributions of some taxa relative to one another, notably at the border between the mucosa and the lumen. Our data suggest that lumen and mucosa in the proximal colon should be conceptualized not as stratified compartments but as components of an incompletely mixed bioreactor. Employing the experimental approaches described should allow direct tests of whether and how specified host and microbial factors influence the nature and functional contributions of “microscale” mixing to the dynamic operations of the microbiota in health and disease.
Cerebral blood flow and substrate utilization in insulin-treated diabetic subjects.

We compared regional cerebral blood flow (rCBF) and arteriojugular vein differences of glucose, ketones, glycerol, lactate, pyruvate, and O2 in eight subjects with well-controlled insulin-dependent diabetes mellitus (IDDM) and in six healthy volunteers. Duration of diabetes was 19.4 +/- 2.1 yr. Measurements were performed before and after 120 min of insulin infusion and concomitant Biostator-controlled normoglycemia. Net uptake of ketones was seen in IDDM subjects before but not after insulin. Net uptake of glucose did not differ significantly between groups. During normoglycemia the molar ratio of O2 to glucose uptake was lower in IDDM than in nondiabetic subjects (4.68 vs. 5.50; P less than 0.05; Wilcoxon test). Small but significant release of lactate and pyruvate was seen in IDDM but not in nondiabetic subjects. The rCBF was measured by 11CH3F and position emission tomography. Global mean CBF was higher in IDDM subjects (64.9 +/- 5.9 vs. 49.3 +/- 2.7 ml.100 g-1.min-1, means +/- SE in nondiabetic subjects, P less than 0.05). rCBF was enhanced in many cortical and subcortical areas, whereas it was decreased in the head of the caudate nucleus. Neuropsychological testing did not reveal obvious cognitive dysfunction. The results imply that a larger fraction of glucose is nonoxidatively metabolized in the IDDM subjects and furthermore indicate an abnormal rCBF pattern in these subjects.
Caregiver speech and children's use of nouns versus verbs: A comparison of English, Italian, and Mandarin

This paper examines naturalistic samples of adult-to-child speech to determine if variations in the input are consistent with reported variations in the proportions of nouns and verbs in children's early vocabularies. It contrasts two PRO-DROP languages, Italian and Mandarin, with English. Naturalistic speech samples from six 2;0 English-, six 1;11 Italian-, and ten 1;10 Mandarin-speaking children and their caregivers were examined. Adult-to-child speech was coded for the type frequency, token frequency, utterance position, and morphological variation of nouns and verbs as well as the types and placements of syntactic subjects and the pragmatic focus of adult questions. Children's spontaneous productions of nouns and verbs and their responses to adult questions were also examined. The results suggest a pattern consistent with the children's spontaneous production data. Namely, the speech of English-speaking caregivers emphasized nouns over verbs, whereas that of Mandarin-speaking caregivers emphasized verbs over nouns. The data from the Italian-speaking caregivers were more equivocal, though still noun-oriented, across these various input measures.
Tertiary prophylaxis in adults: is there a rationale?

There is lack of evidence‐based recommendations or clear‐cut consensus regarding the clinical and economic utility of regular prophylaxis started in adulthood, with the aim of keeping the clinical situation from getting worse by prevention of further bleeds contributing to increasing musculo‐skeletal or other morbidity in haemophilia. Such a prophylaxis program has been shown in relatively small cohorts to be effective in reducing bleeding occurrence, with a variable effect on the joint status, but with significantly higher factor consumption and consequently higher costs than on‐demand therapy. There has been no attempt to identify subsets of patients who may benefit from “tertiary” prophylaxis more than others, for example, due to their bleeding phenotype and/or requirements for product issued on‐demand or to identify the dosage that provides the optimal balance of clinical benefit and cost effectiveness. This article reviews the published literature on prophylaxis started beyond the age of 18 years, the barriers to the uptake of prophylaxis programs particularly in adults and highlights areas in need of further research.
Taxonomy of nesomyine rodents (Muroidea: Nesomyidae: Nesomyinae): Designation of lectotypes and restriction of type localities for species-group taxa in the genus Nesomys Peters

Abstract Key foundational elements of taxonomic description were omitted in the original naming of species-group taxa now recognized in the Malagasy genus Nesomys: N. rufus Peters, 1870, N. audeberti (Jentink, 1879), and N. lambertoni G. Grandidier, 1928. Based on our review of the material available to the authors, we identified the holotype by monotypy of N. rufus, designated lectotypes of N. audeberti and N. lambertoni, restricted the type localities of N. audeberti and N. lambertoni, and localized the probable geographic source of the holotype of N. rufus. Refinement of the geographic source of N. lambertoni and N. rufus illuminates the incorrect placement of their type localities as currently interpreted and brings them within the presently understood distributions of those species. Extensive discussion is devoted to the travels of J. Audebert and A. Crossley, collectors not only of the types of N. audeberti and N. rufus, respectively, but also of important series of lemurs that remain relevant to understanding the taxonomy and distribution of these endangered mammals.
The response of broilers to the feeding of mash or pelleted diets containing maize of varying particle sizes

1. The effects of maize particle size and steam pelleting on growth and nutrient utilisation were studied with broiler chicks. 2. The presence or absence of 10 μg/kg of 1,25 dihydroxycholecalciferol in diets adequate or deficient in phosphorus was also investigated. Food efficiency was superior with the fine maize diets but calcium retention and phytate phosphorus retention were greatest with the coarse maize diets. Pelleting improved food efficiency and growth in both experiments while phytate phosphorus utilisation was decreased. 3. Addition of 1,25-dihydroxycholecalciferol to the diet increased 16-d body weight, bone ash, plasma dialysable phosphorus and retentions of total phosphorus and phytate phosphorus while decreasing phosphorus deficiency rickets and tibial dyschondroplasia. 4. There were significant interactions between maize particle size and food form. The improvement in calcium retention observed with the coarse maize diets was reduced when the diets were pelleted. When fed as a mash, coarse maize diets resulted in increased plasma dialysable phosphorus levels but when the diet was pelleted this response was eliminated. 5. There was also a significant interaction between particle size and phosphorus concentration in that chicks given diets deficient in phosphorus had improved bone ash when fed coarse maize as compared to fine maize. However, this response was eliminated when the diets were adequate in phosphorus. 6. In one experiment, fine maize diets had higher metabolisable energy values and there was a significant interaction between maize particle size and food form as pelleting improved the metabolisable energy value of coarse maize diets but not fine maize diets. In another experiment only pelleting of the factors studied improved the metabolisable energy value of the diets.
Viral infections in the pediatric oncology patient.

The incidence of children diagnosed with all forms of invasive cancer has significantly increased over the past 30 years. At the same time, high cure rates have also been achieved, with 5-year survival rates reaching 70-80% for most childhood malignancies. This improvement has been accomplished through significant advances in treatment, also resulting in the better management of infections during the immunosuppression period. Treatment failure is usually associated with a negative response to chemotherapy (no remission status or relapse) and immunocompromise. The latter is usually caused from the disease itself, especially in the case of lymphoid immune system malignancies, but chemotherapy and radiotherapy can also enhance immunosuppression in the pediatric oncology patient. The direct consequence of the above therapeutic modalities results in prolonged immunosuppression, which constitutes the particular patient group highly susceptible to emerging viral pathogens, sometimes with serious complications that could lead to infectious morbidity. The current chapter aims to present an updated review of the viral infections encountered in the field of pediatric oncology. First, we give a brief overview of the nature of immunosuppression in the particular type of pediatric host, the factors contributing to it, and the current principles in managing immunocompromise. Secondly, we review the types of viral infection, both from the international literature and from the experience of our Oncology Unit, which resides in a tertiary referral hospital serving 5 million people, and the available treatment strategies. Finally, we discuss possible ways for prevention of infection in childhood cancer patients, including medicinal prophylactic treatments, special dietary regimes, as well as active and passive immunisation strategies. At the same time we highlight the need for raising awareness in medical providers and patient relatives about the essential prophylactic measures involved in the evaluation and management of immunocompromised pediatric oncology patients. It is only through achieving a deeper understanding of the factors contributing to viral infections and of the procedures that we can follow to treat or prevent them that we can improve the quality of life of the children with cancer.
Influence of external bacterial structures on the efficiency of photodynamic inactivation by a cationic porphyrin

The main targets of photodynamic inactivation (PDI) are the external bacterial structures, cytoplasmic membrane and cell wall. In this work it was evaluated how the external bacterial structures influence the PDI efficiency. To reach this objective 8 bacteria with distinct external structures were selected; 4 Gram-negative bacteria ( Escherichia coli , with typical Gram-negative external structures; Aeromonas salmonicida , Aeromonas hydrophila both with an S-layer and Rhodopirellula sp., with a peptidoglycan-less proteinaceous cell wall and with cytoplasm compartmentalization) and 4 Gram-positive bacteria ( Staphylococcus aureus , with typical Gram-positive external structures; Truepera radiovictrix , Deinococcus geothermalis and Deinococcus radiodurans , all with thick cell walls that give them Gram-positive stains, but including a second complex multi-layered membrane and structurally analogous to that of Gram-negative bacteria). The studies were performed in the presence of 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin tetraiodide (Tetra-Py^+-Me) at 5.0 μM with white light (40 W m^−2). The susceptibility of each bacteria to PDI by Tetra-Py^+-Me was dependent on bacteria external structures. Although all Gram-positive bacteria were inactivated to the detection limit (reduction of ∼8 log) after 60–180 min of irradiation, the inactivation followed distinct patterns. Among the Gram-negative bacteria, E. coli was the only species to be inactivated to the detection limit (∼8 log after 180 min). The efficiency of inactivation of the two species of Aeromonas was similar (reduction of ∼5–6 log after 270 min). Rhodopirellula was less susceptible (reduction of ∼4 log after 270 min). As previously observed, the Gram-positive bacteria are more easily inactivated than Gram-negative strains, and this is even true for T. radiovictrix , D. geothermalis and D. radiodurans , which have a complex multi-layered cell wall. The results support the theory that the outer cell structures are major bacterial targets for PDI. Moreover, the chemical composition of the external structures has a stronger effect on PDI efficiency than complexity and the number of layers of the external coating, and lipids seem to be an important target of PDI.
Selective Blast Cell Reduction in Elderly Patients with Acute Myeloid Leukemia Secondary to Myelodysplastic Syndrome Treated with Methylprednisolone

The management of elderly patients with acute myeloid leukemia (AML) and a poor performance status is challenging. An 89-year-old man with AML secondary to myelodysplastic syndrome (MDS) and a poor performance status (4) underwent treatment with methylprednisolone (mPSL) (125 mg/body), which resulted in a remarkable reduction of blast cells in the peripheral blood. Neutrophil counts were maintained or increased. Although the suppression was of short duration, mPSL was useful for disease control because it selectively reduced blast counts while maintaining the patient’s performance status. In vivo and in vitro findings suggested that mPSL had direct inhibitory actions on the survival of blast cells. On the basis of this experience, we gave the same mPSL dose to other elderly patients with MDS/AML (n = 5) or AML-M4 (n = 1) who had a poor performance status (3 or higher) and appeared unable to tolerate standard cytotoxic chemotherapies. Selective and significant blast cell reduction was observed in 4 of the 5 patients with MDS/AML, whereas no effects were seen in the AML patient. Although our experience is limited, these findings may provide a clue to understanding the mechanisms regulating the survival of blast cells of MDS/AML and indicate that mPSL may provide a benefit to a subset of these patients.
Alternating Plane Smoothers For Multiblock Grids

Standard multigrid methods are not well suited for problems with anisotropic discrete operators, which can occur, for example, on grids that are stretched in order to resolve a boundary layer. One of the most efficient approaches to yield robust methods is the combination of standard coarsening with alternating-direction plane relaxation in the three dimensions. However, this approach may be difficult to implement in codes with multiblock structured grids because there may be no natural definition of global lines or planes. This inherent obstacle limits the range of an implicit smoother to only the portion of the computational domain in the current block. This report studies in detail, both numerically and analytically, the behavior of blockwise plane smoothers in order to provide guidance to engineers who use block-structured grids. The results obtained so far show alternating-direction plane smoothers to be very robust, even on multiblock grids. In common computational fluid dynamics multiblock simulations, where the number of subdomains crossed by the line of a strong anisotropy is low (up to four), textbook multigrid convergence rates can be obtained with a small overlap of cells between neighboring blocks.
Mosquito (Diptera: Culicidae) Fauna in an Area Endemic for West Nile Virus

ABSTRACT: Mosquito collections with CDC light traps using dry ice and pigeon-baited traps were carried out in south Moravia (Czech Republic) from April to October in 2007 and 2008 at two study sites. In 2007, 11 two-day captures were carried out in two-week intervals, and 1,490 female mosquitoes of nine species were caught. In 2008, 15 two-day trappings of mosquitoes were carried out: 6,778 females of 22 species of mosquitoes were trapped. The results showed marked differences in abundance and species composition of mosquitoes between both study sites and between the trapping methods. In the floodplain forest ecosystem of the Soutok study area, Aedes vexans predominated. The species composition in the Nesyt study site was more varied and the most common species was Culex pipiens. At the latter study site, Anopheles hyrcanus (var. pseudopictus) and Uranotaenia unguiculata, mosquito species with largely southern Eurasian distribution, were repeatedly demonstrated. The largest capture of mosquitoes was in traps with CO2 placed at a height 1 m above the ground. The capture of mosquitoes in the pigeon-baited traps as well as in the traps with CO2 placed in the canopy of trees was markedly lower in both study sites, with the predominant species being Culex pipiens.
Expression Changes of Apoptotic Genes in Tissues from Mice Exposed to Nicotine

Objective: Smoking is the leading preventable cause of various diseases such as lung cancer, chronic obstructive pulmonary disease and cardiovascular disease. Nicotine, one of the major toxic components of tobacco, contributes to the pathogenesis of different diseases. Methods: Given the controversy about nicotine toxicity, the present study was conducted to determine apoptotic effects of nicotine on the heart, kidney, lung and liver of male mice. Real-time PCR was performed to identify mRNA expression changes in apoptotic-related genes between nicotine treated and control mice. Result: In the heart and lung, nicotine caused significant decrease in P53, Bax and Caspase-3 mRNA expression levels compared to the control group. However, in the kidney and liver, the result was significant increase in Bax, Caspase-2, Caspase-3 and a significant decrease in P53 mRNA expression (p<0.01). DNA fragmentation assays indicated no fragmentation in the heart and lung, but in the kidney and liver of nicotine treated mice, isolated DNA was fragmented. Conclusion: Our study provided insight into the molecular mechanisms of nicotine anti-apoptotic effects on the heart and lung as well as pro-apoptotic effects on kidney and liver via a P53-independent pathway.