Miracle-dz/UniFAR-FTUs huggingface dataset:
ABioTrans: A Biostatistical Tool for Transcriptomics Analysis

Here we report a bio-statistical/informatics tool, ABioTrans, developed in R for gene expression analysis. The tool allows the user to directly read RNA-Seq data files deposited in the Gene Expression Omnibus or GEO database. Operated using any web browser application, ABioTrans provides easy options for multiple statistical distribution fitting, Pearson and Spearman rank correlations, PCA, k-means and hierarchical clustering, differential expression analysis, Shannon entropy and noise (square of coefficient of variation) analyses, as well as Gene ontology classifications. Availability and implementation ABioTrans is available at https://github.com/buithuytien/ABioTrans Operating system(s): Platform independent (web browser) Programming language: R (R studio) Other requirements: Bioconductor genome wide annotation databases, R-packages (shiny, LSD, fitdistrplus, actuar, entropy, moments, RUVSeq, edgeR, DESeq2, NOISeq, AnnotationDbi, ComplexHeatmap, circlize, clusterProfiler, reshape2, DT, plotly, shinycssloaders, dplyr, ggplot2). These packages will automatically be installed when the ABioTrans.R is executed in R studio. No restriction of usage for non-academic.
Impaired endothelial prostacyclin production of the canine vein graft in a poor distal runoff limb.

BACKGROUND Because blood flow modulates endothelial prostacyclin production, the extent of this production in autologous vein grafts implanted in poor distal runoff limbs needed to be examined. METHODS Endothelial prostacyclin production in canine autologous vein grafts was measured in poor distal runoff limbs (poor runoff group) and compared with findings in normal runoff limbs (control group). Vein grafts were perfused in a closed circuit at 3 days and 1, 2, 3, and 4 weeks after implantation; after perfusion for the first 30 minutes in a steady flow (basal prostacyclin production), the grafts were exposed to arachidonic acid (stimulated prostacyclin production) for the following 30 minutes. Prostacyclin, as the metabolite 6-keto-PGF1 alpha, was radioimmunoassayed. RESULTS Basal and stimulated prostacyclin production increased in both groups during a period of time after implantation. At 2 weeks when endothelialization was complete, prostacyclin production in the poor runoff group was impaired, compared with the findings in the control group, and this difference increased with time. At 4 weeks the stimulated prostacyclin production was 18.91 +/- 4.03 ng/cm2 in the control group and 11.60 +/- 1.67 ng/cm2 in the poor runoff group (p < 0.05). CONCLUSIONS We propose that the impaired capacity of the vein graft to produce prostacyclin in a poor distal runoff may lead to loss of graft patency in reconstructed arteries.
Heat shock protein 70 – the next chaperone to target in the treatment of human acute myelogenous leukemia?

Introduction: Heat shock proteins (HSPs) are molecular chaperones that stabilize folding and conformation of mature proteins. HSPs are, therefore, considered as possible therapeutic targets in the treatment of human cancers, including acute myeloid leukemia (AML). This strategy offers the possibility of targeting several oncogenic proteins or several intracellular signaling pathways through the use of a single therapeutic agent. Areas covered: Several specific HSP70 inhibitors have now been developed. We describe: i) the molecular structure of HSP70 and the molecular interactions especially with its co-chaperones; ii) the immunoregulatory functions of HSP70; iii) the expression and function of HSP70 in human AML cells; iv) the molecular and pharmacological characteristics of potential HSP70 inhibitors; and v) the clinical and experimental studies of HSP70 inhibition in human AML. Our review is based on careful selection of relevant publications identified in the PubMed database. Expert opinion: HSP70 inhibitors have antileukemic activity in human AML. However, additional experimental studies using in vitro models as well as animal models are required, including detailed toxicology studies, as a scientific basis for the optimal design of future clinical studies.
Voltage comparison based high speed & low power domino circuit for wide fan-in gates

This paper presents design of wide fan-in gate for low power and high speed operations with reduced transistor count. In this work some circuital modifications are done to reduce the number of stacked transistor between input and output hence reducing the delay of the designed wide fan-in OR-gate. Also the average power dissipation of the circuit is reduced as it has less number of switching nodes. The idea used in this technique is the use of basic sense amplifier for comparing voltage generated at the two terminals of the logic block of designed circuit. This logic block represents 8, 16, 32 and 64-input OR-gate. The simulations are done for wide fan-in OR-gates using 90nm CMOS technology model with supply voltage of 1V at 110°C of temperature at clock frequency of 1GHz. The simulation results obtained is compared for 32-input OR-gate with standard voltage comparison based domino circuit for delay, average power and PDP which gives 2.5%, 6% and 9% improvements over it respectively.
Méthode des éléments finis max-plus pour la résolution numérique de problèmes de commande optimale déterministe

Nous introduisons un analogue max-plus de la methode des elements finis de Petrov-Galerkin pour la resolution numerique de problemes de controle optimal deterministe. Cette methode s'appuie sur la linearite max-plus du semi-groupe de Lax-Oleinik, laquelle permet de definir une formulation variationnelle max-plus du probleme de controle. Le systeme discret qui en resulte s'interprete comme l'equation de la programmation dynamique d'un probleme de jeu deterministe a somme nulle a deux joueurs. L'erreur de la methode des elements finis max-plus est controlee par l'erreur de projection de la fonction valeur sur des semimodules max-plus et min-plus et par l'erreur d'approximation de la matrice de rigidite. Nous estimons l'erreur totale de la methode selon la regularite de la fonction valeur et le choix des elements finis, et la comparons a celle de methodes classiques. Enfin, nous illustrons la methode par des exemples numeriques en dimension 1 et 2.
Oscillations of the Taylor polynomials for the sin function

With the advent of graphing calculators, it has become a nice and rather easy activity to plot Taylor polynomials and to check how well or bad they approximate a given function. After having done that up to some degree, say N ≤ 10, the more mathematically minded students wonder what happens in the limit of large N. The remainder formula of the Taylor series gives an upper bound for the error, which one expects to be of the right order of magnitude. In this note we get to more precise information about a specific example. We have chosen the function y = sin x with its infinitely many zeros. But its N-th MacLaurin polynomial PN can have at most N zeros. How much of that “ability to oscillate” is actually occuring? We prove
Turbulence modulation by variable density and viscosity

We investigate the eﬀectiveness of the semi-local Reynolds number Re τ to parametrize wall-bounded ﬂows with strong density, ρ, and viscosity, µ, gradients. Several cases are considered, namely, volumetrically heated low-Mach-number turbulent channel ﬂows, a simultaneously heated and cooled ﬂow with CO2 at supercritical pressure, and heated and cooled supersonic boundary layer ﬂows. The mean density and viscosity in some of these cases vary up to a factor of nine and six, respectively. We show that, even for such high gradients in mean properties, the velocity transformation based on the semi-local Reynolds number is able to collapse the mean streamwise velocity proﬁles. We further-more provide evidence that the turbulent kinetic energy and streamwise vorticity budget equations are also governed by the semi-local Reynolds number. For cases with strong property variations, additional mechanisms appear that are caused by individual density (e.g., baroclinicity) or viscosity gradients. However, in the cases investigated herein, these additional mechanisms are small. The insights gained are used to improve a wall model, which is then tested in a wall-modeled large-eddy simulation (LES) of a compressible channel ﬂow with isothermal walls.
Validating software measures

There are two distinct notions of validation for software measures. On the one hand there is the informal notion that a measure is only valid if it is useful and practical. Although this view of validation is important, it is almost impossible to test. On the other hand there is a formal notion of validation of measures and it is this view which is addressed here. By considering software measures in the context of measurement theory, and by considering a classification of software entities into products, processes and resources the paper describes what the authors believe are the necessary (but not sufficient) activities required for validation, and show how far this deviates from the ‘accepted’ view of validation.
Treatment of renovascular hypertension by transluminal angioplasty – 13 years experience in a single centre

Objective. The study is a follow‐up on treatment of renovascular hypertension (RVH) with percutaneous transluminal renal angioplasty (PTRA). Methods. Patients were screened on the basis of clinical criteria of increased probability of RVH with renography and in selected cases with renal vein renin measurements. A positive work‐up suggesting a functionally important renal artery stenosis led to renal angiography and PTRA if stenosis was confirmed; in 59%, an intravascular stent was inserted. Results. Outcome of treatment was classified as follows – group I: normotensive without medication; group II: with improved control of blood pressure; group III: unchanged blood pressure control. Grouping was performed immediately after treatment, at 1 month, 6 months and at the latest follow‐up. One hundred‐and‐twenty‐two patients (124 atherosclerotic and 12 fibromuscular lesions) were treated during 13 years. Immediately after PTRA the patients were grouped as follows – I: 31%, II: 59%, III: 10%. At 1 month, I: 13%, II: 72%, III: 15%; at 6 months, I: 11%, II: 74%, III: 15%, and at the latest follow‐up, I: 11%, II: 78%, III: 11%. There were few significant complications, and renal function remained on average stable. Conclusion. PTRA is an effective treatment of RVH in patients selected by signs of a flow‐restricting stenosis. Twelve percent were normotensive after angioplasty and a further 77% had better controlled hypertension. Few complications were seen and renal function was on average unchanged as measured by serum creatinine.
Detection and Quantification of Oral Treponemes in Subgingival Plaque by Real-Time PCR

ABSTRACT Oral treponemes have been associated with periodontal diseases. We developed a highly sensitive and specific method to detect and quantify cultivable oral treponemes (Treponema denticola, Treponema vincentii, and Treponema medium) in 50 subgingival plaque samples from 13 healthy subjects as well as 37 patients with periodontal diseases using real-time PCR assays with specific primers and a TaqMan probe for each 16S rRNA sequence. The specificity for each assay was examined by using DNA specimens from various treponemal and other bacterial species. The TaqMan real-time PCR was able to detect from 103 to 108 cells of the oral treponemes, with correlation coefficients as follows: T. denticola, 0.984; T. vincentii, 0.991; and T. medium, 0.984. The frequencies of occurrence of these three oral treponemes in subgingival plaque samples were as follows: T. denticola, 68.0%; T. vincentii, 36.0%; and T. medium, 48.0%. In addition, the number of T. denticola, T. vincentii, and T. medium cells in plaque samples detected by real-time PCR ranged from 3 to 15,184, 1 to 447, and 1 to 7,301 cells/pg of plaque DNA, respectively. Increased numbers of T. denticola cells were detected in plaque samples from deep periodontal pockets, and T. medium was also detected in deep pockets. On the other hand, T. vincentii was mainly found in shallow pockets. These results suggest that various oral treponemes are associated with the formation of each stage of periodontal disease.
Razonamiento basado en casos aplicado a problemas de clasificación

Se pretende analizar la adecuacion y aplicacion del Razonamiento Basado en Casos (R.B.C.) a problemas de clasificacion. La nocion de similitud entre casos se suelen definir mediante distancias, por lo que se emplean diferentes distancias clasicas de la Geometria y algunas de sus variantes. Para comparar los diferentes metodos de clasificacion se han realizado pruebas con 68 Bases de Casos: 19 bases del UCI- Repository (Iris, Pima, Led7 y 24, Wave Form 21 y 40, Letter-Recognition, .) y 49 bases sinteticas con diferentes densidades de puntos y formas de las clases. Ademas de calcular el porcentaje de cierto medio se ha realizado una prueba de contraste de hipotesis t-Student con un nivel de significacion del 95%. Se proponen nuevos metodos de clasificacion basados en distancias mediante la adiccion de hasta 3 caracteristicas sobre el metodo clasico k-NN: *-entornos, *-entornosk-NN (y *-entornos1-NN), y una Heuristica para seleccionar la medida de distancia. Tenemos 6 combinaciones posibles segun se anadan o no estas caracteristicas: k-NN (sirve como referencia), *-entornos, k-NN Heur, *-entornosk-NN, *-entornos Heur, *-entornosk-NN Heur. Se comprueba experimentalmente que todos los metodos propuestos mejoran a k-NN y que la principal fuente de mejora proviene del uso de la Heuristica para seleccionar la distancia. En algunos problemas las medidas de distancia clasicas de la Geometria no resultan adecuadas. Se estudia un tipo de estos problemas y se propone una nueva medida de distancia: la distancia basada en bandas o Hiperplanos. Siguiendo con las ideas del R.B.C., se realiza un cambio de enfoque: cada punto va a tener asociada una banda o medida de distancia local que recoge la informacion de lo que sucede en los alrededores del punto. Cada punto elegira su banda intentando apuntar hacia direcciones donde se encuentran puntos cercanos de su misma clase y alejandose de direcciones donde hay puntos de otras
A web-based, component-oriented application for spatial modelling of habitat suitability of mosquito vectors

Abstract This paper proposes a web-enabled computational environment for the spatial modelling of habitat suitability of mosquito vectors. Under a component-based architecture and implemented using an object-oriented data model, we integrate database interfaces, Web feature services (WFS) based on the open GIS consortium (OGC) protocols, and the data-mining tool WEKA, coupled through Java servlet scripts (JSP). The prototype, based exclusively on freely available libraries and software components, provides basic dynamic spatial simulation capabilities using logistic regression to end-users engaged in local and regional health administration and planning but who lack access to specific software and/or detailed knowledge of spatial modelling techniques. The component-based approach facilitates system maintenance and future expansion of functionality, and guarantees the reusability of developed modules in new spatial modelling applications of health and environmental-related phenomena. Functionality of the WWW-application was validated in a study of habitat suitability mapping of the Malaria vector Anopheles darlingi, in an area surrounding the Manso River hydropower plant, Central Brazil.
RISK FACTORS IN THE OCCURRENCE OF ASTHMA IN CHILDREN

Asthma is still one of the most common chronic inflammatory disease of the airways who determines a high rate of morbidity and mortality in children population. This paper aims to highlight the main risk factors for asthma in children. It is a prospective study and was conducted on a sample of 199 cases with obstructive respiratory disease admitted in the Pediatric Clinic Emergency Hospital Constanta. After a four years period, we identified 126 cases of children that developed asthma. Assessment of risk factors for asthma showed high frequency for the following risk factors: male gender (57.1%), urban (60%), prematurity (29.51%), family atopy (53.2), artificial nutrition, exposure to cigarette smoke.
Pulmonary abnormalities at long-term follow-up of patients with Langerhans cell histiocytosis.

BACKGROUND In Langerhans cell histiocytosis (LCH) pulmonary involvement, which is often initially asymptomatic, may contribute to significant morbidity and mortality. To determine the long-term prognosis, a cross-sectional study was undertaken. PROCEDURE Forty-one patients with > or = 5 years follow-up after the diagnosis of LCH were interviewed and underwent physical examination, blood tests, a chest X-ray and a high-resolution CT (HRCT) of the lungs. All patients included had been referred to the Department of Pediatrics at the Karolinska Hospital in Stockholm between July 1962 and February 1990 (median follow-up 16 years). Biopsies from all patients were reviewed and confirmed to be consistent with LCH. Information on previous clinical features including treatment and the results of chest X-rays were also collected for risk factor analysis. RESULTS Radiographic abnormalities of the lungs (cysts and/or emphysema), found in 10/41 (24%) at follow-up, were classified into five groups according to the extent of the cysts. These patients had more often suffered from multisystem than from single-system disease (P = 0.01), were significantly older at diagnosis (P < 0.001), and had been more heavily treated with chemotherapy and/or radiotherapy. They were also more frequently smokers (P < 0.0001) and 7/10 (70%) had suffered lung involvement at diagnosis. At the time of diagnosis of the pulmonary involvement, 4/10 (40%) patients had respiratory symptoms, but only 2/10 (20%) had symptoms at follow-up. CONCLUSIONS Ten (24%) of the 41 patients had abnormal findings on radiological examination of the lungs at long-term follow-up and seven are or had been smokers. It is of great importance that patients with LCH be informed about smoking-related pulmonary morbidity. Prolonged monitoring of the lungs for smokers and patients with known pulmonary involvement is recommended.
Cytochalasin B induces cellular DNA fragmentation

Cellular DNA fragmentation can be induced in many biological instances without plasma membrane damage. The fungal metabolite, cytochalasin B, is capable of modifying numerous cellular functions related to DNA synthesis. In this work it is demonstrated that cytochalasin B is capable of inducing DNA fragmentation in a number of cells lines. This DNA fragmentation occurs before plasma membrane lysis and over a period of hours. Cytochalasin E and villin, agents that act on the microfilaments, also induce DNA fragmentation. Phorbol dibutyrate, a diacylglyceral analog, is able to inhibit cytochalasin B‐induced DNA fragmentation in a dose‐dependent fashion. These findings support the interpretation that cytochalasin B is inducing DNA fragmentation via its effect on the actin filaments. — Kolber, M. A. , Broschat, K. O. , Landa‐Gonzalez, B. Cytochalasin B induces cellular DNA fragmentation. FASEB J. 4: 3021‐3027; 1990.
Secondary Aftershocks and Their Importance for Aftershock Forecasting

The potential locations of aftershocks, which can be large and damaging, are often forecast by calculating where the mainshock increased stress. We find, however, that the mainshock-induced stress field is often rapidly altered by aftershock-induced stresses. We find that the percentage of aftershocks that are secondary aftershocks, or aftershocks triggered by previous aftershocks, increases with time after the mainshock. If we only consider aftershock sequences in which all aftershocks are smaller than the mainshock, the percentage of aftershocks that are secondary also increases with mainshock magnitude. Using the California earthquake catalog and Monte Carlo trials we estimate that on average more than 50% of aftershocks produced 8 or more days after M ≥5 mainshocks, and more than 50% of all aftershocks produced by M ≥7 mainshocks that have aftershock sequences lasting at least 15 days, are triggered by previous aftershocks. These results suggest that previous aftershock times and locations may be important predictors for new aftershocks. We find that for four large aftershock sequences in California, an updated forecast method using previous aftershock data (and neglecting mainshock-induced stress changes) can outperform forecasts made by calculating the static Coulomb stress change induced solely by the mainshock. Manuscript received 20 November 2002.
Generic User-Level PCI Drivers

Linux has become a popular foundation for systems with real-time requirements such as industrial control applications. In order to run such workloads on Linux, the kernel needs to provide certain properties, such as low interrupt latencies. For this purpose, the kernel has been thoroughly examined, tuned, and verified. This examination includes all aspects of the kernel, including the device drivers necessary to run the system. However, hardware may change and therefore require device driver updates or replacements. Such an update might require reevaluation of the whole kernel because of the tight integration of device drivers into the system and the manyfold ways of potential interactions. This approach is time-consuming and might require revalidation by a third party. To mitigate these costs, we propose to run device drivers in user-space applications. This allows to rely on the unmodified and already analyzed latency characteristics of the kernel when updating drivers, so that only the drivers themselves remain in the need of evaluation. In this paper, we present the Device Driver Environment (DDE), which uses the UIO framework supplemented by some modifications, which allow running any recent PCI driver from the Linux kernel without modifications in user space. We report on our implementation, discuss problems related to DMA from user space and evaluate the achieved performance.
Projeto de um Processador de Rede Intra-Chip para Controle de Comunicação entre Múltiplos Cores

O projeto de processadores com arquiteturas multicore é a atual alternativa para o aumento de desempenho demandado pelo grande volume de processamento de informação. Estes projetos levam à necessidade da definição de mecanismos eficientes de comunicação entre os núcleos do chip. Neste artigo é apresentado o projeto de um processador de rede intra-chip responsável por gerenciar e controlar a comunicação entre os múltiplos núcleos do chip. Para análise do desempenho do processador de rede foi utilizada a linguagem ArchC, que permitiu a simulação do comportamento da arquitetura com precisão de ciclos. Na conclusão verificou-se, através dos experimentos, que a nova arquitetura apresenta um ganho de desempenho relação aos processadores R2NP e IXP1200, devido à organização interna e do controle dos periféricos responsáveis por estabelecer a comunicação.