Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Methylation Impacts Gene Expression and Ensures Hypoxic Survival of Mycobacterium tuberculosis

DNA methylation regulates gene expression in many organisms. In eukaryotes, DNA methylation is associated with gene repression, while it exerts both activating and repressive effects in the Proteobacteria through largely locus-specific mechanisms. Here, we identify a critical DNA methyltransferase in M. tuberculosis, which we term MamA. MamA creates N6-methyladenine in a six base pair recognition sequence present in approximately 2,000 copies on each strand of the genome. Loss of MamA reduces the expression of a number of genes. Each has a MamA site located at a conserved position relative to the sigma factor −10 binding site and transcriptional start site, suggesting that MamA modulates their expression through a shared, not locus-specific, mechanism. While strains lacking MamA grow normally in vitro, they are attenuated in hypoxic conditions, suggesting that methylation promotes survival in discrete host microenvironments. Interestingly, we demonstrate strikingly different patterns of DNA methyltransferase activity in different lineages of M. tuberculosis, which have been associated with preferences for distinct host environments and different disease courses in humans. Thus, MamA is the major functional adenine methyltransferase in M. tuberculosis strains of the Euro-American lineage while strains of the Beijing lineage harbor a point mutation that largely inactivates MamA but possess a second functional DNA methyltransferase. Our results indicate that MamA influences gene expression in M. tuberculosis and plays an important but strain-specific role in fitness during hypoxia.
Sample Path Bounds for Long Memory FBM Traffic

Fractional Brownian motion (fBm) emerged as a useful model for self-similar and long-range dependent Internet traffic. Asymptotic, respectively, approximate performance measures are known from large deviations theory for single queuing systems with fBm traffic. In this paper we prove a rigorous sample path envelope for fBm that complements previous results. We find that both approaches agree in their outcome that overflow probabilities for fBm traffic have a Weibull tail. We show numerical results on the impact of the variability and the correlation of fBm traffic on the queuing performance.
Integrin-Linked Kinase: It’s Role in the Vascular System

Integrin-linked kinase (ILK) is an intracellular molecule that binds to the cytoplasmic domain of β1 and β3-integrin. It has been previously demonstrated in various epithelial cell lines to mediate the ‘outside-in’ signals into the cells and to control the survival of these cells by controlling the phosphorylation of various downstream proteins, such as protein kinase B/Akt (PKB/Akt). We now present in this review the important role of ILK in the vascular system with particular emphasis on its role in endothelial cells (ECs). The results presented here demonstrate that ILK is essential for the proper function, structure and survival of ECs and finally, for the process of neovascularization.
Performance Characteristics of Lightweight Aggregate Cellular Concrete Containing Polypropylene Fibers

This article presents results of an experimental investigation conducted to determine the mix proportion and to characterize the corresponding engineering characteristics of a fiber-reinforced lightweight aggregate, cellular concrete (FRLACC) that was produced without autoclaves. A special foam agent was used to produce air bubbles in the cement matrix. A preliminary compression test was conducted to determine the mix proportion for FRLACC. A series of characterization tests on FRLACC specimens were then carried out to investigate engineering characteristics of FRLACC. The strength aspects of FRLACC were further evaluated by comparing the performance of FRLACC with that of other types of lightweight cellular concrete. It is shown that polypropylene fibers remarkably increase the compressive and splitting tensile strengths of lightweight cellular concrete, whereas the flexural strength of the lightweight cellular concrete is slightly decreased by adding the fibers. It is also shown that FRLACC has superior engineering characteristics in comparison with other types of lightweight cellular concrete.
Selected Nutrient Intakes of Free-Living White Children Ages 6–19 Years. The Lipid Research Clinics Program Prevalence Study(40, 41)

Summary: We report energy intake and selected nutrient intakes–protein, fat (total, saturated, and polyunsaturated), carbohydrate (total, starch, and sucrose), and cholesterol–for 1251 white children ages 6–19 years. The data were obtained, by means of a 24-h dietary recall, from children who were randomly selected from the North American populations studied by the Lipid Research Clinics Program. Females (N = 584) consumed about 2000 kcal daily, an intake that remained relatively constant throughout the age groups studied. Males (N = 667) had an energy intake of 2000 kcal/day during childhood that increased to over 3000 kcal/day in adolescence. Energy sources for both sexes were approximately 15% protein, 38% total fat, 15% saturated fat, 6% polyunsaturated fat, 48% total carbohydrate, 19% starch, and 11% sucrose; cholesterol intake averaged about 145 mg/1000 kcal. For both sexes, fat intake increased with age. Compared to females, males ingested greater amounts of cholesterol and total and saturated fat.
Voting Technology, Political Responsiveness, and Infant Health: Evidence From Brazil

This paper studies the introduction of electronic voting technology in Brazilian elections. Estimates exploiting a regression discontinuity design indicate that electronic voting reduced residual (error‐ridden and uncounted) votes and promoted a large de facto enfranchisement of mainly less educated citizens. Estimates exploiting the unique pattern of the technology's phase‐in across states over time suggest that, as predicted by political economy models, it shifted government spending toward health care, which is particularly beneficial to the poor. Positive effects on both the utilization of health services (prenatal visits) and newborn health (low‐weight births) are also found for less educated mothers, but not for the more educated.
Some Families of Orthogonal Polynomials of a Discrete Variable and their Applications to Graphs and Codes

We present some related families of orthogonal polynomials of a discrete variable and survey some of their applications in the study of (distance-regular) graphs and (completely regular) codes. One of the main peculiarities of such orthogonal systems is their non-standard normalization condition, requiring that the square norm of each polynomial must equal its value at a given point of the mesh. For instance, when they are defined from the spectrum of a graph, one of these families is the system of the predistance polynomials which, in the case of distance-regular graphs, turns out to be the sequence of distance polynomials. The applications range from (quasi-spectral) characterizations of distance-regular graphs, walk-regular graphs, local distance-regularity and completely regular codes, to some results on representation theory.
On the design and characterization of femtoampere current-mode circuits

In this paper, we show and validate a reliable circuit design technique based on source voltage shifting for current-mode signal processing down to femtoamperes. The technique involves specific-current extractors and logarithmic current splitters for obtaining on-chip subpicoampere currents. It also uses a special on-chip sawtooth oscillator to monitor and measure currents down to a few femtoamperes. This way, subpicoampere currents are characterized without driving them off chip and requiring expensive instrumentation with complicated low leakage setups. A special current mirror is also introduced for reliably replicating such low currents. As an example, a simple log-domain first-order low-pass filter is implemented that uses a 100-fF capacitor and a 3.5-fA bias current to achieve a cutoff frequency of 0.5 Hz. A technique for characterizing noise at these currents is also described and verified. Finally, transistor mismatch measurements are provided and discussed. Experimental measurements are shown throughout the paper, obtained from prototypes fabricated in the AMS 0.35-/spl mu/m three-metal two-poly standard CMOS process.
Does aflatoxin exposure in the United Kingdom constitute a cancer risk?

Although the aflatoxins were discovered more than 30 years ago, there is still considerable controversy surrounding their human health effects. Most countries have introduced legislation to control the level of aflatoxins in food, but it is not known if these permitted levels still pose a significant cancer risk. Furthermore, it is unlikely that all the sources of human aflatoxin exposure have been discovered, nor if the liver is the only, or indeed, major target organ for aflatoxin-induced cancer in man. In our laboratory we have used both immunological and HPLC methods to examine human DNA from a variety of tissues and organs to identify and quantify aflatoxin DNA-adducts. We have already detected aflatoxin B1 (AFB1)-DNA adducts in formalin-fixed tissue from an acute poisoning incident in Southeast Asia. Here we have examined human colon and rectum DNA from normal and tumorous tissue obtained from cancer patients and colon, liver, pancreas, breast, and cervix DNA from autopsy specimens. AFB1-DNA adducts were detected in all tissue types examined and ranged from 0-60 adducts/10(6) nucleotides. Where sample size allowed, the adduct levels were confirmed by HPLC analysis. Tumor tissues tended to have higher adduct levels than normal tissue from the same individual, and levels generally increased with patient age. In samples analyzed by HPLC, the adducts present had the chromatographic properties of [8,9-dihydro-8-(N5-formyl)-2',5',6'-triamino-4'-oxo-(N5-pyramidyl) -9- hydroxy-aflatoxin B1, the ring-opened form of the AFB1-guanine adduct. (ABSTRACT TRUNCATED AT 250 WORDS)
Phase-Locked Loop Based on Selective Harmonics Elimination for Utility Applications

Phase-locked loops (PLL) are widely used in power electronics equipment connected to the mains. The use of a square wave voltage-controlled oscillator instead of a sinusoidal one eliminates one multiplier, resulting in a simple PLL algorithm, suitable for low-cost processors. In spite of its simplicity, distorted grid voltages cause steady-state phase error. This paper proposes the use of a modified square waveform obtained by the selective harmonics elimination (SHE) method to solve the phase error problem. Simulation and experimental results for the steady state and the transient tests are presented to validate the proposed single-phase and three-phase SHE-PLL methods. The tests using a field-programmable gate array show that the dynamic response of the proposed method is similar to that of classical PLL, with a simpler implementation.
Estimating long-term behavior of periodically driven flows without trajectory integration

Periodically driven flows are fundamental models of chaotic behavior and the study of their transport properties is an active area of research. A well-known analytic construction is the augmentation of phase space with an additional time dimension; in this augmented space, the flow becomes autonomous or time-independent. We prove several results concerning the connections between the original time-periodic representation and the time-extended representation, focusing on transport properties. In the deterministic setting, these include single-period outflows and time-asymptotic escape rates from time-parameterized families of sets. We also consider stochastic differential equations with time-periodic advection term. In this stochastic setting one has a time-periodic generator (the differential operator given by the right-hand-side of the corresponding time-periodic Fokker–Planck equation). We define in a natural way an autonomous generator corresponding to the flow on time-extended phase space. We prove relationships between these two generator representations and use these to quantify decay rates of observables and to determine time-periodic families of sets with slow escape rate. Finally, we use the generator on the time-extended phase space to create efficient numerical schemes to implement the various theoretical constructions. These ideas build on the work of Froyland et al (2013 SIAM J. Numer. Anal. 51 223–47), and no expensive time integration is required. We introduce an efficient new hybrid approach, which treats the space and time dimensions separately.
PRODUCTION AND CHARACTERIZATION OF CdTe WIRE ARRAYS FOR HYBRID INORGANIC/ORGANIC PHOTOVOLTAIC CELLS

A new approach for obtaining hybrid inorganic/organic photovoltaic structures, based on CdTe nanowires and organic dye films is reported. The wire arrays of CdTe (10 6 wires/cm 2 ) were electrochemically grown using a template method. Ion track polycarbonate foils (30 micrometer thick) were used as templates and the growth conditions for obtaining good quality and stoichiometric CdTe nanowires were identified. After dissolving the polycarbonate template, a CdTe thin film (300 nm) has been deposited by thermal vacuum evaporation onto the wire array before the deposition of ZnPc film as organic absorber. Finally a ZnO thin film was deposited by Electron Pulsed Deposition on ZnPc, working as TCO top electrode. The structural, morphological, electrical and optical properties of each component layer are investigated. Typical parameters of the prepared photovoltaic structures are determined. The external quantum efficiency of the Au/wire array CdTe/CdTe(300 nm)/ZnPc/ZnO structures was significantly increased, with respect to that of Au/wire arrays CdTe/ZnPc/ZnO structures.
Advances in Robotic-Assisted Radical Prostatectomy over Time

Since the introduction of robot-assisted radical prostatectomy (RALP), robotics has become increasingly more commonplace in the armamentarium of the urologic surgeon. Robotic utilization has exploded across surgical disciplines well beyond the fields of urology and prostate surgery. The literature detailing technical steps, comparison of large surgical series, and even robotically focused randomized control trials are available for review. RALP, the first robot-assisted surgical procedure to achieve widespread use, has recently become the primary approach for the surgical management of localized prostate cancer. As a result, surgeons are constantly trying to refine and improve upon current technical aspects of the operation. Recent areas of published modifications include bladder neck anastomosis and reconstruction, bladder drainage, nerve sparing approaches and techniques, and perioperative and postoperative management including penile rehabilitation. In this review, we summarize recent advances in perioperative management and surgical technique for RALP.
Foundations for Continuous Time Hierarchical Co-simulation

Complex systems have to decomposed into sub-systems which are developed by specialized teams. Modeling and simulation techniques help each team achieve a locally optimal solution but they fail to help all teams achieve a globally optimal solution. This is due to each team having its own models made in its own tools, and external suppliers having intellectual property. The result is that it is diﬃcult to simulate the coupled system. Co-simulation is proposed as a way to enable such simulation. Simulators communicate and collaborate as black boxes. The technique has been used in a number of domains improving the overall cost of engineered systems. In these use cases, a minimum common denominator is assumed for the capabilities of simulators. Lever-aging the optional capabilities of simulators improves the performance/accuracy of a co-simulation, but the number of decisions the orchestration mechanism has to make grows exponentially. Diﬀerent, conﬂicting concerns have to be addressed in an optimal way. We propose a way to deal with each concern independently and possibly reuse existing orchestration algorithms that perform better with respect to the con-ﬂicting concerns. Our approach leverages Model Driven Development techniques to process a co-simulation scenario into a canonical/trivial version, where fewer decisions remain to be made. Along the process, conﬂicting concerns will be addressed as an optimization problem, and an appropriate cost function identiﬁed. If successful, the result of this research allows co-simulation scenarios that may oﬀer real-time guarantees, bounds in the maximum error made, or packet size in the communication between simulators.
Hypoxia-Inducible Factor-1 (HIF-1)

Adaptation to low oxygen tension (hypoxia) in cells and tissues leads to the transcriptional induction of a series of genes that participate in angiogenesis, iron metabolism, glucose metabolism, and cell proliferation/survival. The primary factor mediating this response is the hypoxia-inducible factor-1 (HIF-1), an oxygen-sensitive transcriptional activator. HIF-1 consists of a constitutively expressed subunit HIF-1β and an oxygen-regulated subunit HIF-1α (or its paralogs HIF-2α and HIF-3α). The stability and activity of the α subunit of HIF are regulated by its post-translational modifications such as hydroxylation, ubiquitination, acetylation, and phosphorylation. In normoxia, hydroxylation of two proline residues and acetylation of a lysine residue at the oxygen-dependent degradation domain (ODDD) of HIF-1α trigger its association with pVHL E3 ligase complex, leading to HIF-1α degradation via ubiquitin-proteasome pathway. In hypoxia, the HIF-1α subunit becomes stable and interacts with coactivators such as cAMP response element-binding protein binding protein/p300 and regulates the expression of target genes. Overexpression of HIF-1 has been found in various cancers, and targeting HIF-1 could represent a novel approach to cancer therapy.
The Teenage Brain

Research efforts to account for elevated risk behavior among adolescents have arrived at an exciting new stage. Moving beyond laboratory studies of age differences in risk perception and reasoning, new approaches have shifted their focus to the influence of social and emotional factors on adolescent decision making. We review recent research suggesting that adolescent risk-taking propensity derives in part from a maturational gap between early adolescent remodeling of the brain’s socioemotional reward system and a gradual, prolonged strengthening of the cognitive-control system. Research has suggested that in adolescence, a time when individuals spend an increasing amount of time with their peers, peer-related stimuli may sensitize the reward system to respond to the reward value of risky behavior. As the cognitive-control system gradually matures over the course of the teenage years, adolescents grow in their capacity to coordinate affect and cognition and to exercise self-regulation, even in emotionally arousing situations. These capacities are reflected in gradual growth in the capacity to resist peer influence.
Multiobjective optimization and multiple constraint handling with evolutionary algorithms. I. A unified formulation

In optimization, multiple objectives and constraints cannot be handled independently of the underlying optimizer. Requirements such as continuity and differentiability of the cost surface add yet another conflicting element to the decision process. While "better" solutions should be rated higher than "worse" ones, the resulting cost landscape must also comply with such requirements. Evolutionary algorithms (EAs), which have found application in many areas not amenable to optimization by other methods, possess many characteristics desirable in a multiobjective optimizer, most notably the concerted handling of multiple candidate solutions. However, EAs are essentially unconstrained search techniques which require the assignment of a scalar measure of quality, or fitness, to such candidate solutions. After reviewing current revolutionary approaches to multiobjective and constrained optimization, the paper proposes that fitness assignment be interpreted as, or at least related to, a multicriterion decision process. A suitable decision making framework based on goals and priorities is subsequently formulated in terms of a relational operator, characterized, and shown to encompass a number of simpler decision strategies. Finally, the ranking of an arbitrary number of candidates is considered. The effect of preference changes on the cost surface seen by an EA is illustrated graphically for a simple problem. The paper concludes with the formulation of a multiobjective genetic algorithm based on the proposed decision strategy. Niche formation techniques are used to promote diversity among preferable candidates, and progressive articulation of preferences is shown to be possible as long as the genetic algorithm can recover from abrupt changes in the cost landscape.
LyS at TASS 2014: A Prototype for Extracting and Analysing Aspects from Spanish tweets

espanolEste articulo describe nuestra participacion en la tercera edicion del taller de analisis del sentimiento de tuits escritos en castellano, el tass 2014. En la evaluacion competitiva de este ano, se han propuesto cuatro retos: (1) analisis del sentimiento a nivel global, (2) clasificacion de topicos, (3) extraccion de aspectos y (4) analisis del sentimiento a nivel aspectual. Para las tareas 1 y 2 empleamos una aproximacion basada en aprendizaje automatico, donde distintos recursos linguisticos e informacion extraida del conjunto de entrenamiento son utilizados para entrenar un clasificador supervisado. Para abordar la tarea 3, nuestra aproximacion recolecta una lista de representaciones que es empleada para identificar los aspectos requeridos por los organizadores. Por ultimo, la tarea 4 delega en heuristicas para identificar el alcance de cada aspecto, para despues determinar su sentimiento a traves de un clasificador supervisado. Los resultados experimentales son prometedores y nos serviran para desarrollar tecnicas mas complejas en el futuro. EnglishThis paper describes our participation at the third edition of the work- shop on Sentiment Analysis focused on Spanish tweets, tass 2014. This year’s eval- uation campaign includes four challenges: (1) global sentiment analysis, (2) topic classification, (3) aspect-extraction and (4) aspect-based sentiment analysis. Tasks 1 and 2 are addressed from a machine learning approach, using several linguistic resources and other information extracted from the training corpus to feed to a su- pervised classifier. With respect to task 3, we develop a naive approach, collecting a set of representations to identify the predefined aspects requested by the organisers. Finally, task 4 uses heuristics to identify the scope of each aspect, to then classify their sentiment via a supervised classifier. The experimental results are promising and will serve us as the starting point to develop more complex techniques.