Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction of UvrA and UvrB Proteins with a Fluorescent Single-stranded DNA

UvrA and UvrB proteins play key roles in the damage recognition step in the nucleotide excision repair. However, the molecular mechanism of damage recognition by these proteins is still not well understood. In this work we analyzed the interaction between single-stranded DNA (ssDNA) labeled with a fluorophore tetramethylrhodamine (TMR) and Thermus thermophilus HB8 UvrA (ttUvrA) and UvrB (ttUvrB) proteins. TMR-labeled ssDNA (TMR-ssDNA) as well as UV-irradiated ssDNA stimulated ATPase activity of ttUvrB more strongly than did normal ssDNA, indicating that this fluorescent ssDNA was recognized as damaged ssDNA. The addition of ttUvrA or ttUvrB enhanced the fluorescence intensity of TMR-ssDNA, and the intensity was much greater in the presence of ATP. Fluorescence titration indicated that ttUvrA has higher specificity for TMR-ssDNA than for normal ssDNA in the absence of ATP. The ttUvrB showed no specificity for TMR-ssDNA, but it took over 200 min for the fluorescence intensity of the ttUvrB-TMR-ssDNA complex to reach saturation in the presence of ATP. This time-dependent change could be separated into two phases. The first phase was rapid, whereas the second phase was slow and dependent on ATP hydrolysis. Time dependence of ATPase activity and fluorescence polarization suggested that changes other than the binding reaction occurred during the second phase. These results strongly suggest that ttUvrB binds ssDNA quickly and that a conformational change in ttUrvB-ssDNA complex occurs slowly. We also found that DNA containing a fluorophore as a lesion is useful for directly investigating the damage recognition by UvrA and UvrB.
Proposta de Novos Sistemas de Aterramento objetivando a redução do Potencial de Passo

Neste trabalho, os autores apresentam metodologias com o objetivo de diminuir o potencial de passo nas bordas das malhas para sistemas de aterramento usando-se o metodo das diferencas finitas no dominio do tempo (metodo FDTD). Com este objetivo, utilizou-se o software SATIF01, o qual foi desenvolvido no Laboratorio de Analise Numerica em Eletromagnetismo (LANE)-UFPA. Na primeira etapa analisouse a distribuicao de potencial, na superficie da terra, considerando-se uma Malha de Aterramento de 5x5 (12m x 12m). Em seguida, sao implementadas algumas metodologias de reducao do potencial de passo tais como fractal e a insercao de “aneis” ao redor da malha. Os resultados obtidos vieram a confirmar a teoria defendida pelos autores.
Design of a Decentralized Peer-to-Peer reviewing and Publishing Market

This normative paper conceptualizes an alternative for the current scientific peer reviewing and publication system. Based on design science research methodology, we propose a distributed peer-to-peer network and transactional data base system (APOLLO) and a cryptocurrency (APL). We conceptualize a market for peer-to-peer reviewing and publishing of research contributions and associated assets that is based on economic market mechanisms and does not require centralized authorities or intermediaries. We discuss how the resulting decentralized and pseudonymous market for research assets could help to mitigate unresolved conflicts of interests and biases prevalent in the current system.
Low grade inflammation is notably suppressed by conventional anti-inflammatory treatment: a randomised crossover trial

Circulating concentrations of C reactive protein (CRP), a hepatic derived inflammatory marker that is secreted in response to specific cytokines, have been shown to predict the risk of coronary heart disease (CHD) and diabetes in large epidemiological studies.1,,2 These data highlight the concept that inflammation is a central component of the pathogenesis of atherosclerosis. The plaque composition of unstable coronary lesions includes an abundance of inflammatory molecules and cells at the shoulder region and these may act to erode the collagen cap separating the atheromatous material of the plaque from blood. The strength of the prospective data linking CRP to CHD are such that a recent American Heart Association/Centers for Disease Control and Prevention consensus report suggested that high sensitivity CRP assays may be employed in helping predict CHD risk.1 The recognition of the contribution of inflammation to atherosclerosis has focused attention on the impact of treatments on inflammatory markers. Treatments with proven effects on cardiovascular mortality, such as the lipid lowering 3-hydroxy-3-methylglutaryl coenzyme A (HMG-Co A) reductase inhibitors (statins) and also the insulin sensitising peroxisome proliferator activated receptor γ activators (thiazolidinediones), exhibit anti-inflammatory effects providing indirect support for the inflammation hypothesis.1 For example, recent trials suggest a …
Precise conditional immortalization of mouse cells using tetracycline‐regulated SV40 large T‐antigen

Cellular immortalization provides a way for expansion and subsequent molecular characterization of rare cell types. Ideally, immortalization can be achieved by the reversible expression of immortalizing proteins. Here, we describe the use of conditional immortalization based on a modified tetracycline‐regulated system for the expression of SV40 large T‐antigen in embryonic stem (ES) cells and mice. The modified system relies on a codon improved reverse tetracycline transactivator (irtTA) fused to the ligand‐binding domain (LBD) of the androgen receptor (irtTA‐ABD) or of a mutated glucocorticoid receptor (irtTA‐GBD*). Induction of T‐antigen is conferred only after addition of two ligands, one to activate the LBD (mibolerone for irtTA‐ABD or dexamethasone for irtTA‐GBD*) and one to activate the tetracycline transactivator (doxycycline). In ES cells, changes in gene expression upon large T induction were limited and reversible upon deinduction. Similarly, expression of T‐antigen was very tightly regulated in mice. We have isolated and expanded bone marrow mesenchymal stem cells that could be genetically manipulated and maintained their differentiation properties after several passages of expansion under conditions that induce the expression of large T‐antigen. genesis 48:220–232 2010. © 2010 Wiley‐Liss, Inc.
Ca2+ controls slow NAD(P)H oscillations in glucose‐stimulated mouse pancreatic islets

Exposure of pancreatic islets of Langerhans to physiological concentrations of glucose leads to secretion of insulin in an oscillatory pattern. The oscillations in insulin secretion are associated with oscillations in cytosolic Ca2+ concentration ([Ca2+]c). Evidence suggests that the oscillations in [Ca2+]c and secretion are driven by oscillations in metabolism, but it is unclear whether metabolic oscillations are intrinsic to metabolism or require Ca2+ feedback. To address this question we explored the interaction of Ca2+ concentration and islet metabolism using simultaneous recordings of NAD(P)H autofluorescence and [Ca2+]c, in parallel with measurements of mitochondrial membrane potential (ΔΨm). All three parameters responded to 10 mm glucose with multiphasic dynamics culminating in slow oscillations with a period of ∼5 min. This was observed in ∼90% of islets examined from various mouse strains. NAD(P)H oscillations preceded those of [Ca2+]c, but their upstroke was often accelerated during the increase in [Ca2+]c, and Ca2+ influx was a prerequisite for their generation. Prolonged elevations of [Ca2+]c augmented NAD(P)H autofluorescence of islets in the presence of 3 mm glucose, but often lowered NAD(P)H autofluorescence of islets exposed to 10 mm glucose. Comparable rises in [Ca2+]c depolarized ΔΨm. The NAD(P)H lowering effect of an elevation of [Ca2+]c was reversed during inhibition of mitochondrial electron transport. These findings reveal the existence of slow oscillations in NAD(P)H autofluorescence in intact pancreatic islets, and suggest that they are shaped by Ca2+ concentration in a dynamic balance between activation of NADH‐generating mitochondrial dehydrogenases and a Ca2+‐induced decrease in NADH. We propose that a component of the latter reflects mitochondrial depolarization by Ca2+, which reduces respiratory control and consequently accelerates oxidation of NADH.
Efficient lip‐synch tool for 3D cartoon animation

We propose a set of algorithms to efficiently make speech animation for 3D cartoon characters. Our prototype system is based on blendshapes, a linear interpolation technique, which is widely used in facial animation practice. In our system, a few base target shapes of the character, prerecorded voice, and its transcription are required as input. We describe a simple technique that amplifies the target shapes from few inputs using a generic database of viseme mouth shapes. We also introduce additional lip‐synch editing parameters that allow designers to quickly tune the lip movements. Based on these, we implement our prototype system as a Maya plug‐in. The demonstration movies created with this system illustrate well the practicality of our approach. Copyright © 2008 John Wiley & Sons, Ltd.
Impaired cognition in depression and Alzheimer (AD): a gradient from depression to depression in AD.

OBJECTIVE To assess cognition in major depressed (MD), Alzheimer's disease (AD), and depression in AD elderly. METHOD Subjects were evaluated by Mini Mental, Rey Auditory Verbal Learning Test, Rey Complex Figure, Digit Span, Similarities, Trail Making A/B, Verbal Fluency and Stroop. One-way ANOVA and multivariate models were used to compare the performance of each group on neuropsychological tests. RESULTS We evaluated 212 subjects. Compared to MD, attention, working memory, processing speed and recall showed significantly better in controls. Controls showed significantly higher performance in all cognitive measures, except in attention compared to AD. Verbal fluency, memory, processing speed and abstract reasoning in MD was significantly higher compared to AD. AD was significantly better in general cognitive state than depression in AD. All other cognitive domains were similar. CONCLUSION A decreasing gradient in cognition appeared from the control to depression in AD, with MD and AD in an intermediate position.
Sulfasalazine-Induced Hepatic Injury in an Ex Vivo Model of Isolated Perfused Rat Liver and the Protective Role of Taurine

Sulfasalazine is one of the most commonly administered drugs for the treatment of rheumatoid arthritis and inflammatory bowel disease in humans. On the other hand, acute liver failure led to liver transplantation and/or patient death might occur after sulfasalazine administration. There is no precise mechanism for hepatic injury induced by sulfasalazine and no specific hepatoprotective agent has been developed against this complication. Current investigation was designed to study oxidative stress as a proposed mechanism for sulfasalazine-induced liver injury and evaluate the role of taurine administration as a safe hepatoprotective agent. Methods: Rat liver was isolated after cannulation through portal vein and perfused with Krebs-Henseleit buffer. The liver was exposed to different concentrations of sulfasalazine and taurine. Results: Sulfasalazine (5 mM) administration caused significant hepatic injury as judged by elevation in liver perfusate level of LDH, AST, ALT, and potassium ion (K+). Significant amounts of reactive oxygen species (ROS) and lipid peroxidation were detected in sulfasalazine treated livers. Furthermore, hepatic glutathione reservoirs were depleted. Histopathological examination of liver tissues confirmed the above mentioned biochemical data. Co-administration of taurine (5, 10 and 20 mM), significantly mitigated sulfasalazine-induced hepatic injury in isolated rat liver. Conclusion: The data obtained from current investigation indicate potential therapeutic properties of taurine against sulfasalazine-induced liver injury.
Kynþroski íslenskra drengja

Gerð var þverskurðarrannsokn a ytri kynþroskaeinkennum hja 2751 heilbrigðum islenskum dreng a aldrinum 6-16 ara. Rannsoknin var hluti af staerri rannsokn sem for fram a arabilinu 1983-1987 en þar var meðal annars maeld haeð, baeði sitjandi og standandi, þyngd og huðfita. Alls toku 5526 born og unglingar þatt i rannsokninni, og var það meira en 95% af upprunalegum urtakshopi. Fyrstu einkenni kynþroska drengja eru talin þegar eistu na 4 ml rummals (T 4). Meðalaldur islenskra drengja við upphaf kynþroska var 11,89 ar, staðalfravik (standard deviation) 1,08 ar. Timalengd sem tekur eistun að vaxa ur 4 ml i 12 ml (T 4 -T 12) var 2,21 ar. Fyrsti voxtur kynhara (PH 2) fannst að meðaltali við 12,74 ar, staðalfravik 1,37 ar. Timalengd milli PH 2 og PH 5, þegar fullum þroska kynhara var nað, var að meðaltali 2,43 ar. Niðurstoður benda til að kynþroski islenskra pilta fylgi svipuðu ferli og hja piltum a Norðurlondum og meginlandi Vestur-Evropu. Samanburður við erlendar rannsoknir er hins vegar að morgu leyti erfiður vegna olikra rannsoknaraðferða.
Multiferroics: Past, present, and future

This article provides a personal guided tour of multiferroic materials, from their early days as a theoretical curiosity, to their position today as a focus of worldwide research activity poised to impact technology. The article begins with the history of, and the answer to, the question of why so few magnetic ferroelectric multiferroics exist, then gives a survey of the mechanisms and materials that support such multiferroicity. After discussing the tremendous progress that has been made in the magnetoelectric control of magnetic properties using an electric field, some unusual applications of multiferroics in high-energy physics and cosmology are outlined. Finally, the most interesting open questions and future research directions are addressed.
Factors controlling epidermal growth factor (EGF) gene expression in the endometrium of the mare

Previous studies showed a dramatic increase in EGF gene expression in the endometrial glands of pregnant mares around day 40 after ovulation. To investigate how the steroid hormones of pregnancy might regulate this expression, in situ hybridization was used to monitor the levels of EGF mRNA in endometrial biopsies obtained from seasonally anoestrous or ovariectomised mares given exogenous progesterone and oestrogen, alone or in combination, for up to 46 days. Biopsies were also taken from mares during the non‐pregnant cycle, during normal pregnancies and pregnancies compromised by endometrial pathology (endometrosis) or because of incompatible extraspecific embryo transfers (donkey‐in‐horse pregnancies).
Dopant and carrier concentration in Si in equilibrium with monoclinic SiP precipitates.

The behavior of silicon slices very heavily implanted (1.5\ifmmode\times\else\texttimes\fi{}${10}^{17}$ ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}2}$) with phosphorus was investigated by transmission electron microscopy and secondary neutral mass spectrometry (SNMS) after annealing at 800, 850, 900, and 1000 \ifmmode^\circ\else\textdegree\fi{}C. Precipitation of large monoclinic, and partially orthorhombic, SiP particles takes place in the most heavily doped region. From the shape of the SNMS profiles in the dissolution stage of these precipitates, we determined the concentration ${\mathit{C}}_{\mathrm{sat}}$ of P in equilibrium with the conjugate phase: ${\mathit{C}}_{\mathrm{sat}}$=2.45\ifmmode\times\else\texttimes\fi{}${10}^{23}$exp(-0.62/kT) ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}3}$. This concentration has to be compared with the equilibrium concentration ${\mathit{n}}_{\mathit{e}}$ of the electrically active dopant. To this end, more accurate determinations of ${\mathit{n}}_{\mathit{e}}$ were performed on heavily P-doped polysilicon films. It was found that ${\mathit{n}}_{\mathit{e}}$=1.3\ifmmode\times\else\texttimes\fi{}${10}^{22}$exp(-0.37/kT) ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}3}$. Hence for T\ensuremath{\gtrsim}750 \ifmmode^\circ\else\textdegree\fi{}C, ${\mathit{C}}_{\mathrm{sat}}$ exceeds ${\mathit{n}}_{\mathit{e}}$ and the concentration (${\mathit{C}}_{\mathrm{sat}}$-${\mathit{n}}_{\mathit{e}}$) of inactive mobile P increases with temperature. The formation and the diffusion behavior of this inactive dopant are in keeping with a preprecipitation phenomenon. \textcopyright{} 1996 The American Physical Society.
Uso do Algoritmo PageRank para Priorização de Requisitos de Software

Este trabalho apresenta uma nova abordagem para reduzir o empirismo existente na priorizacao de requisitos, aplicando o algoritmo PageRank em um grafo representativo das dependencias entre requisitos. Um estudo de caso e apresentado e comparacoes sao realizadas entre as abordagens de priorizacao por votacao acumulativa, com o uso de Pert/CPM e por meio do PageRank , ou seja, a tecnica proposta neste trabalho. Apos comparar os resultados, foi possivel concluir que o PageRank efetua a priorizacao consistentemente e permite que os stakeholders realizem ajustes nas prioridades dos requisitos, diferentemente das outras duas tecnicas.
Una solución multiparadigma para el desarrollo de software

En el proceso de desarrollo de software, es necesario ser capaces de identificar la naturaleza del problema a resolver para elegir las herramientas y tecnicas que mejor se adapten a la situacion, y den respuesta a la naturaleza multidimensional de los problemas de software complejos. Una aproximacion multiparadigma parece ser lo opcion indicada teniendo en cuenta que usualmente un unico paradigma no alcanza en el dominio del problema a resolver. Nuestro objetivo es establecer modelos, procesos y tecnicas para mejorar el desarrollo de sistemas en un ambiente multiparadigma. Palabras clave: Programacion multiparadigma, Lenguajes de Programacion, Abstraccion, Dominios complejos.
Outage Analysis and Power Allocation for Distributed Space-Time Coding-Based Cooperative Systems over Rayleigh Fading Channels

In this research, we study the outage probability for distributed space-time coding-based cooperative (DSTC) systems with amplify-and-forward relaying over Rayleigh fading channels with a high temporal correlation where the direct link between the source and the destination is available. In particular, we derive the upper and lower bounds of the outage probability as well as their corresponding asymptotic expressions. In addition, using only the average channel powers for the source-to-relay and relay-to-destination links, we propose an efficient power allocation scheme between the source and the relay to minimize the asymptotic upper bound of the outage probability. Through a numerical investigation, we verify the analytical expressions as well as the effectiveness of the proposed efficient power allocation. The numerical results show that the lower and upper bounds tightly correspond to the exact outage probability, and the proposed efficient power allocation scheme provides an outage probability similar to that of the optimal power allocation scheme that minimizes the exact outage probability.
Biomechanical Modeling of the Forces Applied to Closed Incisions During Single-Use Negative Pressure Wound Therapy

Objectives: The use of negative pressure wound therapy (NPWT) on closed surgical incisions is an emerging technology that may reduce the incidence of complications such as surgical site infections. One of the mechanisms through which incisional NPWT is thought to operate is the reduction of lateral tension across the wound. Methods: Finite element analysis computer modeling and biomechanical testing with Syndaver SynTissue™ synthetic skin were used to explore the biomechanical forces in the presence of the PICO⋄ (Smith & Nephew Ltd, Hull, United Kingdom) negative pressure wound therapy system on a sutured incision. Results: Finite element analysis modeling showed that the force on an individual suture reduced to 43% of the force without negative pressure (from 1.31 to 0.56 N) at −40 mm Hg and to 31% (from 1.31 to 0.40 N) at −80 mm Hg. Biomechanical testing showed that at a pressure of −80 mm Hg, 55% more force is required for deformations in the tissue compared with the situation where no negative pressure wound therapy dressing is active. The force required for the same deformation at −120 mm Hg is only 10% greater than at −80 mm Hg, suggesting that most of the effect is achieved at −80 mm Hg. Conclusions: The results show that a canister-less single-use NPWT device is able to reduce the lateral tension across a closed incision, which may explain observed clinical reductions in surgical site complications with incisional NPWT.
A Figure of Thought

Me tametaphorical Issues‘ By George Lakoﬁ’ A Figure of Thought For two millenia we were taught a dogma that was largely unquestioned and came to be viewed as deﬁnitional. Metaphor was called a ﬁgure of speech. As such. it was taken to be a matter of special language: poetic or persuasive language. As a matter of language. rather than thought, it was viewed as dispensible. If you had something to say, you could presumably say it straightforwardly without meta- phor; if you chose metaphor it was for some poetic or rhetorical purpose, perhaps for elegance or economy, but not for plain speech and ordinary thought. Metaphor was seen as contrasting with ordinary, everyday literal language, language that could be straightforwardly true or false, that could lit the world directly or not. Teaching Berkeley undergraduates forces one to question traditional values — even if those values have stood for two thousand years. In 1978, I taught a small undergraduate seminar (there were ﬁve students) in which metaphor was one of a number of topics. I had received a pre-publication copy of the Ortony collection on Metaphor and Thought, and we were discussing the papers in the volume. One day one of the students came in too upset to function. She announced that she had a metaphor problem, and asked the small assembled group for help. Her boy- friend had just told her that their relationship qhad hit a dead-end streetq. lt being Berkeley in the '70's. the class came to the rescue. The metaphor makes sense, we soon ﬁgured out, only if you‘re traveling toward some destination. and only if love is viewed as a form of travel. if you happen onto a dead-end street when you're traveling toward a destination. then you can't keep going the way you've been going. You have to turn back. qWhat I really want,“ the woman said, “is for us to go into another dimension‘. There is nothing like a disappointing love-aﬂ'air for calling a philosophy of long standing into question. Metaphor, on the traditional view, was supposed to be a matter of speech, not thought. Yet here was not just a way of talking about love as a journey, but a way of thinking about it in that way and of reasoning on the basis of the metaphor. In our culture, there is a full-blown love-as-journey meta- phor that is used for comprehending and reasoning about certain aspects of love relationships, especially those having to do with duration, closeness, difficulties, and common purpose. English is full of expressions that reflect the conceptualization of love as a journey. Some are necessarily about love; others can be understood that way: Look how far we ’ve come. It’s been a long, bumpy road. We can’t turn back now. We're at a crossroads. We may have to go our separate ways. We’re spinning our wheels. The relationship isn’t going anywhere. The marriage is on the rocks. These are_ordinary, everyday expressions. There is nothing extraordinary about them. They are not poetic, nor are they used for rhetorical eﬁect. The most This is a column which appears regularly in the journal Metaphor and Symbolic Activity, Hillsdale. NJ. : Erlbaum. 3S‘l