Miracle-dz/UniFAR-FTUs huggingface dataset:
Gcn5p, a Transcription-related Histone Acetyltransferase, Acetylates Nucleosomes and Folded Nucleosomal Arrays in the Absence of Other Protein Subunits*

Gcn5p is the catalytic subunit of several type A histone acetyltransferases (HATs). Previous studies performed under a limited range of solution conditions have found that nucleosome core particles and nucleosomal arrays can be acetylated by Gcn5p only when it is complexed with other proteins, e.g. Gcn5-Ada, HAT-A2, and SAGA. Here we demonstrate that when assayed in buffer containing optimum concentrations of either NaCl or MgCl2, purified yeast recombinant Gcn5p (rGcn5p) efficiently acetylates both nucleosome core particles and nucleosomal arrays. Furthermore, under conditions where nucleosomal arrays are extensively folded, rGcn5p acetylates folded arrays ∼40% faster than nucleosome core particles. Finally, rGcn5p polyacetylates the N termini of free histone H3 but only monoacetylates H3 in nucleosomes and nucleosomal arrays. These results demonstrate both that rGcn5p in and of itself is catalytically active when assayed under optimal solution conditions and that this enzyme prefers folded nucleosomal arrays as a substrate. They further suggest that the structure of the histone H3 N terminus, and concomitantly the accessibility of the H3 acetylation sites, changes upon assembly into nucleosomes and nucleosomal arrays.
SCIR-QA at SemEval-2017 Task 3: CNN Model Based on Similar and Dissimilar Information between Keywords for Question Similarity

We describe a method of calculating the similarity of questions in community QA. Question in cQA are usually very long and there are a lot of useless information about calculating the similarity of questions. Therefore,we implement a CNN model based on similar and dissimilar information between question’s keywords. We extract the keywords of questions, and then model the similar and dissimilar information between the keywords, and use the CNN model to calculate the similarity.
Evolution of the Transmission-Blocking Vaccine Candidates Pvs28 and Pvs25 in Plasmodium vivax: Geographic Differentiation and Evidence of Positive Selection

Transmission-blocking (TB) vaccines are considered an important tool for malaria control and elimination. Among all the antigens characterized as TB vaccines against Plasmodium vivax, the ookinete surface proteins Pvs28 and Pvs25 are leading candidates. These proteins likely originated by a gene duplication event that took place before the radiation of the known Plasmodium species to primates. We report an evolutionary genetic analysis of a worldwide sample of pvs28 and pvs25 alleles. Our results show that both genes display low levels of genetic polymorphism when compared to the merozoite surface antigens AMA-1 and MSP-1; however, both ookinete antigens can be as polymorphic as other merozoite antigens such as MSP-8 and MSP-10. We found that parasite populations in Asia and the Americas are geographically differentiated with comparable levels of genetic diversity and specific amino acid replacements found only in the Americas. Furthermore, the observed variation was mainly accumulated in the EGF2- and EGF3-like domains for P. vivax in both proteins. This pattern was shared by other closely related non-human primate parasites such as Plasmodium cynomolgi, suggesting that it could be functionally important. In addition, examination with a suite of evolutionary genetic analyses indicated that the observed patterns are consistent with positive natural selection acting on Pvs28 and Pvs25 polymorphisms. The geographic pattern of genetic differentiation and the evidence for positive selection strongly suggest that the functional consequences of the observed polymorphism should be evaluated during development of TBVs that include Pvs25 and Pvs28.
A model for auto-tagging of research papers based on keyphrase extraction methods

Tagging provides a convenient means to assign tokens of identification to research papers which facilitate recommendation, search and disposition process of research papers. This paper contributes a document centered approach for auto-tagging of research papers. The auto-tagging method mainly comprises of two processes:- classification and tag selection. The classification process involves automatic keyword extraction using Rapid Automatic Keyword Extraction (RAKE) algorithm which uses the keyword — score matrix. The generated top scored keywords are added to the train dataset dynamically, which can be used further. This add-on feature of the system is considered to be one of the main advantages of the system since adding new born phrases is time-consuming and error prone. Cosine similarity is used for classifying the research paper into corresponding domain utilizing the extracted keywords. Tag selection concentrates on the selection of proper tags for the research paper. Tagging facilitates better search facility and determines the dynamics of research areas in terms of number of publications in a domain by each author. The system generates reports for statistical analysis of research papers in each domain and expertise of each faculty in the research community.
Similarity solution of temperature structure functions in decaying homogeneous isotropic turbulence.

An equilibrium similarity analysis is applied to the transport equation for <(deltatheta)(2)>, the second-order temperature structure function, for decaying homogeneous isotropic turbulence. A possible solution is that the temperature variance decays as x(n), and that the characteristic length scale, identifiable with the Taylor microscale lambda, or equivalently the Corrsin microscale lambda(theta), varies as x(1/2). The turbulent Reynolds and Péclet numbers decay as x((m+1)/2) when m<-1, where m is the exponent which characterizes the decay of the turbulent energy , viz., approximately x(m). Measurements downstream of a grid-heated mandoline combination show that, like <(deltaq)(2)>, <(deltatheta)(2)> satisfies similarity approximately over a significant range of scales r, when lambda, lambda(theta), , and are used as the normalizing scales. This approximate similarity is exploited to calculate the third-order structure functions. Satisfactory agreement is found between measured and calculated distributions of and , where deltau is the longitudinal velocity increment.
Secure pairing with biometrics

Secure pairing enables two devices that share no prior context with each other to agree upon a security association, which they can use to protect their subsequent communication. Secure pairing offers guarantees of the association partner identity and it should be resistant to eavesdropping and to a man-in the middle attack. We propose the SAfE pairing system, a user friendly solution to this problem. Details are presented along with a discussion of the security features, experimental validation with two types of biometric data (face recognition and hand grip pressure pattern) and a usability analysis for face recognition biometric pairing.
Short and deep drain MOSFET for space applications: Device and circuit level analysis

We propose a novel short and deep drain (SDD) MOSFET structure and SDD based circuits that are suitable for space applications. The 3-D TCAD simulations for heavy ion radiation with LET of 10 MeV-cm2/mg have been carried out on both SDD MOSFET and SDD inverter. From TCAD simulations, we observe that SET magnitude in SDD inverter is reduced by 43% by using shorter drain and by 17% by using deeper drain compared to conventional MOSFET inverter if the areas of both designs are kept the same. Further, a detailed TCAD simulation on inverter design also showed that SDD inverter has similar power and delay values as those of the conventional MOSFET if areas are the same.
Variant Chromatin Structure of theoriP Region of Epstein-Barr Virus and Regulation of EBER1 Expression by Upstream Sequences andoriP

ABSTRACT Most of the Epstein-Barr virus genome in latently infected cells is in a standard nucleosomal structure, but the region encompassingoriP and the Epstein-Barr virus-encoded small RNA (EBER) genes shows a distinctive pattern when digested with micrococcal nuclease. This pattern corresponds to a previously mapped nuclear matrix attachment region. Although the EBER genes are adjacent to oriP, there is only a two- to fourfold effect oforiP on EBER expression. However, sequences containing a consensus ATF site upstream of EBER1 are important for EBER1 expression.
Distinguishing Vaccinium Species by Chemical Fingerprinting Based on NMR Spectra, Validated with Spectra Collected in Different Laboratories

Abstract A method was developed to distinguish Vaccinium species based on leaf extracts using nuclear magnetic resonance spectroscopy. Reference spectra were measured on leaf extracts from several species, including lowbush blueberry (Vaccinium angustifolium), oval leaf huckleberry (Vaccinium ovalifolium), and cranberry (Vaccinium macrocarpon). Using principal component analysis, these leaf extracts were resolved in the scores plot. Analysis of variance statistical tests demonstrated that the three groups differ significantly on PC2, establishing that the three species can be distinguished by nuclear magnetic resonance. Soft independent modeling of class analogies models for each species also showed discrimination between species. To demonstrate the robustness of nuclear magnetic resonance spectroscopy for botanical identification, spectra of a sample of lowbush blueberry leaf extract were measured at five different sites, with different field strengths (600 versus 700 MHz), different probe types (cryogenic versus room temperature probes), different sample diameters (1.7 mm versus 5 mm), and different consoles (Avance I versus Avance III). Each laboratory independently demonstrated the linearity of their NMR measurements by acquiring a standard curve for chlorogenic acid (R2 = 0.9782 to 0.9998). Spectra acquired on different spectrometers at different sites classifed into the expected group for the Vaccinium spp. , confirming the utility of the method to distinguish Vaccinium species and demonstrating nuclear magnetic resonance fingerprinting for material validation of a natural health product.
Engineering mutations: Deconstructing the mouse gene by gene

Over the past years new vectors and methodologies have been developed to carry out large‐scale genome‐wide insertional mutagenesis screens in the mouse. Gene trapping, the most commonly used technique, is based on the insertion of a retroviral‐ or plasmid‐based vector into a gene, resulting in a loss‐of‐function mutation, while simultaneously reporting its expression pattern and providing a molecular tag to facilitate cloning. The discovery of vertebrate DNA transposons in the mouse and recent improvements has also led to their increased use in insertional mutagenesis screens. Several public resources have been set‐up recently by the academic community to distribute information and materials generated from these large‐scale screens. These new resources should accelerate the study and understanding of biological and developmental processes. Developmental Dynamics 235:2424–2436, 2006. © 2006 Wiley‐Liss, Inc.
Message Type Extraction Based Alert Detection in System Logs

The task of alert detection in event logs, i.e. determining which events in the event log require action from an administrator, is very important in preventing or recovering from downtime events. The ability to do this automatically and accurately provides significant savings in time and cost of downtime events. In this work we combine message type extraction based alert detection with the entropy based approach of the Nodeinfo algorithm, which is in production use at Sandia National Laboratories, to significantly improve its performance. We show that with Message Type Indexing (MTI) and some modifications to the Nodeinfo framework, we can achieve an ∼99% reduction in the computational effort required for Nodeinfo and an F-Measure score of up to 100% in the identification of regions of the event log which contain alerts. Our work demonstrates a practical application of employing MTI on a real world data set using an alert detection framework that is currently in production use in a major government run national laboratory.
Fluid–structure interactions of the mitral valve and left heart: Comprehensive strategies, past, present and future

The remodeling that occurs after a posterolateral myocardial infarction can alter mitral valve function by creating conformational abnormalities in the mitral annulus and in the posteromedial papillary muscle, leading to mitral regurgitation (MR). It is generally assumed that this remodeling is caused by a volume load and is mediated by an increase in diastolic wall stress. Thus, MR can be both the cause and effect of an abnormal cardiac stress environment. Computational modeling of ischemic MR and its surgical correction is attractive because it enables an examination of whether a given intervention addresses the correction of regurgitation (fluid‐flow) at the cost of abnormal tissue stress. This is significant because the negative effects of an increased wall stress due to the intervention will only be evident over time. However, a meaningful fluid–structure interaction (FSI) model of the left heart is not trivial; it requires a careful characterization of the in vivo cardiac geometry, the tissue parameterization through inverse analysis, a robust coupled solver that handles collapsing Lagrangian interfaces, the automatic grid‐generation algorithms that are capable of accurately discretizing the cardiac geometry, the innovations in image analysis, the competent and efficient constitutive models and an understanding of the spatial organization of tissue microstructure. In this paper, we profile our work toward a comprehensive FSI model of the left heart by reviewing our early work, presenting our current work and laying out our future work in four broad categories: data collection, geometry, FSI and validation. Copyright © 2009 John Wiley & Sons, Ltd.
Analysis of galactocerebrosidase activity in the mouse brain by a new histological staining method

Gene therapy of galactocerebrosidase (GALC) deficient mice (Twitcher mutants) requires a fast and sensitive assay to detect transduced cells in vitro and in vivo. We have developed a new rapid histochemical method that specifically detects GALC activity in situ in neural cells using 5‐Br‐3Cl‐β‐galactopiranoside (X‐Gal) in the presence of taurodeoxycholic and oleic acids to enhance suspension of the substrate at low pH. Using this method, we observed robust X‐Gal staining in diverse neuronal populations and interfascicular oligodendrocytes in sections from normal mouse brain. In contrast, sections of Twitcher brain did not show a specific staining pattern in neurons or glial cells. The availability of this new sensitive and rapid in situ detection assay is fundamental for the follow‐up of Twitcher mice under gene or cellular therapies to correct central GALC deficiency. © 2004 Wiley‐Liss, Inc.
Présent et futur des prévisions hydrologiques pour la gestion des crues. Le cas du Rhône alpin

L'objectif prioritaire du projet de la 3eme Correction du Rhone en amont du Leman est d'assurer la protection de la plaine lors des crues. Dans ce contexte, le projet MINERVE poursuit le but de prevoir et d'optimiser la gestion des flux hydrauliques, en profitant des previsions hydrologiques et du reseau d'amenagements hydroelectriques existant sur le bassin versant. Pour ce faire, un modele de previsions hydro-meterologiques et un modele d'aide a la decision pour l'exploitation preventive des amenagements hydroelectriques ont ete developpes. Dans un premier temps, le modele fonctionnait de maniere deterministe, en utilisant les previsions meteologiques COSMO-7 de MeteoSuisse. Par la suite, le projet s'est elargi en considerant les previsions porbabilistes COSMO-LEPS et en integrant la notion d'incertitude hydro-meteorologique dans le processus de decision.
Effects of Ginseng Supplementation on Supramaximal Exercise Performance and Short‐Term Recovery

The purpose of this study was to examine the effects of long-term ginseng supplementation on short, supramaximal exercise performance and short-term recovery. Using a double-blind protocol, 24 healthy, active women were randomly assigned to a ginseng (n = 12) or placebo (n = 12) treatment group. Each participant added a standardized extract of Panax ginseng C.A. Meyer (400 mg per day of G115) or placebo to their normal diet for 8 weeks (56–60 days). Before and after the trial period, each subject performed an all-out-effort, 30-second leg cycle ergometry test (Wingate protocol) followed by a controlled recovery under constant laboratory conditions. Nineteen subjects completed the study. Analysis of variance using pretest to posttest change scores revealed no significant difference between the ginseng and placebo study groups for the following variables measured: peak anaerobic power output, mean anaerobic power output, rate of fatigue, and immediate postexercise recovery heart rates (p > 0.05). In conclusion, the present data indicate that prolonged supplementation with ginseng (P. ginseng C.A. Meyer) has no ergogenic benefits during and in the recovery from short, supramaximal exercise.
The need to incorporate routine cervical cancer counselling and screening in the management of HIV positive women in Nigeria.

OBJECTIVE The study aimed to assess the awareness and utilization of the Pap smear among HIV positive women in Lagos, Nigeria. MATERIALS AND METHODS A descriptive cross sectional survey of women attending the anti-retroviral clinic of the Lagos State University Teaching Hospital, Ikeja, Lagos State, Nigeria was carried out between 1st September and 30th November 2009 using a pre-tested questionnaire. Data were analysed using the Epi-info 3.5 statistical software of the Centre for Disease Control and Prevention, Atlanta USA. RESULTS None of the 300 respondents reported having received any form of counselling about cervical cancer and screening during the post HIV test counseling. Seventy six (25.3%) of them had heard of cervical cancer; Forty eight (16%) were aware of the Pap smear and only 15 (31.3%) of these (5% of the total number of respondents) have ever done the test before. The majority (69.7%) of those who had not been screened despite knowledge of the Pap smear, gave non- recommendation by their doctor as the main reason for not doing the test. CONCLUSION Cervical cancer counseling and screening is not part of the routine management of HIV positive women in Lagos, Nigeria. There is need to address this deficiency with appropriate guidelines.
Potency of Enzymes from Renal Tubules as Biotracers in Rheumatoid Arthritis Patients Treat With Most Used Antirheumatic Drugs

Aim: To estimate the effect of initial therapy with Paracetamol and Ketoprofen on glomerular and tubular integrity in patients with Rheumatoid arthritis (RA), to quantify the toxicity of these drugs through measurements of the enzyme excretion that correlates with the damage degree on the tubular epithelium. Microalbuminuria is used as a marker for glomerular damage, and the urinary excretion of N-Acetyl-? -D-glucozaminidase (NAG) as an indicator of proximal tubular damage. To determine if there is a change in the clinical indicators of renal function (serum urea and creatinine, urine urea and creatinine, glomerular filtration rate - GFR) in the course of disease and if that change correlates with the dynamics of the quantity of excreted enzymes in urine, reactants of the acute pfase and index of disease activity (DAS28). Methods: Using the colorimetric method for the determination of NAG, as well as immunoturbidimetric immunoturbidimetric assay for detection of microalbuminuria, we examined samples of 70 participants (35 RA pts treated only with Paracetamol, 35 RA pts treated with Ketoprofen), followed up in five time intervals in the course of 24 weeks. Rheumatoid factor (RF) is determined by the agglutination test (Lateks RF test) in the same participants. Results: there is a weak correlation between NAG and microalbuminuria (r=0.16) in the group of patients treated with Paracetamol, while in the group treated with Ketoprofen there is a moderate correlation (r=0.28). NAG Arch Clin Biomed Res 2016; 1 (1): 20-31 21 enzymuria in range, in number of examined patients and in the time of appearance is greater and appears earlier in the group with Ketoprofen compared with the group of Paracetamol. Conclusions: Ketoprofen is a more potent NAG inductor and triggers greater tubular enzymuria than Parcetamol.
MOVEMENT ANALYSIS

King, DA, Cummins, C, Hume, PA, and Clark, TN. Physical demands of amateur domestic and representative netball in one season in New Zealand assessed using heart rate and movement analysis. J Strength Cond Res 34(7): 2062–2070, 2020—The purpose of this descriptive cohort study was to describe physical demands of netball for positions and between playing levels using microtechnology. Data were collected from 34 female netball players across 3 teams at different levels (over 19 years representative [O19], under 19 years representative [U19], and open-age amateur club domestic) for 20 games using heart rate and microtechnology data. Total distance, maximal velocity, PlayerLoad ([PL] accumulated accelerometer-derived load), and individual PL vectors (PL forward [PLF], PL sideward [PLS] and PL vertical [PLV]) were examined. Analysis by playing level and netball position were conducted. The O19 players recorded a higher mean distance (3,365.7 6 1,875.1 m) per match than U19 (p = 0.0095) players. The O19 players recorded a higher PL (p = 0.0003), PLF (p = 0.004), PLS (p = 0.0039), and PLV (p = 0.0352) than the domestic players. Domestic players recorded a higher maximal velocity than O19 players (p = 0.0003; d = 0.32) throughout the study. Domestic players recorded a higher average maximal heart rate (202.2 6 28.2 b$min21) than O19 (p , 0.0001) and U19 (p = 0.0002) players. Given the high physical demands of netball, individual playerand position-specific training programs are required to develop players for the specific demands of competition while also reducing the impact of excessive physical exertion to facilitate safer engagement within netball. The identification of the differing physical and physiological profiles of individual positional groups throughout match-play highlights the importance of integrating microtechnology into the routine monitoring of intermittent court-based sports, such as netball.