Miracle-dz/UniFAR-FTUs huggingface dataset:
Codon reassignment in the Escherichia coli genetic code

Most organisms, from Escherichia coli to humans, use the ‘universal’ genetic code, which have been unchanged or ‘frozen’ for billions of years. It has been argued that codon reassignment causes mistranslation of genetic information, and must be lethal. In this study, we successfully reassigned the UAG triplet from a stop to a sense codon in the E. coli genome, by eliminating the UAG-recognizing release factor, an essential cellular component, from the bacterium. Only a few genetic modifications of E. coli were needed to circumvent the lethality of codon reassignment; erasing all UAG triplets from the genome was unnecessary. Thus, UAG was assigned unambiguously to a natural or non-natural amino acid, according to the specificity of the UAG-decoding tRNA. The result reveals the unexpected flexibility of the genetic code.
Intercomparison of inversion algorithms to retrieve rain rate from SSM/I by using an extended validation set over the Mediterranean area

The capability of some inversion algorithms to estimate surface rain rate at the midlatitude basin scale from the Special Sensor Microwave Imager (SSM/I) data is analyzed. For this purpose, an extended database has been derived from coincident SSM/I images and half-hourly rain rate data obtained from a rain gauge network, placed along the Tiber River basin in Central Italy, during nine years (from 1992 to 2000). The database has been divided in a training set, to calibrate the empirical algorithms, and in a validation one, to compare the results of the considered techniques. The proposed retrieval methods are based on both empirical and physical approaches. Among the empirical methods, a regression, an artificial feedforward neural network, and a Bayesian maximum a posteriori (MAP) inversion have been considered. Three algorithms available in the literature are also included as benchmarks. As physical algorithms, the MAP method and the minimum mean square estimator have been used. Moreover, in order to test the behavior of the algorithms with different kinds of precipitation, a classification of rainy events, based on some statistical parameters derived from rain gauge measurements, has been performed. From this classification, an attempt to identify the type of event from radiometric data has been carried out. The purposes of this paper are to determine whether the use of an extended training set, referred to a limited geographical area, can improve the SSM/I skill in rain detection and estimation and, mainly, to confirm the validity of the physical approach adopted in previous works. It will be shown that, among all the estimators, the neural network presents the best performances and that the physical techniques provide results only slightly worse than those given by empirical methods, but with the well-known advantage of an easy application to different geographical zones and different sensors.
Dyadic concordance in mother and preschooler resting cardiovascular function varies by risk status.

This study examined concordance in heart rate (HR) and respiratory sinus arrhythmia (RSA) in a sample of 104 child-maltreating (CM) and nonCM mother-preschooler dyads (208 individuals). In a laboratory setting, mother and child cardiac physiology was simultaneously monitored via ECG in a 5-min resting period. Mothers ranged in age from 20 to 49 years; children ranged in age from 3 to 5 years. Significant within-dyad (WD) and between-dyad (BD) associations were observed for mother HR and both child HR and RSA, and the associations were moderated by CM status. Only CM dyads exhibited BD associations: Higher average maternal HR was associated with higher child HR and lower child RSA. By contrast, when the time interval was divided into 30 s epochs, nonCM dyads exhibited positive WD (dynamic) associations in mother and child HR, and both CM and nonCM dyads showed negative WD associations in mother HR and child RSA. Further, mothers' mean HR levels moderated the extent of epoch-by-epoch WD concordance observed in mother and child, such that elevated average maternal HR was associated with lower levels of WD (dynamic) concordance. No BD or WD concordance in maternal and child RSA was observed. The findings suggest that measures of intraindividual variation provide useful, alternate perspectives in the study of dyadic processes in at-risk families.
Personas for Content Creators via Decomposed Aggregate Audience Statistics

We propose a novel method for generating personas based on online user data for the increasingly common situation of content creators distributing products via online platforms. We use non-negative matrix factorization to identify user segments and develop personas by adding personality such as names and photos. Our approach can develop accurate personas representing real groups of people using online user data, versus relying on manually gathered data.
Lodging resistance and agro-morphological characteristics of Elon-elon and Palawan red sprayed with paclobutrazol.

An experiment was conducted during the wet season of 2010 to determine the effects of paclobutrazol on the lodging resistance, agro-morphological characteristics and yield performance of Elon-elon and Palawan red. Paclobutrazol was effective in shortening the length of the lower internodes which resulted to shorter plants but with increased lodging resistance. There was a reduction of 12.42 % on culm length and 9.59 % on plant height of the two varieties sprayed at 1000 ppm compared to the untreated plants. Lodging resistance increased with increased concentration of paclobutrazol and lodging index was described by the equation Y = -0.007x + 7.234. At all concentrations of paclobutrazol, Palawan red had the longest first and fourth internodes, heavier 1000 grain weight and higher leaf area index but with more unfilled grains per panicle than Elon-elon. On the other hand, smaller stem diameter, more productive tillers per hill and longer panicle length were obtained from Elonelon than Palawan red. Application of increasing concentrations of paclobutrazol did not affect the chlorophyll contents of the leaves at 15, 30 and 50 DAFS. The percentage filled grains/panicle, number of spikelets/panicle, weight of 1000 grains, dry matter yield, harvest index and grain yield were likewise unaffected owing to lodging at later stages of rice maturity.
IMPACT OF TOPOGRAPHY ON DISTRIBUTION OF SOILS FORMED FROM BASEMENT COMPLEX ROCKS IN PART OF KUBANNI BASIN, NORTHERN NIGERIA

A THESIS SUBMITTED TO THE POSTGRADUATE SCHOOL, AHMADU BELLO UNIVERSITY, ZARIA, IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE AWARD OF THE DEGREE OF MASTER OF SCIENCE (SOIL SCIENCE) DEPARTMENT OF SOIL SCIENCE AHMADU BELLO UNIVERSITY ZARIA, NIGERIA.
Blood lead levels in children of Lucknow, India

After implementing measures to control lead pollution in many countries, blood lead levels (BLLs) in children have been declined. The phase‐out of leaded petrol began in Lucknow, the capital of most populated state, Uttar Pradesh in India on April 1, 2000. We evaluated the mean BLL and associated risk factors for lead exposure in Lucknow children (3–12 years) after petrol lead phase‐out activity. The mean BLL of the 200 children was 9.3 μg/dL (range: 1.0–27.9 μg/dL). Seventy‐four children (37%) had BLL above the Centre for Disease Control and Prevention's (CDC) level of concern (10 μg/dL). When these data were compared with BLLs determined by the George Foundation among the children of Mumbai, Bangalore, Kolkata, Chennai, Hyderabad, and Delhi during the year 1997 when leaded petrol was in use, where 62%, 62%, 87%, 96%, 43%, and 95%, respectively, then exceeded the CDC intervention level. Further, BLL of present study was very close to Mumbai children (age ≤12 years) estimated following the introduction of unleaded petrol, and 33% children had BLL above the CDC concern level with an average 8.4 μg/dL. Low socioeconomic status, proximity of home to traffic density, and mother's illiteracy were the factors associated with elevated BLLs in Lucknow children (P < 0.05). Overall, results indicate a declining trend of BLL in Lucknow children when compared with those reported from other cities of India when leaded petrol was in practice. A national population‐based study is recommended to determine the prevalence of elevated BLLs after the phase‐out of leaded‐petrol. In addition, future studies on other sources of lead exposure in Lucknow are warranted for public health purposes. © 2009 Wiley Periodicals, Inc. Environ Toxicol, 2010.
Interictal 99mTc‐HMPAO SPECT in Temporal Lobe Epilepsy: Relation to Clinical Variables

Summary: Purpose: Factors affecting blood flow observed by interictal single‐photon emission computed tomography (SPECT) images in temporal lobe epilepsy (TLE) have not been systematically studied or consistently demonstrated. We evaluated interictal SPECT results with respect to many clinical variables in a large population of TLE patients, all of whom underwent temporal lobectomy.
Lyme disease: Is it or is it not?

This past summer, Lyme disease was the topic of a Focus section in the Globe and Mail (1). In this section, the reporter described her experience of having physicians unable and then unwilling to diagnose her symptoms of "skin on fire, dizziness and chest pains, twitching muscles, and trouble keeping balance" as Lyme disease following a tick bite three years previously on Prince Edward Island. She reported finding support for her diagnosis after obtaining a positive test from a California laboratory and after seeing approximately 20 physicians. In her article, she speaks to the controversy surrounding the diagnosis and treatment of Lyme disease, and the tension it creates between those who believe they have it and the physicians they see.
Dynamic service rate control for a single‐server queue with Markov‐modulated arrivals

We consider the problem of service rate control of a single‐server queueing system with a finite‐state Markov‐modulated Poisson arrival process. We show that the optimal service rate is nondecreasing in the number of customers in the system; higher congestion levels warrant higher service rates. On the contrary, however, we show that the optimal service rate is not necessarily monotone in the current arrival rate. If the modulating process satisfies a stochastic monotonicity property, the monotonicity is recovered. We examine several heuristics and show where heuristics are reasonable substitutes for the optimal control. None of the heuristics perform well in all the regimes and the fluctuation rate of the modulating process plays an important role in deciding the right heuristic. Second, we discuss when the Markov‐modulated Poisson process with service rate control can act as a heuristic itself to approximate the control of a system with a periodic nonhomogeneous Poisson arrival process. Not only is the current model of interest in the control of Internet or mobile networks with bursty traffic, but it is also useful in providing a tractable alternative for the control of service centers with nonstationary arrival rates. © 2013 Wiley Periodicals, Inc. Naval Research Logistics 60: 661–677, 2013
Solution structure of P05-NH2, a scorpion toxin analog with high affinity for the apamin-sensitive potassium channel.

The venom of the scorpion Androctonus mauretanicus mauretanicus contains a toxin--P05--which is structurally and functionally similar to scorpion leiurotoxin I (87% sequence identity), a blocker of the apamin-sensitive Ca(2+)-activated K+ channels. P05, a 31-residue polypeptide cross-linked by three disulfide bridges, also possesses binding and physiological properties similar to those of the bee venom toxin apamin (18 residues, two disulfides). However, the amino acid sequences of these two polypeptides are dissimilar, except for a common Arg-Arg-Cys-Gln motif which is located on an alpha-helix. P05-NH2, a synthetic analog of P05, unlike native P05, was found to bind irreversibly to the apamin receptor. The solution structure of P05-NH2 has been solved by conventional two-dimensional NMR techniques followed by distance geometry and energy minimization. The obtained conformation is composed of two and an half turns of alpha-helix (residues 5-14) connected by a tight turn to a two-stranded antiparallel beta-sheet (sequences 17-22 and 25-29). This beta-sheet has a right-handed twist as usual for such secondary structures. The beta-turn connecting the two strands belongs to type II'. This structure is homologous to all scorpion toxin structures known so far as well as to insect defensins. The three arginines known to be involved in the pharmacological activity, i.e., Arg6, Arg7, and Arg13, are all located on the solvent-exposed side of the helix and form a positively charged surface which includes Gln9. The calculated electrostatic potential is highly asymmetric with the greatest positive potential centered on the Arg-rich alpha-helix side. (ABSTRACT TRUNCATED AT 250 WORDS)
Sensorless Control Strategies for Three - Phase PWM Rectifiers

support and help. His precious advice and numerous discussions enhanced my knowledge and scientific inspiration. preparation of the laboratory setup is especially appreciated. Finally, I am very grateful for my wife Ann's and son Kacper's love, patience and faith. I would also like to thank my whole family, particularly my parents for their care over the years. Introduction 2 1. INTRODUCTION Methods for limitation and elimination of disturbances and harmonic pollution in the power system have been widely investigated. This problem rapidly intensifies with the increasing amount of electronic equipment (computers, radio set, printers, TV sets etc.). This equipment, a nonlinear load, is a source of current harmonics, which produce increase of reactive power and power losses in transmission lines. The harmonics also cause electromagnetic interference and, sometimes, dangerous resonances. They have negative influence on the control and automatic equipment, protection systems, and other electrical loads, resulting in reduced reliability and availability. Moreover, nonlinear loads and non-sinusoidal currents produce non-sinusoidal voltage drops across the network impedance's, so that non-sinusoidal voltages appears at several points of the mains. It brings out overheating of line, transformers and generators due to the iron losses. Reduction of harmonic content in line current to a few percent allows avoiding most of the mentioned problems. Restrictions on current and voltage harmonics maintained in many countries through IEEE 519-1992 in the USA and IEC 61000-3-2/IEC 61000-3-4 in Europe standards, are associated with the popular idea of clean power. Many of harmonic reduction method exist. These technique based on passive components, mixing single and three-phase diode rectifiers, and power electronics techniques as: multipulse rectifiers, active filters and PWM rectifiers (Fig. 1.1). They can be generally divided as: A) harmonic reduction of already installed non-linear load; B) harmonic reduction through linear power electronics load installation;
Differential Gene Expression in Thrombomodulin (TM; CD141)+ and TM− Dendritic Cell Subsets

Previously we have shown in a mouse model of bronchial asthma that thrombomodulin can convert immunogenic conventional dendritic cells into tolerogenic dendritic cells while inducing its own expression on their cell surface. Thrombomodulin+ dendritic cells are tolerogenic while thrombomodulin− dendritic cells are pro-inflammatory and immunogenic. Here we hypothesized that thrombomodulin treatment of dendritic cells would modulate inflammatory gene expression. Murine bone marrow-derived dendritic cells were treated with soluble thrombomodulin and expression of surface markers was determined. Treatment with thrombomodulin reduces the expression of maturation markers and increases the expression of TM on the DC surface. Thrombomodulin treated and control dendritic cells were sorted into thrombomodulin+ and thrombomodulin− dendritic cells before their mRNA was analyzed by microarray. mRNAs encoding pro-inflammatory genes and dendritic cells maturation markers were reduced while expression of cell cycle genes were increased in thrombomodulin-treated and thrombomodulin+ dendritic cells compared to control dendritic cells and thrombomodulin− dendritic cells. Thrombomodulin-treated and thrombomodulin+ dendritic cells had higher expression of 15-lipoxygenase suggesting increased synthesis of lipoxins. Thrombomodulin+ dendritic cells produced more lipoxins than thrombomodulin− dendritic cells, as measured by ELISA, confirming that this pathway was upregulated. There was more phosphorylation of several cell cycle kinases in thrombomodulin+ dendritic cells while phosphorylation of kinases involved with pro-inflammatory cytokine signaling was reduced. Cultures of thrombomodulin+ dendritic cells contained more cells actively dividing than those of thrombomodulin− dendritic cells. Production of IL-10 is increased in thrombomodulin+ dendritic cells. Antagonism of IL-10 with a neutralizing antibody inhibited the effects of thrombomodulin treatment of dendritic cells suggesting a mechanistic role for IL-10. The surface of thrombomodulin+ dendritic cells supported activation of protein C and procarboxypeptidase B2 in a thrombomodulin-dependent manner. Thus thrombomodulin treatment increases the number of thrombomodulin+ dendritic cells, which have significantly altered gene expression compared to thrombomodulin− dendritic cells in key immune function pathways.
Marchenko-Pastur Theorem and Bercovici-Pata bijections for heavy-tailed or localized vectors

The celebrated Marchenko-Pastur theorem gives the asymptotic spectral distribution of sums of random, independent, rank-one projections. Its main hypothesis is that these projections are more or less uniformly distributed on the first grassmannian, which implies for example that the corresponding vectors are delocalized, i.e. are essentially supported by the whole canonical basis. In this paper, we propose a way to drop this delocalization assumption and we generalize this theorem to a quite general framework, including random projections whose corresponding vectors are localized, i.e. with some components much larger than the other ones. The first of our two main examples is given by heavy tailed random vectors (as in a model introduced by Ben Arous and Guionnet or as in a model introduced by Zakharevich where the moments grow very fast as the dimension grows). Our second main example is given by vectors which are distributed as the Brownian motion on the unit sphere, with localized initial law. Our framework is in fact general enough to get new correspondences between classical infinitely divisible laws and some limit spectral distributions of random matrices, generalizing the so-called Bercovici-Pata bijection.
A Bacterial Phosphatase-Like Enzyme of the Malaria Parasite Plasmodium falciparum Possesses Tyrosine Phosphatase Activity and Is Implicated in the Regulation of Band 3 Dynamics during Parasite Invasion

ABSTRACT Eukaryotic parasites of the genus Plasmodium cause malaria by invading and developing within host erythrocytes. Here, we demonstrate that PfShelph2, a gene product of Plasmodium falciparum that belongs to the Shewanella-like phosphatase (Shelph) subfamily, selectively hydrolyzes phosphotyrosine, as shown for other previously studied Shelph family members. In the extracellular merozoite stage, PfShelph2 localizes to vesicles that appear to be distinct from those of rhoptry, dense granule, or microneme organelles. During invasion, PfShelph2 is released from these vesicles and exported to the host erythrocyte. In vitro, PfShelph2 shows tyrosine phosphatase activity against the host erythrocyte protein Band 3, which is the most abundant tyrosine-phosphorylated species of the erythrocyte. During P. falciparum invasion, Band 3 undergoes dynamic and rapid clearance from the invasion junction within 1 to 2 s of parasite attachment to the erythrocyte. Release of Pfshelph2 occurs after clearance of Band 3 from the parasite-host cell interface and when the parasite is nearly or completely enclosed in the nascent vacuole. We propose a model in which the phosphatase modifies Band 3 in time to restore its interaction with the cytoskeleton and thus reestablishes the erythrocyte cytoskeletal network at the end of the invasion process.
Binocular rivalry is not chaotic

Time series of the durations each eye was dominant during binocular rivalry were obtained psychophysically. The oscillations showed an adaptation effect with mean and standard deviations of rivalry dominance durations increasing as a square root function of time over the course of a trial. The data were corrected for this non-stationarity. Dominance durations had a log-normal probability distribution and the autocorrelation function revealed no short term correlations in the time series. In an attempt to distinguish whether the variability of durations was due to a deterministic, low-dimensional chaotic attractor or to a stochastic process, the data were subjected to two tests. The first was calculation of correlation dimensions and the second was nonlinear forecasting of the time series. Both tests included comparisons with randomized ‘surrogate data’ as controls. In neither case was there a large difference between test results for actual data and surrogate data. We conclude that chaos is not a major factor underlying variability in binocular rivalry.
Structure of Hepatitis C Virus Polymerase in Complex with Primer-Template RNA

ABSTRACT The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory β-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesis at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory β-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus.