Miracle-dz/UniFAR-FTUs huggingface dataset:
The Zur-Regulated ZinT Protein Is an Auxiliary Component of the High-Affinity ZnuABC Zinc Transporter That Facilitates Metal Recruitment during Severe Zinc Shortage

ABSTRACT The pathways ensuring the efficient uptake of zinc are crucial for the ability of bacteria to multiply in the infected host. To better understand bacterial responses to zinc deficiency, we have investigated the role of the periplasmic protein ZinT in Salmonella enterica serovar Typhimurium. We have found that zinT expression is regulated by Zur and parallels that of ZnuA, the periplasmic component of the zinc transporter ZnuABC. Despite the fact that ZinT contributes to Salmonella growth in media containing little zinc, disruption of zinT does not significantly affect virulence in mice. The role of ZinT became clear using strains expressing a mutated form of ZnuA lacking a characteristic histidine-rich domain. In fact, Salmonella strains producing this modified form of ZnuA exhibited a ZinT-dependent capability to import zinc either in vitro or in infected mice, suggesting that ZinT and the histidine-rich region of ZnuA have redundant function. The hypothesis that ZinT and ZnuA cooperate in the process of zinc recruitment is supported by the observation that they form a stable binary complex in vitro. Although the presence of ZinT is not strictly required to ensure the functionality of the ZnuABC transporter, our data suggest that ZinT facilitates metal acquisition during severe zinc shortage.
Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-Experienced Patients Are Missed by Standard Genotype Analysis

ABSTRACT To investigate the extent to which drug resistance mutations are missed by standard genotyping methods, we analyzed the same plasma samples from 26 patients with suspected multidrug-resistant human immunodeficiency virus type 1 by using a newly developed single-genome sequencing technique and compared it to standard genotype analysis. Plasma samples were obtained from patients with prior exposure to at least two antiretroviral drug classes and who were on a failing antiretroviral regimen. Standard genotypes were obtained by reverse transcriptase (RT)-PCR and sequencing of the bulk PCR product. For single-genome sequencing, cDNA derived from plasma RNA was serially diluted to 1 copy per reaction, and a region encompassing p6, protease, and a portion of RT was amplified and sequenced. Sequences from 15 to 46 single viral genomes were obtained from each plasma sample. Drug resistance mutations identified by single-genome sequencing were not detected by standard genotype analysis in 24 of the 26 patients studied. Mutations present in less than 10% of single genomes were almost never detected in standard genotypes (1 of 86). Similarly, mutations present in 10 to 35% of single genomes were detected only 25% of the time in standard genotypes. For example, in one patient, 10 mutations identified by single-genome sequencing and conferring resistance to protease inhibitors (PIs), nucleoside analog reverse transcriptase inhibitors, and nonnucleoside reverse transcriptase inhibitors (NNRTIs) were not detected by standard genotyping methods. Each of these mutations was present in 5 to 20% of the 20 genomes analyzed; 15% of the genomes in this sample contained linked PI mutations, none of which were present in the standard genotype. In another patient sample, 33% of genomes contained five linked NNRTI resistance mutations, none of which were detected by standard genotype analysis. These findings illustrate the inadequacy of the standard genotype for detecting low-frequency drug resistance mutations. In addition to having greater sensitivity, single-genome sequencing identifies linked mutations that confer high-level drug resistance. Such linkage cannot be detected by standard genotype analysis.
Transgenic rice plants that overexpress transcription factors RF2a and RF2b are tolerant to rice tungro virus replication and disease

Rice tungro disease (RTD) is a significant yield constraint in rice-growing areas of South and Southeast Asia. Disease symptoms are caused largely by infection by the rice tungro bacilliform virus (RTBV). Two host transcription factors, RF2a and RF2b, regulate expression of the RTBV promoter and are important for plant development. Expression of a dominant negative mutant of these factors in transgenic rice resulted in phenotypes that mimic the symptoms of RTD, whereas overexpression of RF2a and RF2b had essentially no impact on plant development. Conversely, lines with elevated expression of RF2a or RF2b showed weak or no symptoms of infection after Agrobacterium inoculation of RTBV, whereas control plants showed severe stunting and leaf discoloration. Furthermore, transgenic plants exhibited reduced accumulation of RTBV RNA and viral DNA compared with nontransgenic plants. Similar results were obtained in studies after virus inoculation by green leafhoppers. Gaining disease resistance by elevating the expression of host regulators provides another strategy against RTD and may have implications for other pararetrovirus infections.
Collaborative data sharing with mappings and provenance

A key challenge in science today involves integrating data from databases managed by different collaborating scientists. In this dissertation, we develop the foundations and applications of collaborative data sharing systems (CDSSs), which address this challenge. A CDSS allows collaborators to define loose confederations of heterogeneous databases, relating them through schema mappings that establish how data should flow from one site to the next. In addition to simply propagating data along the mappings, it is critical to record data provenance (annotations describing where and how data originated) and to support policies allowing scientists to specify whose data they trust, and when. Since a large data sharing confederation is certain to evolve over time, the CDSS must also efficiently handle incremental changes to data, schemas, and mappings. We focus in this dissertation on the formal foundations of CDSSs, as well as practical issues of its implementation in a prototype CDSS called Orchestra. We propose a novel model of data provenance appropriate for CDSSs, based on a framework of semiring-annotated relations. This framework elegantly generalizes a number of other important database semantics involving annotated relations, including ranked results, prior provenance models, and probabilistic databases. We describe the design and implementation of the Orchestra prototype, which supports update propagation across schema mappings while maintaining data provenance and filtering data according to trust policies. We investigate fundamental questions of query containment and equivalence in the context of provenance information. We use the results of these investigations to develop novel approaches to efficiently propagating changes to data and mappings in a CDSS. Our approaches highlight unexpected connections between the two problems and with the problem of optimizing queries using materialized views. Finally, we show that semiring annotations also make sense for XML and nested relational data, paving the way towards a future extension of CDSS to these richer data models.
Region-of-Interest Coding Based on Saliency Detection and Directional Wavelet for Remote Sensing Images

With growing contradiction between the high-speed acquisition of remote sensing data and the low-speed data storage and transmission, the advantages of giving higher priority to a region of interest (ROI) in compression have become prominent. Previous research focused on ROI coding, rather than automatic ROI extraction. However, accurate ROI extraction can significantly improve coding efficiency. In this letter, we propose an automatic ROI extraction based on the improved normal directional lifting wavelet transform (LWT). Then, the compression efficiency is enhanced by a novel tangent directional LWT to reduce the signal energy of high-frequency subbands. Finally, the autogenerated ROIs are encoded by a new multibitplane alternating shift method, which supports not only arbitrarily shaped ROI coding, but also flexible adjustment of compression quality in the ROI and the background. The experimental results demonstrate that our method can effectively highlight the ROIs with well-defined boundaries, meanwhile improving the ROI coding with better visual quality.
Modeling the Demand for Liquid Assets: An Application to Canada

En este documento se desarrolla y aplica un modelo de la demanda de activos liquidos de los hogares canadienses, basado en el metodo de la “utilidad directa del dinero” propuesto por Milton Friedman. Se demuestra que en modelos anteriores en que se adopto este metodo, no se tuvieron en cuenta importantes consideraciones microeconomicas y econometricas inherentes al uso de un marco de maximizacion de la utilidad. Empleando recientes mejoras de la teoria de la dualidad, el modelo deriva de una representacion generalizada de las preferencias de hogares individuales, un conjunto de funciones de demanda de limitados activos liquidos, cada una de las cuales contiene como variables el precio de arriendo de todos los activos y el gasto total por servicio del dinero y el cuasidinero. Luego, con la suma de todos los hogares, se obtienen las ecuaciones de la demanda agregada de activos liquidos con fines de estimacion. Una caracteristica importante del modelo es que permite probar explicitamente las hipotesis basicas de maximizacion de la utilidad. El modelo, que se aplica a los datos anuales del periodo 1952-74, incluye cuatro activos: depositos de ahorro personal en bancos autorizados; depositos de ahorro en sociedades de prestamos hipotecarios (TML, por trust and mortgage loan company); depositos a mas de un ano en TML, y Canada Savings Bonds. Los resultados indican, primero, que durante casi dos terceras partes del periodo de estimacion, los datos fueron consistentes con la maximizacion de una ordenacion de preferencias basica de comportamiento racional, definida en relacion con el servicio del dinero y los sustitutos del dinero. Segundo, solo hay pruebas insignificantes de sustituibilidad entre dinero y cuasidinero en general; casi todos los activos son mayormente complementos. Tercero, los resultados indican que el dinero es un bien ordinario y el cuasidinero, un bien suntuario. Por lo tanto, el rapido crecimiento de los pasivos cuasibancarios durante el periodo puede atribuirse a mayores elasticidades de gasto, mas que a variaciones de precios relativos a favor de instituciones financieras distintas de los bancos autorizados.
Comparison of different glucocorticoid regimens in the management of classical congenital adrenal hyperplasia due to 21-hydroxylase deficiency

Background: There are recommendations regarding the total dose of hydrocortisone to be administered in the treatment of classical congenital adrenal hyperplasia (CAH) to achieve the twin objectives of glucocorticoid replacement and control of hyperandrogenism. However, there is evidence gap regarding the breakup, timing and type of the steroid regimen. Objectives: Efficacy of three different glucocorticoid regimens having the same total dose of steroid, differing in either the timing or type of evening steroid administered, in achieving biochemical control of the disease was assessed. Materials and Methods: The study was done in 13 prepubertal children with classical CAH over a 6-month period with 2 months devoted to each regimen. We used a prospective cross-over design using 10-15 mg/m2 total dose of hydrocortisone. Two-fifths of the total dose of hydrocortisone was administered in the morning and one-fifth of the total dose was administered at noon in all the regimens. The regimens differed in the timing of the evening dose of hydrocortisone, 06.00-07.00 pm in regimen 1 and 09.00-10.00 pm in regimen 2. The third regimen had the evening dose of hydrocortisone replaced by an equivalent dose of prednisolone suspension which was administered at 10.00 pm. Serum 17-hydroxyprogesterone and testosterone levels were compared to assess the efficacy of treatment regimens. Results: The three different regimens were found to be similar in their ability to control 17-hydroxyprogesterone and testosterone levels. The percentage of patients with predefined criteria for biochemically controlled disease was similar in all the three regimens. However, there was a trend toward better control of 17-hydroxyprogesterone levels in patients receiving evening dose of prednisolone. Conclusions: There is no significant advantage in administering the hydrocortisone dose late at night in patients with classical CAH.
Low-Power Multiple-Valued Source-Coupled Logic Circuits Using Dual-Supply Voltages for a Reconfigurable VLSI

A novel dual-supply-voltage technique is proposed for a low-power multiple-valued VLSI without decreasing speed. A high-supply voltage is required to generate multiple-valued voltage signals in a current-voltage converter, and a low-supply voltage is used to generate binary voltage signals in a comparator whose speed is not decreased by the low-supply voltage. Moreover, level shifters used to prevent direct-path currents in the conventional dual-VDD CMOS circuits are not necessary to be provided because of constant current flow in the multiple-valued source-coupled logic circuits. As a result, the power consumption of a cell using dual-supply voltages for a multiple-valued reconfigurable VLSI is reduced to 79% in comparison with that of the cell using a single-supply voltage.
Salicylaldehyde and dihydroisobenzofuran derivatives from the marine fungus Zopfiella marina

Abstract Two salicylaldehyde derivatives (1 and 2), a hydroxymethylphenol (3), five dihydroisobenzofuran (4–8) derivatives, and a 5-chloro-3-deoxyisoochracinic acid (9), together with a known 3-deoxyisoochracinic acid (10) were isolated from the marine fungus Zopfiella marina BCC 18240 (or NBRC 30420). The structures of these compounds were elucidated by extensive spectroscopic analysis. Compound 1 showed weak antituberculous activity against Mycobacterium tuberculosis H37Ra, and antibacterial activity against Bacillus cereus with MIC values of 25 and 12.5 μg/mL, respectively.
Design and simulation of a novel phase-encoded OCDMA system

The security of optical code division multi-access (OCDMA) system was analyzed, and the results indicate the hidden trouble of security. A scheme of multi-codes to be transmitted single-user information has been proposed, and single-user eavesdropping model has been simulated. The soft platform of system simulation was built by optisystem3.0 and MATLAB. The simulation analysis of the system has been accomplished on the soft platform. The brute-force searching and a code interception have been studied. The simulation results have shown that this system has better security.
Dual-beam radiation from ID leaky-wave antennas

This contribution proposes leaky-wave antennas operating in dual-mode regime in order to achieve dual-beam radiation patterns. Different radiation mechanisms are applied in the guiding structure to induce radiation from two propagative modes. The presented full-wave results show the potential of dual leaky-mode operation when implemented both in Fabry-Perot and substrate integrated technologies.
Chromaffin cell catecholamine secretion: bisindolylmaleimide compounds exhibit novel and potent antagonist effects at the nicotinic cholinergic receptor in pheochromocytoma cells.

Activation of protein kinase C (PKC) stimulates nicotine-induced catecholamine secretion. PKC down-regulation by prolonged pretreatment with phorbol 12-myristate 13-acetate diminished nicotine-induced catecholamine secretion only slightly (approximately 16%), suggesting substantial PKC independence of nicotinic receptor activation. However, we found that bisindolylmaleimide compounds (which are also putative PKC chemical inhibitors) dramatically inhibited nicotine-induced catecholamine secretion (IC(50) values of approximately 24-37 nM). This inhibition was specific for the nicotinic cholinergic receptor. Catecholamine secretion induced by other nicotinic agonists (such as epibatidine, anatoxin, or cytisine) was also powerfully antagonized by bisindolylmaleimide II (IC(50) values of approximately 60-90 nM). Even high-dose nicotinic agonists failed to overcome the inhibition by bisindolylmaleimide II, suggesting noncompetitive nicotinic antagonism by this class of compounds. Nicotinic inhibition by bisindolylmaleimide seemed not to be readily reversible. Structure-activity studies of bisindolylmaleimide compounds revealed that bisindolylmaleimides I through III are the most potent nicotinic antagonists at the nicotinic cholinergic receptor in PC-12 cells (IC(50) < or =37 nM), whereas bisindolylmaleimide IV and V have far less nicotinic antagonist activity (IC(50) >1 microM); the active compounds I through III have cationic tails at an indole nitrogen, whereas the least potent compounds IV and V do not. By contrast, a free NH within the maleimide ring is crucial for PKC inhibition by this class of compounds. We conclude that bisindolylmaleimides I through III are some of the most potent noncompetitive neuronal nicotinic antagonists, indeed the most potent such antagonists we have observed in PC-12 cells. Nicotinic antagonism of these compounds seems to be independent of PKC inhibition.
A Model for Automatically Detecting and Blocking Pornographic Websites

Preventing juveniles from accessing pornographic web pages remains a problem in Vietnam. The existing tools have failed to block these Vietnamese sites automatically and rely only on configuring black list and white list. In fact, the Vietnamese and English are different in both syntax and semantic, therefore, applying methods used for English into Vietnamese will definitely be much less effective. In this article, we present an automatic system that employs Naïve Bayes machine learning method to filter pornographic web pages in Vietnamese without impacting to users and system performance. The system contains 2 components: The classifier is researched and installed in server, and extension is integrated on the end user's browser. The entire system will be managed from 2 sides: server-side and client-side to gain the best result. In this article, our prime concern is to focus only on text, not image.
Monitoring of Enzymatic Proteolysis Using Self-Assembled Quantum Dot-Protein Substrate Sensors

We have previously utilized hybrid semiconductor quantum dot- (QD-) peptide substrates for monitoring of enzymatic proteolysis. In this report, we expand on this sensing strategy to further monitor protein-protease interactions. We utilize QDs self-assembled with multiple copies of dye-labeled proteins as substrates for the sensing of protease activity. Detection of proteolysis is based on changes in the rate of fluorescence resonance energy transfer (FRET) between the QDs and the proximal dye-labeled proteins following protein digestion by added enzyme. Our study focused on two representative proteolytic enzymes: the cysteine protease papain and the serine protease endoproteinase K. Analysis of the enzymatic digestion allowed us to estimate minimal values for the enzymatic activities of each enzyme used. Mechanisms of enzymatic inhibition were also inferred from the FRET data collected in the presence of inhibitors. Potential applications of this technology include drug discovery assays and in vivo cellular monitoring of enzymatic activity.
Fuzzy cognitive analysis and modeling of water quality

In this paper the water quality is explored using the fuzzy cognitive analysis. Fuzzy cognitive maps of Silov are used as a tool for analysis and modeling. The proposed method is based on the iterative calculation and analysis of system indicators of the fuzzy cognitive maps of Silov for a certain period of time. Presented a fuzzy cognitive map, calculated system parameters and the analysis of the dynamics of changes in these indicators.
A Single Species, Micromonas pusilla (Prasinophyceae), Dominates the Eukaryotic Picoplankton in the Western English Channel

ABSTRACT The class Prasinophyceae (Chlorophyta) contains several photosynthetic picoeukaryotic species described from cultured isolates. The ecology of these organisms and their contributions to the picoeukaryotic community in aquatic ecosystems have received little consideration. We have designed and tested eight new 18S ribosomal DNA oligonucleotide probes specific for different Prasinophyceae clades, genera, and species. Using fluorescent in situ hybridization associated with tyramide signal amplification, these probes, along with more general probes, have been applied to samples from a marine coastal site off Roscoff (France) collected every 2 weeks between July 2000 and September 2001. The abundance of eukaryotic picoplankton remained high (>103 cells ml−1) during the sampling period, with maxima in summer (up to 2 × 104 cells ml−1), and a single green algal species, Micromonas pusilla (Prasinophyceae), dominated the community all year round. Members of the order Prasinococcales and the species Bathycoccus prasinos (Mamiellales) displayed sporadic occurrences, while the abundances of all other Prasinophyceae groups targeted remained negligible.
Splicing and 3′ end formation in the definition of nonsense‐mediated decay‐competent human β‐globin mRNPs

Premature translation termination codons are common causes of genetic disorders. mRNAs with such mutations are degraded by a surveillance mechanism termed nonsense‐mediated decay (NMD), which represents a phylogenetically widely conserved post‐transcriptional mechanism for the quality control of gene expression. How NMD‐competent mRNPs are formed and specified remains a central question. Here, we have used human β‐globin mRNA as a model system to address the role of splicing and polyadenylation for human NMD. We show that (i) splicing is an indispensable component of the human β‐globin NMD pathway, which cannot be compensated for by exonic β‐globin ‘failsafe’ sequences; (ii) the spatial requirements of human β‐globin NMD, as signified by the maximal distance of the nonsense mutation to the final exon–exon junction, are less constrained than in yeast; and (iii) non‐polyadenylated mRNAs with a histone 3′ end are NMD competent. Thus, the formation of NMD‐competent mRNP particles critically depends on splicing but does not require the presence of a poly(A) tail.
Extraction of Informative Genes from Multiple Microarray Data Integrated by Rank-Based Approach

By converting the expression values of each sample into the corresponding rank values, the rank-based approach enables the direct integration of multiple microarray data produced by different laboratories and/or different techniques. In this study, we verify through statistical and experimental methods that informative genes can be extracted from multiple microarray data integrated by the rank-based approach (briefly, integrated rank-based microarray data). First, after showing that a non-parametric technique can be used effectively as a scoring metric for rank-based microarray data, we prove that the scoring results from integrated rank-based microarray data are statistically significant. Next, through experimental comparisons, we show that the informative genes from integrated rank-based microarray data are statistically more significant than those of single-microarray data. In addition, by comparing the lists of informative genes extracted from experimental data, we show that the rank-based data integration method extracts more significant genes than the z-score-based normalization technique or the rank products technique. Public cancer microarray data were used for our experiments and the marker genes list from the CGAP database was used to compare the extracted genes. The GO database and the GSEA method were also used to analyze the functionalities of the extracted genes.