Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural insights into the unique single-stranded DNA-binding mode of Helicobacter pylori DprA

Natural transformation (NT) in bacteria is a complex process, including binding, uptake, transport and recombination of exogenous DNA into the chromosome, consequently generating genetic diversity and driving evolution. DNA processing protein A (DprA), which is distributed among virtually all bacterial species, is involved in binding to the internalized single-stranded DNA (ssDNA) and promoting the loading of RecA on ssDNA during NTs. Here we present the structures of DNA_processg_A (DprA) domain of the Helicobacter pylori DprA (HpDprA) and its complex with an ssDNA at 2.20 and 1.80 Å resolutions, respectively. The complex structure revealed for the first time how the conserved DprA domain binds to ssDNA. Based on structural comparisons and binding assays, a unique ssDNA-binding mode is proposed: the dimer of HpDprA binds to ssDNA through two small, positively charged binding pockets of the DprA domains with classical Rossmann folds and the key residue Arg52 is re-oriented to ‘open’ the pocket in order to accommodate one of the bases of ssDNA, thus enabling HpDprA to grasp substrate with high affinity. This mode is consistent with the oligomeric composition of the complex as shown by electrophoretic mobility-shift assays and static light scattering measurements, but differs from the direct polymeric complex of Streptococcus pneumoniae DprA–ssDNA.
Numerical Simulation of Effects of Gravity on the Micro Jet Flame in the Confined Space

A microscale ceramic tube was used as a burner jet, and a coaxial jet flame was established in the confined space between the ceramic tube and the outer quartz glass tube. The effects of gravity on the small jet flame characteristics in the confined space were investigated numerically. Comparisons between the experimental data and the numerical data showed that characteristics of the small jet flame structure and temperature field were in good agreement. It verified the accuracy of the numerical simulation. Numerical simulations of flame characteristics at zero gravity level were performed. The results show that the gravity level has a greater influence on the flame width than that on the flame length. The chemical reaction rate is larger under the condition of normal gravity than that of zero gravity.
A Tool for Generating Interactive Euler Diagrams

We describe a tool for generating Euler diagrams from a set of region connection calculus formulas. The generation is based on a variant of local search capturing default reasoning for improving aesthetic appearance of Euler diagrams. We also describe an optimization for diagrams to be interactive: the user can modify the diagram with the mouse while formulas are still satisfied. We also discuss how such a tool may propose new relevant formulas to add to the specification using an approximation algorithm based on the satisfiability of Horn clauses.
Comparison of ΔrelA Strains of Escherichia coli and Salmonella enterica Serovar Typhimurium Suggests a Role for ppGpp in Attenuation Regulation of Branched-Chain Amino Acid Biosynthesis

ABSTRACT The growth recovery of Escherichia coli K-12 andSalmonella enterica serovar Typhimurium ΔrelAmutants were compared after nutritional downshifts requiring derepression of the branched-chain amino acid pathways. Because wild-type E. coli K-12 and S. enterica serovar Typhimurium LT2 strains are defective in the expression of the genes encoding the branch point acetohydroxy acid synthetase II (ilvGM) and III (ilvIH) isozymes, respectively, ΔrelA derivatives corrected for these mutations were also examined. Results indicate that reduced expression of the known global regulatory factors involved in branched-chain amino acid biosynthesis cannot completely explain the observed growth recovery defects of the ΔrelA strains. In the E. coli K-12 MG1655 ΔrelA background, correction of the preexisting rph-1 allele which causes pyrimidine limitations resulted in complete loss of growth recovery. S. enterica serovar Typhimurium LT2 ΔrelA strains were fully complemented by elevated basal ppGpp levels in an S. enterica serovar Typhimurium LT2 ΔrelA spoT1 mutant or in a strain harboring an RNA polymerase mutation conferring a reduced RNA chain elongation rate. The results are best explained by a dependence on the basal levels of ppGpp, which are determined byrelA-dependent changes in tRNA synthesis resulting from amino acid starvations. Expression of the branched-chain amino acid operons is suggested to require changes in the RNA chain elongation rate of the RNA polymerase, which can be achieved either by elevation of the basal ppGpp levels or, in the case of the E. coli K-12 MG1655 strain, through pyrimidine limitations which partially compensate for reduced ppGpp levels. Roles for ppGpp in branched-chain amino acid biosynthesis are discussed in terms of effects on the synthesis of known global regulatory proteins and current models for the control of global RNA synthesis by ppGpp.
Thermal properties and thermal bridges of the envelope of a modern farm biogas plant: case study

The goal of this paper is experimental detection and evaluation of the thermal defects of modern farm biogas plant envelope by infrared thermography technique. Further goal of this paper is the theoretical calculation of basic thermal properties of envelope and critical structure details. The results of this study indicate that the unsuitable structural design of the biogas station plant can lead to existence of the thermal bridges and high heat losses of the building and degradation of structures.
Pushing the boundaries of resistance: insights from Brachypodium-rust interactions

The implications of global population growth urge transformation of current food and bioenergy production systems to sustainability. Members of the family Poaceae are of particular importance both in food security and for their applications as biofuel substrates. For centuries, rust fungi have threatened the production of valuable crops such as wheat, barley, oat, and other small grains; similarly, biofuel crops can also be susceptible to these pathogens. Emerging rust pathogenic races with increased virulence and recurrent rust epidemics around the world point out the vulnerability of monocultures. Basic research in plant immunity, especially in model plants, can make contributions to understanding plant resistance mechanisms and improve disease management strategies. The development of the grass Brachypodium distachyon as a genetically tractable model for monocots, especially temperate cereals and grasses, offers the possibility to overcome the experimental challenges presented by the genetic and genomic complexities of economically valuable crop plants. The numerous resources and tools available in Brachypodium have opened new doors to investigate the underlying molecular and genetic bases of plant–microbe interactions in grasses and evidence demonstrating the applicability and advantages of working with B. distachyon is increasing. Importantly, several interactions between B. distachyon and devastating plant pathogens, such rust fungi, have been examined in the context of non-host resistance. Here, we discuss the use of B. distachyon in these various pathosystems. Exploiting B. distachyon to understand the mechanisms underpinning disease resistance to non-adapted rust fungi may provide effective and durable approaches to fend off these pathogens. The close phylogenetic relationship among Brachypodium spp. and grasses with industrial and agronomic value support harnessing this model plant to improve cropping systems and encourage its use in translational research.
High-Resolution Genome-Wide Mapping of Transposon Integration in Mammals

ABSTRACT The Sleeping Beauty (SB) transposon is an emerging tool for transgenesis, gene discovery, and therapeutic gene delivery in mammals. Here we studied 1,336 SB insertions in primary and cultured mammalian cells in order to better understand its target site preferences. We report that, although widely distributed, SB integration recurrently targets certain genomic regions and shows a small but significant bias toward genes and their upstream regulatory sequences. Compared to those of most integrating viruses, however, the regional preferences associated with SB-mediated integration were much less pronounced and were not significantly influenced by transcriptional activity. Insertions were also distinctly nonrandom with respect to intergenic sequences, including a strong bias toward microsatellite repeats, which are predominantly enriched in noncoding DNA. Although we detected a consensus sequence consistent with a twofold dyad symmetry at the target site, the most widely used sites did not match this consensus. In conjunction with an observed SB integration preference for bent DNA, these results suggest that physical properties may be the major determining factor in SB target site selection. These findings provide basic insights into the transposition process and reveal important distinctions between transposon- and virus-based integrating vectors.
Integrating Planning and Execution for Information Gathering

Current specialized planners for query processing are designed to work in local, reliable, and predictable environments. However, there are a number of problems that arise in gathering information from large networks of distributed information. In this environment actions can be executed in parallel to exploit distributed resources, new goals come into the system in the midst of execution, actions may fail due to exogenous events and need to be replanned, and there is incomplete information about the world. We have developed a planner called Sage that addresses the issues that arise in this environment. This system integrates previous work on planning, execution, replanning, and sensing and extends this work to support simultaneous and interleaved planning and execution. Sage has been applied to the problem of information gathering to provide a flexible and efficient system for integrating heterogeneous and distributed data and has been used in the domains of logistics planning and trauma care.
METRIC BASED ON MUTUAL INFORMATION

It is known that the information required for the intelligibility of a speech signal is distributed non-uniformly in time. In this paper we propose WSTOI, a modified version of STOI, a speech intelligibility metric. With WSTOI the contribution of each time-frequency cell is weighted by an estimate of its intelligibility content. This estimate is equal to the mutual information between two hypothetical signals at either end of a simplified model of human communication. Listening tests show that the modification improves the prediction accuracy of STOI at all performance levels on both long and short utterances. An improvement was observed across all tested noise types and suppression algorithms.
The Association between Parameters of Socioeconomic Status and Hypertension in Korea: the Korean Genome and Epidemiology Study

We investigated the association between socioeconomic status and hypertension in Korea, a country that has experienced a dynamic socioeconomic transition. We analyzed participants of a prospective cohort study—the Korean Genome and Epidemiology Study—enrolled between 2001 and 2003. We recruited 7,089 subjects who underwent a 4-year follow up till 2007. Education and income levels, which are important parameters for socioeconomic status, were stratified into 4 groups. Education level was defined as short (≤ 6 years), mid-short (7–9 years), mid-long (10–12 years), and long (≥ 12 years). Monthly income level was stratified as low (< 500,000 KRW), mid-low (500,000–1,499,999 KRW), mid-high (1,500,000–2,999,999 KRW) or high (≥ 3,000,000 KRW). At baseline, 2,805 subjects (39.5%) were diagnosed with hypertension. Education and income levels were inversely associated with the prevalence and incidence of hypertension (P < 0.001). In multivariate analysis, a shorter duration of education was significantly associated with a higher prevalence of hypertension (P < 0.001), but income level was not (P = 0.305). During the follow-up, 605 subjects (14.2%) were newly diagnosed with hypertension. In multivariate adjusted analysis, the hazard ratios (95% confidence interval) for incident hypertension across the longer education groups were 0.749 (0.544–1.032), 0.639 (0.462–0.884), and 0.583 (0.387–0.879), compared with the shortest education group. There was no significant association between incident hypertension and income across higher income groups: 0.988 (0.714–1.366), 0.780 (0.542–1.121), and 0.693 (0.454–1.056), compared with the lowest income group. In conclusion, education and income levels are associated with the prevalence and incidence of hypertension, but only education is an independent prognostic factor in Korea.
Computational Research on Seismic Intensity Based on Ground Motion Parameters

After an earthquake event, the spatial distribution of seismic intensity of the event and extremely destructed area could be quickly evaluated by means of the empirical relationship between ground-motion parameters and seismic intensity, which has been proposed for years. This can provide a basis for the government to carry out emergency relief and reasonable distribution of relief supplies. In this paper, the computational methods of instrumental seismic intensity used at home and abroad are briefly introduced. By analyzing the advantages of the methods in the USA and Japan, a relatively simple computational method of seismic intensity is proposed. Firstly, the acceleration time history (Aall) and velocity time history (Vall) of the complete vibration are synthetized by the filtered three-direction acceleration and velocity time histories, and substituted in the empirical formulation. Then, the seismic intensity can be computed by the sorting method. After that, this method is compared with the intensity scale evaluation method and fuzzy algorithm by using the strong motion parameters of Wenchuan earthquake. The results show that the method proposed in this paper is better than the two methods and has certain practical values.
RF-sputtering of iridium oxide to be used as stimulation material in functional medical implants

This paper describes the reactive RF-powered sputter deposition of iridium oxide (IrOx) to be used as the active stimulation layer in functional medical implants. Using an approach based on generic curves, the amount of oxygen gettered by the film is determined for various carrier gas flows and pumping speeds. It is shown that under certain conditions the getter effect peaks in the shape of a plateau when increasing the oxygen supply to the chamber. Films deposited along this curve show strong differences in electrochemical behaviour. At the beginning of the plateau, stable films with high electrochemical activity are deposited, and impedance measurements link the increase in charge delivery to a higher active surface area. On depositing at the far side of the plateau, the maximum deposition rate is recorded; however, unstable films are formed. These films predominantly contain unstable iridium oxide species, with iridium atoms in higher valence states. Protein adsorption, as is known to occur at implanted electrodes, was tested on some samples, and does not deteriorate the IrOx characteristics.
Influence of different methods of collection from the canine epididymides on post-thaw caudal epididymal sperm quality

Canine epididymal sperm was collected from the cauda epididymis using 2 different methods (flushing and mincing) to compare the qualities (the percentage of progressively motile, viable, morphologically abnormal, immature and intact acrosomes) before and after freezing and thawing. No significant difference was noted in the quality of the cauda epididymal sperm immediately after collection and after freezing-thawing between the collection methods, although the mean levels of sperm quality with the flushing method were slightly better than that of the mincing method. The flushing method is simple and free of blood contamination, although the vas deferens was too small to be perfused in only 1 dog, and our results suggest that the flushing method is preferable to the mincing method for collecting sperm from the canine cauda epididymis.
Privacy Preservation for Participatory Sensing Applications

Participatory sensing, which collects environmental information from mobile phone users, is growing in popularity. The collected information can be used for national policy or decision-making for companies. However, sensing users may violate their privacy. Recent studies have proposed negative surveys which can analyze the attributes of users statistically without precise information about each user's information. The traditional negative surveys need a lot of samples for proper estimation. These days, several types of negative surveys are used that can estimate the distribution of user attributes with a high degree of accuracy. However, privacy levels of these methods are relatively low. Moreover, existing studies assume that the privacy levels of all users are the same. In this paper, we propose a new negative survey that can estimate data distributions with more precision and can be used in a situation where the privacy levels are different based on each user's demand. By simulations of a synthetic and a real data set, we prove that our proposed method can estimate more precisely than existing methods.
Sar1, a Novel Regulator of ER-Mitochondrial Contact Sites

Endoplasmic reticulum (ER)—mitochondrial contact sites play a pivotal role in exchange of lipids and ions between the two organelles. How size and function of these contact sites are regulated remains elusive. Here we report a previously unanticipated, but conserved role of the small GTPase Sar1 in the regulation of ER-mitochondrial contact site size. Activated Sar1 introduces membrane curvature through its N-terminal amphiphatic helix at the ER-mitochondria interphase and thereby reducing contact size. Conversely, the S. cerevisiae N3-Sar1 mutant, in which curvature induction is decreased, caused an increase in ER-mitochondrial contacts. As a consequence, ER tubules are no longer able to mark the prospective scission site on mitochondria, thereby impairing mitochondrial dynamics. Consistently, blocking mitochondrial fusion partially rescued, whereas deletion of the dynamin-like protein enhanced the phenotype in the sar1D32G mutant. We conclude that Sar1 regulates the size of ER-mitochondria contact sites through its effects on membrane curvature.
A GIS‐Coupled Hydrological Model System for the Watershed Assessment of Agricultural Nonpoint and Point Sources of Pollution

This paper introduces AVSWAT, a GIS based hydrological system linking the Soil and Water Assessment Tool (SWAT) water quality model and ArcView“ Geographic Information System software. The main purpose of AVSWAT is the combined assess‐ment of nonpoint and point pollution loading at the watershed scale. The GIS component of the system, in addition to the traditional functions of data acquisition, storage, organization and display, implements advanced analytical methods with enhanced flexibility to improve the hydrological characterization of a study watershed. Intuitive user friendly graphic interfaces, also part of the GIS component, have been developed to provide an efficient interaction with the model and the associated parameter databases, and ultimately to simplify water quality assessments, while maintaining and increasing their reliability. This is also supported by SWAT, the core of the system, a complex, conceptual, hydrologic, continuous model with spatially explicit parameterization, building upon the United State Department of Agriculture (USDA) modeling experience. A step‐by‐step example application for a watershed in Central Texas is also included to verify the capability and illustrate some of the characteristics of the system which has been adopted by many users around the world.
Incremental learning for place recognition in dynamic environments

Vision-based place recognition is a desirable feature for an autonomous mobile system. In order to work in realistic scenarios, visual recognition algorithms should be adaptive, i.e. should be able to learn from experience and adapt continuously to changes in the environment. This paper presents a discriminative incremental learning approach to place recognition. We use a recently introduced version of the incremental SVM, which allows to control the memory requirements as the system updates its internal representation. At the same time, it preserves the recognition performance of the batch algorithm. In order to assess the method, we acquired a database capturing the intrinsic variability of places over time. Extensive experiments show the power and the potential of the approach.
A knowledge-based approach to ECG interpretation using fuzzy logic

A rule-based expert system which uses generalized modus ponens (GMP) from fuzzy logic as a rule of inference is described here for classification of abnormalities related to rhythm disorder in the human heart, through interpretation of the patient's electrocardiographic (EGG) patterns. Application of GMP makes diagnosis of a wide range of variations in the input ECG patterns possible even if they differ from the patterns defined in the preconditions of the rules of the rulebase. The work shows how fuzzy logic with suitably drawn possibility distributions of variables of cardiological domain plays a significant role in making the expert system sensitive to finer variations of input ECG patterns, which are very common in bioelectric signals, without enhancing the size of the rulebase.
Direct Connection on the Move: Characterization of User Mobility in Cellular-Assisted D2D Systems

Next-generation device-to-device (D2D) communication technology, in which a cellular network assists proximal users at all stages of their interaction, is rapidly developing. Previous research has thoroughly characterized D2D performance aspects from discovery to connection establishment, security, and service continuity; however, prospective D2Denabled applications and services envision highly opportunistic device contacts as a consequence of unpredictable human user mobility. Therefore, mobility's impact on D2D communication requires careful investigation to understand the practical operational efficiency of future cellular-assisted D2D systems. This article offers a first-hand tutorial on various implications of D2D mobility across different user movement patterns and mobility-related parameters and proposes an assessment methodology for D2D-enabled systems. The rigorous system-level evaluation conducted for this study delivers important conclusions on the effects of user mobility in emerging D2D-centric systems.
Effective Structural Inference for Large XML Documents

This paper investigates methods to automatically infer structural information from large XML documents. Using XML as a reference format, we approach the schema generation problem by application of inductive inference theory. In doing so, we review and extend results relating to the search spaces of grammatical inferences for large data set. We evaluate the result of an inference process using the concept of Minimum Message Length. Comprehensive experimentation reveals our new hybrid method to be the most effective for large documents. Finally tractability issues, including scalability analysis, are discussed.