Miracle-dz/UniFAR-FTUs huggingface dataset:
A Singular Case of Prophage Complementation in Mutational Activation of recET Orthologs in Salmonella enterica Serovar Typhimurium

ABSTRACT A class of mutations that suppress the recombination defects of recB mutants in Salmonella enterica serovar Typhimurium strain LT2 activates the normally silent recET module of the Gifsy-1 prophage. Allele sbcE21 is a 794-bp deletion within the immunity region of the prophage. Concomitant with activating recET, sbcE21 stimulates Gifsy-1 excision, resulting in unstable suppression. Early studies found both recB suppression and its instability to depend on the presence of the related Gifsy-2 prophage elsewhere in the chromosome. In cells lacking Gifsy-2, the sbcE21 allele became stable but no longer corrected recB defects. Here, we show that a single Gifsy-2 gene is required for Gifsy-1 recET activation in the sbcE21 background. This gene encodes GtgR, the Gifsy-2 repressor. Significantly, the sbcE21 deletion has one end point within the corresponding gene in the Gifsy-1 genome, gogR, which in strain LT2 is a perfect duplicate of gtgR. The deletion truncates gogR and places the Gifsy-1 left operon, including the recET and xis genes, under the control of the gogR promoter. The ability of GtgR to trans-activate this promoter therefore implies that GtgR and GogR normally activate the transcription of their own genes. Consistent with the symmetry of the system, a similar deletion in Gifsy-2 results in a Gifsy-1-dependent sbc phenotype (sbcF24). Two additional Gifsy-1 deletions (sbcE23 and sbcE25) were characterized, as well. The latter causes all but the last codon of the gogR gene to fuse, in frame, to the second half of recE. The resulting hybrid protein appears to function as both a transcriptional regulator and a recombination enzyme.
Evolutionary History of Helicobacter pylori Sequences Reflect Past Human Migrations in Southeast Asia

The human population history in Southeast Asia was shaped by numerous migrations and population expansions. Their reconstruction based on archaeological, linguistic or human genetic data is often hampered by the limited number of informative polymorphisms in classical human genetic markers, such as the hypervariable regions of the mitochondrial DNA. Here, we analyse housekeeping gene sequences of the human stomach bacterium Helicobacter pylori from various countries in Southeast Asia and we provide evidence that H. pylori accompanied at least three ancient human migrations into this area: i) a migration from India introducing hpEurope bacteria into Thailand, Cambodia and Malaysia; ii) a migration of the ancestors of Austro-Asiatic speaking people into Vietnam and Cambodia carrying hspEAsia bacteria; and iii) a migration of the ancestors of the Thai people from Southern China into Thailand carrying H. pylori of population hpAsia2. Moreover, the H. pylori sequences reflect iv) the migrations of Chinese to Thailand and Malaysia within the last 200 years spreading hspEasia strains, and v) migrations of Indians to Malaysia within the last 200 years distributing both hpAsia2 and hpEurope bacteria. The distribution of the bacterial populations seems to strongly influence the incidence of gastric cancer as countries with predominantly hspEAsia isolates exhibit a high incidence of gastric cancer while the incidence is low in countries with a high proportion of hpAsia2 or hpEurope strains. In the future, the host range expansion of hpEurope strains among Asian populations, combined with human motility, may have a significant impact on gastric cancer incidence in Asia.
Comparative Study of Cooperation Tools for Mobile Ad Hoc Networks

Mobile ad hoc networks are formed spontaneously to use the wireless medium for communication among nodes. Each node in this type of network is its own authority and has an unpredictable behaviour. These features involve a cooperation challenge that has been addressed in previous proposals with methods based on virtual currencies. In this work, those methods have been simulated in NS-2 and the results have been analyzed, showing several weaknesses. In particular, it has been concluded that existent methods do not provide significant advances compared with networks without any mechanism for promoting cooperation. Consequently, this work presents three new proposals that try to solve those problems. The obtained results show that the new proposals offer significant improvements over previous schemes based on virtual currencies.
An Automatic Method for Generating Sense Tagged Corpora

The unavailability of very large corpora with semantically disambiguated words is a major limitation in text processing research. For example, statistical methods for word sense disambiguation of free text are known to achieve high accuracy results when large corpora are available to develop context rules, to train and test them.This paper presents a novel approach to automatically generate arbitrarily large corpora for word senses. The method is based on (1) the information provided in WordNet, used to formulate queries consisting of synonyms or definitions of word senses, and (2) the information gathered from Internet using existing search engines. The method was tested on 120 word senses and a precision of 91% was observed.
Arbitrary-ratio image resizing using fast DCT of composite length for DCT-based transcoder

We propose a fast arbitrary-ratio image resizing method for transcoding of the compressed images. The downsizing process in the discrete cosine transform (DCT) domain can be implemented by truncating high-frequency coefficients, whereas the upsizing process is implemented in the DCT domain by padding zero coefficients to the high-frequency part. The proposed method combines a fast inverse and forward DCT of composite length for arbitrary-ratio upsizing or downsizing. According to the resizing ratio, truncating the high-frequency coefficients and padding zeros are appropriately considered by combining the inverse DCT and forward DCT. The proposed method shows a good peak signal-to-noise ratio and less computational complexity compared with the spatial-domain and previous DCT-domain image resizing methods.
Flexible Multi-link Ethernet Binding System for PC Clusters with Asymmetric Topology

In current high-performance PC clusters, the performance and cost of interconnection network are essential issues. Very cost-effective Ethernets, such as Gigabit Ethernet, as well as high performance SANs, such as Infiniband and Myrinet, are still widely used. The authors have been developing a multi-link binding network system for Ethernet, called RI2N, for high-throughput and fault-tolerant interconnection with Gigabit Ethernet. It can be used both for internode communication in MPI programs and traditional UNIX network services such as NFS. In this paper, the authors propose an optimized version of RI2N, called RI2N+, that allows asymmetrical multi-link connection for fitting to various cost-effective system configurations. Such a configuration cannot be supported by Linux Channel Bonding, which is widely used in standard Linux distributions. RI2N+ automatically detects the asymmetric network configuration and controls the traffic distribution to multiple links. In the basic performance evaluation under a high traffic rate, it was confirmed that the throughput of the network with the proposed scheme is improved by approximately 30\% compared with the original RI2N. RI2N+ also maintains high performance even in asymmetric configurations, that is up to 86\% of the relative performance compared with the symmetric case.
Simulating RCS of dispersive media using SO-FDTD-DPW method

Perfectly Matched Layer (PML) is modeled by Split-Field FDTD (SF-FDTD) in order to simulate Radar Cross Section (RCS) of a plasma slab. PML is used as an absorbing boundary, and discrete plane wave (DPW) is employed to generate plane wave. DPW method has a power isolation of 300 dB between scattered-field and total-field regions. The Dispersive media is modelled by shift-operator FDTD. Finally, by using Near-to-Far Field Transformation, all fields are transferred to far field region to calculate RCS.
Some simple rules for interpreting outputs of principal components and correspondence analysis

A large literature has been devoted to the assessment of the right number of eigenvaluesin PCA and CA (two-way and multiple). Most of the publications are based ondistributional assuptions for the sample, or on bootstrap techniques. After havingrecalled some of the most important results, we present simple thresholds based on a« control chart » approach for eigenvalues as well as for contributions, distances
Comparing Parallel Simulation of Social Agents Using Cilk and OpenCL

Recent advances in wireless/mobile communication and body worn sensors, together with ambient intelligence and seamless integrated pervasive technology have paved the way for applications operating based on social signals, i.e., sensing and processing of group behavior, interpersonal relationships, or emotions. Thinking in large, it should be apparent that modeling social systems allowing to study crowd behavior emerging from individual entities' (agents') condition and/or characteristics is, in fact, a challenging task. To address the heterogeneity, analytical agent-based models (ABMs) are gaining popularity due to its capability of directly representing individual entities and their interactions, unfortunately, ABMs (in which each agent has unique behavior) are not very well suited for large populations, expressed by exponentially rising simulation time. To solve this problem, the questions (i) how does the parallel execution of such models scale with capabilities of both the machine (number of cores, cluster size, etc.) and agents (behavioral adaptation function, interaction extent, etc.) and (ii) what is, in comparison, the performance coefficient applying the approach of model execution on graphical processors (GPUs) with its different pipelining architecture, need answers. To this end, we have performed simulation runs with parameter variation on a real parallel and distributed hardware platform using Cilk as well as on a GPU employing OpenCL. Simulation efficiency for two realistic models with varying complexity on a scale of 107 agents has shown the usefulness of both approaches.
Detection of the hereditary hemochromatosis gene mutation by real-time fluorescence polymerase chain reaction and peptide nucleic acid clamping.

Hereditary hemochromatosis (HH), an iron overload disease, is the most common known inheritable disease. The most prevalent form of HH is believed to be the result of a single base-pair mutation. We describe a rapid homogeneous mutation analysis method that does not require post-polymerase chain reaction (PCR) manipulations. This method is a marriage of three emerging technologies: rapid cycling PCR thermal cyclers, peptide nucleic acid (PNA) probes, and a new double-stranded DNA-selective fluorescent dye, Sybr Green I. The LightCycler is a rapid thermal cycler that fluorometrically monitors real-time formation of amplicon with Sybr Green I. PNAs are DNA mimics that are more sensitive to mismatches than DNA probes, and will not serve as primers for DNA polymerases. PNA probes were designed to compete with PCR primers hybridizing to the HH mutation site. Fully complemented PNA probes at an 18:1 ratio over DNA primers with a mismatch result in suppression of amplicon formation. Conversely, PNA probes with a mismatch will not impair the binding of a complementary primer, culminating in amplicon formation. A LightCycler-based rapid genetic assay has been developed to distinguish HH patients from HH carriers and normal individuals using PNA clamping technology.
Effects of Argument Scaffolding and Source Credibility on Science Text Comprehension

This study investigated the effects of argument scaffolding and source credibility on science text comprehension. Eighty-seven college students were randomly assigned to an argument scaffolding activity, or no scaffolding, and read 2 science texts, attributed to a high- or a low-credibility source. The argument-scaffolding group recalled less text-based information but generated more knowledge-based inferences than did the no-scaffolding group. High source credibility enhanced readers’ text-based recall but had little effect on knowledge-based inferences or situation models. Overall, results suggest that argumentation facilitates deeper text comprehension and better argument understanding, while at the same time reducing the effect of source credibility on text processing.
The MPI Bioinformatics Toolkit for protein sequence analysis

The MPI Bioinformatics Toolkit is an interactive web service which offers access to a great variety of public and in-house bioinformatics tools. They are grouped into different sections that support sequence searches, multiple alignment, secondary and tertiary structure prediction and classification. Several public tools are offered in customized versions that extend their functionality. For example, PSI-BLAST can be run against regularly updated standard databases, customized user databases or selectable sets of genomes. Another tool, Quick2D, integrates the results of various secondary structure, transmembrane and disorder prediction programs into one view. The Toolkit provides a friendly and intuitive user interface with an online help facility. As a key feature, various tools are interconnected so that the results of one tool can be forwarded to other tools. One could run PSI-BLAST, parse out a multiple alignment of selected hits and send the results to a cluster analysis tool. The Toolkit framework and the tools developed in-house will be packaged and freely available under the GNU Lesser General Public Licence (LGPL). The Toolkit can be accessed at .
Structural Origins for the Loss of Catalytic Activities of Bifunctional Human LTA4H Revealed through Molecular Dynamics Simulations

Human leukotriene A4 hydrolase (hLTA4H), which is the final and rate-limiting enzyme of arachidonic acid pathway, converts the unstable epoxide LTA4 to a proinflammatory lipid mediator LTB4 through its hydrolase function. The LTA4H is a bi-functional enzyme that also exhibits aminopeptidase activity with a preference over arginyl tripeptides. Various mutations including E271Q, R563A, and K565A have completely or partially abolished both the functions of this enzyme. The crystal structures with these mutations have not shown any structural changes to address the loss of functions. Molecular dynamics simulations of LTA4 and tripeptide complex structures with functional mutations were performed to investigate the structural and conformation changes that scripts the observed differences in catalytic functions. The observed protein-ligand hydrogen bonds and distances between the important catalytic components have correlated well with the experimental results. This study also confirms based on the structural observation that E271 is very important for both the functions as it holds the catalytic metal ion at its location for the catalysis and it also acts as N-terminal recognition residue during peptide binding. The comparison of binding modes of substrates revealed the structural changes explaining the importance of R563 and K565 residues and the required alignment of substrate at the active site. The results of this study provide valuable information to be utilized in designing potent hLTA4H inhibitors as anti-inflammatory agents.
A New Approach for Health Monitoring of Structures: Terrestrial Laser Scanning

Abstract: A new approach is presented for health monitoring of structures using terrestrial laser scanning (TLS). Three‐dimensional (3D) coordinates of a target structure acquired using TLS can have maximum errors of about 10 mm, which is insufficient for the purpose of health monitoring of structures. A displacement measurement model is presented to improve the accuracy of the measurement. The model is tested experimentally on a simply supported steel beam. Measurements were made using three different techniques: (1) linear variable displacement transducers (LVDTs), (2) electric strain gages, and (3) a long gage fiber optic sensor. The maximum deflections estimated by the TLS model are less than 1 mm and within 1.6% of those measured directly by LVDT. Although GPS methods allow measurement of displacements only at the GPS receiver antenna location, the proposed TLS method allows measurement of the entire building's or bridge's deformed shape, and thus a realistic solution for monitoring structures at both structure and member level. Furthermore, it can be used to create a 3D finite element model of a structural member or the entire structure at any instance of time automatically. Through periodic measurements of deformations of a structure or a structural member and performing inverse structural analyses with the measured 3D displacements, the health of the structure can be monitored continuously.
Serum levels of nitric oxide as a predictor of survival in acute respiratory distress syndrome caused by H1N1 pneumonia

A large number of studies show elevated levels of nitric oxide (NO) in infective syndromes, but there is an insufficient number of studies which have investigated serum levels of NO in patients with acute respiratory distress syndrome (ARDS), especially in relation to survival. Hence, we created a study with the aim of determining the NO levels in relation to ARDS survival. Serum levels of NO were measured by Griess reaction in 29 patients [16 men (55%), mean age years 52.72±18]. All data were statistically analyzed using one way ANOVA. Our results show significantly higher serum NO levels in ARDS survivors compared to ARDS non-survivors, (p < 0.05). We conclude that higher serum levels of NO are strongly associated with better clinical outcomes, including increased survival.
Dependent Types for Program Termination Verification

Program termination verification is a challenging research subject of significant practical importance. While there is already a rich body of literature on this subject, it is still undeniably a difficult task to design a termination checker for a realistic programming language that supports general recursion. In this paper, we present an approach to program termination verification that makes use of a form of dependent types developed in Dependent ML (DML), demonstrating a novel application of such dependent types to establishing a liveness property. We design a type system that enables the programmer to supply metrics for verifying program termination and prove that every well-typed program in this type system is terminating. We also provide realistic examples, which are all verified in a prototype implementation, to support the effectiveness of our approach to program termination verification as well as its unobtrusiveness to programming. The main contribution of the paper lies in the design of an approach to program termination verification that smoothly combines types with metrics, yielding a type system capable of guaranteeing program termination that supports a general form of recursion (including mutual recursion), higher-order functions, algebraic datatypes, and polymorphism.
Boosted Classification Trees and Class Probability/Quantile Estimation

The standard by which binary classifiers are usually judged, misclassification error, assumes equal costs of misclassifying the two classes or, equivalently, classifying at the 1/2 quantile of the conditional class probability function P[y=1|x]. Boosted classification trees are known to perform quite well for such problems. In this article we consider the use of standard, off-the-shelf boosting for two more general problems: 1) classification with unequal costs or, equivalently, classification at quantiles other than 1/2, and 2) estimation of the conditional class probability function P[y=1|x]. We first examine whether the latter problem, estimation of P[y=1|x], can be solved with LogitBoost, and with AdaBoost when combined with a natural link function. The answer is negative: both approaches are often ineffective because they overfit P[y=1|x] even though they perform well as classifiers. A major negative point of the present article is the disconnect between class probability estimation and classification. Next we consider the practice of over/under-sampling of the two classes. We present an algorithm that uses AdaBoost in conjunction with Over/Under-Sampling and Jittering of the data "JOUS-Boost". This algorithm is simple, yet successful, and it preserves the advantage of relative protection against overfitting, but for arbitrary misclassification costs and, equivalently, arbitrary quantile boundaries. We then use collections of classifiers obtained from a grid of quantiles to form estimators of class probabilities. The estimates of the class probabilities compare favorably to those obtained by a variety of methods across both simulated and real data sets.
El hacinamiento como contexto: estrategias metodológicas para su análisis

Crowding as context: Analytical and methodological strategies. Crowding can be studied theoretically and methodologically as a focal subject matter or as a background stimuli. One of the advantages of their study as a background stimuli is that other focal behavioral processes, like social interactions which can be influenced by "crowding", could be studied analyzing the contributions of group and spatial density. As a strategical point of departure, we propone a model for the observational study of the individual and institutional influences of "crowding". In this strategy we consider as a focal subject matter, one special kind of social interaction regarding the main contemporary models in crowding: Social interference. The flexible observational designs guide lines for the strategy are discussed, where the field formats records are the nucleus of the proposal. Several options for the record's optimization and for the data analysis are revisited.
Understanding spirituality in the workplace - a qualitative study

Although there has been much interest in recent years in developing spirituality in the workplace there is little rigorous research available to support its effectiveness, for example, in respect of work performance. Without this type of research, many CEOs and business leaders are sceptical that spirituality is anything more than a millennium fad. In order to begin developing robust models to demonstrate the relationship that spirituality has with such criterion measures as employee well‐being and performance, it is first necessary to arrive at a common understanding of the construct of spirituality and how this construct applies in the workplace. For this study, five focus groups were conducted, with an opportunity sample that provided a cross‐section of employees, managers and professionals (n = 33). Two main questions were examined: "What does spirituality mean to me? " and "How do I demonstrate my spirituality in the workplace? " Data from these focus groups were analysed using a grounded theory approach and the computer programme NVivo. Results are reported in three major categories: (1) defining and operationalising spirituality; (2) understanding employee spiritual behaviour and needs in the workplace; and (3) identifying organisational blocks to spiritual development. A preliminary model of spirituality is proposed.
Z-grid-based probabilistic retrieval for scaling up content-based copy detection

Scalability is the key issue in making content-based copy de-tection (CBCD) methods practical for very large image and video databases. Since copies are transformed versions of original documents, CBCD involves some form of retrieval by similarity using as queries the descriptions of potential copies. To enhance the scalability of an existing competitive CBCD method, we introduce here three improvements of this retrieval process: a Z-grid for building the index, uniformity-based sorting and adapted partitioning of the components. Retrieval speed is significantly increased, enabling us to monitor with a single computer one TV channel against a database of 120,000 hours of video.