Miracle-dz/UniFAR-FTUs huggingface dataset:
A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage

Lateral gene transfer (LGT) has been crucial in the evolution of the cholera pathogen, Vibrio cholerae. The two major virulence factors are present on two different mobile genetic elements, a bacteriophage containing the cholera toxin genes and a genomic island (GI) containing the intestinal adhesin genes. Non-toxigenic V. cholerae in the aquatic environment are a major source of novel DNA that allows the pathogen to morph via LGT. In this study, we report a novel GI from a non-toxigenic V. cholerae strain containing multiple genes involved in DNA repair including the recombination repair gene recA that is 23% divergent from the indigenous recA and genes involved in the translesion synthesis pathway. This is the first report of a GI containing the critical gene recA and the first report of a GI that targets insertion into a specific site within recA. We show that possession of the island in Escherichia coli is protective against DNA damage induced by UV-irradiation and DNA targeting antibiotics. This study highlights the importance of genetic elements such as GIs in the evolution of V. cholerae and emphasizes the importance of environmental strains as a source of novel DNA that can influence the pathogenicity of toxigenic strains.
EMPIRICAL TESTS OF RANDOMNESS BASED ON ARRIVAL TIMES

We propose new empirical tests for pseudorandom numbers based on random walks on Z m n . The tests focus on the distribution of arrival time at zero starting from a nonzero fixed point x. The exact probability density of the arrival time is obtained by the Fourier analysis on finite groups. This kind of test based on the probability density for a random walk on a finite group is done for the first time. The test results show hidden defects in a Twisted G FSR generator.
Ergonomie assessment on charging station touch screen based on task performance measurement

In the research and development of electric vehicles (EV) in the Research Center for Electrical Power and Mechatronics, Indonesian Institute of Sciences (RCEPM-LIPI), one of the supporting infrastructure in development is charging station. The human factor issues in the man-machine interface of the fast charging station need to be investigated. Therefore, we conducted a task performance assessment on the utilisation of the fast charging station among Indonesian subjects. We examined the reaction time of 16 healthy adult males while they were using a tablet which simulated the charging station interface in five conditions based on the height and tilt angles of the tablet. Subjects were instructed to react to a visual stimulus in a form of target circle and touch it. We measured total reaction time, average reaction time, and error radius of the touching task. Statistical analysis was performed using one-way ANOVA with repeated measures and Bonferroni post-hoc test. The reaction time analysis shows that the longest time of task performance touching the target was in the total reaction time in condition 1 = 105 cm (30°), with response time mean 3.10 ± 0.59 s and the fastest is in condition 2= 122,5 cm (45°) with a mean of 2.92 ± 0.48 s. However, statistical analysis found that there were no significant differences in the conditions measured (p > 0.05). Further study using various sensory input and physiological measurement instruments is necessary. The ergonomics concept of optimal viewing at charging station between human and machine interaction will support the applicability of sustainable transportation in Indonesia. The data that generated from this type of study can be applied to other interfaces (e.g., ATM, Promotion Display, Gas Station, and other displays) that require touchscreen with task performance.
Probabilistic winner-take-all segmentation of images with application to ship detection

A recent neural clustering scheme called "probabilistic winner-take-all (PWTA)" is applied to image segmentation. It is demonstrated that PWTA avoids underutilization of clusters by adapting the form of the cluster-conditional probability density function as clustering proceeds. A modification to PWTA is introduced so as to explicitly utilize the spatial continuity of image regions and thus improve the PWTA segmentation performance. The effectiveness of PWTA is then demonstrated through the segmentation of airborne synthetic aperture radar (SAR) images of ocean surfaces so as to detect ship signatures, where an approach is proposed to find a suitable value for the number of clusters required for this application. Results show that PWTA gives high segmentation quality and significantly outperforms four other segmentation techniques, namely, 1) K-means, 2) maximum likelihood (ML), 3) backpropagation network (BPN), and 4) histogram thresholding.
Eurographics Symposium on Geometry Processing 2015 Continuous Matching via Vector Field Flow

We present a new method for non-rigid shape matching designed to enforce continuity of the resulting correspondence. Our method is based on the recently proposed functional map representation, which allows efficient manipulation and inference but often fails to provide a continuous point-to-point mapping. We address this problem by exploiting the connection between the operator representation of mappings and flows of vector fields. In particular, starting from an arbitrary continuous map between two surfaces we find an optimal flow that makes the final correspondence operator as close as possible to the initial functional map. Our method also helps to address the symmetric ambiguity problem inherent in many intrinsic correspondence methods when matching symmetric shapes. We provide practical and theoretical results showing that our method can be used to obtain an orientation preserving or reversing map starting from a functional map that represents the mixture of the two. We also show how this method can be used to improve the quality of maps produced by existing shape matching methods, and compare the resulting map's continuity with results obtained by other operator-based techniques.
Extrasynaptic αβ subunit GABAA receptors on rat hippocampal pyramidal neurons

Extrasynaptic GABAA receptors that are tonically activated by ambient GABA are important for controlling neuronal excitability. In hippocampal pyramidal neurons, the subunit composition of these extrasynaptic receptors may include α5βγ and/or α4βδ subunits. Our present studies reveal that a component of the tonic current in the hippocampus is highly sensitive to inhibition by Zn2+. This component is probably not mediated by either α5βγ or α4βδ receptors, but might be explained by the presence of αβ isoforms. Using patch‐clamp recording from pyramidal neurons, a small tonic current measured in the absence of exogenous GABA exhibited both high and low sensitivity to Zn2+ inhibition (IC50 values, 1.89 and 223 μm, respectively). Using low nanomolar and micromolar GABA concentrations to replicate tonic currents, we identified two components that are mediated by benzodiazepine‐sensitive and ‐insensitive receptors. The latter indicated that extrasynaptic GABAA receptors exist that are devoid of γ2 subunits. To distinguish whether the benzodiazepine‐insensitive receptors were αβ or αβδ isoforms, we used single‐channel recording. Expressing recombinant α1β3γ2, α5β3γ2, α4β3δ and α1β3 receptors in human embryonic kidney (HEK) or mouse fibroblast (Ltk) cells, revealed similar openings with high main conductances (∼25–28 pS) for γ2 or δ subunit‐containing receptors whereas αβ receptors were characterized by a lower main conductance state (∼11 pS). Recording from pyramidal cell somata revealed a similar range of channel conductances, indicative of a mixture of GABAA receptors in the extrasynaptic membrane. The lowest conductance state (∼11 pS) was the most sensitive to Zn2+ inhibition in accord with the presence of αβ receptors. This receptor type is estimated to account for up to 10% of all extrasynaptic GABAA receptors on hippocampal pyramidal neurons.
Evaluation of a language model using a clustered model backoff

Describes and evaluates a language model using word classes that have been automatically generated from a word clustering algorithm. Class-based language models have been shown to be effective for rapid adaptation, training on small datasets, and reduced memory usage. In terms of model perplexity, prior work has shown diminished returns for class-based language models constructed using very large training sets. This paper describes a method of using a class model as a backoff to a bigram model which produced significant benefits even when trained from a large text corpus. Tests results on the Whisper continuous speech recognition system show that, for a given word error rate, the clustered bigram model uses 2/3 fewer parameters compared to a standard bigram model using unigram backoff.
Detection of Escherichia coli Serogroups O26 and O113 by PCR Amplification of the wzx and wzy Genes

ABSTRACT PCR-based assays for detecting enterohemorrhagic Escherichia coli serogroups O26 and O113 were developed by targeting the wzx (O-antigen flippase) and the wzy (O-antigen polymerase) genes found in the O-antigen gene cluster of each organism. The PCR assays were specific for the respective serogroups, as there was no amplification of DNA from non-O26 and non-O113 E. coli serogroups or from other bacterial genera tested. Using the PCR assays, we were able to detect the organisms in seeded apple juice inoculated at concentration levels as low as ≤10 CFU/ml. The O26- and O113-specific PCR assays can potentially be used for typing E. coli O26 and O113 serogroups; these assays will offer an advantage to food and environmental microbiology laboratories in terms of identifying these non-O157 serogroups by replacing antigen-based serotyping.
A useful variant of the Davis--Kahan theorem for statisticians

The Davis–Kahan theorem is used in the analysis of many statistical procedures to bound the distance between subspaces spanned by population eigenvectors and their sample versions. It relies on an eigenvalue separation condition between certain population and sample eigenvalues. We present a variant of this result that depends only on a population eigenvalue separation condition, making it more natural and convenient for direct application in statistical contexts, and provide an improvement in many cases to the usual bound in the statistical literature. We also give an extension to situations where the matrices under study may be asymmetric or even non-square, and where interest is in the distance between subspaces spanned by corresponding singular vectors.
Face Detection Using Fuzzy Logic and Skin Color Segmentation in Images

Face detection is one of the challenging problems in image processing. A novel face detection system is presented in this paper and we propose a new approach using Takagi-Sugeno (T-S) fuzzy model and Hue Saturation and Value (HSV) color model. The algorithm uses fuzzy classifier in conjunction with HSV color model to quickly locate faces in the image. The fuzzy classifier basically examines small windows of an image to detect presence of faces in that window and the HSV color model detects the skin in the image. The algorithm is characterized by its simplicity and inexpensive computational requirements. The method shows that our system has comparable performance in terms of detection rates and false positive rates.
Silent Data Corruption (SDC) vulnerability of GPU on various GPGPU workloads

GPU (Graphics Processing Unit) is emerging as a key 3D/2D graphics and parallel workload accelerator in various SoC applications. As semiconductor fabrication technology continues to scale, chips (especially those with extremely high transistor counts such as processors) are becoming increasingly vulnerable to faults that could produce unwanted errors in computing. The most severe problem is Silent Data Corruption (SDC) because this fault insidiously generates erroneous outputs without being detected. This paper discusses the characterization of SDC vulnerability of GPU on various GPGPU (General Purpose computing on GPU) workloads.
RPAIR : A Database of Chemical Transformation Patterns in Enzymatic Reactions

Chemical genomics is the next stage of post-genomic analysis. Drugs, environmental substances and various chemical compounds contribute to the fluctuation of bio-systems. Therefore, chemical genomic analysis would require the investigation of relationships between genomes and their extracellular environments. These relationships between bio-systems and environments include complicated biochemical reactions. At present, biochemical reactions are hierarchically classified using EC (Enzyme Commission) numbers [1]. However, the classification is not totally based on chemical reactions, but also includes enzymes or enzyme genes. EC numbers are commonly utilized as identifiers of enzymes or enzyme genes [4]. In order to expand our current limited knowledge on biochemical reactions as represented by EC numbers, we developed a novel database that provides the patterns of the conformational changes between the chemical structures of the substrate and product. This database is integrated into the KEGG resource [3], so other databases in KEGG have links to the entries of this database. All of the data is available from http://www.genome. jp/reaction/.
A Method for Estimating Rigid Object Motion Using Regularized Scene Flow

In this paper, we propose a method for estimating object motion by three-dimensional scene ﬂow using multiple cameras. The scene ﬂow is regularized by applying sub-space constraints and then object motion is estimated us-ing RANSAC estimation. Regularizing the scene ﬂow us-ing subspace constraints results in highly accurate scene ﬂow because it eliminates the effect of noise caused by computing of optical ﬂow. Simulation and experimental results demonstrated that this method can be used to accurately estimate scene ﬂow and object motion parameters for translation and rotation.
Distortion modeling and analysis for multilevel coded APSK with memoryless nonlinearity

In order to improve the bandwidth efficiency of communication systems under strict power limitation, the use of multilevel modulation together with near capacity channel coding is essential. However, such an approach is sensitive to nonlinear distortion associated with high peak-to-average power ratio (PAPR) of the resulting signals. We consider the application of the multilevel coded modulation with multi-stage decoding (MLC/MSD) over nonlinear communication channels and propose a robust unconventional set partitioning approach in conjunction with the metric adjusted to the statistical characteristics of nonlinear distortion. Numerical results show that the proposed method outperforms the system with the conventional labeling in terms of achievable average mutual information (AMI) and frame error rate (FER).
Introductions of West Nile Virus Strains to Mexico

Complete genome sequencing of 22 West Nile virus isolates suggested 2 independent introductions into Mexico. A previously identified mouse-attenuated glycosylation variant was introduced into southern Mexico through the southeastern United States, while a common US genotype appears to have been introduced incrementally into northern Mexico through the southwestern United States.
Assessing patient characteristics and radiation-induced non-targeted effects in vivo for high dose-rate (HDR) brachytherapy

Purpose: To test whether blood, urine, and tissue based colony-forming assays are a useful clinical detection tool for assessing fractionated treatment responses and non-targeted radiation effects in bystander cells. Materials and methods: To assess patients’ responses to radiation treatments, blood serum, urine, and an esophagus explant-based in vivo colony-forming assay were used from oesophageal carcinoma patients. These patients underwent three fractions of high dose rate (HDR) intraluminal brachytherapy (ILBT). Results: Human keratinocyte reporters exposed to blood sera taken after the third fraction of brachytherapy had a significant increase in cloning efficiency compared to baseline samples (p < 0.001). Such results may suggest an induced radioresistance response in bystander cells. The data also revealed a clear inverse dose-rate effect during late treatment fractions for the blood sera data only. Patient characteristics such as gender had no statistically significant effect (p > 0.05). Large variability was observed among the patients’ tissue samples, these colony-forming assays showed no significant changes throughout fractionated brachytherapy (p > 0.05). Conclusion: Large inter-patient variability was found in the urine and tissue based assays, so these techniques were discontinued. However, the simple blood-based assay had much less variability. This technique may have future applications as a biological dosimeter to predict treatment outcome and assess non-targeted radiation effects.
Hand-Based Biometrics Fusing Palmprint and Finger-Knuckle-Print

Although biometrics technology has progressed substantially, its performance is still to be improved for real applications. This paper aims to improve the accuracy of personal identification, when only single sample is registered as template, by integrating multiple hand-based biometrics, i.e. palmprint and finger-knuckle-print. To make fusion much easier, the same feature, so called fusion code, and decision level fusion strategy are used. Experimental results show that much better performance than single modal biometrics has been achieved.
Language: Journal of the Linguistic Society of America

Language Style Sheet Please note that this style should be followed in the preparation of manuscripts that are being submitted to IJLASSO for review. Manuscripts that depart from the style sheet will be returned to the author for corrections in egregious cases. Submissions should be made electronically, via a Microsoft Word document, to the IJLASSO e-mail address (ijlasso@lsu.edu). If you use special symbols in your manuscript, please send a . pdf file of your manuscript along with the other files, for our reference. [NB: Manuscripts for IJLASSO may be submitted in either English or Spanish. ]
Adaptive regularization for image restoration using a variational inequality approach

In this paper, a generalized image restoration method is formulated as a variational inequality problem, whose solution is obtained using a dynamic system approach. In this method, the restored image and the regularization parameter are obtained simultaneously. In particular, the optimum regularization parameter is determined adaptively, depending on noise and image content. The restoration problem is presented in a generalized form so that it maybe be implemented using different norms; only L1 and L2 norms have been implemented in this paper. A comparison based on experimental results shows that the proposed method achieves comparable if not better performance as some of the existing state-of-the-art techniques.
Building a Golden Collection of Parallel Multi-Language Word Alignment

This paper reports an experience on producing manual word alignments over six different language pairs (all combinations between Portuguese, English, French and Spanish) (Graça et al., 2008). Word alignment of each language pair is made over the first 100 sentences of the common test set from the Europarl corpora (Koehn, 2005), corresponding to 600 new annotated sentences. This collection is publicly available at http://www.l2f. inesc- id.pt/resources/translation/. It contains, to our knowledge, the first word alignment gold set for the Portuguese language, with three other languages. Besides, it is to our knowledge, the first multi-language manual word aligned parallel corpus, where the same sentences are annotated for each language pair. We started by using the guidelines presented at (Mariño, 2005) and performed several refinements: some due to under-specifications on the original guidelines, others because of disagreement on some choices. This lead to the development of an extensive new set of guidelines for multi-lingual word alignment annotation that, we believe, makes the alignment process less ambiguous. We evaluate the inter-annotator agreement obtaining an average of 91.6% agreement between the different language pairs.
Optimal control of service rate and reliability in scheduling over wireless channels

This work investigates a problem of scheduling tasks on a single server in which the rate at which the server can complete its tasks is not fixed but can be varied- a higher service rate resulting in correspondingly less reliable service. This is a prevalent trade-off in many practical systems including wireless communication systems. Introducing the idea of mode of service, we formulate the rate-reliability problem as a Markov control problem. We obtain existence results and show that the optimal policy has a threshold mode. The optimal policy is also shown to provide average delay guarantee while maximizing goodput. We provide numerical results supporting our analysis and showing advantage of the optimal policy over fixed rate policies.
Paraphrasing of Synonyms for a Fine-grained Data Representation

The paper addressed the question how the paraphrasing of synonyms can be linked with a fine-gained ontology based data representation. Our challenge is to identify for a set of synonyms (including terms and multiword expressions) the best lexical paraphrases suitable for given contexts. Our hypothesis is that: i. the minimal context in which the paraphrasing can be validated is different for different (semantic) word classes; ii. paraphrasing is defined by patterns within the minimal context containing the synonym and its dependent. For each minimal context a different set of rules is defined with respect to the modifiers and complements the words are licensed for. The extracted dependency collocations are linked with the WordNet synonyms. With this we achieve two goals: to define the lexical paraphrases suitable for a given context and to augment available lexicalsemantic resources with linguistic information (the dependency collocations in which synonyms are interchangeable).
An evaluation of the clinical potential of tissue diffraction studies

Medical imaging is a long established part of patient management in the treatment of disease. However, in most cases it only provides anatomical detail and does not provide any form of tissue characterisation. This is particularly true for X-ray imaging. Recent studies on tissue diffraction have shown that true molecular signatures can be derived for different tissue types. Breast cancer samples and liver tissue have been studied. It has been shown that diffraction profiles can be traced away from the primary tumour in excised breast tissue samples and that potentially 3mm fat nodules in liver tissue can be identified in patients at acceptable doses.