Miracle-dz/UniFAR-FTUs huggingface dataset:
A genome‐wide strategy for the identification of essential genes in Staphylococcus

 aureus

To address the need for new approaches to antibiotic drug development, we have identified a large number of essential genes for the bacterial pathogen, Staphylococcus aureus, using a rapid shotgun antisense RNA method. Staphylococcus aureus chromosomal DNA fragments were cloned into a xylose‐inducible expression plasmid and transformed into S. aureus. Homology comparisons between 658 S. aureus genes identified in this particular antisense screen and the Mycoplasma genitalium genome, which contains 517 genes in total, yielded 168 conserved genes, many of which appear to be essential in M. genitalium and other bacteria. Examples are presented in which expression of an antisense RNA specifically reduces its cognate mRNA. A cell‐based, drug‐screening assay is also described, wherein expression of an antisense RNA confers specific sensitivity to compounds targeting that gene product. This approach enables facile assay development for high throughput screening for any essential gene, independent of its biochemical function, thereby greatly facilitating the search for new antibiotics.
On the Solution of the Stokes Equation on Regions with Corners

The detailed behavior of solutions to Stokes equations on regions with corners has been historically difficult to characterize. The solutions to Stokes equations on regions with corners are known to develop singularities in the vicinity of corners; in particular, the solutions are known to have infinite oscillations along almost every ray that meet at the corner. While the nature of singularities for the differential equation have been analyzed in great detail, very little is known about the nature of singularities for the corresponding integral equations. In this paper, we observe that, when the Stokes equation is formulated as a boundary integral equation, the solutions are representable by rapidly convergent series of the form ∑jcjtμjsinβjlogt+djtμjcosβjlogt , where t is the distance from the corner and the parameters μj, βj are real, and are determined via an explicit formula depending on the angle at the corner. In addition to being analytically perspicuous, these representations lend themselves to the construction of highly accurate and efficient numerical discretizations, significantly reducing the number of degrees of freedom required for the solution of the corresponding integral equations. The results are illustrated by several numerical examples. © 2020 Wiley Periodicals LLC
Interactions of a DNA-bound Transcriptional Activator with the TBP-TFIIA-TFIIB-Promoter Quaternary Complex*

Site-specific protein-DNA photo-cross-linking was used to show that, when bound to its cognate site at various distances upstream of the TATA element, the chimeric transcriptional activator GAL4-VP16 can physically interact with a TATA box-binding protein (TBP)- transcription factor IIA (TFIIA)-TFIIB complex assembled on the TATA element. This result implies DNA bending and looping of promoter DNA as a result of the physical interaction between GAL4-VP16 and an interface of the TBP-TFIIA-TFIIB complex. This protein-protein interaction on promoter DNA minimally requires the presence of one GAL4 binding site and the formation of a quaternary complex containing TBP, TFIIB, and TFIIA on the TATA element. Notably, the topology of the TBP-TFIIA-TFIIB-promoter complex is not altered significantly by the interaction with DNA-bound activators. We also show that the ability of GAL4-VP16 to activate transcription through a single GAL4 binding site varies according to its precise location and orientation relative to the TATA element and that it can approach the efficiency obtained with multiple binding sites. Taken together, our results indicate that the spatial positioning of the DNA-bound activation domain is important for efficient activation, possibly by maximizing its interactions with the transcriptional machinery including the TBP-TFIIA-TFIIB-promoter quaternary complex.
Further the Effectiveness of Software Testability Measure

Software testability is proposed to address the problem of increasing cost of test and the quality of software. Testability measure provides a quantified way to denote the testability of software. Since 1990s, many testability measure models are proposed to address the problem. By discussing the contradiction between domain testability and domain range ratio (DRR), a new testability measure, semantic fault distance, is proposed. Its validity is discussed. Keywords—Software testability, DRR, Domain testability.
Nitrogen and Organic Matter Removal from Slaughterhouse Wastewater in a Lab-Scale Aerobic Fixed-Film Bioreactor

This paper presents the behaviour of a laboratory scale Aerobic Fixed-Film Bioreactor (Ae-FFB) with arranged media including its initial start up phase. It examines the viability of the Ae-FFB to remove nitrogen and organic matter from poultry slaughterhouse wastewater. After 12 days of operation while rapid growth of nitrifying bacteria took place, nitrogen and organic loading rates were increased progressively by up to 0.2 kg TKN m-3 day-1 and 0.8 kg COD m-3 day-1 respectively, reaching nitrogen and organic matter removal efficiencies of up to 92%. Heterotrophic bacteria, mainly placed in the suspended biomass accumulated at the bottom of the reactor, were found to be competing with nitrifying bacteria for oxygen, which limited nitrification efficiency. Despite operating with dissolved oxygen concentrations of around 3.5 mg l-1, an important contribution of the denitrification process was observed that removed up to 50% of oxidised nitrogen, depending on the availability of biodegradable organic matter.
The use of 3D face shape modelling in dysmorphology

Facial appearance can be a significant clue in the initial identification of genetic conditions, but their low incidence limits exposure during training and inhibits the development of skills in recognising the facial “gestalt” characteristic of many dysmorphic syndromes. Here we describe the potential of computer-based models of three-dimensional (3D) facial morphology to assist in dysmorphology training, in clinical diagnosis and in multidisciplinary studies of phenotype–genotype correlations.
Long-term quality of life after intensified multi-modality treatment of oral cancer including intra-arterial induction chemotherapy and adjuvant chemoradiation

Background: Quality of life (QoL) studies are well established when accompanying trials in head and neck cancer, but studies on long-term survivors are rare. Aims: The aim was to evaluate long-term follow-up patients treated with an intensified multi-modality therapy. Setting and Design: Cross-sectional study, tertiary care center. Patients and Methods: A total of 135 oral/oropharyngeal cancer survivors having been treated with an effective four modality treatment (intra-arterial induction chemotherapy, radical surgery, adjuvant radiation, concurrent systemic chemotherapy) filled European Organisation for Research and Treatment of Cancer (EORTC) QLQ-C30 and HN35 questionnaires. Mean distance to treatment was 6.1 (1.3-16.6) years. Results were compared with a reference patient population (EORTC reference manual). In-study group comparison was also carried out. Statistical Analysis: One-sample t-test, Mann-Whitney-test, Kruskal-Wallis analysis. Results: QoL scores of both populations were well comparable. Global health status, cognitive and social functioning, fatigue, social eating, status of teeth, mouth opening and dryness, and sticky saliva were significantly worse in the study population; pain and need for pain killers, cough, need for nutritional support, problems with weight loss and gain were judged to be significantly less. Patients 1-year posttreatment had generally worse scores as compared to patients with two or more years distance to treatment. Complex reconstructive measures and adjuvant (chemo) radiation were main reasons for significant impairment of QoL. Conclusion : Subjective disease status of patients following a maximized multi-modality treatment showed an expectable high degree of limitations, but was generally comparable to a reference group treated less intensively, suggesting that the administration of an intensified multi-modality treatment is feasible in terms of QoL/effectivity ratio.
Role of Cystathionine β-Lyase in Catabolism of Amino Acids to Sulfur Volatiles by Genetic Variants of Lactobacillus helveticus CNRZ 32

ABSTRACT Catabolism of sulfur-containing amino acids plays an important role in the development of cheese flavor. During ripening, cystathionine β-lyase (CBL) is believed to contribute to the formation of volatile sulfur compounds (VSCs) such as methanethiol and dimethyl disulfide. However, the role of CBL in the generation of VSCs from the catabolism of specific sulfur-containing amino acids is not well characterized. The objective of this study was to investigate the role of CBL in VSC formation by Lactobacillus helveticus CNRZ 32 using genetic variants of L. helveticus CNRZ 32 including the CBL-null mutant, complementation of the CBL-null mutant, and the CBL overexpression mutant. The formation of VSCs from methionine, cystathionine, and cysteine was determined in a model system using gas chromatography-mass spectrometry with solid-phase microextraction. With methionine as a substrate, CBL overexpression resulted in higher VSC production than that of wild-type L. helveticus CNRZ 32 or the CBL-null mutant. However, there were no differences in VSC production between the wild type and the CBL-null mutant. With cystathionine, methanethiol production was detected from the CBL overexpression variant and complementation of the CBL-null mutant, implying that CBL may be involved in the conversion of cystathionine to methanethiol. With cysteine, no differences in VSC formation were observed between the wild type and genetic variants, indicating that CBL does not contribute to the conversion of cysteine.
Universal Computation in Simple One-Dimensional Cellular Automata

The existence of computation-universal one-dimensional cellular automata with seven states per cell for a transition function depending on the cell itself and its nearest neighbors (r= 1), and four states per cell for r= 2 (when next-nearest neighbors also are included), is shown. It is also demonstrated that a Turing machine with m tape symbols and n internal states can be simulated by a cellular automaton of range r= 1 with m+ n+ 2 states per cell.
A Cohesion Based Friend Recommendation System

Social network sites have attracted millions of users with the social revolution in Web2.0. A social network is composed by communities of individuals or organizations that are connected by a common interest. Online social networking sites like Twitter, Facebook and Orkut are among the most visited sites in the Internet chew, (2008). In the social network sites, a user can register other users as friends and enjoy communication. However, the large amount of online users and their diverse and dynamic interests possess great challenges to support such a novel feature in online social networks kwon, (2010). In this work, we design a general friend recommendation framework based on cohesion after analyzing the current method of friend recommendation. The main idea of the proposed method is consisted of the following stagesmeasuring the link strength in a network and find out possible link on this network that is yet to be established; detecting communities among the network using modularity and recommending friends. Considering the noticeable attraction of users to social networking sites, lots of research has been carried out to take advantage of the users ‘information available in these sites. Knowledge mining techniques have been developed in order to extract valuable pieces of information from the users’ activities. This paper deals with a methodology to generate a social graph of users’ actions and predict the future social activities of the users based upon the existing relationships. This graph is updated dynamically based on the changes in the selected social network. The forecasting performed is based upon some predefined rules applied on the graph.
Influence of physical and chemical factors on the hydrogen transfer capacity of murine leprosy bacilli.

Another paper (6) summarizes certain implications for leprosy research involved in successful application of metabolic methods to washed suspensions of M. leprae murium and by similar studies with cultivable mycobacteria. It must be emphasized that no attempt has been made previously to utilize metabolic methods in such manner that the data obtained could substitute for cultivation or infection data. It should be obvious that premature application of these methods to M. leprae has been avoided because the mere compilation of data is futile unless there be also a secure foundation to inform us when metabolic activity can be interpreted in terms of the viability or infectiousness of the microorganisms, and when it cannot. The preparation of this foundation has depended upon simultaneous study of two fundamental metabolic processes: (a) the enzymatic transfer of hydrogen in order to accomplish oxidation of the complex endogenous materials stored in the bacilli, and (b) the derivation of useful energy by finally burning this hydrogen in the presence of oxygen. Since neither infection data nor colony counts can be obtained with M. leprae, whereas infection data can be obtained with M. leprae murium, the latter has been employed during the past four years to represent the noncultivated mycobacteria, and also to measure the infectiousness of suspensions on which metabolic data were obtained. Cultivable mycobacteria have been employed for comparisons, for plate counts, for analysis of principle, or to provide insight as seemed necessary. Measurement of hydrogen transfer capacity (HTC) permits comprehensive study of many variables with modest numbers of bacilli. This procedure has been used in a search for correlation with results obtained previously when tissue homogenates containing M. leprae murium were inoculated into rats after exposure to different experimental conditions in vitro (5). Since the HTC method permits adequate repetition of rapid and accurate determinations, our knowledge of the physiological requirements of murine leprosy bacilli has expanded rapidly. Conditions with respect to pH, oxygen, carbon dioxide, and electrolytes required for optimal conduct of endogenous metabolism coincide with those for cult i-
On the structure and origin of pressure fluctuations in wall turbulence: predictions based on the resolvent analysis

Abstract We generate predictions for the fluctuating pressure field in turbulent pipe flow by reformulating the resolvent analysis of McKeon and Sharma (J. Fluid Mech., vol. 658, 2010, pp. 336–382) in terms of the so-called primitive variables. Under this analysis, the nonlinear convective terms in the Fourier-transformed Navier–Stokes equations (NSE) are treated as a forcing that is mapped to a velocity and pressure response by the resolvent of the linearized Navier–Stokes operator. At each wavenumber–frequency combination, the turbulent velocity and pressure field are represented by the most-amplified (rank-1) response modes, identified via a singular value decomposition of the resolvent. We show that these rank-1 response modes reconcile many of the key relationships among the velocity field, coherent structure (i.e. hairpin vortices), and the high-amplitude wall-pressure events observed in previous experiments and direct numerical simulations (DNS). A Green’s function representation shows that the pressure fields obtained under this analysis correspond primarily to the fast pressure contribution arising from the linear interaction between the mean shear and the turbulent wall-normal velocity. Recovering the slow pressure requires an explicit treatment of the nonlinear interactions between the Fourier response modes. By considering the velocity and pressure fields associated with the triadically consistent mode combination studied by Sharma and McKeon (J. Fluid Mech., vol. 728, 2013, pp. 196–238), we identify the possibility of an apparent amplitude modulation effect in the pressure field, similar to that observed for the streamwise velocity field. However, unlike the streamwise velocity, for which the large scales of the flow are in phase with the envelope of the small-scale activity close to the wall, we expect there to be a $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}\pi /2$ phase difference between the large-scale wall-pressure and the envelope of the small-scale activity. Finally, we generate spectral predictions based on a rank-1 model assuming broadband forcing across all wavenumber–frequency combinations. Despite the significant simplifying assumptions, this approach reproduces trends observed in previous DNS for the wavenumber spectra of velocity and pressure, and for the scale-dependence of wall-pressure propagation speed.
Sociocultural and Academic Considerations for School-Age d/Deaf and Hard of Hearing Multilingual Learners: A Case Study of a Deaf Latina

For decades , research has focused on American Sign Language/English bilingual education for d/Deaf and hard of hearing students whose families used English or ASL. However, a growing population of d/Dhh children come from households where languages other than English (e.g., Spanish, Chinese, Vietnamese) are used. In a longitudinal case study, the authors document the K–12 educational pathway of a deaf Latina student. Anecdotal records, semistructured interviews, assessment data, and document reviews of the participant’s school and clinical records are used to develop the case study. The findings provide the basis for recommendations for future research and for critical factors to consider to improve the education of d/Dhh Multilingual Learners (DMLs). These include ensuring appropriate educational placements, addressing early communication and language needs, determining effective instructional techniques and assessments, strengthening the L1 to support L2 learning, and providing students with opportunities to learn their heritage language.
Location of the initiation site of calcium transients and sparks in rabbit heart Purkinje cells

1 The distribution and localization of Ca2+ transients and Ca2+ sparks in isolated adult rabbit Purkinje cells were examined using confocal microscopy and the Ca2+ indicator fluo‐3. 2 When cells were field stimulated in 2.0 mm Ca2+ buffer, a transverse confocal line scan (500 Hz) showed that the fluorescence intensity was greatest at the cell periphery during the onset of the Ca2+ transient ([Ca2+]i). In contrast, the [Ca2+]i of ventricular cells showed a more uniform pattern of activation across the cell. Staining with di‐8‐ANEPPS revealed that Purkinje cells lack t‐tubules, whereas ventricular cells have an extensive t‐tubular system. 3 When we superfused both cell types with a buffer containing 5 mm Ca2+‐1 μm isoproterenol (isoprenaline) they produced Ca2+ sparks spontaneously. Ca2+ sparks occurred only at the periphery of Purkinje cells but occurred throughout ventricular cells. Sparks in both cell types could be completely abolished by addition of the SR inhibitor thapsigargin (500 nm). Brief exposure to nifedipine (10 μm) did not reduce the number of spontaneous sparks. 4 Immunofluorescence staining of Purkinje cells with anti‐ryanodine antibody revealed that ryanodine receptors (RyRs) are present at both peripheral and central locations. 5 Computer simulations of experiments in which the calcium transient was evoked by voltage clamp depolarizations suggested that the increase in calcium observed in the centre of the cell could be explained by simple buffered diffusion of calcium. These computations suggested that the RyRs deep within the cell do not contribute significantly to the calcium transient. 6 These results provide the first detailed, spatially resolved data describing Ca2+ transients and Ca2+ sparks in rabbit cardiac Purkinje cells. Both types of events are initiated only at subsarcolemmal SR Ca2+ release sites suggesting that in Purkinje cells, Ca2+ sparks only originate where the sarcolemma and sarcoplasmic reticulum form junctions. The role of the centrally located RyRs remains unclear. It is possible that because of the lack of t‐tubules these RyRs do not experience a sufficiently large Ca2+ trigger during excitation‐contraction (E‐C) coupling to become active.
Pseudo-Supervised Latent Dirichlet Allocation for Image Annotation

Latent Dirichlet allocation (LDA) is a generative probabilistic model of discrete data, where each observed item is represented as a finite mixture over latent topics. Several multi-modal extensions of LDA to model annotated data are available for image annotation. Most of existing methods model the joint distribution of image features and caption texts, in order to capture statistical correlations between the two modalities, introducing an association module to correlate two sets of hidden topics. In this paper we present an alternative probabilistic model, referred to as pseudo-supervised LDA (psLDA), for image annotation, where we directly explore the caption topics to train the image model. Our model consists of two LDAs, each of which corresponds to caption model and image model, respectively, which are trained individually. However, empirical frequencies of the topics in the caption model are served as pseudo-labels for the image model, so that image and caption models are correlated via these pseudo-labels, instead of via latent variables as in most of existing methods. Numerical experiments on 2688-image Label Me dataset demonstrate the outstanding performance of psLDA, compared to existing methods such as corresponding LDA (cLDA) and topic-regression multi-modal LDA (trmmLDA), as measured by caption perplexity.
The double-assignment method for the exponential chaotic tabu search in quadratic assignment problems

The quadratic assignment problem (QAP) is one of the NP-hard combinatorial optimization problems. An exponential chaotic tabu search using a 2-opt algorithm driven by chaotic neuro-dynamics has been proposed as one heuristic method for solving QAPs. In this paper we first propose a new local search, the double-assignment method, suitable for the exponential chaotic tabu search, which adopts features of the Lin-Kernighan algorithm. We then introduce chaotic neuro-dynamics into the double-assignment method to propose a novel exponential chaotic tabu search. We further improve the proposed exponential chaotic tabu search with the double-assignment method by enhancing the effect of chaotic neuro-dynamics.
Inverted index search in data mining

Data mining has its origins in various disciplines. Two most important data mining disciplines are statistics and machine learning. Data mining is a process of finding new, useful knowledge from data using different techniques. These techniques provide faster and better search for large amounts of data. Inverted index is structure that can be used in data mining process. That is a sorted list of words, with the list of corresponding documents attached to each word. Authors explored inverted index structure for a big corpus of documents. For that purpose, authors created application that use inverted index structure. Application uses open source library named Lucene.