Miracle-dz/UniFAR-FTUs huggingface dataset:
The NEAT Domain-Containing Proteins of Clostridium perfringens Bind Heme

The ability of a pathogenic bacterium to scavenge iron from its host is important for its growth and survival during an infection. Our studies on C. perfringens gas gangrene strain JIR325, a derivative of strain 13, showed that it is capable of utilizing both human hemoglobin and ferric chloride, but not human holo-transferrin, as an iron source for in vitro growth. Analysis of the C. perfringens strain 13 genome sequence identified a putative heme acquisition system encoded by an iron-regulated surface gene region that we have named the Cht (Clostridium perfringens heme transport) locus. This locus comprises eight genes that are co-transcribed and includes genes that encode NEAT domain-containing proteins (ChtD and ChtE) and a putative sortase (Srt). The ChtD, ChtE and Srt proteins were shown to be expressed in JIR325 cells grown under iron-limited conditions and were localized to the cell envelope. Moreover, the NEAT proteins, ChtD and ChtE, were found to bind heme. Both chtDE and srt mutants were constructed, but these mutants were not defective in hemoglobin or ferric chloride utilization. They were, however, attenuated for virulence when tested in a mouse myonecrosis model, although the virulence phenotype could not be restored via complementation and, as is common with such systems, secondary mutations were identified in these strains. In summary, this study provides evidence for the functional redundancies that occur in the heme transport pathways of this life threatening pathogen.
The association between dog ownership and physical activity in adults – a brief review

The following key messages have been found as a result of this rapid review: 1. Dog walking may be used to encourage physical activity at a population level. 2. Dog owners are not more active than non-dog owners unless they walk their dogs. 3. Currently, there is a lack of robust evidence to suggest a correlation between dog ownership and an increase in physical activity and/or weight loss.
Feature-Based Classification of Amino Acid Substitutions outside Conserved Functional Protein Domains

There are more than 500 amino acid substitutions in each human genome, and bioinformatics tools irreplaceably contribute to determination of their functional effects. We have developed feature-based algorithm for the detection of mutations outside conserved functional domains (CFDs) and compared its classification efficacy with the most commonly used phylogeny-based tools, PolyPhen-2 and SIFT. The new algorithm is based on the informational spectrum method (ISM), a feature-based technique, and statistical analysis. Our dataset contained neutral polymorphisms and mutations associated with myeloid malignancies from epigenetic regulators ASXL1, DNMT3A, EZH2, and TET2. PolyPhen-2 and SIFT had significantly lower accuracies in predicting the effects of amino acid substitutions outside CFDs than expected, with especially low sensitivity. On the other hand, only ISM algorithm showed statistically significant classification of these sequences. It outperformed PolyPhen-2 and SIFT by 15% and 13%, respectively. These results suggest that feature-based methods, like ISM, are more suitable for the classification of amino acid substitutions outside CFDs than phylogeny-based tools.
An Ecient First-order Horn-clause Abduction System Based on the Atms 3 Hwee Tou Ng

This paper presents an algorithm for rst-order Horn-clause abduction that uses an ATMS to avoid redundant computation. This algorithm is either more e cient or more general than any other previous abduction algorithm. Since computing all minimal abductive explanations is intractable, we also present a heuristic version of the algorithm that uses beam search to compute a subset of the simplest explanations. We present empirical results on a broad range of abduction problems from text understanding, plan recognition, and device diagnosis which demonstrate that our algorithm is at least an order of magnitude faster than an alternative abduction algorithm that does not use an ATMS.
PDFX: fully-automated PDF-to-XML conversion of scientific literature

PDFX is a rule-based system designed to reconstruct the logical structure of scholarly articles in PDF form, regardless of their formatting style. The system's output is an XML document that describes the input article's logical structure in terms of title, sections, tables, references, etc. and also links it to geometrical typesetting markers in the original PDF, such as paragraph and column breaks. The key aspect of the presented approach is that the rule set used relies on relative parameters derived from font and layout specifics of each article, rather than on a template-matching paradigm. The system thus obviates the need for domain- or layout-specific tuning or prior training, exploiting only typographical conventions inherent in scientific literature. Evaluated against a significantly varied corpus of articles from nearly 2000 different journals, PDFX gives a 77.45 F1 measure for top-level heading identification and 74.03 for extracting individual bibliographic items. The service is freely available for use at http://pdfx.cs. man.ac. uk/.
Natural Transformation of Campylobacter jejuni Occurs Beyond Limits of Growth

Campylobacter jejuni is a human bacterial pathogen. While poultry is considered to be a major source of food borne campylobacteriosis, C. jejuni is frequently found in the external environment, and water is another well-known source of human infections. Natural transformation is considered to be one of the main mechanisms for mediating transfer of genetic material and evolution of the organism. Given the diverse habitats of C. jejuni we set out to examine how environmental conditions and physiological processes affect natural transformation of C. jejuni. We show that the efficiency of transformation is correlated to the growth conditions, but more importantly that transformation occurs at growth-restrictive conditions as well as in the late stationary phase; hence revealing that growth per se is not required for C. jejuni to be competent. Yet, natural transformation of C. jejuni is an energy dependent process, that occurs in the absence of transcription but requires an active translational machinery. Moreover, we show the ATP dependent ClpP protease to be important for transformation, which possibly could be associated with reduced protein glycosylation in the ClpP mutant. In contrast, competence of C. jejuni was neither found to be involved in DNA repair following DNA damage nor to provide a growth benefit. Kinetic studies revealed that several transformation events occur per cell cycle indicating that natural transformation of C. jejuni is a highly efficient process. Thus, our findings suggest that horizontal gene transfer by natural transformation takes place in various habitats occupied by C. jejuni.
Multipoint Aerodynamic Shape Optimization Investigations of the Common Research Model Wing

The aerodynamic shape optimization of wings in transonic flow is an inherently challenging problem. In addition to the high computational cost of solving the Reynolds-averaged Navier–Stokes equations, there is a complex interdependence between the cross-sectional shape, wave drag, and viscous effects. Furthermore, it is necessary to perform multipoint optimizations to ensure good performance for a range of flight conditions. The choice of which flight conditions should be considered in a multipoint optimization and how many of these should be considered is still not well understood. This paper addresses this issue by solving a series of seven benchmark optimizations developed by the AIAA Aerodynamic Optimization Discussion Group. These optimization cases include a single-point optimization, four three-point optimizations, a nine-point optimization, and a five-point optimization. The optimizations consist in minimizing the weighted drag coefficient subject to lift, moment, thickness, and volume constraints.
Multimodal rigid-body registration of 3D brain images using bilateral symmetry

In this paper we show how to use the approximate bilateral symmetry of the brain with respect to its interhemispheric fissure for intra-subject (rigid-body) mono- and multimodal 3D image registration. We propose to define and compute an approximate symmetry plane in the two images to register and to use these two planes as constraints in the registration problem. This 6-parameter problem is thus turned into three successive 3-parameter problems. Our hope is that the lower dimension of the parameter space makes these three subproblems easier and faster to solve than the initial one. We implement two algorithms to solve these three subproblems in the exact same way, within a common intensity-based framework using mutual information as the similarity measure. We compare this symmetry-based strategy with the standard approach (i.e. direct estimation of a 6-parameter rigid-body transformation), also implemented within the same framework, using synthetic and real datasets. We show our symmetry-based method to achieve subvoxel accuracy with better robustness and larger capture range than the standard approach, while being slightly less accurate and slower. Our method also succeeds in registering clinical MR and PET images with a much better accuracy than the standard approach. Finally, we propose a third strategy to decrease the run time of the symmetry-based approach and we give some ideas, to be tested in future works, on how to improve its accuracy.
Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments

No microorganism capable of anaerobic growth on methane as the sole carbon source has yet been cultivated. Consequently, information about these microbes has been inferred from geochemical and microbiological observations of field samples. Stable isotope analysis of lipid biomarkers and rRNA gene surveys have implicated specific microbes in the anaerobic oxidation of methane (AOM). Here we use combined fluorescent in situ hybridization and secondary ion mass spectrometry analyses, to identify anaerobic methanotrophs in marine methane-seep sediments. The results provide direct evidence for the involvement of at least two distinct archaeal groups (ANME-1 and ANME-2) in AOM at methane seeps. Although both archaeal groups often occurred in direct physical association with bacteria, they also were observed as monospecific aggregations and as single cells. The ANME-1 archaeal group more frequently existed in monospecific aggregations or as single filaments, apparently without a bacterial partner. Bacteria associated with both archaeal groups included, but were not limited to, close relatives of Desulfosarcina species. Isotopic analyses suggest that monospecific archaeal cells and cell aggregates were active in anaerobic methanotrophy, as were multispecies consortia. In total, the data indicate that the microbial species and biotic interactions mediating anaerobic methanotrophy are diverse and complex. The data also clearly show that highly structured ANME-2/Desulfosarcina consortia are not the sole entities responsible for AOM at marine methane seeps. Other microbial groups, including ANME-1 archaea, are capable of anaerobic methane consumption either as single cells, in monospecific aggregates, or in multispecies consortia.
WIYN open cluster study. XXVI. Improved kinematic membership and spectroscopy of IC 2391

Context. Young open clusters provide important clues to the interface between the main sequence and pre-main-sequence phases of stellar evolution. The young and nearby open cluster IC 2391 is well-suited to studies of these two evolutionary phases. Aims. We establish a bona fide set of cluster members and then analyze this set in terms of binary frequency, projected rotational velocities, [Fe/H], and lithium abundance. In the wake of the Hipparcos distance controversy for the Pleiades, we compare the main-sequence fitting distance modulus to the Hipparcos mean parallax for IC 2391. Methods. We have obtained new proper motions for 6991 stars down to $V \sim 13$–16 over a ~9-deg 2 area of the sky comprising IC 2391. The precision of proper motions, $\sigma_\mu=1.7$ mas yr -1 , allowed us to calculate reliable membership probabilities. We also obtained precise radial velocity and $v \sin i$ measurements with Coravel and FEROS for 76 probable cluster members. The cluster's mean radial velocity is $+14.8\pm0.7$ km s -1 . The FEROS high-resolution spectra were used to determine both the [Fe/H] abundance in the four main sequence dwarfs of IC 2391 and the Li abundance in 47 stars. In addition, new BV CCD photometry was obtained for the majority of probable cluster members. Results. The proper-motion survey covers a 6 times larger sky area than the prior targeted searches for cluster members in IC 2391. A total of 66 stars are considered bona fide cluster members down to a mass equivalent to 0.5 $M_{\odot}$. A quarter of them have been newly identified with many in the F2-K5 spectral range, which is crucial for a main-sequence fit. We find a mean [Fe/H] value of $+0.06\pm0.06$, when a solar abundance of $\log \epsilon$(Fe) = 7.45 is adopted. The main sequence fitting yields a distance modulus that is 0.19 mag larger than that derived from Hipparcos parallaxes; thus this offset nearly has the size of a similar offset found for the Pleiades. The Li abundance pattern is similar to the earlier findings and is typical for a 40 Myr old open cluster. Conclusions. A variety of new data on the probable members of IC 2391 improve essentially all observational parameters of this young open cluster.
Semantic Web Enabled, Open Source Language Technology

This paper motivates the need for Semantic Web enabled language technology tools and introduces a set of freely available, customisable components which integrate data about language with Semantic Web data in the form of ontologies. We also argue for a closer integration between Natural Language Processing (NLP) and Semantic Web tools and infrastructures and present an integrated platform for knowledge and information management, that uses RDF to encode and store language data and resources.
Galaxy groups in the 2dF Galaxy Redshift Survey: large-scale structure with groups

We use the 2dF Galaxy Group Catalogue constructed by Merchan & Zandivarez to study the large-scale structure of the Universe traced by galaxy groups. We concentrate on the computation of the power spectrum and the two-point correlation function. The resulting group power spectrum shows a similar shape to the galaxy power spectrum obtained from the 2dF Galaxy Redshift Survey by Percival et al., but with a higher amplitude quantified by a relative bias in redshift space of bs(k) ∼ 1.5 on the range of scales analysed in this work, 0.025 < k/h Mpc−1 < 0.45. The group two-point correlation function for the total sample is well described by a power law with correlation length s0= 8.9 ± 0.3 h−1 Mpc and slope γ=−1.6 ± 0.1 on scales of s < 20 h−1 Mpc. In order to study the dependence of the clustering properties on group mass, we split the catalogue into four subsamples defined by different ranges of group virial masses. Our results are consistent with a 40 per cent increase of the correlation length s0 when the minimum mass of the sample increases from to . These computations allow a fair estimate of the relation described by the correlation length s0 and the mean intergroup separation dc for galaxy systems of low mass. Our results show that an empirical scaling law s0= 4.7d0.32c provides a very good fit to the results from this work, as well as to previous results obtained for groups and clusters of galaxies. The same law describes the predictions for dark matter haloes in N-body simulations of Λ cold dark matter (ΛCDM) models. We also extend our study to the redshift space distortions of galaxy groups, where we find that the anisotropies in the clustering pattern of the 2dF Galaxy Group Catalogue are consistent with gravitational instability, with a flattening of the redshift-space correlation function contours in the direction of the line of sight. The group pairwise velocities found from this analysis for a sample of groups with masses are consistent with 〈w2〉1/2= (280+50−110) km s−1, in agreement with ΛCDM cosmological simulations. The bias factor for the 2dF groups of moderate masses is consistent with the values predicted by the combination of a CDM model and the ellipsoidal collapse model for the formation of structures.
Widespread mRNA Association with Cytoskeletal Motor Proteins and Identification and Dynamics of Myosin-Associated mRNAs in S. cerevisiae

Programmed mRNA localization to specific subcellular compartments for localized translation is a fundamental mechanism of post-transcriptional regulation that affects many, and possibly all, mRNAs in eukaryotes. We describe her e a systematic approach to identify the RNA cargoes associated with the cytoskeletal motor proteins of Saccharomyces cerevisiae in combination with live-cell 3D super-localization microscopy of endogenously tagged mRNAs. Our analysis identified widespread association of mRNAs with cytoskeletal motor proteins, including association of Myo3 with mRNAs encoding key regulators of actin branching and endocytosis such as WASP and WIP. Using conventional fluorescence microscopy and expression of MS2-tagged mRNAs from endogenous loci, we observed a strong bias for actin patch nucleator mRNAs to localize to the cell cortex and the actin patch in a Myo3- and F-actin dependent manner. Use of a double-helix point spread function (DH-PSF) microscope allowed super-localization measurements of single mRNPs at a spatial precision of 25 nm in x and y and 50 nm in z in live cells with 50 ms exposure times, allowing quantitative profiling of mRNP dynamics. The actin patch mRNA exhibited distinct and characteristic diffusion coefficients when compared to a control mRNA. In addition, disruption of F-actin significantly expanded the 3D confinement radius of an actin patch nucleator mRNA, providing a quantitative assessment of the contribution of the actin cytoskeleton to mRNP dynamic localization. Our results provide evidence for specific association of mRNAs with cytoskeletal motor proteins in yeast, suggest that different mRNPs have distinct and characteristic dynamics, and lend insight into the mechanism of actin patch nucleator mRNA localization to actin patches.
The Identification of Tax Multipliers in Structural VARs ∗

Structural Vector Autoregressions (SVARs) are identified imposing parametric restrictions. Each set of restrictions corresponds to a different structural model with potentially different implications. Yet the link between assumptions on the structural model and results has not been systematically explored. This paper contributes to fill this gap in the literature. First, we show how to solve analytically the translation of reduced-form residuals into policy shocks. Second, we use the closed-form solution to derive analytically impulse response functions. This theoretical framework is applied to explore identification of tax shocks. We derive an analytical relation between the output elasticity of tax revenue (restriction) and the impact tax multiplier. We show that all identification schemes used in the literature can be recasted in terms of the elasticity. Two results emerge from our analysis. First, differences in elasticity explain differences in the estimates of the tax multiplier reported in the literature. Second, empirically plausible elasticities are consistent with positive and negative tax multipliers. This finding contradicts conjectures in the literature ruling out negative tax multipliers. JEL Classification: E62; C52.
Educational Inequalities Among School Leavers in Ireland 1979-1994

The extent to which inequalities in educational outcomes persist in modern Ireland has been the subject of much debate. This paper investigates whether the rapid expansion in educational participation rates over the 1980s and early 1990s has led to a reduction in social class and gender inequalities. Using data from the annual surveys of school leavers conducted by the Economic and Social Research Institute, analyses highlight marked changes in female educational participation, particularly in the third-level sector, but a remarkable persistence in class inequalities in educational attainment. Contrary to findings based on other sources (Clancy, 1995), no reduction in socio-economic inequalities is apparent in access to third-level education.
An Auxiliary Variable-Aided Hybrid Message Passing Approach to Joint Channel Estimation and Decoding for MIMO-OFDM

This letter deals with message passing receiver design for joint channel estimation and decoding in MIMO-OFDM with unknown noise variance. The conventional factor graph representation for the system involves observation factors, which are functions of a number of variables in the form of multiplication and summation. In this work, by introducing some auxiliary variables, we further break each of the observation factors into several factors, which enables the use of hybrid mean field (MF), belief propagation (BP), and expectation propagation (EP) message passing to tackle the observation factors. It turns out that our approach is much more efficient than the existing approaches, leading to remarkable performance improvement as shown by simulation results.
The Top 30 Problems with the Big Bang

Earlier, we presented a simple list of the top ten problems with the Big Bang. [1] Since that publication, we have had many requests for citations and additional details , which we provide here. We also respond to a few rebuttal arguments to the earlier list. Then we supplement the list based on the last four years of developments—with another 20 problems for the theory. 1. Static universe models fit observational data better than expanding universe models. Static universe models match most observations with no adjustable parameters. The Big Bang can match each of the critical observations, but only with adjustable parameters, one of which (the cosmic deceleration parameter) requires mutually exclusive values to match different tests. [ 2,3] Without ad hoc theorizing, this point alone falsifies the Big Bang. Even if the discrepancy could be explained, Occam's razor favors the model with fewer adjustable parameters— the static universe model. 2. The microwave " background " makes more sense as the limiting temperature of space heated by starlight than as the remnant of a fireball. The expression " the temperature of space " is the title of chapter 13 of Sir Arthur Eddington's famous 1926 work. [4] Eddington calculated the minimum temperature any body in space would cool to, given that
Physical layer security of MIMO frequency selective channels by beamforming and noise generation

This paper addresses physical layer security in MIMO communications over frequency selective wireless channels in the presence of passive eavesdroppers, i.e. the associated channels are unknown to the legitimate transmitter. Signalling is based on orthogonal frequency division multiplexing (OFDM). Spatial beamforming is performed to improve the quality of the legitimate link. With the aim of confusing the eavesdroppers, a fraction of the available power is allocated to transmit artificial noise. Frequency diversity is shown to significantly improve secrecy. A probabilistic analysis of secrecy is presented.