Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Spore Peptidoglycan Hydrolase of Bacillus cereus: Biochemical Characterization and Nucleotide Sequence of the Corresponding Gene, sleL

ABSTRACT The exudate of germinated spores of B. cereus IFO 13597 in 0.15 M KCl–50 mM potassium phosphate (pH 7.0) contained a spore-lytic enzyme which has substrate specificity for fragmented spore cortex from wild-type organisms (cortical-fragment-lytic enzyme [CFLE]), in addition to a previously characterized germination-specific hydrolase which acts on intact spore cortex (spore cortex-lytic enzyme [SCLE]) (R. Moriyama, S. Kudoh, S. Miyata, S. Nonobe, A. Hattori, and S. Makino, J. Bacteriol. 178:5330–5332, 1996). CFLE was not capable of degrading isolated cortical fragments from spores of Bacillus subtilis ADD1, which lacks muramic acid δ-lactam. This suggests that CFLE cooperates with SCLE in cortex hydrolysis during germination. CFLE was purified in an active form and identified as a 48-kDa protein which functions as anN-acetylglucosaminidase. Immunochemical studies suggested that the mature enzyme is localized on a rather peripheral region of the dormant spore, probably the exterior of the cortex layer. A gene encoding the enzyme, sleL, was cloned in Escherichia coli, and the nucleotide sequence was determined. The gene encodes a protein of 430 amino acids with a deduced molecular weight of 48,136. The N-terminal region contains a repeated motif common to several peptidoglycan binding proteins. Inspection of the data banks showed no similarity of CFLE with N-acetylglucosaminidases found so far, suggesting that CFLE is a novel type ofN-acetylglucosaminidase. The B. subtilis genome sequence contains genes, yaaH and ydhD, which encode putative proteins showing similarity to SleL.
Who Tweets in the United Kingdom? Profiling the Twitter Population Using the British Social Attitudes Survey 2015

The headache any researcher faces while using Twitter data for social scientific analysis is that we do not know who tweets. In this article, we report on results from the British Social Attitudes Survey (BSA) 2015 on Twitter use. We focus on associations between using Twitter and three demographic characteristics—age, sex, and class (defined here as National Statistics Socio-Economic Classification [NS-SEC]). In addition to this, we compare findings from BSA 2015, treated as ground truth (known characteristics), with previous attempts to map the demographic nature of UK Twitter users using computational methods resulting in demographic proxies. Where appropriate, the datasets are compared with UK Census 2011 data to illustrate that Twitter users are not representative of the wider population. We find that there are a disproportionate number of male Twitter users, in relation to both the Census 2011 and previous proxy estimates; that Twitter users are predominantly young, but there are more older users than previously estimated; and that there are strong class effects associated with Twitter use.
First observation of top quark production in the forward region.

Top quark production in the forward region in proton-proton collisions is observed for the first time. The W+b final state with W→μν is reconstructed using muons with a transverse momentum, p_{T}, larger than 25 GeV in the pseudorapidity range 2.0<η<4.5. The b jets are required to have 50<p_{T}<100 GeV and 2.2<η<4.2, while the transverse component of the sum of the muon and b-jet momenta must satisfy p_{T}>20 GeV. The results are based on data corresponding to integrated luminosities of 1.0 and 2.0 fb^{-1} collected at center-of-mass energies of 7 and 8 TeV by LHCb. The inclusive top quark production cross sections in the fiducial region are σ(top)[7 TeV]=239±53(stat)±33(syst)±24(theory) fb,σ(top)[8 TeV]=289±43(stat)±40(syst)±29(theory) fb.These results, along with the observed differential yields and charge asymmetries, are in agreement with next-to-leading order standard model predictions.
Holons and Agents

The future of the manufacturing sector in the world will be determined by how it meets the challenges of the 21st century. Two paradigms promise to meet these challenges, multi-agent systems (MAS) and holonic system (HS). Currently, there is some misunderstanding about the relationships between these two approaches. The aim of this work is to make a study of all the characteristics of the HS and the MAS approach, in order to illustrate a comprehensive comparison of holons and agents, and, at the same time, to present a survey about the main research works in both areas.
Budding yeast RSI1/APC2, a novel gene necessary for initiation of anaphase, encodes an APC subunit

SIC1 is a non‐essential gene encoding a CDK inhibitor of Cdc28‐Clb kinase activity. Sic1p is involved in both mitotic exit and the timing of DNA synthesis. To identify other genes involved in controlling Clb‐kinase activity, we have undertaken a genetic screen for mutations which render SIC1 essential. Here we describe a gene we have identified by this means, RSI1/APC2. Temperature‐sensitive rsi1/apc2 mutants arrest in metaphase and are unable to degrade Clb2p, suggesting that Rsi1p/Apc2p is associated with the anaphase promoting complex (APC). This is an E3 ubiquitin‐ligase that controls anaphase initiation through degradation of Pds1p and mitotic exit via degradation of Clb cyclins. Indeed, the anaphase block in rsi1/apc2 temperature‐sensitive mutants is overcome by removal of PDS1, consistent with Rsi1p/Apc2p being part of the APC. In addition, like our rsi1/apc2 mutations, cdc23‐1, encoding a known APC subunit, is also lethal with sic1Δ. Thus SIC1 clearly becomes essential when APC function is compromised. Finally, we find that Rsi1p/Apc2p co‐immunoprecipitates with Cdc23p. Taken together, our results suggest that RSI1/APC2 is a subunit of APC.
Nighttime Vehicle Detection Based on Bio-Inspired Image Enhancement and Weighted Score-Level Feature Fusion

This paper presents an effective nighttime vehicle detection system that combines a novel bioinspired image enhancement approach with a weighted feature fusion technique. Inspired by the retinal mechanism in natural visual processing, we develop a nighttime image enhancement method by modeling the adaptive feedback from horizontal cells and the center-surround antagonistic receptive fields of bipolar cells. Furthermore, we extract features based on the convolutional neural network, histogram of oriented gradient, and local binary pattern to train the classifiers with support vector machine. These features are fused by combining the score vectors of each feature with the learnt weights. During detection, we generate accurate regions of interest by combining vehicle taillight detection with object proposals. Experimental results demonstrate that the proposed bioinspired image enhancement method contributes well to vehicle detection. Our vehicle detection method demonstrates a 95.95% detection rate at 0.0575 false positives per image and outperforms some state-of-the-art techniques. Our proposed method can deal with various scenes including vehicles of different types and sizes and those with occlusions and in blurred zones. It can also detect vehicles at various locations and multiple vehicles.
Human Reinforcement Learning Subdivides Structured Action Spaces by Learning Effector-Specific Values

Humans and animals are endowed with a large number of effectors. Although this enables great behavioral flexibility, it presents an equally formidable reinforcement learning problem of discovering which actions are most valuable because of the high dimensionality of the action space. An unresolved question is how neural systems for reinforcement learning—such as prediction error signals for action valuation associated with dopamine and the striatum—can cope with this “curse of dimensionality. ” We propose a reinforcement learning framework that allows for learned action valuations to be decomposed into effector-specific components when appropriate to a task, and test it by studying to what extent human behavior and blood oxygen level-dependent (BOLD) activity can exploit such a decomposition in a multieffector choice task. Subjects made simultaneous decisions with their left and right hands and received separate reward feedback for each hand movement. We found that choice behavior was better described by a learning model that decomposed the values of bimanual movements into separate values for each effector, rather than a traditional model that treated the bimanual actions as unitary with a single value. A decomposition of value into effector-specific components was also observed in value-related BOLD signaling, in the form of lateralized biases in striatal correlates of prediction error and anticipatory value correlates in the intraparietal sulcus. These results suggest that the human brain can use decomposed value representations to “divide and conquer” reinforcement learning over high-dimensional action spaces.
Determination of optimal parameters and feasibility for imaging epileptic seizures by Electrical Impedance Tomography

Electrical Impedance Tomography (EIT) may potentially provide a novel noninvasive method for imaging the sources of epileptic seizures, but so far initial clinical studies were unsuccessful, as baseline noise obscured any signal. The purpose of this study was to guideline specification for improved recording equipment, by estimating signal magnitude in relation to noise and the optimal frequency and current level for recording, using a realistic 3D finite element model of the human head with isotropic layers representing the brain, cerebrospinal fluid, skull and scalp. EIT recordings were simulated for all the possible combinations of injection and measurement pairs derived from 31 electrodes on the scalp; noise was estimated for recording systems with a serial, semi-parallel or fully-parallel design, as these permitted greater degrees of averaging. Simulated applied current frequency ranged between 5Hz and 4MHz and the amplitude was set in accordance to the safety regulations. Seizures were simulated as conductivity decreases of 3-16%, depending on frequency, for right hippocampus, parahippocampal structures or temporal lobe. The largest real scalp voltage changes were 1.0% at 50 kHz for the superficial temporal lobe seizures and up to ten times smaller for the deeper sites; in comparison, noise was 0.035, 0.01, and 0.002% after averaging over the required resolution of 1s for the serial, semior parallel systems. Changes in the correct location could be obtained in reconstructed real component images during temporal lobe seizures with all systems, but for the other three regions only with a fully-parallel system. These findings suggest that EIT of epileptic seizures is feasible before clonic or tonic movement occurs and would be best undertaken at 50 kHz and with a parallel recording system.
Age Dependent Differences in Collagen Alignment of Glutaraldehyde Fixed Bovine Pericardium

Bovine pericardium is used for heart valve leaflet replacement where the strength and thinness are critical properties. Pericardium from neonatal animals (4–7 days old) is advantageously thinner and is considered as an alternative to that from adult animals. Here, the structures of adult and neonatal bovine pericardium tissues fixed with glutaraldehyde are characterized by synchrotron-based small angle X-ray scattering (SAXS) and compared with the mechanical properties of these materials. Significant differences are observed between adult and neonatal tissue. The glutaraldehyde fixed neonatal tissue has a higher modulus of elasticity (83.7 MPa) than adult pericardium (33.5 MPa) and a higher normalised ultimate tensile strength (32.9 MPa) than adult pericardium (19.1 MPa). Measured edge on to the tissue, the collagen in neonatal pericardium is significantly more aligned (orientation index (OI) 0.78) than that in adult pericardium (OI 0.62). There is no difference in the fibril diameter between neonatal and adult pericardium. It is shown that high alignment in the plane of the tissue provides the mechanism for the increased strength of the neonatal material. The superior strength of neonatal compared with adult tissue supports the use of neonatal bovine pericardium in heterografts.
Universal Citizenship and the Problem of Alienage

Many commentators have noted the "return of the citizen" to normative political and legal theory. Yet there is a widespread tendency among theorists to treat the subject of national citizenship status as thematically and analytically separate from the rest of the citizenship field. Something of a division of labor in the literature has developed, according to which threshold questions regarding both access to, and the significance of, formal national citizenship status are treated as distinct from questions about the nature and quality of citizenship as practiced within the political community. The former questions are usually consigned to the domain of immigration scholarship, while the latter are treated as political and legal theory's core enterprise. This essay argues that the prevailing tendency to bracket citizenship's threshold questions is intellectually problematic because it has the effect of limiting, and perhaps distorting, analysts' ability to theorize the nature of citizenship as it exists within the political community. Questions concerning citizenship's threshold and it's substantive character are, in fact, deeply interwoven. Regulation of citizenship's boundaries reaches deep into the heart of the national political community, and profoundly affects the nature of relations among those residing within. To make the argument, the essay focuses on one recent development in normative citizenship theory - the growing perception that rights and status-based approaches to citizenship are exhausted or otherwise obsolete. This perception reflects a theoretical world in which citizenship's threshold, national questions are assumed away - a world in which everyone is presumed to be a formal citizen and in which citizenship's basic rights are presumed to be universally available. To the extent these presumptions are problematized, however, and citizenship's national dimension is taken into account, the ideal of universal citizenship can no longer be so easily presumed. The challenge to universal citizenship becomes especially clear if we focus on the condition of non-citizens, or aliens, who reside within the liberal democratic community. Aliens, by definition, are outsiders to citizenship. Yet they are also persons residing within the liberal democratic political community, and their presence in the community raises pressing questions about the practice of citizenship within, including questions about precisely how far the rights and status of citizenship can, and should, be understood to extend. Attending to alienage serves to underscore the continuing salience - and the continuing intractability - of liberal status and rights questions in citizenship theory, their current unfashionability notwithstanding.
Screening of CD96 and ASXL1 in 11 patients with Opitz C or Bohring–Opitz syndromes

Opitz C trigonocephaly (or Opitz C syndrome, OTCS) and Bohring‐Opitz syndrome (BOS or C‐like syndrome) are two rare genetic disorders with phenotypic overlap. The genetic causes of these diseases are not understood. However, two genes have been associated with OTCS or BOS with dominantly inherited de novo mutations. Whereas CD96 has been related to OTCS (one case) and to BOS (one case), ASXL1 has been related to BOS only (several cases). In this study we analyze CD96 and ASXL1 in a group of 11 affected individuals, including 2 sibs, 10 of them were diagnosed with OTCS, and one had a BOS phenotype. Exome sequences were available on six patients with OTCS and three parent pairs. Thus, we could analyze the CD96 and ASXL1 sequences in these patients bioinformatically. Sanger sequencing of all exons of CD96 and ASXL1 was carried out in the remaining patients. Detailed scrutiny of the sequences and assessment of variants allowed us to exclude putative pathogenic and private mutations in all but one of the patients. In this patient (with BOS) we identified a de novo mutation in ASXL1 (c.2100dupT). By nature and location within the gene, this mutation resembles those previously described in other BOS patients and we conclude that it may be responsible for the condition. Our results indicate that in 10 of 11, the disease (OTCS or BOS) cannot be explained by small changes in CD96 or ASXL1. However, the cohort is too small to make generalizations about the genetic etiology of these diseases. © 2015 Wiley Periodicals, Inc.
Transcriptome analysis of Vibrio parahaemolyticus in type III secretion system 1 inducing conditions

Vibrio parahaemolyticus is an emerging bacterial pathogen capable of causing inflammatory gastroenteritis, wound infections, and septicemia. As a food-borne illness, infection is most frequently associated with the consumption of raw or undercooked seafood, particularly shellfish. It is the primary cause of Vibrio-associated food-borne illness in the United States and the leading cause of food-borne illness in Japan. The larger of its two chromosomes harbors a set of genes encoding type III section system 1 (T3SS1), a virulence factor present in all V. parahaemolyticus strains that is similar to the Yersinia ysc T3SS. T3SS1 translocates effector proteins into eukaryotic cells where they induce changes to cellular physiology and modulate host-pathogen interactions. T3SS1 is also responsible for cytotoxicity toward several different cultured cell lines as well as mortality in a mouse model. Herein we used RNA-seq to obtain global transcriptome patterns of V. parahaemolyticus under conditions that either induce [growth in Dulbecco's Modified Eagle Medium (DMEM) media, in trans expression of transcriptional regulator exsA] or repress T3SS1 expression (growth in LB-S media, in trans exsD expression) and during infection of HeLa cells over time. Comparative transcriptomic analysis demonstrated notable differences in the expression patterns under inducing conditions and was also used to generate an expression profile of V. parahaemolyticus during infection of HeLa cells. In addition, we identified several new genes that are associated with T3SS1 expression and may warrant further study.
The who, what, why and how of high performance computing applications in the cloud

Cloud computing is emerging as an alternative to supercomputers for some of the high-performance computing (HPC) applications that do not require a fully dedicated machine. With cloud as an additional deployment option, HPC users are faced with the challenges of dealing with highly heterogeneous resources, where the variability spans across a wide range of processor configurations, interconnections, virtualization environments and pricing rates and models. In this paper, we take a holistic viewpoint to answer the question ? why and who should choose (or not choose) cloud for HPC, for what applications, and how should cloud be used for HPC? To this end, we perform a comprehensive performance evaluation of a set of benchmarks and complex HPC applications on a range of platforms, varying from supercomputers to commodity clusters, both in-house and in the cloud. Having identified the performance bottlenecks in cloud, we demonstrate that alternative lightweight virtualization mechanisms such as thin VMs and OS-level containers, and hypervisor and applicationlevel CPU affinity can greatly lower the overhead and noise of virtualization. Next, we discuss the economic aspects of HPC in the cloud, which we believe is an important area that has not been sufficiently addressed by past research. Finally, we explore the benefits of an intelligent matching of an HPC application to the best deployment platform within a given set, discussing how we can combine a cloud deployment with a supercomputer. Overall results indicate that current public clouds are cost-effective only at small scale ? 4 to 16 cores for the chosen HPC applications, when considered in isolation, but can complement (and co-exist with) supercomputers using models such as cloud burst and application-aware mapping to achieve significant cost benefits.
Greater rate of decline in maximal aerobic capacity with age in physically active vs. sedentary healthy women.

Using a meta-analytic approach, we recently reported that the rate of decline in maximal oxygen uptake (VO2 max) with age in healthy women is greatest in the most physically active and smallest in the least active when expressed in milliliters per kilogram per minute per decade. We tested this hypothesis prospectively under well-controlled laboratory conditions by studying 156 healthy, nonobese women (age 20-75 yr): 84 endurance-trained runners (ET) and 72 sedentary subjects (S). ET were matched across the age range for age-adjusted 10-km running performance. Body mass was positively related with age in S but not in ET. Fat-free mass was not different with age in ET or S. Maximal respiratory exchange ratio and rating of perceived exertion were similar across age in ET and S, suggesting equivalent voluntary maximal efforts. There was a significant but modest decline in running mileage, frequency, and speed with advancing age in ET. VO2 max (ml . kg-1 . min-1) was inversely related to age (P < 0.001) in ET (r = -0.82) and S (r = -0.71) and was higher at any age in ET. Consistent with our meta-analysic findings, the absolute rate of decline in VO2 max was greater in ET (-5.7 ml . kg-1 . min-1 . decade-1) compared with S (-3.2 ml . kg-1 . min-1 . decade-1; P < 0. 01), but the relative (%) rate of decline was similar (-9.7 vs -9. 1%/decade; not significant). The greater absolute rate of decline in VO2 max in ET compared with S was not associated with a greater rate of decline in maximal heart rate (-5.6 vs. -6.2 beats . min-1 . decade-1), nor was it related to training factors. The present cross-sectional findings provide additional evidence that the absolute, but not the relative, rate of decline in maximal aerobic capacity with age may be greater in highly physically active women compared with their sedentary healthy peers. This difference does not appear to be related to age-associated changes in maximal heart rate, body composition, or training factors.
Properties of dynamic earthquake ruptures with heterogeneous stress drop

Earthquake rupture is a notoriously complex process, at all observable scales. We introduce a simplified semi-dynamic crack model to investigate the connection between the statistical properties of stress and those of macroscopic source parameters such as rupture size, seismic moment, apparent stress drop and radiated energy. Rupture initiation is treated consistently with nucleation on a linear slip-weakening fault, whereas rupture propagation and arrest are treated according to the Griffith criterion. The available stress drop is prescribed as a spatially correlated random field and is shown to potentially sustain a broad range of magnitudes. By decreasing the amplitude of the stress heterogeneities or increasing their correlation length the distribution of earthquake sizes presents a transition from Gutenberg- Richter to characteristic earthquake behavior. This transition is studied through a mean-field analysis. The bifurcation to characteristic earthquake behavior is sharp, reminiscent of a first-order phase transition. A lower roll-off magnitude observed in the Gutenberg-Richter regime is shown to depend on the correlation length of the available stress drop, rather than being a direct signature of the nucleation process. More generally, we highlight the possible role of the stress correlation length scale on deviations from earthquake source self-similarity. The present reduced model is a building block towards understanding the effect of structural and dynamic fault heterogeneities on the scaling of source parameters and on basic properties of seismicity.