Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence Analysis of 96 Genomic Regions Identifies Distinct Evolutionary Lineages within CC156, the Largest Streptococcus pneumoniae Clonal Complex in the MLST Database

Multi-Locus Sequence Typing (MLST) of Streptococcus pneumoniae is based on the sequence of seven housekeeping gene fragments. The analysis of MLST allelic profiles by eBURST allows the grouping of genetically related strains into Clonal Complexes (CCs) including those genotypes with a common descent from a predicted ancestor. However, the increasing use of MLST to characterize S. pneumoniae strains has led to the identification of a large number of new Sequence Types (STs) causing the merger of formerly distinct lineages into larger CCs. An example of this is the CC156, displaying a high level of complexity and including strains with allelic profiles differing in all seven of the MLST loci, capsular type and the presence of the Pilus Islet-1 (PI-1). Detailed analysis of the CC156 indicates that the identification of new STs, such as ST4945, induced the merging of formerly distinct clonal complexes. In order to discriminate the strain diversity within CC156, a recently developed typing schema, 96-MLST, was used to analyse 66 strains representative of 41 different STs. Analysis of allelic profiles by hierarchical clustering and a minimum spanning tree identified ten genetically distinct evolutionary lineages. Similar results were obtained by phylogenetic analysis on the concatenated sequences with different methods. The identified lineages are homogenous in capsular type and PI-1 presence. ST4945 strains were unequivocally assigned to one of the lineages. In conclusion, the identification of new STs through an exhaustive analysis of pneumococcal strains from various laboratories has highlighted that potentially unrelated subgroups can be grouped into a single CC by eBURST. The analysis of additional loci, such as those included in the 96-MLST schema, will be necessary to accurately discriminate the clonal evolution of the pneumococcal population.
Benefit Finding and Psychological Adjustment Following a Non-Marital Relationship Breakup

Many people experience a non-marital relationship breakup, which can lead to poor adjustment outcomes; however, relative to divorce, non-marital breakups have received less research attention, particularly on factors that may predict positive adjustment outcomes. We examined the adaptive role of finding benefits in a non-marital breakup in 140 participants who completed measures of benefit finding, the impact of the event, and adjustment. Regression analyses found that benefit finding related to positive adjustment outcomes and that the benefit finding-depression relationship was moderated by the impact of the event. This study provides empirical support for benefit finding in a non-marital relationship breakup.
Melanoma Differentiation-Associated Gene 5 Is Critical for Protection against Theiler's Virus-Induced Demyelinating Disease

ABSTRACT Infection of dendritic and glial cells with Theiler's murine encephalomyelitis virus (TMEV) induces various cytokines via Toll-like receptor- and melanoma differentiation-associated gene 5 (MDA5)-dependent pathways. However, the involvement and role of MDA5 in cytokine gene activation and the pathogenesis of TMEV-induced demyelinating disease are largely unknown. In this study, we demonstrate that MDA5 plays a critical role in the production of TMEV-induced alpha interferon (IFN-α) during early viral infection and in protection against the development of virus-induced demyelinating disease. Our results indicate that MDA5-deficient 129SvJ mice display significantly higher viral loads and apparent demyelinating lesions in the central nerve system (CNS) accompanied by clinical symptoms compared with wild-type 129SvJ mice. During acute viral infection, MDA5-deficient mice produced elevated levels of chemokines, consistent with increased cellular infiltration, but reduced levels of IFN-α, known to control T cell responses and cellular infiltration. Additional studies with isolated CNS glial cells from these mice suggest that cells from MDA5-deficient mice are severely compromised in the production of IFN-α upon viral infection, which results in increased cellular infiltration and viral loads in the CNS. Despite inadequate stimulation, the overall T cell responses to the viral determinants were significantly elevated in MDA5-deficient mice, reflecting the increased cellular infiltration. Therefore, the lack of MDA5-mediated IFN-α production may facilitate a massive viral load and elevated cellular infiltration in the CNS during early viral infection, leading to the pathogenesis of demyelinating disease.
Does object naming aid 12-month-olds' formation of novel object categories?

An experiment with 64 twelve-month-olds investigated the influence of object naming on their formation of novel object categories. Stimuli were constructed to represent 2 broad categories consisting of 3 narrow categories each. Objects representing the same narrow or broad category were presented with either a labelling or non-labelling phrase in a modified word extension procedure. Only infants in the narrow category-level condition who heard labelling phrases demonstrated categorization, and categorization performance in the narrow label condition was superior to that in the narrow no-label condition. Consistent with studies utilizing conventional objects, results indicate that object naming can facilitate infants' formation of novel object categories early in the process of lexical acquisition.
Characterizing the dynamic nature of the Yersinia pestis periplasmic proteome in response to nutrient exhaustion and temperature change

The periplasmic proteome of Yersinia pestis strain KIM6+ was characterized using differential 2‐DE display of proteins isolated from several subcellular fractions. Circa 160 proteins were designated as periplasmic, including 62 (putative) solute‐binding proteins of ATP‐binding cassette (ABC) transporters (SBPs) and 46 (putative) metabolic enzymes. More than 30 SBPs were significantly increased in abundance during stationary phase cell growth, compared to the exponential phase. The data suggest that nutrient exhaustion in the stationary phase triggers cellular responses resulting in the induced expression of numerous ABC transporters, which are responsible for the import of solutes/nutrients. Limited availability of inorganic phosphate (Pi) also caused dramatic proteomic changes. Nine proteins were functionally linked to the mobilization and import of three small molecules (Pi, phosphonate and glycerol‐3‐phosphate) and accounted for nearly half of the total protein mass in the periplasm of Pi‐starved cells. When cells were grown at 26°C versus 37°C, corresponding to ambient temperatures in the flea vector and mammalian hosts, respectively, several periplasmic proteins with no known roles in the Y. pestis life cycle were strongly altered in abundance. This included a putative nitrate/sulfonate/bicarbonate‐specific SBP (Y1004), encoded by the virulence‐associated plasmid pMT1 and increased in abundance at 37°C.
Performance analysis with a memory-bound Monte Carlo simulation on Xeon Phi

Physics simulations are known to be great resources exhausters (CPU, memory). Hardware acceleration can help reduce the need for CPU time and increase the available memory bandwidth. In this paper, we present the performance gain when running a memory-bound muon Monte Carlo simulation on an Intel Xeon Phi and an Intel Xeon CPU. We show how to increase performance on the Xeon Phi without modifying the Physics software frameworks we are using for our application. We investigate distributed simulations on multicore and manycore systems and also the impact of hyper-threading on performance. We extend this to a hybrid computing model, balancing the computing burden between both the manycore and multicore processors of a computing node. Finally, we improved memory usage on the Xeon Phi by sharing Kernel Memory pages using KSM, and we show that, using this approach, we can run 16% more simulation instances.
Polymorphism of glycogen synthetase gene in polycystic ovary syndrome

OBJECTIVE Polycystic ovary syndrome is a heterogeneous disorder associated with a moderate degree of insulin resistance and a higher risk of developing NIDDM. The exact mechanism of insulin resistance is unclear. This study examines the frequency of an Xbal polymorphism of the glycogen synthetase gene (A2 allele) as a marker of insulin resistance and seeks to relate the presence of the A2 allele to indices of insulin sensitivity in women with polycystic ovary syndrome (PCOS).
Metal oxide film formation from coordination complex solutions by surface layer-by-layer chemical deposition technique

The layer-by-layer deposition technique for metal oxide thin films from solutions of complex compounds is proposed and considered by examples of copper and titanium oxides from ammonia copper and titanium citrate-peroxide complexes as sources respectively. The films were deposited on glass substrates and flexible substrates made of polyester. The resulting films were investigated by atomic force microscopy and transmission spectroscopy. For both materials the grain structure is obtained, measured energy gap values (3.2 eV for titania and 2.1 eV for copper(I) oxide) are in agreement with literature data.
Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform

Macromolecular surfaces are fundamental representations of their three-dimensional geometric shape. Accurate calculation of protein surfaces is of critical importance in the protein structural and functional studies including ligand-protein docking and virtual screening. In contrast to analytical or parametric representation of macromolecular surfaces, triangulated mesh surfaces have been proved to be easy to describe, visualize and manipulate by computer programs. Here, we develop a new algorithm of EDTSurf for generating three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface, using the technique of fast Euclidean Distance Transform (EDT). The triangulated surfaces are constructed directly from volumetric solids by a Vertex-Connected Marching Cube algorithm that forms triangles from grid points. Compared to the analytical result, the relative error of the surface calculations by EDTSurf is <2–4% depending on the grid resolution, which is 1.5–4 times lower than the methods in the literature; and yet, the algorithm is faster and costs less computer memory than the comparative methods. The improvements in both accuracy and speed of the macromolecular surface determination should make EDTSurf a useful tool for the detailed study of protein docking and structure predictions. Both source code and the executable program of EDTSurf are freely available at http://zhang.bioinformatics. ku.edu/EDTSurf.
Memory benefits during visual search depend on difficulty

In three experiments we explored whether memory for previous locations of search items influences search efficiency more as the difficulty of exhaustive search increases. Difficulty was manipulated by varying item eccentricity and item similarity (discriminability). Participants searched through items placed at three levels of eccentricity. The search displays were either identical on every trial (repeated condition) or the items were randomly reorganised from trial to trial (random condition), and search items were either relatively easy or difficult to discriminate from each other. Search was both faster and more efficient (i.e., search slopes were shallower) in the repeated condition than in the random condition. More importantly, this advantage for repeated displays was greater (1) for items that were more difficult to discriminate and (2) for eccentric targets when items were easily discriminable. Thus, increasing target eccentricity and reducing item discriminability both increase the influence of memory during search.
Scale invariant feature transform evaluation in small dataset

This paper investigates how we can achieve object recognition in an image by looking at some examples of training images. Scale Invariant Feature Transform (SIFT) is one proposal method to detect features in an image and then can use those features to distinguish between different objects. Therefore, my aim was to implement SIFT code to do recognition tasks using simple thresholding and evaluating this algorithm to find its strength and weakness points for a small dataset. The challenge here is to find the best threshold for examples of training images, which can work properly with query images.
Degenerate parabolic stochastic partial differential equations: Quasilinear case

We study the Cauchy problem for a quasilinear degenerate parabolic stochastic partial differential equation driven by a cylindrical Wiener process. In particular, we adapt the notion of kinetic formulation and kinetic solution and develop a well-posedness theory that includes also an $L^1$-contraction property. In comparison to the first-order case (Debussche and Vovelle, 2010) and to the semilinear degenerate parabolic case (Hofmanova, 2013), the present result contains two new ingredients: a generalized Ito formula that permits a rigorous derivation of the kinetic formulation even in the case of weak solutions of certain nondegenerate approximations and a direct proof of strong convergence of these approximations to the desired kinetic solution of the degenerate problem.
The Toll-IL-1R Member Tir8/SIGIRR Negatively Regulates Adaptive Immunity against Kidney Grafts1

Members of the TLR/IL-1R superfamily mediate ischemia/reperfusion injury and initiate immune response in transplanted organs. In this study, we tested the hypothesis that Toll-IL-1R8 (TIR8), a negative regulator of TLR/IL-1R highly expressed in the kidney, modulates immune cell activation underlying kidney rejection. In a mouse model of fully mismatched kidney allotransplantation in which the graft is spontaneously accepted, intragraft Tir8 expression was enhanced compared with naive kidneys. Targeted deletion of Tir8 in the graft exerted a powerful antitolerogenic action leading to acute rejection. Similarly, in a mouse model of kidney graft acceptance induced by costimulation blockade, most Tir8−/− grafts were acutely rejected. Despite similar levels of TLR4, IL-1R, and their ligands, the posttransplant ischemia/reperfusion-induced inflammatory response was more severe in Tir8−/− than in Tir8+/+ grafts and was followed by expansion and maturation of resident dendritic cell precursors. In vitro, Tir8−/− dendritic cell precursors acquired higher allostimulatory activity and released more IL-6 upon stimulation with a TLR4 ligand and TNF-α than Tir8+/+ cells, which may explain the increased frequency of antidonor-reactive T cells and the block of regulatory T cell formation in recipients of a Tir8−/− kidney. Thus, TIR8 acts locally as a key regulator of allogeneic immune response in the kidney. Tir8 expression and/or signaling in donor tissue are envisaged as a novel target for control of innate immunity and amelioration of graft survival.
Congestion Management of Electricity Markets Using FACTS Controllers

Within the deregulated electricity markets of today a major issue for the Independent System Operator (ISO) is to deal effectively with congestion management. This paper provides an investigation into the benefit of the Unified Power Flow Controller (UPFC) as a viable solution to the problem of congestion management. Many deregulated electricity markets now operate in a bilateral manner, and carry out as many transactions per hour as was previously performed in a single day. The bilateral market environment is reflected in this investigation. A mathematical model of the UPFC has been incorporated into a general two-step optimization methodology for finding the optimal rating of the UPFC located at congested transmission lines. Numerical examples are presented based on the IEEE 30-bus system, and the results demonstrate the method used to find the optimum rating of the UPFC and the reduction in congestion costs the UPFC brings to a heavily congested system.
Nature of Protein Family Signatures: Insights from Singular Value Analysis of Position-Specific Scoring Matrices

Position-specific scoring matrices (PSSMs) are useful for detecting weak homology in protein sequence analysis, and they are thought to contain some essential signatures of the protein families. In order to elucidate what kind of ingredients constitute such family-specific signatures, we apply singular value decomposition to a set of PSSMs and examine the properties of dominant right and left singular vectors. The first right singular vectors were correlated with various amino acid indices including relative mutability, amino acid composition in protein interior, hydropathy, or turn propensity, depending on proteins. A significant correlation between the first left singular vector and a measure of site conservation was observed. It is shown that the contribution of the first singular component to the PSSMs act to disfavor potentially but falsely functionally important residues at conserved sites. The second right singular vectors were highly correlated with hydrophobicity scales, and the corresponding left singular vectors with contact numbers of protein structures. It is suggested that sequence alignment with a PSSM is essentially equivalent to threading supplemented with functional information. In addition, singular vectors may be useful for analyzing and annotating the characteristics of conserved sites in protein families.
N-grams-based File Signatures for Malware Detection

Malware is any malicious code that has the potential to harm any computer or network. The amount of malware is increasing faster every year and poses a serious security threat. Thus, malware detection is a critical topic in computer security. Currently, signature-based detection is the most extended method for detecting malware. Although this method is still used on most popular commercial computer antivirus software, it can only achieve detection once the virus has already caused damage and it is registered. Therefore, it fails to detect new malware. Applying a methodology proven successful in similar problem-domains, we propose the use of ngrams (every substring of a larger string, of a fixed lenght n) as file signatures in order to detect unknown malware whilst keeping low false positive ratio. We show that n-grams signatures provide an effective way to detect unknown malware.
The Rey Auditory Verbal Learning Test: normative data for the Brazilian population and analysis of the influence of demographic variables

Rey Auditory Verbal Learning Test (RAVLT) is an efficient neuropsychological instrument for testing episodic declarative memory. Performance on this test can be influenced by demographic and cultural variables. The objective of the present study was to analyze the influence of demographics variables, such as age, gender, and education, on RAVLT performance in young and elderly adults. A Portuguese version of the RAVLT was administered to 302 healthy participants. Subjects were from both genders, ranging in age from 17 to 85 years (mean 50.6 ± 15.9 years) and in education from 1 to 20 years (mean 11.3 ± 3.7 years). Participants were grouped by age: 17-34 years old, 34-49 years old, 50-64 years old, and 65-85 years old. Pearson's Correlation analysis showed a significant association between RAVLT performance and both age and education ( p < .001), but not between RAVLT performance and gender. Two-way analysis of variance revealed significant effects of age on all RAVLT measurements and significant effects of years of education on all measurements, with the exception of recognition. The present data indicate that participant age and education significantly influence performance on the RAVLT. Keywords: memory, neuropsychological tests, neuropsychology.
Hegemony, postcolonialism and sport-for-development: a response to Lindsey and Grattan

In their article in this volume, entitled ‘An “international movement”? Decentering sport for development within Zambian communities”, Iain Lindsey and Alan Grattan (2012) highlight important issues of agency, locality, diversity and culture within the current mobilization of sport to meet international development goals. Drawing on valuable fieldwork in Zambia, the authors suggest that prior research may have overstated the solidity and boundaries of an ‘international’ movement towards sport-for-development and exaggerated the influence of northern initiatives in the Global South and the hegemony of neoliberal development policy. As two of the authors whose work is evaluated, we offer a rejoinder in which we suggest that Lindsey and Grattan's analyses are important and insightful but best viewed as complementary to the critical analyses of northern-led development and neoliberalism. Drawing on Gramscian hegemony and postcolonial theory, we make the case for a renewed commitment to the issues of power and resistance in the mobilization of sport to meet international development goals.
Local structural disorder imparts plasticity on linear motifs

MOTIVATION The dynamic nature of protein interaction networks requires fast and transient molecular switches. The underlying recognition motifs (linear motifs, LMs) are usually short and evolutionarily variable segments, which in several cases, such as phosphorylation sites or SH3-binding regions, fall into locally disordered regions. We probed the generality of this phenomenon by predicting the intrinsic disorder of all LM-containing proteins enlisted in the Eukaryotic Linear Motif (ELM) database. RESULTS We demonstrated that LMs in average are embedded in locally unstructured regions, while their amino acid composition and charge/hydropathy properties exhibit a mixture characteristic of folded and disordered proteins. Overall, LMs are constructed by grafting a few specificity-determining residues favoring structural order on a highly flexible carrier region. These results establish a connection between LMs and molecular recognition elements of intrinsically unstructured proteins (IUPs), which realize a non-conventional mode of partner binding mostly in regulatory functions.
The Process and Phases of Arthur Inman's Suicidal Career

This study attempted to understand the process of Arthur Crew Inman's suicidal career, and the phases and pathways leading to his eventual suicide. There remains an inadequate understanding of the phases of the suicide process, even though research has produced insight into the possible pathways leading to the suicide act. Using The Inman diary, which documents, amongst other things, the suicidal behaviour of Arthur Inman, grounded theory techniques were implemented in this study in order to understand such a process. These techniques included the constant comparative method, coding as proposed by Strauss's concept indicator model, memoing and integrative diagramming. The results revealed the existence of four phases of the suicide process, subsuming several pathways. Whilst contemporary studies have focused on pathways to the suicide act, mostly comprising relationships between different variables, it is argued that identifying phases of the process may provide a means of structuring such pathways within certain phases. These phases are characterised by specific cognito-emotive and behavioural properties. Validity and reliability issues are also addressed, together with possible methodological limitations.