Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure and Assembly of Group B Streptococcus Pilus 2b Backbone Protein

Group B Streptococcus (GBS) is a major cause of invasive disease in infants. Like other Gram-positive bacteria, GBS uses a sortase C-catalyzed transpeptidation mechanism to generate cell surface pili from backbone and ancillary pilin precursor substrates. The three pilus types identified in GBS contain structural subunits that are highly immunogenic and are promising candidates for the development of a broadly-protective vaccine. Here we report the X-ray crystal structure of the backbone protein of pilus 2b (BP-2b) at 1. 06Å resolution. The structure reveals a classical IgG-like fold typical of the pilin subunits of other Gram-positive bacteria. The crystallized portion of the protein (residues 185-468) encompasses domains D2 and D3 that together confer high stability to the protein due to the presence of an internal isopeptide bond within each domain. The D2+D3 region, lacking the N-terminal D1 domain, was as potent as the entire protein in conferring protection against GBS challenge in a well-established mouse model. By site-directed mutagenesis and complementation studies in GBS knock-out strains we identified the residues and motives essential for assembly of the BP-2b monomers into high-molecular weight complexes, thus providing new insights into pilus 2b polymerization.
Naming problems in dementia: Semantic or lexical?

Abstract The naming behaviour was explored of patients moderately deteriorated with probable Alzheimer's disease (pAD) by analysing responses made on a picture naming and two word-picture matching tasks for the same items. Naming responses were classified into target and non-target and the relationship between non-target responses and their targets were explored. It was found that semantic relatedness influenced these non-target responses but frequency and imageability did not. The pAD participants performed significantly better on the two word-picture matching tasks than the naming task, while there was no difference on these within- and between-category tasks. These findings are explored with reference to a two-stage model of lexical access, which has separate storage of semantic, lexical and phonological information. The participants' difficulties appear to lie largely in retrieving the labels for items they comprehend.
Possible involvement of the OKT4 molecule in T cell recognition of class II HLA antigens. Evidence from studies of cytotoxic T lymphocytes specific for SB antigens

A recently described HLA gene, SB, which maps between GLO and HLA-DR, codes for Ia-like molecules that are similar to but distinct from HLA- DR molecules. Cytotoxic T lymphocytes (CTL) specific for SB1, SB2, SB3, and SB4 were compared with HLA-A2-specific CTL with respect to their surface expression of the T cell differentiation antigens OKT3, OKT4, and OKT8. All CTL activity was eliminated by treatment with OKT3 and C'. The SB-specific cytotoxicity was eliminated by OKT4 plus C' but not by OKT8 plus C'. In contrast, HLA-A2-specific killing was completely susceptible to treatment with OKT8 plus C' but not with OKT4 plus C'. Cytotoxicity was analyzed in the presence of OKT8 and a series of monoclonal antibodies (OKT4A, 4B, 4C, and 4D) that react with distinct epitopes on the OKT4 molecule. SB1-, SB3-, and SB4-specific CTL were partially inhibited by OKT4A and 4B (45-75%), whereas HLA-A2-specific CTL were partially inhibited by OKT8 (48-63%) but not by OKT4. SB2- specific CTL were not inhibited (less than 26%) by OKT8 or by any of the OKT4-related antibodies. These results suggest that the OKT4 marker may be expressed on most T cells that recognize allogeneic Ia or self Ia plus foreign antigens; OKT4+ cells do not appear to be functionally homogeneous in that they can act both as helper/inducer and cytotoxic cells. Models are proposed for the functional involvement of the OKT4 molecule in T cell-Ia antigen interactions.
Processing SPARQL Queries Over Linked Data-A Distributed Graph-based Approach

We propose techniques for processing SPARQL queries over linked data. We follow a graph-based approach where answering a query Q is equivalent to finding its matches over a distributed RDF data graph G. We adopt a “partial evaluation and assembly” framework. Partial evaluation results of query Q over each repository—called local partial match—are found. In the assembly stage, we pro- pose a centralized and a distributed assembly strategy. We analyze our algorithms both theoretically and the experimentally. Extensive experiments over both real and benchmark RDF repositories with billion triples demonstrate the high performance and scalability of our methods compared with that of the existing solutions.
Adaptive video background modeling using color and depth

A new algorithm for background estimation and removal in video sequences obtained with stereo cameras is presented. Per-pixel Gaussian mixtures are used to model recent scene observations in the combined space of depth and luminance-invariant color. These mixture models adapt over time, and are used to build a new model of the background at each time step. This combination in itself is novel, but we also introduce the idea of modulating the learning rate of the background model according to the scene activity level on a per-pixel basis, so that dynamic foreground objects are incorporated into the background more slowly than are static scene changes. Our results show much greater robustness than prior state-of-the-art methods to challenging phenomena such as video displays, non-static background objects, areas of high foreground traffic, and similar color of foreground and background. Our method is also well-suited for use in real-time systems.
A Thermodynamic Model for Prebiotic Protein Function

We propose a scenario for the prebiotic co-evolution of RNA and of fast folding proteins with large entropy gaps as observed today. We show from very general principles that the folding and unfolding of the proteins synthesized by RNA can function as a heat pump. Rock surfaces can facilitate the folding of amino acid chains having polar and hydrophobic residues, with an accompanying heat loss to the surrounding rock. These chains then absorb heat from the soup as they unfold. This opens the way to the enhancement of RNA replication rates, by the enzymatic action of folded proteins present in greater numbers at reduced temperatures. This gives an evolutionary advantage to those RNA coding amino acid sequences with non-degenerate folded states which would provide the most efficient refrigeration.
The EUA Institutional Evaluation Programme: an account of institutional best practices

When evaluating the EUA Institutional Evaluation Programme (IEP), Nilsson et al. emphasised the interest in creating a data bank on good practices derived from its reports that would contribute to disseminating examples of effective quality management practices and to supporting mutual learning among universities. In IEP, evaluated institutions present a SWOT analysis that is examined by the external reviewers. This article identifies and systematises the strengths identified by external evaluators, related to good management practices, which may contribute to the data bank. The paper also suggests that the IEP reports present a set of strengths that define a certain type of university, namely a centralised institution, with strong leadership, well-defined strategic management practices, capacity to change and an institutional identity and culture promoting its worldwide competitiveness. Along with other prioritised characteristics the IEP process potentially contributes to convergence towards a more uniform European higher education model. The analysis of the strengths identified by reviewers does not show a significant regional influence.
An Empirical Bayesian Approach for Identifying Differential Coexpression in High‐Throughput Experiments

Summary A common goal of microarray and related high‐throughput genomic experiments is to identify genes that vary across biological condition. Most often this is accomplished by identifying genes with changes in mean expression level, so called differentially expressed (DE) genes, and a number of effective methods for identifying DE genes have been developed. Although useful, these approaches do not accommodate other types of differential regulation. An important example concerns differential coexpression (DC). Investigations of this class of genes are hampered by the large cardinality of the space to be interrogated as well as by influential outliers. As a result, existing DC approaches are often underpowered, exceedingly prone to false discoveries, and/or computationally intractable for even a moderately large number of pairs. To address this, an empirical Bayesian approach for identifying DC gene pairs is developed. The approach provides a false discovery rate controlled list of significant DC gene pairs without sacrificing power. It is applicable within a single study as well as across multiple studies. Computations are greatly facilitated by a modification to the expectation–maximization algorithm and a procedural heuristic. Simulations suggest that the proposed approach outperforms existing methods in far less computational time; and case study results suggest that the approach will likely prove to be a useful complement to current DE methods in high‐throughput genomic studies.
Effects of visual clutter on pilot workload, flight performance and gaze pattern

Visual clutter has received an increased interest by the aerospace community to characterize the negative impacts of information overload on pilots. Past studies found mixed effects of the primary flight display (PFD) visual clutter on flight performance. In this study, we created three experimental PFDs with different clutter levels (low, medium, high) and the same flight guidance function. Twelve pilots completed an instrument landing using all three PFDs. We found that pilots reported lower workload level (p < .005) and had better lateral control during the approach (p < .05) using the medium-clutter PFD. These results show the relevancy to optimize visual clutter of complex aerospace displays, as it impacts subjective and objective performance of experienced pilots.
Difficulties in collaboration: A critical incident study of interprofessional healthcare teamwork

The challenge for members of interprofessional teams is to manage the team processes that occur in all teamwork while simultaneously managing their individual professional identities. The aim of this study was to identify and describe difficulties perceived by health professionals in interprofessional teamwork. Utterances on verbal actions and resolutions were also explored to enable a discussion of the implications for interprofessional learning. Individual interviews using a Critical Incident Technique were performed with 18 Swedish professionals working in healthcare teams, and examined with qualitative content analysis. The main findings show difficulties related to the team dynamic that arose when team members acted towards one another as representatives of their professions, difficulties that occurred when the members' various knowledge contributions interacted in the team, and difficulties related to the influence of the surrounding organization. The perceived consequences of the difficulties, beyond individual consequences, were restrictions on the use of collaborative resources to arrive at a holistic view of the patient's problem, and barriers to providing patient care and service in the desired manner. This paper also discusses how experiences of managing difficulties entailed various forms of interprofessional learning situations.
Protection from experimental ventilator-induced acute lung injury by IL-1 receptor blockade

Background: Clinical studies have shown that injurious mechanical ventilation is associated with increased airspace and plasma levels of interleukin-1β (IL-1β); however, the potential therapeutic value of IL-1 inhibition in acute lung injury has not been thoroughly investigated. A study was undertaken to determine if IL-1 signalling is a necessary early event in the pathogenesis of experimental ventilator-induced lung injury. Methods: Mice deficient in IL-1 receptor type 1 (IL1R1) and rats treated with IL-1 receptor antagonist (IL-1Ra) were mechanically ventilated with high tidal volume (30 ml/kg) and the effect of IL-1 signalling blockade on the severity of lung injury was determined. Results: Permeability, as measured by radiolabelled albumin flux, was significantly lower in IL1R1 null mice than in wild-type mice during injurious ventilation (p<0.05). IL-1Ra significantly decreased protein permeability and pulmonary oedema in rats during injurious ventilation and also decreased airspace and plasma levels of the chemokine CXCL1 and airspace neutrophils. IL-1Ra decreased expression of NOS2 and ICAM-1 mRNA in whole lung. Bronchoalveolar lavage fluid levels of RTI40, a marker of type I cell injury, were 2.5 times lower following IL-1Ra treatment (p<0.05). In isolated type II pneumocytes, IL-1β reduced electrical resistance and increased transepithelial permeability. Conclusions: IL-1 contributes to alveolar barrier dysfunction in VILI by promoting lung neutrophil recruitment and by increasing epithelial injury and permeability. Because preserved alveolar barrier function is associated with better outcomes in patients with acute lung injury, these data support further testing of IL-1Ra for the treatment of acute lung injury.
Binocular Training Reduces Amblyopic Visual Acuity Impairment

Abstract Amblyopia is the most common cause of monocular visual impairment. Patching, which is modestly effective, is the current treatment of amblyopia in children. There is no clinically approved treatment for adults. The present study is a clinical trial (non-sham controlled and non-randomized) that assessed the efficacy of binocular training for improvement of the visual acuity in children and adults with amblyopia. Twenty-two amblyopic subjects ranging in age from 5 to 73 (mean: 36.2) years for whom patching and/or surgical treatments did not correct their visual impairment completed an average of 14.5 sessions of binocular training over a period of 4 to 6 weeks. Random dot kinematograms were presented dichoptically to the two eyes and the participants’ task was to identify the direction of motion of the targets. Mean visual acuity improvement was 0.34 LogMAR (range: 0.1–0.58 LogMAR) and was shown to persist 6 months following the cessation of binocular training. Our study provides results in a large number of patients that confirm the clinical effectiveness of binocular training as a treatment for amblyopia in improving visual acuity in both children and adults. Moreover, this study is the first to demonstrate that the improvements in visual function were maintained for 6 months in the absence of any additional treatment.
The Social-Support Systems of Black Families

Since kin-support systems were recognized by Robert Hill in 1971 as one of the main sources of strength in Black families, discussion and inquiry about them have been a central theme in Black family studies. In fact, social-support systems consisting of kin, friends, and neighbors have become a focal point of studies of families on the whole, although there is still disagreement over their definition and their component parts. This paper will review contemporary literature on Black families' social-support systems, using a broad definition of socialsupport systems as "a set of personal contacts through which the individual maintains his social identity and receives emotional supports, material aid and services, information and new social contacts" (Walker et al., 1977). ' First, this review takes a theoretical perspective. It is unclear whether variables used to describe socialsupport systems in general, i.e., network composition and durability, have also been used or are applicable to describe social-support systems of Black families. Second, the review will describe the empirical work done on Black families' social-support systems, assess our knowledge about these systems in different kinds of Black families, and identify the areas where more empirical work on this topic is needed. Black families have historically been involved in support systems, particularly those that connect extended kin. Frazier (1939), in one of the earliest examinations of Black families, described the
Rigidity and flexibility of gender stereotypes in childhood: Developmental or differential?

Previous research has shown that the early learning of male–female categories is characterized by rigid beliefs about stereotypic differences, but that once gender knowledge is well established, the beliefs become more flexible. Because most studies are cross-sectional, it is not known if the early rigidity represents a normative transitional developmental stage that passes, or if early individual differences in rigidity continue into later childhood. To answer that question, analyses were performed on longitudinal data of 64 children who had been questioned about their gender concepts yearly from ages 5 to 10 years. Supporting a cognitive-developmental approach, the findings showed that the period of rigidity was short-lived whether rigidity began early or late or whether the level of peak rigidity was high or low. Copyright © 2005 John Wiley & Sons, Ltd.
Clinical and ultrasonographic changes of the breast after use of soy isoflavones.

BACKGROUND Phytoestrogens may be an alternative therapy in control of menopausal symptoms but their definite effects on breast tissue must be determined. Our study aimed to define the clinical and ultrasonographic changes of the breast after use of soy isoflavones in menopausal women. MATERIALS AND METHODS Menopausal women with hot flashes were randomly grouped as cases and controls and cases received soy isoflavones for 12 weeks. Breast examination (BE) and ultrasonography (US) were done at 0, 6 and 12 weeks. Tenderness and nodularity on BE were graded 1-4 by breast surgeons. RESULTS There were 30 women in the case and 26 in the control group. The mean age was 51.3 years and the mean age of menopause was 49.2 years. There was no change in the BE and US at 6 weeks in controls. In the case group, 10% had grade 1 tenderness and 13.3% grade 2 tenderness and grade 1 nodularity in BE accompanied with diffuse small cysts in US. At 12 weeks, there was no change in BE and US in the 2 groups. CONCLUSIONS There was no statistically significant difference in the BE of the 2 groups at 6 and 12 weeks (p value=0.36 and 0.41 for nodularity and tenderness respectively) and in the US results. Although the literature contains many facts concerning PEs and the breast, further prospective studies are needed to identify structural breast changes produced by PEs in order to identify the appropriate dosage and indications of use.
Pilot contamination alleviated coding and decoding for multicell massive MIMO systems

In this paper, we propose a new space-time block coding scheme to mitigate the effect of pilot contamination in multi-cell, massive Multiple-Input Multiple-Output (MIMO) systems. We derive the code design criterion and give some code design examples. Moreover, we present a new decoding method based on an oblique projection, which has a low decoding complexity. Simulation results show that our coding and decoding scheme has better performance than the systems with the Minimum Mean-Square Error (MMSE) decoder.
Treatment of Multiply Controlled Problem Behavior With Procedural Variations of Differential Reinforcement

We describe the assessment and treatment of 2 children with autism spectrum disorder whose problem behaviors (self-injury, aggression, and disruption) were multiply controlled. Results of functional analyses indicated that the children's problem behaviors were maintained by both positive reinforcement (attention) and negative reinforcement (escape from task demands). Subsequently, procedural variations of differential reinforcement and extinction were implemented in different contexts (attention and demand) and were effective in reducing problem behavior, increasing appropriate communication, and increasing compliance.
An Architecture for Structured, Concurrent, Real-Time Action

I present a computational architecture designed to capture certain properties essential to actions, including compositionality, concurrency, quick reactions, and resilience in the face of unexpected events. It uses a structured internal state model and complex inference about the environment to inform decision-making. The properties above are achieved by combining interacting procedural and probabilistic representations, so that the structure of actions is captured by Petri Nets, which are informed by, and affect, a model of the world represented as a Probabilistic Relational Model. I give both a theoretical analysis of the architecture and a demonstration of its use in a simulated robotic environment.
A Portable MIMO Testbed and Selected Channel Measurements

A portable multiple-input multiple-output (MIMO) testbed that is based on field programmable gate arrays (FPGAs) and which operates in the 902–928 MHz industrial, scientific, and medical (ISM) band has been developed by the High Capacity Digital Communications (HCDC) Laboratory at the University of Alberta. We present a description of the HCDC testbed along with MIMO channel capacities that were derived from measurements taken with the HCDC testbed for three special locations: a narrow corridor, an athletics field that is surrounded by a metal fence, and a parkade. These locations are special because the channel capacities are different from what is expected for a typical indoor or outdoor channel. For two of the cases, a ray-tracing analysis has been performed and the simulated channel capacity values closely match the values calculated from the measured data. A ray-tracing analysis, however, requires accurate geometrical measurements and sophisticated modeling for each specific location. A MIMO testbed is ideal for quickly obtaining accurate channel capacity information.
What Do We Know When We Know a Person

Individual differences in personality may be described at three different levels. Level I consists of those broad, decontextualized, and rela- tively nonconditional constructs called "traits," which provide a dispositional signature for personality description. No description of a person is adequate without trait attributions, but trait attributions themselves yield little beyond a "psychology ofthe stranger. " At Level II (called "personal concems"), per- sonality descriptions invoke personal strivings, life tasks, defense mechanisms, coping strategies, domain-specific skills and values, and a wide assortment of other motivational, developmental, or strategic constructs that are contextual- ized in time, place, or role. While dispositional traits and personal concerns appear to have near-universal applicability. Level III presents frameworks and constructs that may be uniquely relevant to adulthood only, and perhaps only within modern societies that put a premium on the individuation of the self. Thus, in contemporary Western societies, a full description of personality commonly requires a consideration of the extent to which a human life ex- presses unity and purpose, which are the hallmarks of identity. Identity in adulthood is an inner story of the self that integrates the reconstmcted past, perceived present, and anticipated future to provide a life with unity, purpose, and meaning. At Level III, psychologists may explore the person's identity as an internalized and evolving life story. Each of the three levels has its own geography and requires its own indigenous nomenclatures, taxonomies, theories, frameworks, and laws.