Miracle-dz/UniFAR-FTUs huggingface dataset:
Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages

ABSTRACT Numerous experimental studies have demonstrated that CD8+ T cells contribute to immunity against influenza by limiting viral replication. It is therefore surprising that rigorous statistical tests have failed to find evidence of positive selection in the epitopes targeted by CD8+ T cells. Here we use a novel computational approach to test for selection in CD8+ T-cell epitopes. We define all epitopes in the nucleoprotein (NP) and matrix protein (M1) with experimentally identified human CD8+ T-cell responses and then compare the evolution of these epitopes in parallel lineages of human and swine influenza viruses that have been diverging since roughly 1918. We find a significant enrichment of substitutions that alter human CD8+ T-cell epitopes in NP of human versus swine influenza virus, consistent with the idea that these epitopes are under positive selection. Furthermore, we show that epitope-altering substitutions in human influenza virus NP are enriched on the trunk versus the branches of the phylogenetic tree, indicating that viruses that acquire these mutations have a selective advantage. However, even in human influenza virus NP, sites in T-cell epitopes evolve more slowly than do nonepitope sites, presumably because these epitopes are under stronger inherent functional constraint. Overall, our work demonstrates that there is clear selection from CD8+ T cells in human influenza virus NP and illustrates how comparative analyses of viral lineages from different hosts can identify positive selection that is otherwise obscured by strong functional constraint. IMPORTANCE There is a strong interest in correlates of anti-influenza immunity that are protective against diverse virus strains. CD8+ T cells provide such broad immunity, since they target conserved viral proteins. An important question is whether T-cell immunity is sufficiently strong to drive influenza virus evolution. Although many studies have shown that T cells limit viral replication in animal models and are associated with decreased symptoms in humans, no studies have proven with statistical significance that influenza virus evolves under positive selection to escape T cells. Here we use comparisons of human and swine influenza viruses to rigorously demonstrate that human influenza virus evolves under pressure to fix mutations in the nucleoprotein that promote escape from T cells. We further show that viruses with these mutations have a selective advantage since they are preferentially located on the “trunk” of the phylogenetic tree. Overall, our results show that CD8+ T cells targeting nucleoprotein play an important role in shaping influenza virus evolution.
Reduction among bracket polynomials

In this paper, we propose an <i>SL</i>(<i>n</i>)-invariant division of <i>SL</i>(<i>n</i>)-invariant polynomials by establishing an admissible order among the invariant polynomials in normal form. The invariant division leads to an invariant Gröbner basis theory. The invariant division is closely related to multivariate coordinate polynomial division. This feature leads to a proof of the result that if <i>f</i><sub>1</sub>,. , <i>f</i><sub><i>k</i></sub> are <i>SL</i>(<i>n</i>,K)-invariant where K is an arbitrary field, possibly of positive characteristic, then the invariant ideal generated by them is the intersection of the ideal generated by the <i>f</i><sub><i>i</i></sub> in the polynomial ring of coordinates with the algebra of invariants.
Preparing Students for College: The Implementation and Impact of the Early College High School Model

As implemented in North Carolina, Early College High Schools are small, autonomous schools designed to increase the number of students who graduate from high school and are prepared for postsecondary education. Targeted at students who are underrepresented in college, these schools are most frequently located on college campuses and are intended to provide students with 2 years of college credit upon graduation from high school. This article reports on preliminary 9th-grade results from 285 students in 2 sites participating in a longitudinal experimental study of the impact of the model. These early results show that significantly more Early College High School students are enrolling and progressing in a college preparatory course of study. This expanded access, however, is associated with somewhat lower pass rates for some courses, suggesting the need for strong academic support to accompany increased enrollment in more rigorous courses. Implementation data collected on one school indicate that it is successfully implementing the model's components.
Facilitating conversational learning in a project team practice

Purpose – This paper seeks to provide an empirical insight into the facilitation dilemmas for conversational learning in a project team environment.Design/methodology/approach – This paper is an outcome of a participative action research process into the dynamics of situated learning activity in a case study project team. As part of their organizational change project (which included an explicit project goal of developing their collective and individual learning competencies) the case study project team initiated and undertook a series of participative “learning‐how‐to‐learn” workshops. These workshops were “learning spaces” that were centred on engaging “conversations” to both initiate and promote interpersonal understanding and critical reflective practice between the participants.Findings – In evaluating the discontinuities experienced between the planned phases and activities in these “learning space” workshop processes, three key lessons that the participants learnt about facilitating conversational .
Diagnosis of vascular diseases. Ultrasound investigations--guidelines.

The management of carotid artery disease includes both modifications in life style as well treatment of vascular risk factors. However, strict risk factor modification, including improved antihypertensive therapy, lipid management, smoking cessation, and antiplatelet therapy, promise for reducing the vascular event rate in patients with carotid atherosclerosis. The best medical management for stroke prevention was highlighted in clinical practice guidelines issued jointly in 2006 by the American Heart Association and the American Stroke Association, and co-sponsored by the Council on Cardiovascular Radiology and Intervention and the American Academy of Neurology. Lowering blood pressure to a target below 120/80 mm Hg by life style interventions and antihypertensive treatment. Glucose control to near-normoglycemic levels (target hemoglobin A1C ≤7%) is recommended among diabetics to reduce micro-vascular complications and, with lesser certainty, macrovascular complications. The primary objective of this review is to summarize the current evidence and standards for the advanced diagnostic and management strategies used in asymptomatic and symptomatic patients with carotid atherosclerosis.
Teaching personal and social responsibility to juniors through physical education

The teaching personal and social responsibility (TPSR) in physical education (PE) has a research base dating back some years. There is significant literature pertaining to senior students, the underserved, problem youth in America, teaching responsibility in gym settings, and through PE and in special projects. At the fore-front of this literature is the work of Don Hellison and his levels of responsibility, which are widely known and respected. While there is recent literature relating to New Zealand educational settings, however there is very little pertaining to junior primary school students. It is this silence that has been explored in this action research study as an area for innovation in teaching, where a working model based on Hellison's levels has been adapted, trialled and refined in a New Zealand junior school setting, and has met with considerable ongoing success.
Dual Recovery Among People With Serious Mental Illnesses and Substance Problems: A Qualitative Analysis

Objective: Individuals with serious mental illnesses are more likely to have substance-related problems than those without mental health problems. They also face more difficult recovery trajectories as they cope with dual disorders. Nevertheless, little is known about individuals’ perspectives regarding their dual recovery experiences. Methods: This qualitative analysis was conducted as part of an exploratory mixed-methods study of mental health recovery. Members of Kaiser Permanente Northwest (a group-model, not-for-profit, integrated health plan) who had serious mental illness diagnoses were interviewed four times over two years about factors affecting their mental health recovery. Interviews were recorded, transcribed, and coded with inductively derived codes. Themes were identified by reviewing text coded “alcohol or other drugs. ” Results: Participants (N = 177) had diagnosed schizophrenia/schizoaffective disorder (n = 75, 42%), bipolar I/II disorder (n = 84, 48%), or affective psychosis (n = 18, 10%). At baseline, 63% (n = 112) spontaneously described addressing substance use as part of their mental health recovery. When asked at follow-up, 97% (n = 171) provided codeable answers about substances and mental health. We identified differing pathways to recovery, including through formal treatment, self-help groups or peer support, “natural” recovery (without the help of others), and continued but controlled use of alcohol. We found three overarching themes in participants’ experiences of recovering from serious mental illnesses and substance-related problems: Learning about the effects of alcohol and drugs provided motivation and a foundation for sobriety; achieving sobriety helped people to initiate their mental health recovery processes; and achieving and maintaining sobriety built self-efficacy, self-confidence, improved functioning and a sense of personal growth. Non-judgmental support from clinicians adopting chronic disease approaches also facilitated recovery. Conclusions: Irrespective of how people achieved sobriety, quitting or severely limiting use of substances was important to initiating and continuing mental health recovery processes. Substance abuse treatment approaches that are flexible, reduce barriers to engagement, support learning about effects of substances on mental health and quality of life, and adopt a chronic disease model of addiction may increase engagement and success. Peer-based support like Alcoholics or Narcotics Anonymous can be helpful for people with serious mental illnesses, particularly when programs accept use of mental health medications.
Quantifying the biophysical characteristics of Plasmodium-falciparum-parasitized red blood cells in microcirculation

The pathogenicity of Plasmodium falciparum (Pf) malaria results from the stiffening of red blood cells (RBCs) and its ability to adhere to endothelial cells (cytoadherence). The dynamics of Pf-parasitized RBCs is studied by three-dimensional mesoscopic simulations of flow in cylindrical capillaries in order to predict the flow resistance enhancement at different parasitemia levels. In addition, the adhesive dynamics of Pf-RBCs is explored for various parameters revealing several types of cell dynamics such as firm adhesion, very slow slipping along the wall, and intermittent flipping. The parasite inside the RBC is modeled explicitly in order to capture phenomena such as “hindered tumbling” motion of the RBC and the sudden transition from firm RBC cytoadherence to flipping on the endothelial surface. These predictions are in quantitative agreement with recent experimental observations, and thus the three-dimensional modeling method presented here provides new capabilities for guiding and interpreting future in vitro and in vivo studies of malaria.
A connectivity monitoring model of opportunistic sensor network based on evolving graph

Connectivity is one of the most important parameters in network monitoring. The connectivity model of Opportunistic Sensor Networks (OSN) can hardly be established by traditional graph models due to the fact that its connectivity is timing correlative and evolutionary, which makes it extremely difficult to monitor an OSN. In order to solve the monitoring problem, this paper builds an evolving graph model based on the theory of evolving graph as a description of an OSN. It defines a series of parameters to measure the connectivity of the OSN and establishes an monitoring model. Meanwhile, this paper gives the key algorithms in building the model, the Evolving-Graph-Modeling (EGM) algorithm and the Connected-Journey (CJ) algorithm. The rationality of the monitoring model has been proven by a prototype system and the simulation results. Extensive simulation results show that the proposed connectivity monitoring model can indicate real circumstances of OSN’ connectivity, and it is applicable to monitoring an opportunistic sensor network.
Comparison of a S-VHS Camcorder and a High-Resolutio n CCD-Camera for use in Architectural Photogrammetry

Improvements and new developments in the fields of sensor and computer technology have had a major impact on photogrammetry. Nowadays a variety of cameras and photogrammetric systems is available. The application of a S-VHS camcorder and a high-resolution CCD-camera together with a system for Digital Photogrammetry and Architectural Design in architectural photogrammetry is demonstrated on a practical object. Both imaging systems provide sufficient accuracy for architectural tasks. The high-resolution CCDcamera provides for a high accuracy and a large number of details measurable in the images, whereas the inexpensive camcorder is easy to use, transportable and provides a large integrated storage capacity. An automatic data transfer of the photogrammetrically generated three-dimensional object description to a CAAD system provides new capabilities for architects and conservationists.
Loop-free multipath routing using generalized diffusing computations

A new distributed algorithm for the dynamic computation of multiple loop-free paths from source to destination in a computer network or Internet are presented, validated, and analyzed. According to this algorithm, which is called DASM (diffusing algorithm for shortest multipath), each router maintains a set of entries for each destination in its routing table, and each such entry consists of a set of tuples specifying the next router and distance in a loop-free path to the destination. DASM guarantees instantaneous loop freedom of multipath routing tables by means of a generalization of Dijkstra and Scholten's diffusing computations. With generalized diffusing computations, a node in a directed acyclic graph (DAG) defined for a given destination has multiple next nodes in the DAG and is able to modify the DAG without creating a directed loop. DASM is shown to be loop-free at every instant, and its average performance is analyzed by simulation and compared against an ideal link-state algorithm and the diffusing update algorithm (DUAL).
T1 cortical hypointensities and their association with cognitive disability in multiple sclerosis

Background: Neocortical lesions (NLs) largely contribute to the pathology of multiple sclerosis (MS), although their relevance in patients’ disability remains unknown. Objective: To assess the incidence of T1 hypointense NLs by 3.0-Tesla magnetic resonance imaging (MRI) in patients with MS and examine neocortical lesion association with cognitive impairment. Methods: In this case-control study, 21 MS patients and 21 age-, sex- and years of education-matched healthy volunteers underwent: (i) a neuropsychological examination rating cognitive impairment (Minimal Assessment of Cognitive Function in MS); (ii) a 3.0-Tesla MRI inclusive of an isotropic 1.0 mm3 three-dimensional inversion prepared spoiled gradient-recalled-echo (3D-IRSPGR) image and T1- and T2-weighted images. Hypointensities on 3D-IRSPGR lying in the cortex, either entirely or partially were counted and association between NLs and cognitive impairment investigated. Results: A total of 95 NLs were observed in 14 (66.7%) patients. NL+ patients performed poorer (p = 0.020) than NLpatients only on the delayed recall component of the California Verbal Learning Test. This difference lost statistical significance when a correction for white matter lesion volume was employed. Conclusions: Although T 1 hypointense NLs may be present in a relatively high proportion of multiple sclerosis patients, the impact that they have in cognitive impairment is not independent from white matter disease.
Air Pollution and Activation of Implantable Cardioverter Defibrillators in London

Background: Air pollution may increase the incidence of ventricular cardiac arrhythmias. We investigated this in patients with implantable cardioverter defibrillators attending London clinics. Method: We explored associations between dates of activation of defibrillators and daily concentrations of various metrics of particulate matter and of pollutant gases at lags from 0 to 5 days, using a fixed-stratum case-crossover analysis controlling for confounding factors. Results: Over an average of 1200 days of observation, 705 patients experienced 5462 activation days. Of 11 pollutants considered, we found positive associations with particle sulfate, particulate matter with aerodynamic diameter less than 10 &mgr;m and less than 2.5 &mgr;m, ozone, and sulfur dioxide. Only the association for particle sulfate was not easily explainable by chance (for 1 &mgr;g/m3, lag 0–1 day, odds ratio = 1.025 [95% confidence interval = 1.003 to 1.047]). There was little or no evidence of associations with markers of primary vehicle emissions (particle number concentration, black smoke, nitrogen oxides, and carbon monoxide). There was little evidence of interactions with clinical factors such as ischemic heart disease, frequency of activation, or cardiac drugs. Conclusion: Overall there was little evidence of an association between air pollution and activation of implantable cardioverter defibrillators. The pollutants with positive associations tended to be those of secondary origin with a regional distribution, rather than primary pollutants emitted from transport sources.
Outdoor recreation interests and environmental attitudes in Norway

In a survey among a representative sample of the Norwegian population (N = 2449), the associations between environmental attitudes and interest in 15 outdoor recreation activities were assessed. Environmental attitudes were measured by a short version of the New Ecological Paradigm (NEP) scale. Results suggest that most Norwegians agree with the environmental values tapped by the NEP scale. NEP scores were higher among women than among men and they were negatively associated with age. Rural inhabitants expressed lower NEP scores than did urban respondents, but educational level did not affect NEP scale scores. Multiple regression models explained only limited parts of the variance in respondents' NEP score and interests in outdoor recreation activities. The NEP scale yielded different regression coefficients across the 15 activities. However, the scale did contribute significantly to the prediction of interest in ten out of 15 activities. The results show that ‘appreciative’ and ‘consumptive’ activities do not constitute homogenous categories that relate to environmental attitudes in opposing ways. For example, various types of fishing and various types of hunting show different associations with environmental attitudes as measured by the NEP scale. The combined picture of the regression models suggests a complex relationship between recreational interests and the predictor variables. To obtain better explanations, other variables and more complex models will most likely be needed
Formamide-Free Genomic in situ Hybridization Allows Unambiguous Discrimination of Highly Similar Parental Genomes in Diploid Hybrids and Allopolyploids

Polyploidy and hybridization play an important role in plant diversification and speciation. The application of genomic in situ hybridization (GISH) allows the identification of parental genomes in hybrids, thus elucidating their origins and allowing for analysis of their genomic evolution. The performance of GISH depends on the similarity of the parental genomes and on the age of hybrids. Here, we present the formamide-free GISH (ff-GISH) protocol applied to diploid and polyploid hybrids of monocots (Prospero, Hyacinthaceae) and dicots (Melampodium, Asteraceae) differing in similarity of the parental genomes and in chromosome and genome sizes. The efficiency of the new protocol is compared to the standard GISH protocol. As a result, ff-GISH allowed efficient labeling and discrimination of the parental chromosome sets in diploid and allopolyploid hybrids in Prospero autumnale species complex. In contrast, the standard GISH protocol failed to differentiate the parental genomes due to high levels of similar repetitive DNA. Likewise, an unambiguous identification of parental genomes in allotetraploid Melampodium nayaritense (Asteraceae) was possible after ff-GISH, whereas the standard GISH hybridization performance was suboptimal. The modified method is simple and non-toxic and allows the discrimination of very similar parental genomes in hybrids. This method lends itself to modifications and improvements and can also be used for FISH.
Confessions and reflections of the black sheep of the learning disabilities field

The educational systems in all countries have failed to adequately address the problems of students with learning disabilities. Antisocial behaviour, homelessness, mental health problems and even suicide are a result. This article will explore the reasons for this state of affairs. One of the major reasons is excessive reliance on testing without developing a more efficient and streamlined system. Related to this excessive testing is reliance on intelligence quotient (IQ) scores. I argue and present evidence that the IQ score is unnecessary in the diagnosis of whether or not there is a learning disability. Intelligence quotient tests also do not provide useful information that can be used in the treatment of a learning disability. In addition, one of the latest, and very regressive, trends is to demand testing for ‘processing deficits’, even though there is no evidence that processing deficits are useful for either diagnosis or remediation. One recent and promising approach, Response-to-Intervention, has been developed. This approach emphasizes early identification and intervention and remediation as soon as problems are discovered. A longitudinal study of early identification and intervention will be described. Educators have solutions to the problem of learning disabilities within their grasp. Society will benefit if these solutions are pursued.
Contemporary Cosmological Beliefs

We report the results of a new survey of the American public to explore cosmological beliefs and the reasons for those beliefs. We find that cosmological knowledge is associated with age, gender, education, and membership in a church or religious organization. The majority of people believe that the universe is static. In reaction to the idea of an expanding universe, some respondents expressed fear of unknown change and danger to earth. The identification of such factors may provide insight into the psychological and social environment in which science is done.