Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-Exome Sequencing Reveals a Rapid Change in the Frequency of Rare Functional Variants in a Founding Population of Humans

Whole-exome or gene targeted resequencing in hundreds to thousands of individuals has shown that the majority of genetic variants are at low frequency in human populations. Rare variants are enriched for functional mutations and are expected to explain an important fraction of the genetic etiology of human disease, therefore having a potential medical interest. In this work, we analyze the whole-exome sequences of French-Canadian individuals, a founder population with a unique demographic history that includes an original population bottleneck less than 20 generations ago, followed by a demographic explosion, and the whole exomes of French individuals sampled from France. We show that in less than 20 generations of genetic isolation from the French population, the genetic pool of French-Canadians shows reduced levels of diversity, higher homozygosity, and an excess of rare variants with low variant sharing with Europeans. Furthermore, the French-Canadian population contains a larger proportion of putatively damaging functional variants, which could partially explain the increased incidence of genetic disease in the province. Our results highlight the impact of population demography on genetic fitness and the contribution of rare variants to the human genetic variation landscape, emphasizing the need for deep cataloguing of genetic variants by resequencing worldwide human populations in order to truly assess disease risk.
A role for TNF in limiting the duration of CTL effector phase and magnitude of CD8 T cell memory

It is known that TNF‐α (TNF) exerts distinct tissue‐protective or ‐destructive effects in the pathogenesis of T cell‐dependent immunopathology, depending on the context and amount of cytokine produced. To better understand the cellular mechanisms underlying the regulation of T cells by TNF, we have analyzed the role of TNF in regulating various facets of the antigen‐specific CD8 T cell response to lymphocytic choriomeningitis virus (LCMV) in mice. We show that expansion and differentiation of virus‐specific effector CD8 T cells and LCMV clearance are not dependent on TNF. Instead, we demonstrate that TNF limits the duration of the effector phase of the CD8 T cell response by regulating apoptosis and not proliferation of effector cells in vivo. We further show that attenuation of effector cell apoptosis induced by TNF deficiency led to a substantial increase in the number of virus‐specific memory CD8 T cells without affecting their function. The enhancement in the number of memory CD8 T cells in TNF‐deficient (TNF−/−) mice was not associated with up‐regulation of IL‐7Rα or Bcl‐2 in effector cells, which indicated that TNF might limit differentiation of memory cells from IL‐7Rlo effector cells. Collectively, these data are strongly suggestive of a role for TNF in down‐regulating CD8 T cell responses and the establishment of CD8 T cell memory during an acute viral infection. These findings further our understanding of the regulation of CD8 T cell homeostasis and have implications in vaccine development and clinical use of anti‐TNF therapies to treat T cell‐dependent, inflammatory disorders.
The Structure and Emission of the Accretion Shock in T Tauri Stars. II. The Ultraviolet-Continuum Emission

We compare accretion-shock models with optical and ultraviolet spectra of pre-main-sequence stars to (1) make the first determinations of accretion rates in intermediate-mass T Tauri stars from continuum emission and (2) derive improved estimates of accretion rates and extinctions for continuum T Tauri stars. Our method extends the shock models developed by Calvet & Gullbring to enable comparisons with optical and archival International Ultraviolet Explorer ultraviolet spectra. We find good agreement between the observations and the model predictions, supporting the basic model of magnetospheric accretion shocks as well as previous determinations of accretion rates and interstellar reddening for the low-mass T Tauri stars. The accretion rates determined for the intermediate-mass T Tauri stars agree well with values obtained through the other methods of Muzerolle and coworkers that use near-infrared hydrogen line strengths.
Positive Counseling with College Students

College students face multiple challenges and can find college life to be overwhelming at times. In this paper, we examine how positive psychology, which embraces a strengthsbased focus, has much to offer college students and their counselors. After providing an overview of positive psychology, we examine how positive psychology can be integrated into counseling generally and then more specifically into working with college students. We examine a number of different issues that college students face, and we offer different positive psychology techniques that have been found to be beneficial. Moreover, we provide a case study to demonstrate the benefits of taking a positive psychology approach to enhance counseling effectiveness. We also give attention to the potential benefits of taking a strengths-based approach to improving student retention and to how positive psychology can be applied to enhance the well-being of the counselor.
Amortized supersampling

We present a real-time rendering scheme that reuses shading samples from earlier time frames to achieve practical antialiasing of procedural shaders. Using a reprojection strategy, we maintain several sets of shading estimates at subpixel precision, and incrementally update these such that for most pixels only one new shaded sample is evaluated per frame. The key difficulty is to prevent accumulated blurring during successive reprojections. We present a theoretical analysis of the blur introduced by reprojection methods. Based on this analysis, we introduce a nonuniform spatial filter, an adaptive recursive temporal filter, and a principled scheme for locally estimating the spatial blur. Our scheme is appropriate for antialiasing shading attributes that vary slowly over time. It works in a single rendering pass on commodity graphics hardware, and offers results that surpass 4x4 stratified supersampling in quality, at a fraction of the cost.
Fundamental problems in provable security and cryptography

This paper examines methods for formally proving the security of cryptographic schemes. We show that, despite many years of active research and dozens of significant results, there are fundamental problems which have yet to be solved. We also present a new approach to one of the more controversial aspects of provable security, the random oracle model.
On the path density of a gradient field

We consider the problem of reliably finding filaments in point clouds. Realistic data sets often have numerous filaments of various sizes and shapes. Statistical techniques exist for finding one (or a few) filaments but these methods do not handle noisy data sets with many filaments. Other methods can be found in the astronomy literature but they do not have rigorous statistical guarantees. We propose the following method. Starting at each data point we construct the steepest ascent path along a kernel density estimator. We locate filaments by finding regions where these paths are highly concentrated. Formally, we define the density of these paths and we construct a consistent estimator of this path density.
The cap in the hat: unoriented 2D strings and matrix(-vector) models

We classify the possible bosonic and type 0 unoriented open and closed string theories in two dimensions, and find their dual matrix(-vector) models. There are no RP2 R-R tadpoles in any of the models, but many of them possess a massless tachyon tadpole. Thus all the models we find are consistent two-dimensional string vacua, but some get quantum corrections to their classical tachyon background. Where possible, we solve the tadpole cancellation condition, and find all the tachyon tadpole-free theories.
The time course of emotional picture processing: an event-related potential study using a rapid serial visual presentation paradigm

The present study recorded event-related potentials using rapid serial visual presentation paradigm to explore the time course of emotionally charged pictures. Participants completed a dual-target task as quickly and accurately as possible, in which they were asked to judge the gender of the person depicted (task 1) and the valence (positive, neutral, or negative) of the given picture (task 2). The results showed that the amplitudes of the P2 component were larger for emotional pictures than they were for neutral pictures, and this finding represents brain processes that distinguish emotional stimuli from non-emotional stimuli. Furthermore, positive, neutral, and negative pictures elicited late positive potentials with different amplitudes, implying that the differences between emotions are recognized. Additionally, the time course for emotional picture processing was consistent with the latter two stages of a three-stage model derived from studies on emotional facial expression processing and emotional adjective processing. The results of the present study indicate that in the three-stage model of emotion processing, the middle and late stages are more universal and stable, and thus occur at similar time points when using different stimuli (faces, words, or scenes).
Impacts of Urban Development on Precipitation in the Tropical Maritime Climate of Puerto Rico

Water is critical for sustaining natural and managed ecosystems, and precipitation is a key component in the water cycle. To understand controls on long-term changes in precipitation for scientific and environmental management applications it is necessary to examine whether local land use and land cover change (LULCC) has played a significant role in changing historical precipitation patterns and trends. For the small tropical island of Puerto Rico, where maritime climate is dominant, we used long-term precipitation and land use and land cover data to assess whether there were any detectable impacts of LULCC on monthly and yearly precipitation patterns and trends over the past century. Particular focus was given to detecting impacts from the urban landscape on mesoscale climates across Puerto Rico. We found no statistical evidence for significant differences between average monthly precipitation in urban and non-urban areas directly from surface stations, but, after subdividing by Holdridge Ecological Life Zones (HELZs) in a GIS, there were statistically significant differences (α = 0.05) in yearly average total precipitation between urban and non-urban areas in most HELZs. Precipitation in Puerto Rico has been decreasing over the past century as a result of a decrease in precipitation during periods (months or years) of low rain. However, precipitation trends at particular stations contradict synoptic-scale long-term trends, which suggests that local land use/land cover effects are driving precipitation variability at local scales.
Connecting Emotions to Behavioral Outcomes

The field of positive psychology has emerged within the last decade and focuses on investigating happiness and what constitutes a satisfying life (Seligman, 2011; Seligman & Csikszentmihalyi, 2000). One of the main purposes of positive psychology is to identify resources that can be used to promote psychologically beneficial outcomes (Fredrickson, 2001). Two positive psychological outcomes that can build resources to overcome negative circumstances and lead to a fulfilling life are resilience and well-being. A theory proposed by Fredrickson (1998) that offers a process by which individuals can enhance well-being and resilience is the broaden-and-build theory. Through this theory, it is hypothesized that experiencing positive affect can broaden an individual’s thoughts and actions, which can in turn build lasting personal outcomes (i.e., resilience and well-being; Fredrickson, 2001). The current study draws upon the tenets of the broaden-and-build theory to identify processes that may help clarify the connection between positive affect and positive psychological outcomes. Specifically, the main purpose of the current study was to determine if savoring strategies mediate the relationships between positive affect and positive psychological outcomes. Participants included two hundred and eighty-nine college students who were recruited to complete a series of online surveys. In regard to gender, 186 (64.4%) participants identified as a woman and 101 (34.9%) participants identified as a man. Results of the study revealed that positive affect was directly and indirectly related to positive psychological outcomes (i.e., resilience and well-being). Of importance, savoring in the moment partially explained the link between positive affect and positive psychological outcomes. Implications to theory and clinical practice are discussed. Index Words: Positive Psychology, Positive Affect, Savoring, Resilience, Well-Being CONNECTING EMOTIONS TO BEHAVIORAL OUTCOMES by WHITNEY L. SPEARS B.S., Virginia Commonwealth University, 2011 M.S., Georgia Southern University, 2015 A Dissertation Proposed to the Graduate Faculty of Georgia Southern University in Partial Fulfillment of the Requirements for the Degree DOCTOR OF PSYCHOLOGY
Knowledge Sharing in a Community of Practice

The aim of this study is to develop an understanding of the factors influencing participants’ knowledge-sharing in an electronic network of practice. The study builds on a theoretical framework derived from the theory of reasoned action and theories of social capital and social exchange. A model of knowledge sharing in an electronic network of practice has been developed based on this framework, which attempts to integrate factors validated through recent empirical studies (Kankanhalli et al., 2005; Wasko and Faraj, 2005; Bock et al., 2005). The model that considers the factors influencing the knowledge contributor and the knowledge seeker has been empirically tested using a survey in the Financial Management Community of Practice (COP) in the USAF Portal. Figure 1 shows the research model adopted for the study, which incorporates constructs from social exchange theory and social capital theory. Data were collected from members of the Financial Management (FM) Communities of Practice (COP) on the AF portal. Partial least squares (PLS) was chosen as the structural equation analysis method to the test the hypotheses. The study demonstrated that experience in the profession influenced the amount of contribution, but that self-rated expertise did not. The findings indicate that relational capital may not be as important to usage, but it is strongly related to the intention to share knowledge. The study also indicated that commitment to the community of practice was not a factor in knowledge contribution. Concerning anticipated extrinsic benefits, the results show that individuals are not motivated by these types of rewards whether monetary in nature or reputation-based. The hypothesis regarding the sense of self-worth through the intention to share knowledge was not supported. Secondly, the results showed that the anticipated loss of knowledge power that occurs when an individual shares personal knowledge, did not influence an individual’s intention to share knowledge in the COP. Finally, an individual’s codification effort indicated only a relationship with number of messages posted. The results provide some evidence that cognitive social capital influences intention to share knowledge.
Validity of Self-Reported Pedometer Steps per Day in College Students

ABSTRACT The purpose of this article was to examine the validity of self-reported pedometer steps/day. Forty-seven participants were provided a New Lifestyles NL-2000 (NL-2000; Lees Summit, MO, USA) pedometer and a physical activity (PA) diary for 3 weeks, but not informed of the data-storing capabilities. For weeks 2 and 3, each participant was given a step goal of 3,000 steps/day above week 1 average. A 2 × 3 repeated measures analysis of variance (ANOVA) was used to examine differences between reported steps/day. Bland–Altman plots assessed the mean bias and limits of agreement between reporting methods. Mean self-reported and NL-2000 steps/day were 9,264 ± 3,555 and 8,971 ± 3,590 steps/day (n = 26, p > .05). Mean biases were 216 ± 1,753 (week 1), –506 ± 1,355 (week 2), and –590 ± 1,360 (week 3) steps/day. Negative mean bias values indicate higher self-reported steps/day. Mean steps/day were similar between recording methods, but large differences were observed among individuals, suggesting self-reported steps/day may be valid for PA research at the population level, but not the individual level.
A Survey on Software Architecture Analysis Methods

The purpose of the architecture evaluation of a software system is to analyze the architecture to identify potential risks and to verify that the quality requirements have been addressed in the design. This survey shows the state of the research at this moment, in this domain, by presenting and discussing eight of the most representative architecture analysis methods. The selection of the studied methods tries to cover as many particular views of objective reflections as possible to be derived from the general goal. The role of the discussion is to offer guidelines related to the use of the most suitable method for an architecture assessment process. We will concentrate on discovering similarities and differences between these eight available methods by making classifications, comparisons and appropriateness studies.
What's in a Smile? Maternal Brain Responses to Infant Facial Cues

OBJECTIVES. Our goal was to determine how a mother's brain responds to her own infant's facial expressions, comparing happy, neutral, and sad face affect. METHODS. In an event-related functional MRI study, 28 first-time mothers were shown novel face images of their own 5- to 10-month-old infant and a matched unknown infant. Sixty unique stimuli from 6 categories (own-happy, own-neutral, own-sad, unknown-happy, unknown-neutral, and unknown-sad) were presented randomly for 2 seconds each, with a variable 2- to 6-second interstimulus interval. RESULTS. Key dopamine-associated reward-processing regions of the brain were activated when mothers viewed their own infant's face compared with an unknown infant's face. These included the ventral tegmental area/substantia nigra regions, the striatum, and frontal lobe regions involved in (1) emotion processing (medial prefrontal, anterior cingulate, and insula cortex), (2) cognition (dorsolateral prefrontal cortex), and (3) motor/behavioral outputs (primary motor area). Happy, but not neutral or sad own-infant faces, activated nigrostriatal brain regions interconnected by dopaminergic neurons, including the substantia nigra and dorsal putamen. A region-of-interest analysis revealed that activation in these regions was related to positive infant affect (happy > neutral > sad) for each own–unknown infant-face contrast. CONCLUSIONS. When first-time mothers see their own infant's face, an extensive brain network seems to be activated, wherein affective and cognitive information may be integrated and directed toward motor/behavioral outputs. Dopaminergic reward-related brain regions are activated specifically in response to happy, but not sad, infant faces. Understanding how a mother responds uniquely to her own infant, when smiling or crying, may be the first step in understanding the neural basis of mother–infant attachment.
Battery runtime optimization toolbox for wearable biomedical sensors

Battery runtime is a critical concern for practical usage of wearable biomedical sensor systems. A long runtime requires an interdisciplinary low-power knowledge and appropriate design tools. We addressed this issue designing a toolbox in three parts: (1) Modular evaluation kit for development of wearable ultra-low-power biomedical sensors; (2) Miniaturized, wearable, and code compatible sensor system with the same properties as the development kit; (3) Web-based battery runtime calculator for our sensor systems. The purpose of the development kit is optimization of the power consumption. Once optimization is finished, the same embedded software can be transferred to the miniaturized body worn sensor. The web-based application supports development quantifying the effects of use case and design decisions on battery runtime. A sensor developer can select sensor modules, configure sensor parameters, enter use case specific requirements, and select a battery to predict the battery runtime for a specific application. Our concept adds value to development of ultra-low-power biomedical wearable sensors. The concept is effective for professional work and educational purposes.
Non-Tuberculous Mycobacteria and the Performance of Interferon Gamma Release Assays in Denmark

Background The QuantiFERON-TB-Gold Test (QFT) is more specific than the Mantoux skin-test to discriminate between Mycobacterium tuberculosis (MTB) and non-tuberculous mycobacterial (NTM) infections. Here we study the performance of the QFT in patients with NTM disease. Methods From 2005 to 2011, nationwide patient data on positive NTM cultures (n = 925) were combined with nationwide data on QFT results (n = 16,133), both retrieved from the International Reference Laboratory of Mycobacteriology, Denmark. A total of 112 patients with NTM infections had a QFT performed, 53 patients had definite NTM disease, 10 had possible disease and 49 had NTM colonization. Results QFT was positive in 8% (4/53) of patients with definite disease, 40% (4/10) with possible disease and 31% (15/49) with colonization. Positivity rate was lowest among patients with definite disease infected with NTM without the RD1 region 4% (2/50). None of the 15 children with MAC lymphadenitis had a positive QFT. Conclusion This study is one of the largest assessing IGRAs in patients with NTM disease in a TB low-incidence setting. Our study showed that the QFT holds potential to discriminate between NTM and MTB infections. We found no positive IGRA test results among children with NTM not sharing the RD1-region of MTB resulting in a 100% specificity and we suggest that a QFT in a child presenting with cervical lymphadenitis may be helpful in distinguishing NTM from TB lymphadenitis.
Library and Archives Canada Cataloguing in Publication

All rights reserved. Up to 10 copies of this document may be made for your noncommercial personal use, provided that credit is given to the original source. You must have prior written permission for any other reproductions, storage in a retrieval system or transmission, in any form or by any means. Please note that the CMA is a member of Access Copyright, The Canadian Copyright Licensing Agency (formerly known as CANCOPY). As such, we have an agreement in place with ACCESS to grant to organizations and individuals, on our behalf, permission to make photocopies from our publications. Should you wish to pursue this request, we ask that you contact ACCESS COPYRIGHT, THE CANADIAN COPY-Handbook on clinical practice guidelines / Canadian Medical Association. Issued also in French under title: Manuel sur les guides de pratique clinique. Includes bibliographical references. 1. Medical protocols—Canada. 2. Medical care—Standards—Canada.