Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast and Robust Association Tests for Untyped SNPs in Case-Control Studies

Genome-wide association studies (GWASs) aim to genotype enough single nucleotide polymorphisms (SNPs) to effectively capture common genetic variants across the genome. Even though the number of SNPs genotyped in such studies can exceed a million, there is still interest in testing association with SNPs that were not genotyped in the study sample. Analyses of such untyped SNPs can assist in signal localization, permit cross-platform integration of samples from separate studies, and can improve power – especially for rarer SNPs. External information on a larger collection of SNPs from an appropriate reference panel, comprising both SNPs typed in the sample and the untyped SNPs we wish to test for association, is necessary for an untyped variant analysis to proceed. Linkage disequilibrium patterns observed in the reference panel are then used to infer the likely genotype at the untyped SNPs in the study sample. We propose here a novel statistical approach for testing untyped SNPs in case-control GWAS, based on an efficient score function derived from a prospective likelihood, that automatically accounts for the variability in the process of estimating the untyped variant. Computationally efficient methods of phasing can be used without affecting the validity of the test, and simple measures of haplotype sharing can be used to infer genotypes at the untyped SNPs, making our approach computationally much faster than existing approaches for untyped analysis. At the same time, we show, using simulated data, that our approach often has performance nearly equivalent to hidden Markov methods of untyped analysis. The software package ‘untyped’ is available to implement our approach.
Understanding Process Tracing

Abstract Process tracing is a fundamental tool of qualitative analysis. This method is often invoked by scholars who carry out within-case analysis based on qualitative data, yet frequently it is neither adequately understood nor rigorously applied. This deficit motivates this article, which offers a new framework for carrying out process tracing. The reformulation integrates discussions of process tracing and causal-process observations, gives greater attention to description as a key contribution, and emphasizes the causal sequence in which process-tracing observations can be situated. In the current period of major innovation in quantitative tools for causal inference, this reformulation is part of a wider, parallel effort to achieve greater systematization of qualitative methods. A key point here is that these methods can add inferential leverage that is often lacking in quantitative analysis. This article is accompanied by online teaching exercises, focused on four examples from American politics, two from comparative politics, three from international relations, and one from public health/epidemiology.
WITHIN-YEAR PERSISTENCE OF STUDENTS AT TWO-YEAR COLLEGES

Two previous studies have used the National Postsecondary Student Aid Survey ( NPSAS ) to examine the persistence of two-year college students. We used NPSAS:96 and found that tuition had a small negative effect on within-year persistence. Debtload was significant and negatively associated with persistence at low and middle levels of debt, but significant and positively associated with persistence at high levels of debt. We explored the implications of these findings and compared our research to the previous studies. This study used NPSAS:96 to research the persistence of two-year college students. We found that, while background and college experience variables influenced persistence, students were 0.18% less likely to persist for each $100increase intuition, more likely to persist if they received subsidies, and 15.96% more likely to persist for every $1,000 in student loan debt outstanding.
THE STRENGTH OF INDIRECT RELATIONS IN SOCIAL NETWORKS

Here, our goal is to develop a formal analysis of dual network structures taking into account transitive completions of higher order than the usually considered triadic closure, i.e., allowing quadruple closure and any other higher order transitive completion of open n-paths traversing two dual social networks. In this way, a sequence of indirect relations might be generated in each social network, right next to the inherent direct relations in these networks. For this purpose, we introduce the setting of a “dual social network system” and we discuss how this setting might be produced in empirical situations, in which social networks are composed or partitioned in terms of various forms of actors’ categorizations from an attributional, attitudinal, typological or structural point of view. Furthermore, we are concerned with the issue of adjusting the concepts of Granovetter’s thesis on the strength of the weak ties to the case of direct and (any order) indirect relations in such dual social network systems.
An Analysis of Digital Media Holograms Usage Intentions: An Extension of the Technology Acceptance Model

This study confirms the impact of information quality and system quality on consumers' technology experience, it specifically shows that the perceived quality of content and system were found to have a significant effect on users' perceived usefulness and perceived enjoyment. In addition, social influences had a positive effect on the intention to use digital media holograms. Using the 200 data points from the initial sample, the three constructs and their indicators were subjected to confirmation through a measurement model in AMOS 4.0. The results showed that the effect of enjoyment on PU yielded a value of -. 39 (p<.01), indicating a negative relationship that was in contrast to initial predictions. In addition, the effect of enjoyment on PEOU yielded a value of . 29 (p<.01), but the effect of engagement on PEOU yielded a value of -. 29 (p<.01), also shown to support the TAM, given that the effect of PU on PEOU was . 29 (p<.01). Finally the effect of attitudes toward using digital media holograms on behavioral intentions to use media yielded a value of 34 (p<.01). These findings suggest an extension of the TAM model for convergence technologies. This research advances theory and contributes to the foundation for future research aimed at improving the understanding of users' adoption behavior of convergence technologies. The research and practice implications are also discussed.
Context-aware Entity Morph Decoding

People create morphs, a special type of fake alternative names, to achieve certain communication goals such as expressing strong sentiment or evading censors. For example, “Black Mamba”, the name for a highly venomous snake, is a morph that Kobe Bryant created for himself due to his agility and aggressiveness in playing basketball games. This paper presents the first end-to-end context-aware entity morph decoding system that can automatically identify, disambiguate, verify morph mentions based on specific contexts, and resolve them to target entities. Our approach is based on an absolute “cold-start” it does not require any candidate morph or target entity lists as input, nor any manually constructed morph-target pairs for training. We design a semi-supervised collective inference framework for morph mention extraction, and compare various deep learning based approaches for morph resolution. Our approach achieved significant improvement over the state-of-the-art method (Huang et al., 2013), which used a large amount of training data. 1
The Dynamics of Autism Spectrum Disorders: How Neurotoxic Compounds and Neurotransmitters Interact

In recent years concern has risen about the increasing prevalence of Autism Spectrum Disorders (ASD). Accumulating evidence shows that exposure to neurotoxic compounds is related to ASD. Neurotransmitters might play a key role, as research has indicated a connection between neurotoxic compounds, neurotransmitters and ASD. In the current review a literature overview with respect to neurotoxic exposure and the effects on neurotransmitter systems is presented. The aim was to identify mechanisms and related factors which together might result in ASD. The literature reported in the current review supports the hypothesis that exposure to neurotoxic compounds can lead to alterations in the GABAergic, glutamatergic, serotonergic and dopaminergic system which have been related to ASD in previous work. However, in several studies findings were reported that are not supportive of this hypothesis. Other factors also might be related, possibly altering the mechanisms at work, such as time and length of exposure as well as dose of the compound. Future research should focus on identifying the pathway through which these factors interact with exposure to neurotoxic compounds making use of human studies.
Childhood Predictors of Later Creativity in Early Adolescence

Play is an important part of the everyday life of children. Play allows children to practice and master new skills, explore their environment, and add to their understanding of the physical and social world. The purpose of this study was to investigate the relations among the complexity of pretend play, child temperament, and parent creativity as they predict later creativity at ages 10-14. All children in this study participated in the Southern Illinois Twins and Sibling Study (SITTS; DiLalla, 2002) at age five. Pretend play behaviors and parent ratings of child temperament were assessed at age 5. When the children were ages 10-14 the families were invited to participate in a follow-up study, part of which involved children completing an alternative use task. It was hypothesized that pretend play at age 5, temperament, and parent creativity would predict later creativity. Path analyses indicated that preschool realistic pretend play and temperament were significant predictors of creativity in early adolescence. An additional path analysis was conducted to include the correlation between the play behaviors of the non-target child and the target child. Results indicated that the social aspects of the play session superseded temperamental aspects at age 5; when other child’s play behaviors were included in the model, temperament no longer significantly predicted play behavior. Parent creativity did not predict later creativity or pretend play behaviors at age 5. These results indicate that early pretend play behaviors are important in the development of later creativity.
Temporal Plasticity Involved in Recovery from Manual Dexterity Deficit after Motor Cortex Lesion in Macaque Monkeys

The question of how intensive motor training restores motor function after brain damage or stroke remains unresolved. Here we show that the ipsilesional ventral premotor cortex (PMv) and perilesional primary motor cortex (M1) of rhesus macaque monkeys are involved in the recovery of manual dexterity after a lesion of M1. A focal lesion of the hand digit area in M1 was made by means of ibotenic acid injection. This lesion initially caused flaccid paralysis in the contralateral hand but was followed by functional recovery of hand movements, including precision grip, during the course of daily postlesion motor training. Brain imaging of regional cerebral blood flow by means of H215O-positron emission tomography revealed enhanced activity of the PMv during the early postrecovery period and increased functional connectivity within M1 during the late postrecovery period. The causal role of these areas in motor recovery was confirmed by means of pharmacological inactivation by muscimol during the different recovery periods. These findings indicate that, in both the remaining primary motor and premotor cortical areas, time-dependent plastic changes in neural activity and connectivity are involved in functional recovery from the motor deficit caused by the M1 lesion. Therefore, it is likely that the PMv, an area distant from the core of the lesion, plays an important role during the early postrecovery period, whereas the perilesional M1 contributes to functional recovery especially during the late postrecovery period.
TWEAK Is an Endothelial Cell Growth and Chemotactic Factor That Also Potentiates FGF-2 and VEGF-A Mitogenic Activity

Objective—TWEAK, a member of the tumor necrosis factor superfamily, binds to the Fn14 receptor and stimulates angiogenesis in vivo. In this study, we investigated Fn14 gene expression in human endothelial cells (ECs) and examined the effect of TWEAK, added either alone or in combination with fibroblast growth factor-2 (FGF-2) or vascular endothelial growth factor-A (VEGF-A), on EC proliferation, migration, and survival in vitro. We also determined whether a soluble Fn14-Fc fusion protein could inhibit TWEAK biologic activity on ECs and investigated TWEAK signal transduction in ECs. Methods and Results—We found that both FGF-2 and VEGF-A could induce Fn14 mRNA expression in ECs. TWEAK was a mitogen for ECs, and this proliferative activity could be inhibited by an Fn14-Fc decoy receptor. Furthermore, TWEAK treatment activated several intracellular signaling pathways in ECs and potentiated FGF-2– and VEGF-A–stimulated EC proliferation. TWEAK also had EC chemotactic activity, but it did not promote EC survival. Conclusions—These results indicate that TWEAK is an EC growth and migration factor but not a survival factor. TWEAK can also enhance both FGF-2 and VEGF-A mitogenic activity on ECs. Thus, TWEAK may act alone as well as in combination with FGF-2 or VEGF-A to regulate pathological angiogenesis.
Prediction of high-power EMI effects in CMOS operational amplifiers

In this paper, a new analytical model for the prediction of the effects of high-power electromagnetic interference in CMOS operational amplifiers is presented. This model provides a closed-form expression of the operational amplifiers (opamp) output offset voltage that is induced if radio frequency interference (RFI) is superimposed onto the opamp input voltages in terms of technology and design parameters. Such a model is very useful both to predict the susceptibility of a given opamp circuit and to design opamp topologies with a high immunity to RFI. Model predictions are compared with experimental results
Embedded wafer level ball grid array (eWLB) technology for millimeter-wave applications

The embedded wafer level ball grid array (eWLB) is a novel packaging technology that shows excellent performance for millimeter-wave (mm-wave) applications. We present simulation and measurement results of single-ended and differential transmission lines realized using the thin-film redistribution layers (RDL) of an eWLB. We demonstrate the capabilities for the integration of passives on example of a configurable 17/18 GHz down-converter circuit realized in silicon-germanium (SiGe) technology with a fan-in eWLB differential inductor used for the LC tank. We compare the performance of differential chip-package-board transitions realized in an eWLB and in other common package types. We report an optimized compact chip-package-board transition in the eWLB. We obtain a simulated insertion loss as low as −0.65 dB and a return loss below −16 dB at 77 GHz without external matching networks. We introduce the concept of antenna integration in the eWLB and show examples of single-ended and differential antenna structures. Finally, we present for the first time a single-chip four-channel 77 GHz transceiver in SiGe integrated in the eWLB package together with four dipole antennas. The presented examples demonstrate that the eWLB technology is an attractive candidate for mm-wave applications including system-in-package (SiP).
Some Analogies Between Thermodynamics and Shannon Theory

In this paper we present some analogies between thermodynamics and certain Shannon theory results. We revisit the previously published results that relate notion of energy and information. We then introduce a thermodynamic system that could be used to store information. The ideal gas is considered. We present the corresponding thermodynamic analysis and establish equivalence with the additive white Gaussian noise (AWGN) channel capacity formula. Specifically, we show that the average energy needed for adiabatic compression of the ideal gas to 1/N of its initial volume is the same as the average energy needed to achieve the capacity C = log, N of the equivalent AWGN channel. In addition, the analysis is extended to show a link between the gas volume and minimum squared codeword distance. Furthermore, we show that the ideal gas which went through the adiabatic compression, and later settled according to the second law of thermodynamics, will reach an equilibrium state which is directly related to Shannon random coding and joint typicality decoding.
Intensive family preservation services in Flanders: An outcome study

Set up as a one-group pre-test-post-test follow-up design, this study examines the outcomes of intensive family preservation services (IFPS) in Flanders addressing the following research questions: Does IFPS make a significant difference concerning (1) the interaction between parent and child? (2) social support as experienced by the parent? (3) stress and empowerment of the parent? and (4) the strengths and difficulties of the minor? Families seem to indicate that their family situation is more manageable, although still, professional help is needed. Parents feel more resilient about the situation and indicate that they can get along with their child better than before the crisis intervention. Parents still feel uncertain about the future and about their role as a parent. There seems to be no indications that their level and quality of social contacts have changed. Further research is suggested to provide more in-depth information about the conditions associated with processes of change during an IFPS intervention.
The Fragile Wisdom: An Evolutionary View on Women’s Biology and Health

The Fragile Wisdom brings the biology and anthropology of sex differences to life by taking an evolutionary perspective on why certain health problems that never affected our ancestors, plague women today. A biological anthropologist specializing in reproductive ecology, Grazyna Jasienska postulates that women's biology and health are evolutionarily distinct from men's because of the relative energetic investment in reproduction and consequently executes her analysis of medical questions using the lens of sex. In this text intended for an academic adult audience, Jasienska investigates emerging medical concerns by juxtaposing the biological demands of the world that human bodies evolved in with those of current industrialized society. She presents a very well-cited argument based on a broad spectrum of primary literature findings, from biochemistry bench work to anthropological field studies, yet the book has a narrative style reminiscent of story-telling. Jasienska frames her book around the important distinction that " Health and evolutionary fitness are not synonymous " (p. 2). She explores how this disjunction relates to reproductive cost/benefit balancing acts. Jasienska discusses hormone variation, agriculture and estrogen levels, developmental programming, case studies of childhood diet and heart disease, intergenera-tional effects of slavery, the physical burdens of reproducing , factors affecting life span, how modern diet and exercise patterns are distinct from historical circumstances , evolutionary trade-offs, benefits of philanthropy, and gene-lifestyle interactions. Jasienska also offers a basic biological introduction to each topic she considers before delving into larger questions, which makes The Fragile Wisdom accessible regardless of the reader's particular background and specialty. The way that Jasienska revisits hormone levels and energy storage from a variety of perspectives gives her argument a high level of coherency and stresses the broad implications of her work. It is rare to find a book that is able to simultaneously consider such a myriad of causes for biological disease. However, The Fragile Wisdom would be strengthened by exploring additional issues or by drawing on public health research to suggest interventions to combat the problems it presents. Of note, Jasienka never attempts to advise the reader how to live a long and healthy life. Indeed, one of the main conundrums she grapples with is the fact that we are all products of our genetics, environment, and choices, in often-uncontrollable ways. She begins by explaining that " healthy " is a generally unattainable ideal. Returning to earlier hunter-forager subsistence patterns is not only impossible, but would also …
Video-based facial re-animation

Generating photorealistic facial animations is still a challenging task in computer graphics, and synthetically generated facial animations often do not meet the visual quality of captured video sequences. Video sequences on the other hand need to be captured prior to the animation stage and do not offer the same animation flexibility as computer graphics models. We present an inexpensive method for video-based facial animation, which combines the photorealism of real videos with the flexibility of CGI-based animation by extracting dynamic texture sequences from existing multi-view footage. To synthesize new facial performances, these texture sequences are concatenated in a motion-graph-like way. In order to ensure realistic appearance, we combine a warp-based optimization scheme with a modified cross dissolve to prevent visual artefacts during the transition between texture sequences. Our approach makes photorealistic facial re-animation from existing video footage possible, which is especially useful in applications like video editing or the animation of digital characters.
Timing and entrainment of multimodal backchanneling behavior for an embodied conversational agent

We report on an analysis of feedback behavior in an Active Listening Corpus as produced verbally, visually (head movement) and bimodally. The behavior is modeled in an embodied conversational agent and displayed in a conversation with a real human to human participants for perceptual evaluation. Five strategies for the timing of backchannels are compared: copying the timing of the original human listener, producing backchannels at randomly selected times, producing backchannels according to high level timing distributions relative to the interlocutor's utterance and pauses, or according to local entrainment to the interlocutors' vowels, or according to both. Human observers judge that models with global timing distributions miss less opportunities for backchanneling than random timing.
A Comparison of Fuzzy Clustering Algorithms to Cluster Web Messages

— Our objective in this paper is to propose an approach capable of clustering web messages. The clustering is carried out by assigning, with a certain probability, texts written by the same web user to the same cluster based on Stylometric features and using fuzzy clustering algorithms. Focus in the present work is on comparing the most popular algorithms in fuzzy clustering theory namely, Fuzzy C-means, Possibilistic C-means and Fuzzy Possibilistic C-Means.