Miracle-dz/UniFAR-FTUs huggingface dataset:
Rare Variation Facilitates Inferences of Fine-Scale Population Structure in Humans

Understanding the genetic structure of human populations has important implications for the design and interpretation of disease mapping studies and reconstructing human evolutionary history. To date, inferences of human population structure have primarily been made with common variants. However, recent large-scale resequencing studies have shown an abundance of rare variation in humans, which may be particularly useful for making inferences of fine-scale population structure. To this end, we used an information theory framework and extensive coalescent simulations to rigorously quantify the informativeness of rare and common variation to detect signatures of fine-scale population structure. We show that rare variation affords unique insights into patterns of recent population structure. Furthermore, to empirically assess our theoretical findings, we analyzed high-coverage exome sequences in 6,515 European and African American individuals. As predicted, rare variants are more informative than common polymorphisms in revealing a distinct cluster of European–American individuals, and subsequent analyses demonstrate that these individuals are likely of Ashkenazi Jewish ancestry. Our results provide new insights into the population structure using rare variation, which will be an important factor to account for in rare variant association studies.
BambooTrust: practical scalable trust management for global public computing

Global public computing platforms, such as PlanetLab, grid computing systems, and XenoServers, require facilities for managing trust to allow their participants to interact effectively in an open and untrusted environment. In this paper, we describe BambooTrust, a practical, high-performance distributed trust management system for global public computing platforms. We present our peer-to-peer architecture, based on the XenoTrust model and the Bamboo distributed hash table. We describe the initial BambooTrust implementation and deployment, and demonstrate that the system performs and scales more than adequately well by means of experimental evaluation.
Humanoid Robots in Soccer: Robots Versus Humans in RoboCup 2050

This article describes the history and major achievements of the RoboCup Humanoid League from its start in 2002 to today. Furthermore, it gives an indication on how the league may evolve over the coming years until 2050, when a team of autonomous humanoid robots shall play soccer against the human world champion. We show how the competition drives humanoid robot research and serves as a benchmark to measure progress.
Wheat dependent exercise induced anaphylaxis: is this an appropriate terminology?

Background The presentation of wheat dependent exercise induced anaphylaxis (WDEIA) can be variable. A high index of clinical suspicion is required to initiate the investigation pathway. Double blind placebo controlled food-exercise challenge is the gold standard investigation but the practicality of this test limits its application. Aim To critically analyse the symptoms of WDEIA and their correlation with serum specific IgE (sIgE) to rω-5-gliadin. Methods 17 patients were tested for serum sIgE to rω-5-gliadin. The clinical response to a diet/exercise intervention protocol was used to assess specificity of a positive sIgE to rω-5-gliadin. Length of time to diagnosis, clinical likelihood scores, exercise intensity involved and the severity of allergic reactions were examined retrospectively. Result 8/10 patients with positive sIgE to rω-5-gliadin had a confirmed diagnosis of WDEIA. Half of the WDEIA patients had a prolonged time lag to diagnosis (32–62 months) and were initially diagnosed with idiopathic anaphylaxis or chronic idiopathic urticaria and angioedema. Only three patients had experienced life threatening symptoms (Mueller grading 4). A close association was observed between requirements of lower exercise intensity to provoke a reaction and diagnostic delay. Conclusion Specific IgE to rω-5-gliadin can provide supportive evidence for WDEIA without the need of a food-exercise challenge. The wheat-exercise association is not obvious in many patients, highlighting the need to consider WDEIA in the differential diagnosis of all patients presenting with idiopathic systemic reactions. The term anaphylaxis may be inappropriate and it is therefore worth considering an alternative terminology such as ‘activity dependent wheat allergy’ to describe this condition.
Bioactive Whey Protein Concentrate and Lactose Stimulate Gut Function in Formula-fed Preterm Pigs

Objective: Formula feeding is associated with compromised intestinal health in preterm neonates compared with maternal milk, but the mechanisms behind this are unclear. We hypothesized that the use of maltodextrin and whey protein concentrates (WPCs) with reduced bioactivity owing to thermal processing are important factors. Method: Ninety-two cesarean-delivered preterm pigs were fed increasing doses of formulas for 5 days (24–120 mL · kg−1 · day−1). In experiment 1, 4 groups of pigs (n = 15–16) were fed lactose- or maltodextrin-dominant formulas (lactose/maltodextrin ratios 3:1 or 1:3, respectively), containing WPC with either high or low levels of IgG (WPC1 or WPC2, respectively). In experiment 2, 2 groups of pigs (n = 15–16) were fed lactose-dominant formulas with either a bioactive WPC (BioWPC, produced by reduced thermal-processing) or a conventional WPC (ConWPC). Results: In experiment 1, pigs fed formula with WPC1 had higher villi, hexose absorption, and lactase activity in small intestine, relative to WPC2, but predominantly with the lactose-dominant formula (all P < 0.05). In experiment 2, the BioWPC product had higher bioactivity, as indicated by higher IgG, lactoferrin, and TGF-&bgr;2 levels, and better enterocyte proliferation in vitro. Pigs fed the BioWPC formula showed better feeding tolerance and higher intestinal villi and lactase activity (all P < 0.05). The BioWPC formula-fed pigs also had greater physical activity (P < 0.05 on day 4) and tended to show improved hexose absorption and decreased gut permeability (both P ⩽ 0.09). Conclusions: Infant formulas containing lactose as the main carbohydrate, and WPC with reduced thermal processing, may support gut maturation and health in sensitive, preterm neonates.
An Eye Tracking Study on Text Customization for User Performance and Preference

This paper presents a user study which compares reading performance versus user preference in customization of the text. We study the following parameters: grey scales for the font and the background, colors combinations, font size, column width and spacing of characters, lines and paragraphs. We used eye tracking to measure the reading performance of 92 participants, and questionnaires to collect their preferences. The study shows correlations on larger contrast and sizes, but there is no concluding evidence for the other parameters. Based on our results, we propose a set of text customization guidelines for reading text on screen combining the results of both kind of data.
Expression of p15INK4b and p57KIP2 and Relationship with Clinicopathological Features and Prognosis in Patients with Vulvar Squamous Cell Carcinoma

Background The cyclin-dependent kinase inhibitors p15INK4b and p57KIP2 are important regulators of the cell cycle, and their abnormal expression has been detected in various tumors. However, little is known about the role of p15INK4b and p57KIP2 in the pathogenesis of vulvar carcinoma, and the prognostic impact is still unknown. In our current study, we examined the expression of p15INK4b and p57KIP2 in a large series of vulvar squamous cell carcinomas to elucidate the prognostic impact. Methods Expression of p15INK4b and p57KIP2 were examined in 297 vulvar squamous cell carcinomas using immunohistochemistry. Both uni- and multivariate analysis of prognostic factors were performed, and correlations with clinicopathologic parameters were examined. Results Compared to the high levels of p15INK4b and p57KIP2 in normal vulvar squamous epithelium, low levels of p15INK4b and p57KIP2 were found in 82% and 44% of vulvar carcinomas, respectively. Low levels of p15INK4b and p57KIP2 correlated significantly with malignant features, including large tumor diameter (p = 0.03 and p = 0.001, respectively) and increased invasiveness (p = 0.003 and p = 0.04, respectively). Although p15INK4b and p57KIP2 levels could not be identified as prognostic markers, combined analysis of p14ARF/p15INK4b/p16INK4a showed that patients whose tumors expressed low levels of two or three of these INK4 proteins had a worse prognosis than those with only low levels of one or no protein (univariate analysis p = 0.02). The independent prognostic significance of these INK4 proteins was confirmed by multivariate analysis (p = 0.008). Conclusions We show for the first time that p15INK4b and p57KIP2 may be involved in the progression of vulvar carcinomas and the combined p14ARF/p15INK4b/p16INK4a status was a statistically independent prognostic factor.
Convergence Results for Unanimous Voting

We develop a unidimensional spatial model of two party competition in which parties are better informed than voters about the bliss point of voters. The announced positions of the two parties serve as signals to the voters concerning the parties' private information. Surprisingly, in all separating equilibria the policies implemented by the left-wing party, when it attains power, are to the right of the policies implemented by the right-wing party when it attains power in turn. The driving force behind this result is that, in the event of a shock making right-wing policies more attractive, the incentives pushing the left party to the right are strong, since by winning the election it can avoid the right party implementing extreme policies, while the right-wing party can stay put in a radical stance with the prospect of seeing relatively attractive policies implemented by the rival party.
Regimvid at ImageCLEF 2015 Scalable Concept Image Annotation Task: Ontology based Hierarchical Image Annotation

In this paper, we describe our participation in the Image- CLEF 2015 Scalable Concept Image Annotation task. In this participa- tion, we display our approach for an automatic image annotation by the use of an ontology-based semantic hierarchy handled at both learning and annotation steps. While recent works focused on the use of semantic hierarchies to improve concept detector accuracy, we are investigating the use of such hierarchies to reduce detector complexity and then, to handle eciently large-scale image datasets. Our framework is based on two steps: (1) constructing a fuzzy ontology through analyzing learning dataset, and (2) guiding the annotation process through a reasoning en- gine. The obtained results conrm that this approach is promising for scalable image annotation.
AN IN SILICO DESCRIPTION OF AN ALZHEIMER NETWORK

Alzheimer’s disease (AD) is the most well known form of dementia. Already in 1907 Alois Alzheimer published a first paper about the symptoms of this disease, of which we know that it afflicts one in three people above 85. By now it is broadly accepted that indeed the loss of short-term memory is among the first symptoms of AD, followed by behavioural changes and difficulties with motor activities. In the end, Alzheimer is a terminal disease, and with its huge direct impact on caregivers and financial impact on society it is an essential topic in several research fields. Additionally, by the increasing average age of current society it only becomes more urgent. Among these fields of research, computational neuroscience can be helpful as a first step in deciphering phenomena that occur with the appearance of Alzheimer’s disease. For many years after the first descriptions about AD there was no clue about a possible cause. Nowadays it is known that the appearance of the disease is mediated by a protein called Amyloid beta (A�). The exact role of A� remains unknown, though a prominent hypothesis is that it affects several presynaptic processes, thereby suppressing neuron efficiency. We model networks containing up to 600 neurons as computational networks in which the vertices represent a neuron. The internal dynamics of the neuron are governed by the so-called Izhikevich model. The connections represent the synapses between neurons. In this way, the behaviour of neural networks can be simulated by using computational mathematics. In this thesis a computational framework designed to map experimental data to synaptic parameters is constructed. In this way, having in vitro measurements of A�-treated neuronal networks and untreated control networks, the existence of significant differences in the synaptic properties of the two types of networks can be systematically investigated. Taking our cues from previous research by Philip Hahn & Cameron McIntyre [2010], we attempt to use a Gauss-Newton least mean square error optimisation. The computational framework then extracts the first two statistical moments, Mean Firing Rate (MFR) and Coefficient of Variation (CV), from measurements. This Gauss-Newton method subsequently searches for synaptic properties yielding networks with comparable MFR and CV. We conclude that this Gauss-Newton method should be handled with great care. In particular, we find that, for our particular model the algorithm either diverges or converges at a poor rate. Besides this statement and giving an overview on how varying the synaptic parameters affects the behaviour of neural networks, this thesis gives elaborate suggestions for future computational research on Alzheimer’s disease.
Age-Related Changes of Adaptive and Neuropsychological Features in Persons with Down Syndrome

Down Syndrome (DS) is characterised by premature aging and an accelerated decline of cognitive functions in the vast majority of cases. As the life expectancy of DS persons is rapidly increasing, this decline is becoming a dramatic health problem. The aim of this study was to thoroughly evaluate a group of 67 non-demented persons with DS of different ages (11 to 66 years), from a neuropsychological, neuropsychiatric and psychomotor point of view in order to evaluate in a cross-sectional study the age-related adaptive and neuropsychological features, and to possibly identify early signs predictive of cognitive decline. The main finding of this study is that both neuropsychological functions and adaptive skills are lower in adult DS persons over 40 years old, compared to younger ones. In particular, language and short memory skills, frontal lobe functions, visuo-spatial abilities and adaptive behaviour appear to be the more affected domains. A growing deficit in verbal comprehension, along with social isolation, loss of interest and greater fatigue in daily tasks, are the main features found in older, non demented DS persons evaluated in our study. It is proposed that these signs can be alarm bells for incipient dementia, and that neuro-cognitive rehabilitation and psycho-pharmacological interventions must start as soon as the fourth decade (or even earlier) in DS persons, i.e. at an age where interventions can have the greatest efficacy.
On the radio emitting high mass X-ray binary LS 5039

We present new optical { near{IR spectroscopic and photometric observations of the newly discovered galactic microquasar LS 5039, which indicate a classication for the mass donor in the system of O6.5V((f)). Optical spectroscopy and photometry shows no variability over a timescale of years, and we nd no evidence of modulation by, or emission from the compact companion in these data. However signicant photometric variability (0:4 mag) is present in the H and K bands between 1995{2000. Such variability has been observed in other radio bright X-ray binaries where it has been attributed to synchrotron emission from the jet. However, given the non{thermal spectral index of the radio emission in LS 5039 this explanation appears unlikely, predicting a near{IR flux3 orders of magnitude too small to contribute signicantly at such wavelengths. Nightly optical photometry over a 21 day period between 2000 May{June reveals variability at a level of a few hundredths of a magnitude, with no periodicity or long term trend visible. Likewise, while the radio lightcurves show moderate variability (20 per cent of the mean flux density) we nd no evidence of periodic modulation { Monte Carlo simulations constrain any such periodic variability to <4 per cent modulation at 2.25 GHz. The dierences in behaviour between LS 5039 and Cygnus X-1 { the most closely related radio emitting High Mass X-ray Binary { are likely to be a result of the weaker stellar wind and probable greater orbital separation of LS 5039 compared to Cyg X-1.
Vines and vineyards by updating persistence in linear time

Persistent homology is the mathematical core of recent work on shape, including reconstruction, recognition, and matching. Its pertinent information is encapsulated by a pairing of the critical values of a function, visualized by points forming a diagram in the plane. The original algorithm in [10] computes the pairs from an ordering of the simplices in a triangulation and takes worst-case time cubic in the number of simplices. The main result of this paper is an algorithm that maintains the pairing in worst-case linear time per transposition in the ordering. A side-effect of the algorithm's analysis is an elementary proof of the stability of persistence diagrams [7] in the special case of piecewise-linear functions. We use the algorithm to compute 1-parameter families of diagrams which we apply to the study of protein folding trajectories.
The Sage handbook of quantitative methodology for the social sciences

Preface Acknowledgments Section I: Scaling Chapter 1: Dual Scaling - Shizuhiko Nishisato Chapter 2: Multidimensional Scaling and Unfolding of Symmetric and Asymmetric Proximity Relations - Willem J. Heiser and Frank M.T. A. Busing Chapter 3: Principal Components Analysis With Nonlinear Optimal Scaling Transformations for Ordinal and Nominal Data - Jacqueline J. Muelman, Anita J. Van der Kooij, and Willem J. Heiser Section II: Testing and Measurement Chapter 4: Responsible Modeling of Measurement Data for Appropriate Inferences: Important Advances in Reliability and Validity Theory - Bruno D. Zumbo and Andre A. Rupp Chapter 5: Test Modeling - Ratna Nandakumar and Terry Ackerman Chapter 6: Differential Item Functioning Analysis: Detecting DIF Items and Testing DIF Hypotheses - Louis A. Roussos and William Stout Chapter 7: Understanding Computerized Adaptive Testing: from Robbins-Monro to Lord and Beyond - Hua-Hua Chang Section III: Models for Categorical Data Chapter 8: Trends in Categorical Data Analysis: New, Semi-New, and Recycled Ideas - David Rindskopf Chapter 9: Ordinal Regression Models - Valen E. Johnson and James H. Albert Chapter 10: Latent Class Models - Jay Magidson and Jeroen K. Vermunt Chapter 11: Discrete-Time Survival Analysis - John B. Willett and Judith D. Singer Section IV: Models for Multilevel Data Chapter 12: An Introduction to Growth Modeling - Donald Hedecker Chapter 13: Multilevel Models for School Effectiveness Research - Russell W. Rumberger and Gregory J. Palardy Chapter 14: The Use of Hierarchical Models in Analyzing Data from Experiments and Quasi-Experiments Conducted in Field Settings - Michael Seltzer Chapter 15: Meta-Analysis - Spyros Konstantopoulos and Larry V. Hedges Section V: Models for Latent Variables Chapter 16: Determining the Number of Factors in Exploratory and Confirmatory Factor Analysis - Rick H. Hoyle and Jamieson L. Duvall Chapter 17: Experimental, Quasi-Experimental, and Nonexperimental Design and Analysis with Latent Variables - Gregory R. Hancock Chapter 18: Applying Dynamic Factor Analysis in Behavioral and Social Science Research - John R. Nesselroade and Peter C. M. Molenaar Chapter 19: Latent Variable Analysis: Growth Mixture Modeling and Related Techniques for Longitudinal Data - Bengt Muthen Section VI: Foundational Issues Chapter 20: Probabalistic Modeling with Bayesian Networks - Richard E. Neapolitan and Scott Morris Chapter 21: The Null Ritual: What You Always Wanted to Know About Significance Testing but Were Afraid to Ask - Gerd Gigerenzer, Stefan Krauss, and Oliver Vitouch Chapter 22: On Exogeneity - David Kaplan Chapter 23: Objectivity in Science and Structural Equation Modeling - Stanley A. Mulaik Chapter 24: Causal Inference - Peter Spirtes, Richard Scheines, Clark Glymour, Thomas Richardson, and Christopher Meek Index
RUMA has it: Rewired User-space Memory Access is Possible!

Memory management is one of the most boring topics in database research. It plays a minor role in tasks like free-space management or efficient space usage. Here and there we also realize its impact on database performance when worrying about NUMA-aware memory allocation, data compacting, snapshotting, and defragmentation. But, overall, let's face it: the entire topic sounds as exciting as 'garbage collection' or 'debugging a program for memory leaks'. What if there were a technique that would promote memory management from a third class helper thingie to a first class citizen in algorithm and systems design? What if that technique turned the role of memory management in a database system (and any other data processing system) upside-down? What if that technique could be identified as a key for re-designing various core algorithms with the effect of outperforming existing state-of-the-art methods considerably? Then we would write this paper. We introduce RUMA: Rewired User-space Memory Access. It allows for physiological data management, i.e. we allow developers to freely rewire the mappings from virtual to physical memory (in user space) while at the same time exploiting the virtual memory support offered by hardware and operating system. We show that fundamental database building blocks such as array operations, partitioning, sorting, and snapshotting benefit strongly from RUMA.
Property and Lighting Manipulations for Static Volume Stylization Using a Painting Metaphor

Although volumetric phenomena are important for realistic rendering and can even be a crucial component in the image, the artistic control of the volume's appearance is challenging. Appropriate tools to edit volume properties are missing, which can make it necessary to use simulation results directly. Alternatively, high-level modifications that are rarely intuitive, e.g., the tweaking of noise function parameters, can be utilized. Our work introduces a solution to stylize single-scattering volumetric effects in static volumes. Hereby, an artistic and intuitive control of emission, scattering and extinction becomes possible, while ensuring a smooth and coherent appearance when changing the viewpoint. Our method is based on tomographic reconstruction, which we link to the volumetric rendering equation. It analyzes a number of target views provided by the artist and adapts the volume properties to match the appearance for the given perspectives. Additionally, we describe how we can optimize for the environmental lighting to match a desired scene appearance, while keeping volume properties constant. Finally, both techniques can be combined. We demonstrate several use cases of our approach and illustrate its effectiveness.