Miracle-dz/UniFAR-FTUs huggingface dataset:
Male-Biased Autosomal Effect of 16p13.11 Copy Number Variation in Neurodevelopmental Disorders

Copy number variants (CNVs) at chromosome 16p13.11 have been associated with a range of neurodevelopmental disorders including autism, ADHD, intellectual disability and schizophrenia. Significant sex differences in prevalence, course and severity have been described for a number of these conditions but the biological and environmental factors underlying such sex-specific features remain unclear. We tested the burden and the possible sex-biased effect of CNVs at 16p13.11 in a sample of 10,397 individuals with a range of neurodevelopmental conditions, clinically referred for array comparative genomic hybridisation (aCGH); cases were compared with 11,277 controls. In order to identify candidate phenotype-associated genes, we performed an interval-based analysis and investigated the presence of ohnologs at 16p13.11; finally, we searched the DECIPHER database for previously identified 16p13.11 copy number variants. In the clinical referral series, we identified 46 cases with CNVs of variable size at 16p13.11, including 28 duplications and 18 deletions. Patients were referred for various phenotypes, including developmental delay, autism, speech delay, learning difficulties, behavioural problems, epilepsy, microcephaly and physical dysmorphisms. CNVs at 16p13.11 were also present in 17 controls. Association analysis revealed an excess of CNVs in cases compared with controls (OR = 2.59; p = 0.0005), and a sex-biased effect, with a significant enrichment of CNVs only in the male subgroup of cases (OR = 5.62; p = 0.0002), but not in females (OR = 1.19, p = 0.673). The same pattern of results was also observed in the DECIPHER sample. Interval-based analysis showed a significant enrichment of case CNVs containing interval II (OR = 2.59; p = 0.0005), located in the 0.83 Mb genomic region between 15.49–16.32 Mb, and encompassing the four ohnologs NDE1, MYH11, ABCC1 and ABCC6. Our data confirm that duplications and deletions at 16p13.11 represent incompletely penetrant pathogenic mutations that predispose to a range of neurodevelopmental disorders, and suggest a sex-limited effect on the penetrance of the pathological phenotypes at the 16p13.11 locus.
Genomic Survey of Cryptococcus neoformans-Induced Gene Expression Profiling in Human Brain Micro-Vascular Endothelial Cells

Cryptococcus neoformans is able to infect brain microvascular endothelial cells (BMEC). We performed microarray analysis of the changes in gene expression of human BMEC (HBMEC) to dissect the pathogenesis of this infection. Changes in mRNA levels were monitored at 0, 4, 8, 12, 16, 20 and 24 hours. Principal component analysis (PCA) revealed a fluctuation of gene groups during the pathogen-host interaction. Based on the time-course analysis, there are 91 and 89 genes that persistently increase and decrease their mRNA levels, respectively. The significant changes are immune responses to C. neoformans infection. Hierarchical cluster profile showed that 61 out of 66 listed interferon genes were changed at least at one time point. The active responses in expression ofMHC genes were also detected at all stages of the interaction. Taken together, our infectomic studies with linear PCA approach suggest that HBMEC significantly changes its gene profiling and also actively participates in immuno-regulations in the central nervous system during C. neoformans infection.
Heavy tails, generalized coding, and optimal Web layout

This paper considers Web layout design in the spirit of source coding for data compression and rate distortion theory, with the aim of minimizing the average size of files downloaded during Web browsing sessions. The novel aspect here is that the object of design is layout rather than codeword selection, and is subject to navigability constraints. This produces statistics for file transfers that are heavy tailed, completely unlike standard Shannon theory, and provides a natural and plausible explanation for the origin of observed power laws in Web traffic. We introduce a series of theoretical and simulation models for optimal Web layout design with varying levels of analytic tractability and realism with respect to modeling of structure, hyperlinks, and user behavior. All models produce power laws which are striking both for their consistency with each other and with observed data, and their robustness to modeling assumptions. These results suggest that heavy tails are a permanent and ubiquitous feature of Internet traffic, and not an artifice of current applications or user behavior. They also suggest new ways of thinking about protocol design that combines insights from information and control theory with traditional networking.
Selection of Early-Occurring Mutations Dictates Hormone-Independent Progressionin Mouse Mammary TumorLines

ABSTRACT Mice harboring three mouse mammary tumor virus (MMTV) variants develop pregnancy-dependent (PD) tumors that progress to pregnancy-independent (PI) behavior through successive passages. Herein, we identified 10 predominant insertions in PI transplants from 8 independent tumor lines. These mutations were also detected in small cell populations in the early PD passages. In addition, we identified a new viral insertion upstream of the gene Rspo3, which is overexpressed in three of the eight independent tumor lines and codes for a protein very similar to the recently described protein encoded by Int7. This study suggests that during progression towards hormone independence, clonal expansion of cells with specific mutations might be more relevant than the occurrence of new MMTV insertions.
Association of cord blood levels of IL-17A, but not TGF-β with pre-term neonate

Background: It has been documented that cytokines play important roles in the induction of normal functions of the placenta. It has been hypothesized that abnormal expression of the cytokines may be associated with unsuccessful pregnancy. Objective: The aim of this study was to compare the serum levels of interleukin-17A (IL-17A) and tumor growth factor (TGF-β) in pre-term, term neonates, and their corresponding mothers. Materials and Methods: This study was performed on 100 term and 60 pre-term neonates, and also on their corresponded mothers. Serum levels of IL-17A and TGF-β were examined by enzyme linked immunosorbent assay (ELISA). Results: Our results revealed that the serum levels of IL-17A were significantly decreased in pre-term neonates in comparison to full-term neonates. However, the serum levels of IL-17A in the mothers either with pre-term or full-term neonates were not different. Also the serum levels of TGF-β were not changed in pre-term neonates and their mothers when compared with full-term neonates and their mothers, respectively. Conclusion: Based on these findings, it can be concluded that IL-17A may play crucial roles in induction of normal pregnancies and also probably participates in normal growth of fetus.
EU Kids Online: national perspectives

This comparative report summarises the internet related experiences of children in the 33 countries now participating in EU Kids Online. Findings for eight new countries are added to the 25 included in our previous reports – Croatia, Iceland, Latvia, Luxembourg, Malta, Russia, Slovakia and Switzerland. For each country, we present the key statistics and country-specific commentary on children’s internet access and use, activities and skills, risks and harm parental mediation and safety, and national policy implications.
EngineeringComputer Architecture and Parallel Systems LaboratoryA Quantitative Study on Performance-Power Impact ofDual-Speed Pipeline

The drastic increase in power consumption by modern processors emphasizes the need for power-performance trade-o s in architecture design space exploration and compiler optimizations. This paper reports a quantitative study on the power-performance trade-o s in software pipelined schedules for an Itanium-like EPIC architecture with dual-speed pipelines, in which functional units are partitioned into fast ones and slow ones. We have developed an integer linear programming formulation to capture the energy/performance tradeo s for software pipelined loops. The proposed integer linear programming formulation and its solution method have been implemented and tested on a set of SPEC2000 benchmarks. The results are compared with an Itanium-like architecture(baseline) in which there are four functional units(FUs) and all of them are fast units. Our quantitative study reveals: 1. There is considerable energy saving by introducing a few slow FUs in place of fast FUs in the baseline architecture. When 2 out 4 FUs are set as slow, the total energy consumed by FUs is reduced by up to 31.1% (with an average reduction of 25.2%) compared to the baseline con guration. 2. Although using slow FUs may cause some performance degradation, our results show that such degradation is small in a large majority of cases. The average performance degradation for a con guration with 2 out of 4 FUs being slow is only 6.2%. Even when 3 out of the 4 FUs are slow units, the average performance degradation is within 15% compared to that achieved by the baseline con guration with all fast FUs. 3. If performance demand is less critical, then further energy reduction can be achieved by trading performance for energy. For example, if 30% decrease in the performance can be tolerated, then an energy saving of up to to 40.3% can be achieved, with an average of 34%.
Empirical Analysis of Limit Order Markets

We analyse order placement strategies in a limit order market, using data on the order flow from the Stockholm Stock Exchange. Traders submitting market or limit orders trade off the order price against both the execution probability and the winner’s curse risk associated with different order choices. The optimal order strategy is characterized by a monotone function, which maps the liquidity demand of the investors into their order choice. We develop and implement a semiparametric test of this monotonicity property, and find no evidence against the monotonicity property for buy orders or sell orders. We do find evidence against the hypothesis that the trader’s decision to be a buyer or a seller depends only on the trading profits available in the limit order book. We estimate that traders submitting market buy orders have private valuations that exceed the asset value by 2.3% on average and receive an average payoff of at least 1.8% of the asset value. Traders submitting limit buy orders at the price below the best ask quote have private valuations between 0.1% and 2.3% above the asset value and earn an average payoff of between 0.3% and 1.8% of the asset value. Although the distribution of liquidity demand does not depend on conditioning information, conditioning information helps us to predict the composition of the order flow in our data. These findings imply that variation in the composition of the order flow can be explained by empirical variation in the relative profitability of alternative order choices and movements in the common value of the asset.
An Empirical Analysis of Business Cycles in a New Keynesian Model with Inventories

This paper introduces inventories in an otherwise standard dynamic stochastic general equilibrium model. Firms accumulate inventories to facilitate sales, but face a cost of doing so in terms of costly storage of intermediate goods. Based on U.S. data we estimate the parameters of our model using Bayesian methods. The results show that accounting for inventory dynamics has a significant impact on parameter estimates and the following analyses. We find that inventories enter the New Keynesian Phillips curve as an additional and significant driving variable and make the inflation process less backward-looking. Moreover, impulse responses can change in terms of magnitude and persistence. The variance decompositionreveals substantial changes regarding the driving forces of inflation and the nominal interest rate when we consider inventory holding.
Interpersonal Relations and Group Processes What Do People Desire in Others? a Sociofunctional Perspective on the Importance of Different Valued Characteristics

Humans, as discriminately social creatures, make frequent judgments about others' suitability for interdependent social relations. Which characteristics of others guide these judgments and, thus, shape patterns of human affiliation? Extant research is only minimally useful for answering this question. On the basis of a sociofunctional analysis of human sociality, the authors hypothesized that people highly value trustworthiness and (to a lesser extent) cooperativeness in others with whom they may be interdependent, regardless of the specific tasks, goals, or functions of the group or relationship, but value other favorable characteristics (e.g., intelligence) differentially across such tasks, goals, or functions. Participants in 3 studies considered various characteristics for ideal members of interdependent groups (e.g., work teams, athletic teams) and relationships (e.g., family members, employees). Across different measures of trait importance and different groups and relationships, trustworthiness was considered extremely important for all interdependent others; the evidence for the enhanced importance of cooper-ativeness across different interdependence contexts was more equivocal. In contrast, people valued other characteristics primarily as they were relevant to the specific nature of the interdependent group or relationship. These empirical investigations illuminate the essence of human sociality with its foundation of trust and highlight the usefulness of a theoretically derived framework of valued characteristics. Imagine we could design our perfect relationship partners and group members—ideal romantic partners, family members, work group members, athletic team members, and so on. What characteristics would we give them? Would some characteristics emerge as more important than others? If so, which ones? Why these qualities instead of others? In a world in which humans have some degree of choice about whom to affiliate with, the above questions force us to peek into the very core of what it means to be social. Affiliation choices are necessarily discriminatory in the sharpest sense of the word, in that people must choose some individuals over others (Kurzban & Leary, 2001; Kurzban & Neuberg, 2005): Although the number of possible affiliates appears to be nearly limitless in modern society, the reality is that we each have " room " for only so many friends, so many business partners, so many research collaborators, and so many lovers (Dunbar, 1993; Tooby & Cosmides, 1996). So we must discriminate among potential associates, partially on the basis of our assessments of their personal attributes. An in-depth understanding of valued characteristics should therefore benefit substantially both theoretical and applied investigations of friendship networks, organizational …
Reach control problem: Well-posedness and structural stability

We study well-posedness and structural stability of the reach control problem (RCP) for affine systems. We demonstrate that the affine and piecewise affine feedbacks introduced in previous papers for solving RCP on a simplex are well-posed and structurally stable in the presence of small perturbations of system parameters. We also present general results on well-posedness and structural stability of RCP on polytopes by continuous state feedback. Some results echo classical findings on well-posedness for the robust regulator problem.
Deterministic and Statistical Properties of Multi-Resolution 3 D Modeling

Multi-resolution schemes for 3D modeling from an input video sequence are becoming very popular. However, multi-resolution techniques may not be the best solution strategy in many scenarios and it is important to understand the characteristics of such algorithms. In this paper, we present a multiresolution structure from motion algorithm, using monocular video as input, that exploits the bilinear relationship between depth and translation parameters to propagate the estimates through a coarseto-fine reconstruction framework. We present a detailed analysis of the deterministic and statistical properties of such an algorithm. We show that our optimization procedure is guaranteed to converge to the local minimum at each resolution. We also derive analytical expressions for the error covariances of depth and motion estimates, obtained using a multi-resolution structure from motion reconstruction algorithm, as a function of the error covariance of the feature tracks in the the input video. The method is based on using the implicit function theorem for deriving the error covariance at each resolution, and propagating the statistics from coarse to fine resolution, again taking advantage of the bilinear nature of the problem. The statistical calculations do not require the assumptions of Gaussianity of the error distributions and are valid for dense depth reconstruction estimates. Simulations have been carried out using real-life video sequences. It is shown how multi-resolution techniques can either succeed or fail in reconstructing the same scene depending on the quality of the input video of that scene, thus justifying the need for a theoretical analysis of error propagation in the 3D modeling from video.
Design as you see FIT: System-level soft error analysis of sequential circuits

Soft errors in combinational and sequential elements of digital circuits are an increasing concern as a result of technology scaling. Several techniques for gate and latch hardening have been proposed to synthesize circuits that are tolerant to soft errors. However, each such technique has associated overheads of power, area, and performance. In this paper, we present a new methodology to compute the failures in time (FIT) rate of a sequential circuit where the failures are at the system-level. System-level failures are detected by monitors derived from functional specifications. Our approach includes efficient methods to compute the FIT rate of combinational circuits (CFIT), incorporating effects of logical, timing, and electrical masking. The contribution of circuit components to the FIT rate of the overall circuit can be computed from the CFIT and probabilities of system-level failure due to soft errors in those elements. Designers can use this information to perform Pareto-optimal hardening of selected sequential and combinational components against soft errors. We present experimental results demonstrating that our analysis is efficient, accurate, and provides data that can be used to synthesize a low-overhead, low-FIT sequential circuit.
Measuring Feature Diversity in Native Language Identification

The task of Native Language Identification (NLI) is typically solved with machine learning methods, and systems make use of a wide variety of features. Some preliminary studies have been conducted to examine the effectiveness of individual features, however, no systematic study of feature interaction has been carried out. We propose a function to measure feature independence and analyze its effectiveness on a standard NLI corpus.
Optimal Behavioral Hierarchy

Human behavior has long been recognized to display hierarchical structure: actions fit together into subtasks, which cohere into extended goal-directed activities. Arranging actions hierarchically has well established benefits, allowing behaviors to be represented efficiently by the brain, and allowing solutions to new tasks to be discovered easily. However, these payoffs depend on the particular way in which actions are organized into a hierarchy, the specific way in which tasks are carved up into subtasks. We provide a mathematical account for what makes some hierarchies better than others, an account that allows an optimal hierarchy to be identified for any set of tasks. We then present results from four behavioral experiments, suggesting that human learners spontaneously discover optimal action hierarchies.
NIMH Project Accept (HPTN 043): Results from In-Depth Interviews with a Longitudinal Cohort of Community Members

Introduction NIMH Project Accept (HPTN 043) is a community- randomized trial to test the safety and efficacy of a community-level intervention designed to increase testing and lower HIV incidence in Tanzania, Zimbabwe, South Africa and Thailand. The evaluation design included a longitudinal study with community members to assess attitudinal and behavioral changes in study outcomes including HIV testing norms, HIV-related discussions, and HIV-related stigma. Methods A cohort of 657 individuals across all sites was selected to participate in a qualitative study that involved 4 interviews during the study period. Baseline and 30-month data were summarized according to each outcome, and a qualitative assessment of changes was made at the community level over time. Results Members from intervention communities described fewer barriers and greater motivation for testing than those from comparison communities. HIV-related discussions in intervention communities were more grounded in personal testing experiences. A change in HIV-related stigma over time was most pronounced in Tanzania and Zimbabwe. Participants in the intervention communities from these two sites attributed community-level changes in attitudes to project specific activities. Discussion The Project Accept intervention was associated with more favorable social norms regarding HIV testing, more personal content in HIV discussions in all study sites, and qualitative changes in HIV-related stigma in two of five sites.
Modelling legal and administrative cadastral domain : implementation in the Portuguese legal framework

The objective of this thesis is to develop a conceptual model for classification of real property rights and public regulations. The model is called the Legal Cadastral Domain Model.The model is intended to be a terminological framework for cross-border exchange of cadastral information. Parties exchanging cadastral information via the model do not require detailed knowledge of the legal system in which the right or regulation is created.The model is based on the principle that real property rights and public regulations influence real property ownership by being either beneficial or encumbering for the real property owner.The theoretical departure of the research presented in this thesis is in comparative legal theory and terminology. Real property rights and public regulations are important parts of real property legislation as they describe and secure the use and other exploitation of land, water and air.The research is conducted through studies in real property legislation and associated literature. The model has been developed through case studies on real property rights in Portugal, Germany, Ireland, the Netherlands and Sweden and public regulations in Portugal and Sweden.The generated results show that it seems possible to describe real property rights and public regulations regardless of their legal origin, at least in Western legal systems.The thesis also includes a discussion of terminological aspects concerning definitions of three-dimensional (3D) real property.The thesis consists of a summary and 6 papers.