Miracle-dz/UniFAR-FTUs huggingface dataset:
Examining the Impact of Imputation Errors on Fine-Mapping Using DNA Methylation QTL as a Model Trait

This study highlights dangers in over-interpreting fine-mapping results. Chundru et al. show that genotype imputation accuracy has a large impact on fine-mapping accuracy. They used DNA methylation at CpG-sites with a variant. Genetic variants disrupting DNA methylation at CpG dinucleotides (CpG-SNP) provide a set of known causal variants to serve as models to test fine-mapping methodology. We use 1716 CpG-SNPs to test three fine-mapping approaches (Bayesian imputation-based association mapping, Bayesian sparse linear mixed model, and the J-test), assessing the impact of imputation errors and the choice of reference panel by using both whole-genome sequence (WGS), and genotype array data on the same individuals (n = 1166). The choice of imputation reference panel had a strong effect on imputation accuracy, with the 1000 Genomes Project Phase 3 (1000G) reference panel (n = 2504 from 26 populations) giving a mean nonreference discordance rate between imputed and sequenced genotypes of 3.2% compared to 1.6% when using the Haplotype Reference Consortium (HRC) reference panel (n = 32,470 Europeans). These imputation errors had an impact on whether the CpG-SNP was included in the 95% credible set, with a difference of ∼23% and ∼7% between the WGS and the 1000G and HRC imputed datasets, respectively. All of the fine-mapping methods failed to reach the expected 95% coverage of the CpG-SNP. This is attributed to secondary cis genetic effects that are unable to be statistically separated from the CpG-SNP, and through a masking mechanism where the effect of the methylation disrupting allele at the CpG-SNP is hidden by the effect of a nearby SNP that has strong linkage disequilibrium with the CpG-SNP. The reduced accuracy in fine-mapping a known causal variant in a low-level biological trait with imputed genetic data has implications for the study of higher-order complex traits and disease.
A stokes flow boundary integral measurement of tubular structure cross sections in two dimensions

In this paper we will develop a method to determine cross sections of arbitrary two-dimensional tubular structures, which are allowed to branch, by means of a Stokes flow based boundary integral formulation. The measure for the cross sections for a point on the boundary of a given structure will be the path obtained by integrating perpendicularly to the flow lines from one side of the boundary to the other. Special emphasis will be put on the behavior at branching points, the behavior at vortices, and the necessary boundary conditions. The method can be extended to three dimensional problems.
Processing of SMOS level 1c data onto a Discrete Global Grid

The SMOS data product steps from raw data to brightness temperature maps are described. Originally ordered in the sequence of snapshots, the data are rearranged for the level 1c Brightness Temperature maps according to their location in a Discrete Global Grid (DGG). A number of candidate DGGs are introduced and their suitability is evaluated
Exact Covers via Determinants

Given a $k$-uniform hypergraph on $n$ vertices, partitioned in $k$ equal parts such that every hyperedge includes one vertex from each part, the $k$-Dimensional Matching problem asks whether there is a disjoint collection of the hyperedges which covers all vertices. We show it can be solved by a randomized polynomial space algorithm in $O^*(2^{n(k-2)/k})$ time. The $O^*()$ notation hides factors polynomial in $n$ and $k$. The general Exact Cover by $k$-Sets problem asks the same when the partition constraint is dropped and arbitrary hyperedges of cardinality $k$ are permitted. We show it can be solved by a randomized polynomial space algorithm in $O^*(c_k^n)$ time, where $c_3=1.496, c_4=1.642, c_5=1.721$, and provide a general bound for larger $k$. Both results substantially improve on the previous best algorithms for these problems, especially for small $k$. They follow from the new observation that Lov\'asz' perfect matching detection via determinants (Lov\'asz, 1979) admits an embedding in the recently proposed inclusion--exclusion counting scheme for set covers, \emph{despite} its inability to count the perfect matchings.
Short text categorization exploiting contextual enrichment and external knowledge

We address the problem of the categorization of short texts, like those posted by users on social networks and microblogging platforms. We specifically focus on Twitter. Since short texts do not provide sufficient word occurrences, and they often contain abbreviations and acronyms, traditional classification methods such as "Bag-of-Words" have limitations. Our proposed method enriches the original text with a new set of words, to add more semantic value by using information extracted from webpages of the same temporal context. Then we use those words to query Wikipedia, as an external knowledge base, with the final goal to categorize the original text using a predefined set of Wikipedia categories. We also present a first experimental evaluation that confirms the effectiveness of the algorithm design and implementation choices, highlighting some critical issues with short texts.
Generic programming with fixed points for mutually recursive datatypes

Many datatype-generic functions need access to the recursive positions in the structure of the datatype, and therefore adopt a fixed point view on datatypes. Examples include variants of fold that traverse the data following the recursive structure, or the Zipper data structure that enables navigation along the recursive positions. However, Hindley-Milner-inspired type systems with algebraic datatypes make it difficult to express fixed points for anything but regular datatypes. Many real-life examples such as abstract syntax trees are in fact systems of mutually recursive datatypes and therefore excluded. Using Haskell's GADTs and type families, we describe a technique that allows a fixed-point view for systems of mutually recursive datatypes. We demonstrate that our approach is widely applicable by giving several examples of generic functions for this view, most prominently the Zipper.
Expectation Suppression in Early Visual Cortex Depends on Task Set

Stimulus expectation can modulate neural responses in early sensory cortical regions, with expected stimuli often leading to a reduced neural response. However, it is unclear whether this expectation suppression is an automatic phenomenon or is instead dependent on the type of task a subject is engaged in. To investigate this, human subjects were presented with visual grating stimuli in the periphery that were either predictable or non-predictable while they performed three tasks that differently engaged cognitive resources. In two of the tasks, the predictable stimulus was task-irrelevant and spatial attention was engaged at fixation, with a high load on either perceptual or working memory resources. In the third task, the predictable stimulus was task-relevant, and therefore spatially attended. We observed that expectation suppression is dependent on the cognitive resources engaged by a subjects’ current task. When the grating was task-irrelevant, expectation suppression for predictable items was visible in retinotopically specific areas of early visual cortex (V1-V3) during the perceptual task, but it was abolished when working memory was loaded. When the grating was task-relevant and spatially attended, there was no significant effect of expectation in early visual cortex. These results suggest that expectation suppression is not an automatic phenomenon, but dependent on attentional state and type of available cognitive resources.
Testing of high current transformer by non-uniform equivalent magnetomotive force method

Abstrac t In the testing of high current transformer performance under interference from external current, it is very difficult to reproduce the high current in adjacent bus-bar or eccentric primary bus-bar. To overcome the testing difficulty, this manuscript presents an effective and simple method named as Non-uniform Equivalent Magnetomotive Force (NEMMF) Method, which uses a single non-uniformly distributed testing winding to reproduce the magnetic field from adjacent and concentric primary bus-bars simultaneously. The principle of the NEMMF method is demonstrated and proved by magnetic circuit method, and some key formulas determining the parameters of testing winding have been derived. The NEMMF method is then verified by numerical simulation using Finite Element Method (FEM).
Hybrid 3D registration approach using RGB and depth images

We propose a novel technique for registration of 3D point sets using both the RGB data as well as the depth data. The main advantage of any RGB-D sensor is the pixel wise correspondence between RGB values and depth values, which can be leveraged to register two RGB-D datasets. RGB images are used for correspondence identification and these correspondences are transferred to depth images to be used for the registration algorithm. RANSAC is used for rejection of noisy data points, which increases the registration accuracy. We also analyze and present an error threshold selection strategy for fitting 3D points. Our approach achieves faster execution, thus enabling real-time implementation of change detection and 3D mapping of the environment, etc. Multiple feature extraction methods have been tested to evaluate tradeoffs between accuracy and time.
Coding for noisy channels with input-dependent insertions

Tree encoding and sequential decoding are considered for noisy channels that respond a random number of times to each input. Such channels appear in mathematical models of certain speech recognition systems. The decoding error probability and the channel capacity are bounded by extension of the methods of Jelinek and Zigangirov to noisy multilevel channels with input-dependent insertions. Certain analytical difficulties peculiar to the channels in question are indicated.
Multi-feature stationary foreground detection for crowded video-surveillance

We propose a novel approach for stationary foreground detection in crowds based on the spatio-temporal evolution of multiple features. A generic framework is presented to detect stationarity where history images model the spatio-temporal feature patterns. A feature is proposed based on structural information over each pixel neighborhood for dealing with shadows and illumination changes. A multifeature detector is composed by combining the history images of three features (namely, foreground, motion and structural information) to estimate the foreground stationarity over time, which is later thresholded to detect stationary regions. Experimental results over challenging video-surveillance sequences show the improvement of the proposed approach against related work as structural information reduces false detections, which are common in crowded places.
Facilitating Argument in Physical Space

We have created a ubiquitous computing application which will facilitate discussion. The system applies radio frequency identification (RFID) and tangible user interfaces (TUIs) to the World Wide Web. It uses TUIs to permit users to explore and construct both sides of a debate. While our initial evaluation focuses on school children, during our demo conference attendees use our interface to participate in the debate of pertinent Ubicomp topic; “Will ubiquitous computers replace paper? ” Our interface moves beyond WIMP to bring argumentation and debate into the tangible realm.
Projected Impact of Dengue Vaccination in Yucatán, Mexico

Dengue vaccines will soon provide a new tool for reducing dengue disease, but the effectiveness of widespread vaccination campaigns has not yet been determined. We developed an agent-based dengue model representing movement of and transmission dynamics among people and mosquitoes in Yucatán, Mexico, and simulated various vaccine scenarios to evaluate effectiveness under those conditions. This model includes detailed spatial representation of the Yucatán population, including the location and movement of 1.8 million people between 375,000 households and 100,000 workplaces and schools. Where possible, we designed the model to use data sources with international coverage, to simplify re-parameterization for other regions. The simulation and analysis integrate 35 years of mild and severe case data (including dengue serotype when available), results of a seroprevalence survey, satellite imagery, and climatological, census, and economic data. To fit model parameters that are not directly informed by available data, such as disease reporting rates and dengue transmission parameters, we developed a parameter estimation toolkit called AbcSmc, which we have made publicly available. After fitting the simulation model to dengue case data, we forecasted transmission and assessed the relative effectiveness of several vaccination strategies over a 20 year period. Vaccine efficacy is based on phase III trial results for the Sanofi-Pasteur vaccine, Dengvaxia. We consider routine vaccination of 2, 9, or 16 year-olds, with and without a one-time catch-up campaign to age 30. Because the durability of Dengvaxia is not yet established, we consider hypothetical vaccines that confer either durable or waning immunity, and we evaluate the use of booster doses to counter waning. We find that plausible vaccination scenarios with a durable vaccine reduce annual dengue incidence by as much as 80% within five years. However, if vaccine efficacy wanes after administration, we find that there can be years with larger epidemics than would occur without any vaccination, and that vaccine booster doses are necessary to prevent this outcome.
Quality and Quantity of Education in the Process of Development

We develop a theory of human capital investment to study through which channels students react to school quality when deciding about their investment in higher education (secondary and above) and how educational quality affects the growth process of an economy. In a dynamic general equilibrium closed economy. higher education requires an extra investment of private resources. whereas primary education is mandatory. The theory states that human capital accumulation raises with quality through two main effects: larger quality increases the number ofpeople with higher education (extensive channel). and it increases the volume of investment in higher schooling per individual (intensive channel). That is. even with perfect capital markets. relatively low quality could discourage opportunities to pursue education beyond primary school. since low quality decreases the returns from higher education. As a result, agents could get stuck at primary levels. The intensive channel establishes that once individuals decide to participate in higher schooling. the larger the quality of educational system. the larger the investment made by each agent. Educational quality may allow for different steps of development and that depending on quality the economy may follow different paths, Using cross-country data, empirical evidence shows that the proposed channels seem to be quantitatively important and that the effect of quality and quantity of education on growth depends on the stage of development.
Concept Forgetting for ALCOI-Ontologies using an Ackermann Approach

We present a method for forgetting concept symbols in ontologies speciﬁed in the description logic ALCOI . The method is an adaptation and improvement of a second-order quantiﬁer elimination method developed for modal logics and used for computing correspondence properties for modal axioms. It follows an approach exploiting a result of Ackermann adapted to description logics. An important feature inherited from the modal approach is that the inference rules are guided by an ordering compatible with the elimination order of the concept symbols. This provides more control over the inference process and reduces non-determinism, resulting in a smaller search space. The method is extended with a new case splitting inference rule, and several simpliﬁcation rules. Compared to related forgetting and uniform interpolation methods for description logics, the method can handle inverse roles, nominals and ABoxes. Compared to the modal approach on which it is based, it is more eﬃcient in time and improves the success rates. The method has been implemented in Java using the OWL API. Experimental results show that the order in which the concept symbols are eliminated signiﬁcantly aﬀects the success rate and eﬃciency.
Biological control of locusts and grasshoppers.

Control of grasshoppers and locusts has traditionally relied on synthetic insecticides, and for emergency situations this is unlikely to change. However, a growing awareness of the environmental issues associated with acridid control as well as the high costs of emergency control are expanding the demand for biological control. In particular, preventive, integrated control strategies with early interventions will reduce the financial and environmental costs associated with large-scale plague treatments. The recent development of effective oil formulations of Metarhizium anisopliae spores in Africa, Australia, and Brazil opens new possibilities for environmentally safe control operations. Metarhizium biopesticide kills 70%-90% of treated locusts within 14-20 days, with no measurable impact on nontarget organisms. An integrated pest management strategy, with an emphasis on the use of Metarhizium, that incorporates rational use of chemical pesticides with biological options such as the microsporidian Nosema locustae and the hymenopteran egg parasitoids Scelio spp. , has become a realistic option.
Enhanced Apoptotic Cell Clearance Capacity and B Cell Survival Factor Production by IL-10-Activated Macrophages: Implications for Burkitt’s Lymphoma1

Burkitt’s lymphoma (BL) is typified by frequent tumor cell apoptosis and significant macrophage infiltration. Since BL cells have an inherent tendency to undergo apoptosis at a high rate, we reasoned that macrophages in BL are functionally enhanced in at least two activities that have implications for tumor pathogenesis: 1) engulfment of apoptotic cells, an anti-inflammatory process known to suppress immune responses, and 2) production of BL cell survival factors that limit the extent of tumor cell apoptosis. In this study, we show that the microenvironment of BL is rich in the pleiotropic cytokine IL-10, which can be produced by both tumor cells and macrophages, and that IL-10-activated human macrophages have enhanced capacity to engulf apoptotic cells in vitro. This was found to be dependent on the macrophage tethering receptor of apoptotic cells, CD14. Furthermore, IL-10-activated macrophages were found to produce markedly higher levels of the B cell survival factor, B cell-activating factor of the TNF family/B lymphocyte stimulator (BAFF/BLyS) than macrophages matured in the absence of IL-10. Coculture of macrophages with BL cells further enhanced BAFF secretion. Significantly, we show that enhancement of BL cell survival by IL-10-activated macrophages is mediated by a BAFF-dependent component and that BAFF is produced at high levels by tumor-associated macrophages in situ. These results indicate that macrophages, regulated by IL-10, have the potential to promote BL pathogenesis, first, through suppression of antitumor immunity following enhanced engulfment of apoptotic tumor cells and, second, through increased production of tumor cell growth/survival factors.
Association of menopause age and N-terminal pro brain natriuretic peptide: the Multi-Ethnic Study of Atherosclerosis

ObjectiveMenopause age can affect the risk of developing cardiovascular disease (CVD). The purpose of this study was to investigate the associations of early menopause (menopause occurring before age 45 y) and menopause age with N-terminal pro brain natriuretic peptide (NT-proBNP), a potential risk marker of CVD and heart failure. MethodsOur cross-sectional study included 2,275 postmenopausal women, aged 45 to 85 years and without clinical CVD (2000-2002), from the Multi-Ethnic Study of Atherosclerosis. Participants were classified as having or not having early menopause. NT-proBNP was log-transformed. Multivariable linear regression was used for analysis. ResultsFive hundred sixty-one women had early menopause. The median (25th-75th percentiles) NT-proBNP value was 79.0 (41.1-151.6) pg/mL for all participants, 83.4 (41.4-164.9) pg/mL for women with early menopause, and 78.0 (40.8-148.3) pg/mL for women without early menopause. The mean (SD) age was 65 (10.1) and 65 (8.9) years for women with and without early menopause, respectively. No significant interactions between menopause age and ethnicity were observed. In multivariable analysis, early menopause was associated with a 10.7% increase in NT-proBNP levels, whereas each 1-year increase in menopause age was associated with a 0.7% decrease in NT-proBNP levels. ConclusionsEarly menopause is associated with greater NT-proBNP levels, whereas each 1-year increase in menopause age is associated with lower NT-proBNP levels, in postmenopausal women.
Some planar algebras related to graphs

Let X denote a finite nonempty set, and let W denote a matrix whose rows and columns are indexed by X and whose entries belong to some field K. We study three planar algebras related to W. Briefly, a planar algebra is a graded vector space ν = ∪ b ∈ Z+ ∪ {+,-} ν n which is closed under planar operators. The first planar algebra which we study, F W = ∪F W n , is defined by the group theoretic properties of W. For n E Z + , F W n is the vector space of functions from X to K which are constant on the? ut(W)-orbits of X n , and F W + , F W - are identified with K. The second planar algebra, P W = ∪P W n , is the planar algebra generated W. We define it combinatorially: P W n is spanned by functions from X to K defined via statistical mechanical sums on certain planar open graphs. The third planar algebra, O W = ∪O W n , differs from P W only in that the open graphs defining the functions need not be planar. It turns out that P W ⊆ O W ⊂ F W . We show that P W = O W if and only if P W 4 contains a single special function known as the transposition. We show that O W = F W whenever |X|! is not divisible by the characteristic of K.
Towards an Understanding about Complexities of Alternative Media: Portrayals of Power in Alternative Media

In this study I conducted qualitative content analysis of alternative media in order to uncover the different categories about corporate power presented to activist audiences in social justice movements. I found that there were two dominant categories about corporate power disseminated through alternative media: (1) “traditional” corporate power and (2) hegemonic corporate power. “Traditional” corporate power is based on the idea that corporations dominate resources in society. Hegemonic corporate power is based on the idea that corporations dominate the ideological assumptions in contemporary society. Both of these categories hold significant implications for comprehension and classification of alternative media.