Miracle-dz/UniFAR-FTUs huggingface dataset:
Smoothing Splines on Unit Ball Domains with Application to Corneal Topography

Optical coherence tomography (OCT) is a non-invasive imaging technique used to study and understand internal structures of biological tissues such as the anterior chamber of the human eye. An interesting problem is the reconstruction of the shape of the biological tissue from OCT images, that is not only a good fit of the data but also respects the smoothness properties observed in the images. A similar problem arises in Magnetic Resonance Imaging (MRI). We cast the problem as a penalized weighted least squares regression with a penalty on the magnitude of the second derivative (Laplacian) of the surface. We present a novel algorithm to construct the Kimeldorf-Wahba solution for unit ball domains. Our method unifies the ad-hoc approaches currently in the literature. Application of the theory to data from an anterior segment optical coherence tomographer is presented. A detailed comparison of the reconstructed surface using different approaches is presented.
Changing opportunities: refugees and host communities in western Tanzania

Introduction Refugees and host populations Changing opportunities in the local context Agricultural opportunities Competition for scarce resources Economic opportunities Infrastructure and development resources Social dynamics Varying host experiences during the refugee presence Vulnerable individuals: older persons and people with disabilities Poor farmers and casual laborers Employees on fixed incomes Creative strategies Conclusion REFERENCES NEW ISSUES IN REFUGEE RESEARCH
Information-Based Heterogeneity in Expectations and Optimal Monetary Policy

This paper analyses optimal monetary policy and welfare implications of three endogenous processes in forming inflation expectations, which depart from the standard case of rational expectations. Two processes assume heterogeneous expectations driven either by discretionary central banks through the release of information or by agents through discrete choice among two forecast rules; the third process is a Bayesian learning about the central bank’s inflation target. Transitional dynamics towards steady-state show that, overall, an active and transparent monetary policy promoting rationality and learning may raise welfare during disinflations, while a passive and less transparent attitude may stabilise output and raise welfare through inflationary surprises.
South African Mutations of the CCR5 Coreceptor for HIV Modify Interaction With Chemokines and HIV Envelope Protein

The CCR5 chemokine receptor is the major coreceptor for HIV-1 and the receptor for CC-chemokines, MIP-1α, MIP-1β, and regulated upon activation normal T-cell-expressed and secreted. Individuals, who are homozygous for the nonfunctional CCR5Δ32 allele, are largely resistant to HIV-1 infection. Four unique mutations that affect the amino acid sequence of CCR5 have been identified in South Africa. We have assessed the effect of these mutations on CCR5 interactions with chemokines and HIV Envelope protein. The Leu107Phe mutation did not affect CCR5 expression, chemokine binding, intracellular signaling, or interaction with Envelope. The Arg225Gln mutant was similar to wild-type CCR5, but ligand-independent intracellular signaling suggests that it is partially constitutively active. The Asp2Val mutation decreased chemokine-binding affinity, chemokine-stimulated intracellular signaling, and receptor expression. It also decreased HIV Envelope-mediated cell fusion. The Arg225Stop mutant showed no measurable chemokine binding or signaling and no measurable expression of CCR5 at the cell surface or within the cell. Consistent with lack of cell surface expression, it did not support envelope-mediated cell fusion. These results show that South African CCR5 variants have a range of phenotypes in vitro that may reflect altered chemokine responses and susceptibility to HIV infection in individuals who carry these alleles.
Measuring and mitigating security and privacy issues on android applications

Over time, the increasing popularity of the Android operating system (OS) has resulted in its user-base surging past 1 billion unique devices. As a result, cybercriminals and other non-criminal actors are attracted to the OS due to the amount of user information they can access. Aiming to investigate security and privacy issues on the Android ecosystem, previous work has shown that it is possible for malevolent actors to steal users' sensitive personal information over the network, via malicious applications, or vulnerability exploits etc., presenting proof of concepts or evidences of exploits. Due to the ever-changing nature of the Android ecosystem and the arms race involved in detecting and mitigating malicious applications, it is important to continuously examine the ecosystem for security and privacy issues. This thesis presents research contributions in this space, and it is divided into two parts. The first part focuses on measuring and mitigating vulnerabilities in applications due to poor implementation of security and privacy protocols. In particular, we investigate the implementation of the SSL/TLS protocol validation logic, and properties such as ephemerality, anonymity, and end-to-end encryption. We show that, despite increased awareness of vulnerabilities in SSL/TLS implementation by application developers, these vulnerabilities are still present in popular applications, allowing malicious actors steal users' information. To help developers mitigate them, we provide useful recommendations such as enabling SSL/TLS pinning and using the same certificate validation logic in their test and development environments. The second part of this thesis focuses on the detection of malicious applications that compromise users' security and privacy, the detection performance of the different program analysis approach, and the influence of different input generators during dynamic analysis on detection performance. We present a novel method for detecting malicious applications, which is less susceptible to the evolution of the Android ecosystem (i.e., changes in the Android framework as a result of the addition/removal of API calls in new releases) and malware (i.e., changes in techniques to evade detection) compared to previous methods. Overall, this thesis contributes to knowledge around Android apps with respect to, vulnerability discovery that leads to loss of users' security and privacy, and the design of robust Android malware detection tools. It highlights the need for continual evaluation of apps as the ecosystem changes to detect and prevent vulnerabilities and malware that results in a compromise of users' security and privacy.
Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes

International standardization and coordination of the nomenclature of variants of hepatitis C virus (HCV) is increasingly needed as more is discovered about the scale of HCV‐related liver disease and important biological and antigenic differences that exist between variants. A group of scientists expert in the field of HCV genetic variability, and those involved in development of HCV sequence databases, the Hepatitis Virus Database (Japan), euHCVdb (France), and Los Alamos (United States), met to re‐examine the status of HCV genotype nomenclature, resolve conflicting genotype or subtype names among described variants of HCV, and draw up revised criteria for the assignment of new genotypes as they are discovered in the future. A comprehensive listing of all currently classified variants of HCV incorporates a number of agreed genotype and subtype name reassignments to create consistency in nomenclature. The paper also contains consensus proposals for the classification of new variants into genotypes and subtypes, which recognizes and incorporates new knowledge of HCV genetic diversity and epidemiology. A proposal was made that HCV variants be classified into 6 genotypes (representing the 6 genetic groups defined by phylogenetic analysis). Subtype name assignment will be either confirmed or provisional, depending on the availability of complete or partial nucleotide sequence data, or remain unassigned where fewer than 3 examples of a new subtype have been described. In conclusion, these proposals provide the framework by which the HCV databases store and provide access to data on HCV, which will internationally coordinate the assignment of new genotypes and subtypes in the future. (HEPATOLOGY 2005.)
Direct Inhibition of Plant Mitochondrial Respiration by Elevated CO2

Doubling the concentration of atmospheric CO2 often inhibits plant respiration, but the mechanistic basis of this effect is unknown. We investigated the direct effects of increasing the concentration of CO2 by 360 [mu]L L-1 above ambient on O2 uptake in isolated mitochondria from soybean (Glycine max L. cv Ransom) cotyledons. Increasing the CO2 concentration inhibited the oxidation of succinate, external NADH, and succinate and external NADH combined. The inhibition was greater when mitochondria were preincubated for 10 min in the presence of the elevated CO2 concentration prior to the measurement of O2 uptake. Elevated CO2 concentration inhibited the salicylhydroxamic acid-resistant cytochrome pathway, but had no direct effect on the cyanide-resistant alternative pathway. We also investigated the direct effects of elevated CO2 concentration on the activities of cytochrome c oxidase and succinate dehydrogenase (SDH) and found that the activity of both enzymes was inhibited. The kinetics of inhibition of cytochrome c oxidase were time-dependent. The level of SDH inhibition depended on the concentration of succinate in the reaction mixture. Direct inhibition of respiration by elevated CO2 in plants and intact tissues may be due at least in part to the inhibition of cytochrome c oxidase and SDH.
Gender and Informal Sector Employment in Indonesia

The decision whether to participate in the labor market is frequently modeled as a decision between two choices: to work or not to work. While this may be the appropriate way to model that decision for men, there is some question as to how well it explains the labor force participation decisions of women. Paid work is the standard for defining what constitutes work in most economic models, and typically no distinction is drawn between paid work that takes place in the formal sector of the economy and paid work in the informal sector. From a feminist perspective this is problematic on both counts. For women, even though the work they do in the home is not considered "work" in the economic sense, it affects their decision whether or not to participate in the labor market. Their choices may be more accurately represented as (1) to work (in the home without pay) or (2) to work (for pay in the labor market). Further, in developing countries a large percent of economically active women and men work in the informal sector. Women in particular are disproportionately represented in this sector. Given the general perception of the informal sector as an inferior alternative to the formal sector for employment, feminists have voiced concerns about women being marginalized in this sector (Bernasek 1999). Another dimension in the labor force participation decision may then also be these choices: to work (in the informal sector for pay) or to work (in the formal sector for pay). At least for women, that suggests a more appropriate modeling of the labor force participation decision in terms of a multi-choice framework: to work at home without pay, to work for pay in the informal sector, or to work for pay in the formal sector.
A Collaborative Ranking Model for Cross-Domain Recommendations

With the advent of social media, generating high quality cross-domain recommendations has become more and more important for users of heterogeneous domains. In this study, we propose a collaborative ranking model to generate cross-domain recommendations. Given a target domain, we design an objective function aimed at performing push of relevant items at the top of a recommendation list. Also, as users may have different behaviours in multiple domains in our collaborative ranking model we propose a weighting strategy to control the influence of user preferences from auxiliary domains when producing the recommendation lists. Our experiments on ten cross-domain recommendation tasks show that the proposed approach achieves higher recommendation accuracy than other state-of-the-art methods.
Do the dimensions of the temperament and character inventory map a simple genetic architecture? Evidence from molecular genetics and factor analysis.

OBJECTIVE It has been reported that the human temperament dimensions of novelty seeking and harm avoidance are associated with polymorphisms in the D(4) dopamine receptor gene (D4DR) and the serotonin-transporter-linked promoter region (5-HTTLPR), respectively. Although these findings are consistent with Cloninger's hypothesized psychobiological model of temperament and character, many studies failed to replicate these findings. In the present study the authors tested whether the psychobiological model taps the genetic architecture of personality by exploring associations between these candidate genes and the dimensions of the Temperament and Character Inventory and by examining its phenotypic structure. METHOD Of the 946 male and female participants in the Baltimore Longitudinal Study of Aging to whom the Temperament and Character Inventory was administered, 587 were genotyped for a polymorphism with a 48-base-pair repeat in the D4DR gene and 425 were genotyped for a 44-base-pair insertion or deletion in the 5-HTTLPR polymorphism. RESULTS There was no significant association between D4DR polymorphisms and novelty seeking. The authors also failed to find an association between 5-HTTLPR polymorphisms and harm avoidance. The factor structure of the Temperament and Character Inventory did not reveal the hypothesized phenotypic structure. CONCLUSIONS This investigation produced no support for the temperament-character model at either the biological or psychological level.
Alterations in enzymatic antioxidant defence in diabetes mellitus − a rational approach

Defence against the reactive oxidants produced during aerobic metabolism is a complex process and is provided by a system of enzymes and antioxidant compounds capable of preventing excess radical production, neutralising free radicals and repairing the damage caused by them. Regulation of the antioxidant system must provide sufficient, properly located, antioxidant compounds and enzymes. Damage to this system has been proved to play a role in various disorders. Long-term complications of diabetes mellitus are supposed to be partially mediated by oxidative stress. The authors summarise experimental and clinical investigations in this field and analyse the possible importance of the changes in the antioxidant system in the development of diabetic vascular complications.
Positive unlabeled learning via wrapper-based adaptive sampling

Learning from positive and unlabeled data frequently occurs in applications where only a sub-set of positive instances is available while the rest of the data are unlabeled. In such scenarios, often the goal is to create a discriminant model that can accurately classify both positive and negative data by modelling from labeled and unlabeled instances. In this study, we propose an adaptive sampling (AdaSampling) approach that utilises prediction probabilities from a model to iteratively up-date the training data. Starting with equal prior probabilities for all unlabeled data, our method “wraps” around a predictive model to iteratively update these probabilities to distinguish positive and negative instances in unlabeled data. Subse-quently, one or more robust negative set(s) can be drawn from unlabeled data, according to the likelihood of each instance being negative, to train a single classiﬁcation model or ensemble of models.
Rotation of Meiotic Spindle Is Controlled by Microfilaments in Mouse Oocytes1

Abstract The completion of meiosis requires the spatial and temporal coordination of cytokinesis and karyokinesis. During meiotic maturation, many events, such as formation, location, and rotation of the meiotic spindle as well as chromosomal movement, polar body extrusion, and pronuclear migration, are dependent on regulation of the cytoskeleton system. To study functions of microfilaments in meiosis, we induced metaphase II (MII) mouse oocytes to resume meiosis by in vitro fertilization or parthenogenetic activation, and we treated such oocytes with cytochalasin B (CB). The changes of the meiotic spindle, as visualized in preparations stained for β-tubulin and chromatin, were observed by fluorescent confocal microscopy. The meiotic spindle of MII oocytes was observed to be parallel to the plasmalemma. After meiosis had resumed, the spindle rotated to the vertical position so that the second polar body could be extruded into the perivitelline space. When meiosis resumed and oocytes were treated with 10 μg/ml of CB, the spindle rotation was inhibited. Consequently, the oocyte formed an extra pronucleus instead of extruding a second polar body. These results indicate that spindle rotation is essential for polar body extrusion; it is the microfilaments that play a crucial role in regulating rotation of the meiotic spindle.
The E2F6 repressor activates gene expression in myocardium resulting in dilated cardiomyopathy

The E2F/Rb pathway regulates cardiac growth and development and holds great potential as a therapeutic target. The E2F6 repressor is a unique E2F member that acts independently of pocket proteins. Forced expression of E2F6 in mouse myocardium induced heart failure and mortality, with severity of symptoms correlating to E2F6 levels. Echocardiography demonstrated a 37% increase (P>0.05) in left ventricular end‐diastolic diameter and reduced ejection fraction (<40%, P>0.05) in young transgenic (Tg) mice. Microarray and qPCR analysis revealed a paradoxical increase in E2F‐responsive genes, which regulate the cell cycle, without changes in cardiomyocyte cell number or size in Tg mice. Young adult Tg mice displayed a 75% (P>0.01) decrease in gap junction protein connexin‐43, resulting in abnormal electrocardiogram including a 24% (P>0.05) increase in PR interval. Further, mir‐206, which targets connexin‐43, was up‐regulated 10‐fold (P>0.05) in Tg myocardium. The mitogen‐activated protein kinase pathway, which regulates the levels of miR‐206 and connexin‐43, was activated in Tg hearts. Thus, deregulated E2F6 levels evoked abnormal gene expression at transcriptional and post‐transcriptional levels, leading to cardiac remodeling and dilated cardiomyopathy. The data highlight an unprecedented role for the strict regulation of the E2F pathway in normal postnatal cardiac function. —Westendorp, B. , Major, J. L. , Nader, M. , Salih, M. , Leenen, F. H. H. , Tuana, B. S. The E2F6 repressor activates gene expression in myocardium resulting in dilated cardiomyopathy. FASEB J. 26, 2569‐2579 (2012). www.fasebj. org
Estimating agglomeration economies in Spain: evidence from geographically disaggregated data

In this paper we estimate agglomeration economies in Spain in 2009 basing on Ciccone? s (2002) model, which explains average labor productivity in one spatial unit on employment density and other controls. The novelty of our analysis is that the empirical model is estimated at a highly disaggregated spatial scale, oppositely to the convention of taking as unit of analysis NUTS-2 or NUTS-3 regions. Recent contributions to New Economic Geography (NEG) base their theoretical analysis on geographical units defined at a more disaggregated spatial scale than these administratively defined regions. Specifically, from a sample of income-taxpayers published by the Spanish Fiscal Studies Institute -Instituto de Estudios Fiscales- we derive figures on average wages by worker at the scale of Local Labor Markets (LLMs). The empirical analysis bases on several estimation strategies; namely, Ordinary Least Squares (OLS), Two-Stages Least Squares (2SLS), Quantile Regressions (QR) and Instrumental Variable Quantile Regressions (IVQR) estimators, all they finding a significantly positive effect of agglomeration in the conditional mean of labor productivity. Additionally, the QR and IVQR estimators find a progressively decreasing, but still positive, effect of employment density along the conditional distribution of labor productivity.
Differential effects of osteogenic protein‐1 (BMP‐7) on gene expression of BMP and GDF family members during differentiation of the mouse MC615 chondrocyte cells

The mRNA expression patterns of several bone morphogenetic proteins (BMPs) and growth differentiation factors (GDFs) in long‐term cultures of the clonal mouse chondrocyte cell line MC615 were examined. Distinct spatial and temporal patterns of expression of BMPs and GDFs were observed. The temporal orders of expression were correlated with those of several biochemical markers characteristic of chondrocytic cell differentiation. BMP‐1, ‐2, ‐5, and ‐6 mRNA expression increased throughout the chondrogenic process and BMP‐4 mRNA expression was not changed. GDF‐1 and ‐3 mRNA expression increased throughout the chondrogenic process, and GDF‐5, ‐6, ‐8, and ‐9 mRNA expressions were not changed. Effects of osteogenic protein‐1 (OP‐1, BMP‐7) on the expression patterns of several other members of the BMP family and of the GDF family were also examined. OP‐1 downregulated the BMP‐1, ‐4, ‐5, and ‐6 mRNA expression by a maximal 3‐, 5‐, 2.5‐, and 3‐fold, respectively. The BMP‐2 mRNA expression was not changed significantly by a low concentration of OP‐1, but was increased at 200 ng/ml at day 7 of treatment. In contrast to the BMPs, OP‐1 upregulated significantly the six GDF members examined (GDF‐1, ‐3, ‐5, ‐6, ‐8, and ‐9) by three‐ to four‐fold. Our findings demonstrate that OP‐1 differentially regulates the mRNA expression of several related members of the BMP family and upregulates the mRNA expression of several members of the GDF family. The observations suggest that OP‐1 action on cartilage differentiation involves a complex regulation of gene expression of several members of the BMP and the GDF family. © 2002 Wiley‐Liss, Inc.
Multitask regression for condition-specific prioritization of miRNA targets in transcripts

Deregulation of miRNAs is implicated in many diseases in particular cancer, where miRNAs can act as tumour suppressors or oncogenes. As sequence-based miRNA target predictions do not provide condition-specific information, many algorithms combine expression data for miRNAs and genes for prioritization of miRNA targets. However, common strategies prioritize miRNA-gene associations, although a miRNA may only target a subset of the alternative transcripts produced by a gene. Thus, current approaches are suboptimal. Here we address the problem of transcript and not gene based miRNA target prioritization. We show how to leverage methods that were developed for gene expression based miRNA-target prioritization for transcripts. In addition, we introduce a new multitasking based learning (MTL) method that uses structured-sparsity inducing regularization to improve accuracy of the learning. The new MTL approach performs especially favorable in small sample size settings, for genes with many transcripts and with noisy transcript expression level estimates as shown with simulated data. In an analysis of real liver cancer RNA-seq data we show that the MTL approach better predicts transcript expression and outperforms simpler approaches for miRNA-target prediction.