Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of iron and haemochromatosis gene mutations in the progression of liver disease in chronic hepatitis C

Background: Chronic hepatitis C virus (HCV) infection is frequently associated with elevated markers of iron stores. Recessively inherited mutations in the HFE gene are responsible for iron accumulation in most cases of hereditary haemochromatosis and may have a role in HCV infection. They may also be associated with progressive liver fibrosis although this remains controversial. Aims: To assess the prevalence of HFE mutations in Scottish HCV infected patients and to explore the effect of the carrier state on serum and liver iron stores, and the severity of liver disease. Patients: A total of 164 patients with antibodies to HCV who underwent liver biopsy were assessed prospectively. Methods: Each patient was screened for HFE mutations (Cys282Tyr and His63Asp). Iron markers were assessed in serum (ferritin, transferrin saturation) and on liver biopsy (stainable iron, liver iron concentration (LIC) and hepatic iron index). Results: There were 67 (41%, 26 Cys282Tyr, 33 His63Asp, eight compound) heterozygotes. Forty four (28%) patients had elevated serum iron markers, 24 (15%) had stainable liver iron, and five (3%) had elevated LICs. Carriage of HFE mutations was not associated with any clinical, biochemical, virological, or pathological features, including accumulation of liver iron. Elevated serum iron markers were associated with male sex, increased alcohol consumption, and increased liver inflammation and fibrosis. Patients with elevated LICs were older, acquired HCV infection earlier, and had more liver inflammation. Conclusions: Patients with chronic HCV infection frequently have elevated serum iron markers although elevated LICs are uncommon. Elevated serum iron studies and LICs occur in patients with more severe liver disease. Carriage of HFE mutations, although frequently observed in these HCV infected patients, does not have a role in the accumulation of iron or the progression of liver disease in HCV infection.
Father Input and Child Vocabulary Development: The Importance of Wh Questions and Clarification Requests

Abstract Individual differences in children's language skills have been shown to stem in part from variations in the quantity and quality of parent speech input. However, most research focuses on mothers' input whereas less is known about the effects of variability in father input. In this article, we review the relation between parent input and child language development with a focus on low-income families, and review general findings about similarities and differences in mother and father speech. Within this review, we highlight conversation-eliciting speech, such as wh questions and clarification requests, which occur, on average, more frequently in father input than mother input. Conversation-eliciting speech is challenging for 2-year-old children and has been shown in research with mothers to relate to child vocabulary development. We then report a study examining whether fathers' use of conversation-eliciting speech relates to children's developing vocabulary skills at 24 months of age within a sample of low-income African American families. Understanding that speech input varies among fathers, and specific strengths that fathers bring to interactions with their young children can help speech-language pathologists develop and implement more effective interventions.
Tap Model to Improve Input Accuracy of Touch Panels

In recent years, devices that use touch panels as interfaces, such as smart phones and tablet PCs, have spread. These devices have many advantages. For example, operating the panel can be done more intuitively in comparison with using conventional physical buttons, and the devices are quite more flexible than those that use a traditional fixed UI. However, mistakes frequently occur when inputting with a touch panel because the buttons have no physical boundaries and users cannot get tactile feedback with their fingers because the panels never change physically. Thus, the input accuracy of touch-panel devices is lower than that of devices with physical buttons. There are studies on improving input accuracy. Most of them use language models for typing natural language or probabilistic models to describe the errors made when users tap their fingers. However, these models are not practical, and the experiments are preliminary. Thus, in this paper, we propose a more practical model for improving input accuracy, in which the relative relationships between a target object and neighbor object that might influence error making when touching the target are tested. We consider that our model can describe important properties for designing various UIs depending on practical applications. We then make a plan to conduct experiments in order to build our model in a calibrated way and discuss our evaluation of the model.
New Insights into Metabolic Signaling and Cell Survival: The Role of β-O-Linkage of N-Acetylglucosamine

The involvement of glucose in fundamental metabolic pathways represents a core element of biology. Late in the 20th century, a unique glucose-derived signal was discovered, which appeared to be involved in a variety of cellular processes, including mitosis, transcription, insulin signaling, stress responses, and potentially, Alzheimer's disease, and diabetes. By definition, this glucose-fed signaling system was a post-translational modification to proteins. However, unlike classical cotranslational N-glycosylation occurring in the endoplasmic reticulum and Golgi apparatus, this process occurs elsewhere throughout the cell in a highly dynamic fashion, similar to the quintessential post-translational modification, phosphorylation. This more recently described post-translational modification, the β-O-linkage of N-acetylglucosamine (i.e., O-GlcNAc) to nucleocytoplasmic proteins, represents an under-investigated area of biology. This signaling system operates in all of the tissues examined and seems to have persisted throughout all multicellular eukaryotes. Thus, it comes with little surprise that O-GlcNAc signaling is an integral system and viable target for biomedical investigation. This system may be a boundless source for insight into a variety of diseases and yield numerous opportunities for drug design. This Perspective will address recent insights into O-GlcNAc signaling in the cardiovascular system as a paradigm for its involvement in other biological systems.
Pathogenesis of Mycobacterium bovis Infection: the Badger Model As a Paradigm for Understanding Tuberculosis in Animals

Tuberculosis in animals is caused principally by infection with Mycobacterium bovis and the potential for transmission of infection to humans is often the fundamental driver for surveillance of disease in livestock and wild animals. However, with such a vast array of species susceptible to infection, it is often extremely difficult to gain a detailed understanding of the pathogenesis of infection––a key component of the epidemiology in all affected species. This is important because the development of disease control strategies in animals is determined chiefly by an understanding of the epidemiology of the disease. The most revealing data from which to formulate theories on pathogenesis are that observed in susceptible hosts infected by natural transmission. These data are gathered from detailed studies of the distribution of gross and histological lesions, and the presence and distribution of infection as determined by highly sensitive bacteriology procedures. The information can also be used to establish the baseline for evaluating experimental model systems. The European badger (Meles meles) is one of a very small number of wild animal hosts where detailed knowledge of the pathogenesis of M. bovis infection has been generated from observations in natural-infected animals. By drawing parallels from other animal species, an experimental badger infection model has also been established where infection of the lower respiratory tract mimics infection and the disease observed in natural-infected badgers. This has facilitated the development of diagnostic tests and testing of vaccines that have the potential to control the disease in badgers. In this review, we highlight the fundamental principles of how detailed knowledge of pathogenesis can be used to evaluate specific intervention strategies, and how the badger model may be a paradigm for understanding pathogenesis of tuberculosis in any affected wild animal species.
Using Optical and Near-Infrared Photometry to Test MACHO Lens Candidates

We obtained new VLT/ISAAC H-band observations for five MACHO LMC source stars and adjacent LMC field regions. After combining our near-IR photometry with Hubble Space Telescope/PC BVRI optical photometry, we compared the MACHO objects to the adjacent field stars in a variety of color-magnitude and color-color diagrams. These diagnostic diagrams were chosen to be sensitive to our hypothesis that at least some of the MACHO lenses were foreground Galactic disk or thick-disk M dwarfs. For the five lensed objects we studied, our hypothesis could be ruled out for main-sequence lens masses ≳0.1 M☉ for distances out to 4 kpc. On the other hand, the fact that LMC MACHO 5, an object not in our study, has been recently found to have just such a foreground lens highlights that the remainder of the LMC MACHO objects should be searched for the signature of their lenses using our photometric technique or via near-IR spectroscopy. We also constructed diagnostic color-color diagrams sensitive to determining reddening for the individual MACHO source stars and found that these five objects did not show evidence for significant additional reddening. At least these five MACHO objects are thus also inconsistent with the LMC self-lensing hypothesis.
Plant Community and Nutrient Development within Four Estuary Restoration Sites in Kitsap County, Washington

iv Acknowledgments . vi List of Figures . iv List of Tables . v 1.0 Introduction . 1 1.1 Ecosystem Connectivity. 1 1.1.1 Ecosystem Services . 2 1.1.2 Carbon in Estuaries . 3 1.1.3 Vegetation in Estuaries . 5 1.1. 4 Microbes and Nutrients in Estuaries . 6 1.2 Degradation of Estuaries . 9 1.3 Remediation of Estuaries . 12 2.0 Research Objectives and Statistical Hypotheses . 15 3.0 Methods . 18 3.1 Sample Sites . 18 3.1.1 Harper Creek . 20 3.1.2 Carpenter Creek. 22 3.1.3 Beaver Creek . 25 3.1. 4 Dogfish Creek . 28 3.2 Vegetation Community Survey. 30 3.3 Sample Preparation and Analysis . 31 3.3.1 Soil Processing and Homogenization . 31 3.3.2 Vegetation Processing and Homogenization . 32 3.3.3 Weight Loss on Ignition . 32 3.3. 4 Carbon-to-Nitrogen Elemental Analysis. 33 3.3. 5 Calculating Differences . 33 3.3. 6 Quality Control . 34 4.0 Statistical Analyses. 35 4.1 Parametric Analyses. 35 4.2 Non-Parametric Analyses . 36 4.2. 1 Soil and Plant Biomass Correlation . 36 4.2. 2 Plant Community Composition Analysis . 36 4.3 Statistical Errors . 38 5.0 Results . 40 5.1 Soil . 40 5.1.1 Percent Soil Carbon . 40
Human‐in‐the‐loop Control of a Humanoid Robot for Disaster Response: A Report from the DARPA Robotics Challenge Trials

The DARPA Robotics Challenge (DRC) requires teams to integrate mobility, manipulation, and perception to accomplish several disaster‐response tasks. We describe our hardware choices and software architecture, which enable human‐in‐the‐loop control of a 28 degree‐of‐freedom Atlas humanoid robot over a limited bandwidth link. We discuss our methods, results, and lessons learned for the DRC Trials tasks. The effectiveness of our system architecture was demonstrated as the WPI‐CMU DRC Team scored 11 out of a possible 32 points, ranked seventh (out of 16) at the DRC Trials, and was selected as a finalist for the DRC Finals.
Vehicle Model Aided Inertial Navigation For A Uav Using Low-Cost Sensors

This paper considers two different methods of using a dynamic vehicle model in order to aid pose estimates provided by an Inertial Navigation System (INS) for a Un-manned Aerial Vehicle (UAV). We consider low-cost inertial sensors in which errors from sensor noise, bias and scale-factor errors cause a significant growth in pose estimate errors when the navigation system is un-aided by external positioning information such as from GPS or terrain observations. It is shown that an accurate dynamic vehicle model can considerably reduce the error growth in vehicle pose estimates by enhancing the observability of the inertial sensor error sources. Furthermore we analyse the effectiveness of using the vehicle model information given that there are errors in the vehicle model.
Orographic distillation and spatio‐temporal variations of stable isotopes in precipitation in the North Atlantic

Little is known about the spatial and temporal variability of the stable isotopic composition of precipitation in the North Atlantic and its relationship to the North Atlantic Oscillation (NAO) and anthropogenic climate change. The islands of the Azores archipelago are uniquely positioned in the middle of the North Atlantic Ocean to address this knowledge gap. A survey of spatial and temporal variability of the stable isotope composition of precipitation in Azores is discussed using newly presented analyses along with Global Network of Isotopes in Precipitation data. The collected precipitation samples yield a new local meteoric water line (δ2H = 7.1 * δ18O + 8.46) for the Azores region and the North Atlantic Ocean. The annual isotopic mean of precipitation shows a small range for the unweighted and precipitation mass‐weighted δ18O‐H2O values. Results show an inverse relation between the monthly δ18O‐H2O and the amount of precipitation, which increases in elevation and into the interior of the island. Higher amounts of precipitation (from convective storm systems) do not correspond to the most depleted values of stable isotopes in precipitation. Precipitation shows an orographic effect with depleted δ18O‐H2O values related to the Rayleigh effect. Monthly δ18O‐H2O values for individual precipitation sampling stations show little relationship to air temperature. Results show a local source of moisture during the summer with the characteristics of the first vapour condensate. The stable isotope composition of precipitation is strongly correlated to the NAO index, and δ18O‐H2O values show a statistically significantly trend towards enrichment since 1962 coincident with the increased air temperature and relative humidity due to climate change. Results are in line with observations of increasing sea surface temperature and relative humidity.
Learning to Search in Branch and Bound Algorithms

Branch-and-bound is a widely used method in combinatorial optimization, including mixed integer programming, structured prediction and MAP inference. While most work has been focused on developing problem-specific techniques, little is known about how to systematically design the node searching strategy on a branch-and-bound tree. We address the key challenge of learning an adaptive node searching order for any class of problem solvable by branch-and-bound. Our strategies are learned by imitation learning. We apply our algorithm to linear programming based branch-and-bound for solving mixed integer programs (MIP). We compare our method with one of the fastest open-source solvers, SCIP; and a very efficient commercial solver, Gurobi. We demonstrate that our approach achieves better solutions faster on four MIP libraries.
Impact of spatial diversity on spectral efficiency of cooperative relaying

Cooperative relaying takes advantage of spatial diversity to improve the performance of wireless communication systems. In theory, the larger the diversity, the more capability to combat fading. Several cooperative relaying schemes have been proposed in the past. Here we focus on timer-based-best-select, distributed space-time coded, and M-group space-time coded. In this paper, an equal transmission time model and a flexible transmission time model are proposed. The spectral efficiencies with respect to spatial diversity for the three schemes are compared. The results show that, under both models, timer-based-best-select performs better than the other two schemes.
An Optimal Investment Policy in Equity-Debt Financed Firms with Finite and Infinite Maturities

In this paper we examine an optimal investment policy of the firm that is financed by issuing equity and debt. Recently, a number of researchers have studied the interaction among firm’s investment and financing decisions under uncertainty by means of real option framework. In the literature, investment problems for a firm with growth options, that is financed with equity and debt are investigated. In most studies, in order to simplify the problem, the infinite maturity for the investment and debt is assumed. However, in the real case firms are usually considered to have investment policies with finite option. This paper examines the optimal investment policy of the firm which is financed by issuing equity and debt during a period of time. Specifically, we discuss the effect of maturity on the investment timing, the firm value, the optimal leverage and coupon payment. JEL classification: D81; D92; E22; G31
Vascular Accesses for Haemodialysis in the Upper Arm Cause Greater Reduction in the Carotid-Brachial Stiffness than Those in the Forearm: Study of Gender Differences

Purpose. To evaluate in chronically haemodialysed patients (CHPs), if: (1) the vascular access (VA) position (upper arm or forearm) is associated with differential changes in upper limb arterial stiffness; (2) differences in arterial stiffness exist between genders associated with the VA; (3) the vascular substitute (VS) of choice, in biomechanical terms, depends on the previous VA location and CHP gender. Methods. 38 CHPs (18 males; VA in upper arm: 18) were studied. Left and right carotid-brachial pulse wave velocity (PWVc-b) was measured. In in vitro studies, PWV was obtained in ePTFE prostheses and in several arterial and venous homografts obtained from donors. The biomechanical mismatch (BM) between CHP native vessel (NV) and VS was calculated. Results/Conclusions. PWVc-b in upper limbs with VA was lower than in the intact contralateral limbs (P < 0.05), and differences were higher (P < 0.05) when the VA was performed in the upper arm. Differences between PWVc-b in upper limbs with VA (in the upper arm) with respect to intact upper limbs were higher (P < 0.05) in males. Independently of the region in which the VA was performed, the homograft that ensured the minimal BM was the brachial artery. The BM was highly dependent on gender and the location in the upper limb in which the VA was performed.
Optimizing linear counting queries under differential privacy

Differential privacy is a robust privacy standard that has been successfully applied to a range of data analysis tasks. But despite much recent work, optimal strategies for answering a collection of related queries are not known. We propose the matrix mechanism, a new algorithm for answering a workload of predicate counting queries. Given a workload, the mechanism requests answers to a different set of queries, called a query strategy, which are answered using the standard Laplace mechanism. Noisy answers to the workload queries are then derived from the noisy answers to the strategy queries. This two stage process can result in a more complex correlated noise distribution that preserves differential privacy but increases accuracy. We provide a formal analysis of the error of query answers produced by the mechanism and investigate the problem of computing the optimal query strategy in support of a given workload. We show this problem can be formulated as a rank-constrained semidefinite program. Finally, we analyze two seemingly distinct techniques, whose similar behavior is explained by viewing them as instances of the matrix mechanism.
Evaluating food front-of-pack labelling: a pan-European survey on consumers’ attitudes toward food labelling

Abstract Nutrition labels on pre-packaged foods have been widely used as a medium to foster healthier eating habits in the general population, to contribute to a reduction in the incidence and prevalence of diet-related conditions. Yet, there is no convincing evidence that food labels are an effective means to achieve the desired effect at population level. Several factors have been suggested to account for this decoupling of efficacy, e.g. difficulties in understanding the information on food-labels. The present article presents the results of a survey on Europeans’ understanding of nutritional labels and evaluation on the communication tools for their diffusion. A total of 7550 phone interviews were conducted in 16 European Countries: Austria, Belgium, Denmark, France, Germany, Greece, Italy, the Netherlands, Poland, Portugal, Czech Republic, Slovenia, Spain, Sweden, United Kingdom and Hungary. Consumers were asked about their opinion on nutritional information provided at different levels and their commitment to healthy behaviour.
From Averaging to Acceleration, There is Only a Step-size

We show that accelerated gradient descent, averaged gradient descent and the heavy-ball method for non-strongly-convex problems may be reformulated as constant parameter second-order difference equation algorithms, where stability of the system is equivalent to convergence at rate O(1/n 2), where n is the number of iterations. We provide a detailed analysis of the eigenvalues of the corresponding linear dynamical system , showing various oscillatory and non-oscillatory behaviors, together with a sharp stability result with explicit constants. We also consider the situation where noisy gradients are available, where we extend our general convergence result, which suggests an alternative algorithm (i.e., with different step sizes) that exhibits the good aspects of both averaging and acceleration.
A lightweight privacy-preserving truth discovery framework for mobile crowd sensing systems

The recent proliferation of human-carried mobile devices has given rise to the mobile crowd sensing (MCS) systems. However, the sensory data provided by the participating workers are usually not reliable. As an efficient technique to extract truthful information from unreliable data, truth discovery has drawn significant attention. Currently, the privacy concern of the participating workers poses a major challenge on the design of truth discovery mechanisms. Although the existing mechanism can conduct truth discovery with high accuracy and strong privacy guarantee, tremendous overhead is incurred on the worker side. In this paper, we propose a novel lightweight privacy preserving truth discovery framework, L-PPTD, which is implemented by involving two non-colluding cloud platforms and adopting additively homomorphic cryptosystem. This framework not only achieves the protection of each worker's sensory data and reliability information but also introduces little overhead to the workers. In order to further reduce each worker's overhead in the scenarios where only the sensory data need to be protected, we propose another more lightweight framework named L2-PPTD. The desirable performance of the proposed frameworks is verified through extensive experiments conducted on real world MCS systems.