Miracle-dz/UniFAR-FTUs huggingface dataset:
Stratifying Type 2 Diabetes Cases by BMI Identifies Genetic Risk Variants in LAMA1 and Enrichment for Risk Variants in Lean Compared to Obese Cases

Common diseases such as type 2 diabetes are phenotypically heterogeneous. Obesity is a major risk factor for type 2 diabetes, but patients vary appreciably in body mass index. We hypothesized that the genetic predisposition to the disease may be different in lean (BMI<25 Kg/m2) compared to obese cases (BMI≥30 Kg/m2). We performed two case-control genome-wide studies using two accepted cut-offs for defining individuals as overweight or obese. We used 2,112 lean type 2 diabetes cases (BMI<25 kg/m2) or 4,123 obese cases (BMI≥30 kg/m2), and 54,412 un-stratified controls. Replication was performed in 2,881 lean cases or 8,702 obese cases, and 18,957 un-stratified controls. To assess the effects of known signals, we tested the individual and combined effects of SNPs representing 36 type 2 diabetes loci. After combining data from discovery and replication datasets, we identified two signals not previously reported in Europeans. A variant (rs8090011) in the LAMA1 gene was associated with type 2 diabetes in lean cases (P = 8.4×10−9, OR = 1.13 [95% CI 1.09–1.18]), and this association was stronger than that in obese cases (P = 0.04, OR = 1.03 [95% CI 1.00–1.06]). A variant in HMG20A—previously identified in South Asians but not Europeans—was associated with type 2 diabetes in obese cases (P = 1.3×10−8, OR = 1.11 [95% CI 1.07–1.15]), although this association was not significantly stronger than that in lean cases (P = 0.02, OR = 1.09 [95% CI 1.02–1.17]). For 36 known type 2 diabetes loci, 29 had a larger odds ratio in the lean compared to obese (binomial P = 0.0002). In the lean analysis, we observed a weighted per-risk allele OR = 1.13 [95% CI 1.10–1.17], P = 3.2×10−14. This was larger than the same model fitted in the obese analysis where the OR = 1.06 [95% CI 1.05–1.08], P = 2.2×10−16. This study provides evidence that stratification of type 2 diabetes cases by BMI may help identify additional risk variants and that lean cases may have a stronger genetic predisposition to type 2 diabetes.
Electric Machine Goodness : Classic results revisited in light of contemporary machine design

Common understanding among machine designers is that, when scaling down to smaller sizes, most performance parameters will degrade. This principle is embodied in the goodness factor presented by Laithwaite. A derivation of the goodness factor for axial flux geometry is presented, confirming that the result is the same as for radial flux geometry. The paper then discusses the factor with respect to permanent magnet machines, where experience shows that the principle does not hold, in that small machines can have very good characteristics. An initial modification of the factor to cover permanent magnet machines is presented.
Hypoxia and the Hypoxic Response Pathway Protect against Pore-Forming Toxins in C. elegans

Pore-forming toxins (PFTs) are by far the most abundant bacterial protein toxins and are important for the virulence of many important pathogens. As such, cellular responses to PFTs critically modulate host-pathogen interactions. Although many cellular responses to PFTs have been recorded, little is understood about their relevance to pathological or defensive outcomes. To shed light on this important question, we have turned to the only genetic system for studying PFT-host interactions—Caenorhabditis elegans intoxication by Crystal (Cry) protein PFTs. We mutagenized and screened for C. elegans mutants resistant to a Cry PFT and recovered one mutant. Complementation, sequencing, transgenic rescue, and RNA interference data demonstrate that this mutant eliminates a gene normally involved in repression of the hypoxia (low oxygen response) pathway. We find that up-regulation of the C. elegans hypoxia pathway via the inactivation of three different genes that normally repress the pathway results in animals resistant to Cry PFTs. Conversely, mutation in the central activator of the hypoxia response, HIF-1, suppresses this resistance and can result in animals defective in PFT defenses. These results extend to a PFT that attacks mammals since up-regulation of the hypoxia pathway confers resistance to Vibrio cholerae cytolysin (VCC), whereas down-regulation confers hypersusceptibility. The hypoxia PFT defense pathway acts cell autonomously to protect the cells directly under attack and is different from other hypoxia pathway stress responses. Two of the downstream effectors of this pathway include the nuclear receptor nhr-57 and the unfolded protein response. In addition, the hypoxia pathway itself is induced by PFT, and low oxygen is protective against PFT intoxication. These results demonstrate that hypoxia and induction of the hypoxia response protect cells against PFTs, and that the cellular environment can be modulated via the hypoxia pathway to protect against the most prevalent class of weapons used by pathogenic bacteria.
Interactive segmentation with hidden object-based annotations: toward smart media

In this paper a novel "Smart Media" concept for semantic-based multimedia security and management is proposed. This concept is based on interactive object segmentation (considered as side information in visual human-computer interface) with hidden object-based annotations. Information-theoretic formalism is introduced that considers the human-computer interface as a multiple access channel. We do not consider an image as a set of pixels but rather as a set of annotated regions that correspond to objects or their parts, where these objects are associated with some hidden descriptive text about their features. The presented approach for "semantic" segmentation is addressed by means of the human-computer interface that allows a user to easily incorporate information related to image objects and to store them in a secure way. Since each selected image object carries its own embedded description, this makes it self-containing and formally independent from the particular image format used for storage in image databases. The proposed object-based hidden descriptors are invariant to changes of image filename or/and image headers, and are resistant to object cropping/insertion operations, which are usual in multimedia processing and management. This is well harmonized with the "Smart Media" concept where the image contains additional information about itself, and where this information is securely integrated inside the image while remaining perceptually invisible.
Development of a Metal Micro-Textured Thermal Interface Material

Typical thermal interface materials (TIMs) consist of high thermal conductivity solid particles dispersed in a continuous, low thermal conductivity organic compound. Despite using filler materials of very high thermal conductivity, the effective thermal conductivity of these TIMs is often two orders of magnitude lower than the pure filler materials. In addition, dispensing and flow of the particle-matrix composite results in voids being trapped within the bond. To address these issues, a novel metal micro-textured thermal interface material (MMT-TIM) has been developed. This material consists of a thin metal foil with raised micro-scale features that plastically deform under an applied pressure thereby creating a continuous, thermally conductive, path between the mating surfaces. Numerical tools have been developed that couple the mechanical and thermal properties and behaviour of MMT-TIMs as they undergo large-plastic deformation during assembly. This study presents the modelling approach and predictions of MMT-TIM performance based on these numerical techniques. The predictions show good agreement with experimental results, which were obtained using prototype MMT-TIMs and an advanced TIM characterization facility. Finally, a future outlook for this technology is presented based on these promising initial results.Copyright © 2009 by ASME
Adsorption of divalent cations to bilayer membranes containing phosphatidylserine

The Stern equation, a combination of the Langmuir adsorption isotherm, the Boltzmann relation, and the Grahame equation from the theory of the diffuse double layer, provides a simple theoretical framework for describing the adsorption of charged molecules to surfaces. The ability of this equation to describe the adsorption of divalent cations to membranes containing brain phosphatidylserine (PS) was tested in the following manner. Charge reversal measurements were first made to determine the intrinsic 1:1 association constants of the divalent cations with the anionic PS molecules: when the net charge of a PS vesicle is zero one-half of the available sites are occupied by divalent cations. The intrinsic association constant, therefore, is equal to the reciprocal of the divalent cation concentration at which the mobility of a PS vesicle reverses sign. The Stern equation with this association constant is capable of accurately describing both the zeta potential data obtained with PS vesicles at other concentrations of the divalent cations and the data obtained with with vesicles formed from mixtures of PS and zwitterionic phospholipids. Independent measurements of the number of ions adsorbed to sonicated PS vesicles were made with a calcium-sensitive electrode. The results agreed with the zeta potential results obtained with multilamellar vesicles. When membranes are formed at 20 degrees C in 0.1 M NaCl, the intrinsic 1:1 association constants of Ni, Co, Mn, Ba, Sr, Ca, and Mg with PS are 40, 28, 25, 20, 14, 12, and 8 M-1, respectively.
Standing After Spinal Cord Injury With Four-Contact Nerve-Cuff Electrodes for Quadriceps Stimulation

This paper describes the performance of a 16-channel implanted neuroprosthesis for standing and transfers after spinal cord injury including four-contact nerve-cuff electrodes stimulating the femoral nerve for knee extension. Responses of the nerve-cuffs were stable and standing times increased by 600% over time-matched values with a similar eight-channel neuroprosthesis utilizing muscle-based electrodes on vastus lateralis for knee extension.
Chromium Contamination in Silicon: Detection and Impact on Oxide Performances

Introduction Chromium is less effective as a recombination center than other transition metal contaminants, such as iron [1]. Therefore, the sensitivity of lifetime techniques to chromium contamination is lower with respect to other contaminants. As these techniques are very commonly used for metal contamination monitoring, a moderate chromium contamination could be missed by monitoring tests. On the other hand, chromium is sometimes reported [2] to be less harmful than other contaminants for device performances. In this work some techniques for metal contamination control were compared for their ability to reveal chromium contamination. In addition, capacitors were built on chromium-contaminated silicon to check whether chromium contamination can affect the oxide performances.
Application of blue laser triangulation sensors for displacement measurement through fire

This paper explores the use of blue laser triangulation sensors to measure displacement of a target located behind or in the close proximity of natural gas diffusion flames. This measurement is critical for providing high-quality data in structural fire tests. The position of the laser relative to the flame envelope can significantly affect the measurement scatter, but has little influence on the mean values. We observe that the measurement scatter is normally distributed and increases linearly with the distance of the target from the flame along the beam path. Based on these observations, we demonstrate how time-averaging can be used to achieve a standard uncertainty associated with the displacement error of less than 0.1 mm, which is typically sufficient for structural fire testing applications. Measurements with the investigated blue laser sensors were not impeded by the thermal radiation emitted from the flame or the soot generated from the relatively clean-burning natural gas.
Statistics of merging peaks of random Gaussian fluctuations: skeleton tree formalism

Cosmological bound objects are generally considered to be formed from the local maxima of cosmological density fluctuations, which are often assumed to be Gaussian random fields. In order to study the statistics of those objects that are the result of hierarchical merging, we propose skeleton tree formalism, which can analytically distinguish episodic merging from continuous accretion in the mass-growth processes. This distinction was not clear in the extended Press–Schechter (PS) formalism. Skeleton tree formalism is a natural extension of peak theory, which is an alternative formalism for the statistics of bound objects. Fluctuation-field smoothing with a Gaussian filter produces a landscape by adding the extra dimension of the filter-resolution scale to the spatial coordinate of the fluctuation. In this landscape, a smoothed peak is nesting alongside the neighbouring peak and appears as a critical point called a sloping saddle, which can be interpreted as a destroyed object during a merger event in the context of the hierarchical structure formation. The topological properties of the landscape can be abstracted as skeleton trees, which consist of the line process of the smoothing peaks and the point process of the sloping saddles. According to this abstract topological picture, in this paper, we present the concept and the basic results of skeleton tree formalism in describing (1) the distinction between accretion and a merger in the hierarchical structure formation from various initial random Gaussian fields; (2) the instantaneous number density of the sloping saddles, which gives the destruction rate in the mergers; (3) the number densities of all the peaks, nesting and non-nesting, with simple and analytical distinguishing definitions; (4) the self-consistency of the formalism in reproducing the statistics, including the conservation equation, of all the peaks; (5) the instantaneous number density of the reforming objects, which is derived from the conservation formula of the non-nesting peak; and (6) the mean growth history of the objects, which is reproduced from the rates of destruction, reformation, and from the relative accretion growth.
Transductive Pattern Learning for Information Extraction

Abstract : The requirement for large labelled training corpora is widely recognized as a key bottleneck in the use of learning algorithms for information extraction. We present TPLEX, a semi-supervised learning algorithm for information extraction that can acquire extraction patterns from a small amount of labelled text in conjunction with a large amount of unlabelled text. Compared to previous work, TPLEX has two novel features. First, the algorithm does not require redundancy in the fragments to be extracted, but only redundancy of the extraction patterns themselves. Second, most bootstrapping methods identify the highest quality fragments in the unlabelled data and then assume that they are as reliable as manually labelled data in subsequent iterations. In contrast, TPLEX's scoring mechanism prevents errors from snowballing by recording the reliability of fragments extracted from unlabelled data. Our experiments with several benchmarks demonstrate that TPLEX is usually competitive with various fully-supervised algorithms when very little labelled training data is available.
DIETARY FIBRES OF APPLE AND APRICOT PASTES: EFFECT OF HEATING ON PLANT CELL WALLS

Fruit pieces prepared from pastes are now commonly added to breakfast cereals, snack bars and “healthy” confectionery. The objective was to determine the cell wall composition of heat-treated apple paste and apricot paste. The cell walls of apple paste and apricot paste were isolated and sequentially fractionated separately using HEPES, CDTA, Na 2 CO 3 , 1M KOH, 4M KOH leaving a final residue. The monosaccharide composition of the fractions was consistent with the presence of cellulose, pectic polysaccharides, xyloglucans, heteroxylans and galactoglucomannans. The heat treatment during the apple paste and the apricot paste production did not change the overall amounts of neutral monosaccharides. Heat treatment resulted in the considerable solubilization of pectic polymers in water-soluble and CDTA-soluble fractions compared to Na 2 CO 3 , KOH and final residue fractions of the fruit pastes. During heat treatment, tissue softening occurs due to the disruption of the constituent cell wall matrix.
Ultimate Boundedness of Nonlinear Singularly Perturbed System with Measurement Noise

SUMMARY In this letter, we consider the ultimate boundedness of the singularly perturbed system with measurement noise. The composite controller is commonly used to regulate the singularly perturbed system. However, in the presence of measurement noise, the composite controller does not guarantee the ultimate boundedness of the singularly perturbed system. Thus, we propose the modified composite controller to show the ultimate boundedness of the singularly perturbed system with measurement noise.
Anode Sheath Switching in a Carbon Nanotube Arc Plasma

The anode ablation rate is investigated as a function of anode diameter for a carbon nanotube arc plasma. It is found that anomalously high ablation occurs for small anode diameters. This result is explained by the formation of a positive anode sheath. The increased ablation rate due to this positive anode sheath could imply greater production rate for carbon nanotubes.
The Information Dynamics of Phase Transitions in Random Boolean Networks

Random Boolean Networks (RBNs) are discrete dynamical systems which have been used to model Gene Regulatory Networks. We investigate the well-known phase transition between ordered and chaotic behavior in RBNs from the perspective of the distributed computation conducted by their nodes. We use a recently published framework to characterize the distributed computation in terms of its underlying information dynamics: information storage, information transfer and information modification. We find maximizations in information storage and coherent information transfer on either side of the critical point, allowing us to explain the phase transition in RBNs in terms of the intrinsic distributed computations they are undertaking.
Rare Variant Association Testing Under Low-Coverage Sequencing

Deep sequencing technologies enable the study of the effects of rare variants in disease risk. While methods have been developed to increase statistical power for detection of such effects, detecting subtle associations requires studies with hundreds or thousands of individuals, which is prohibitively costly. Recently, low-coverage sequencing has been shown to effectively reduce the cost of genome-wide association studies, using current sequencing technologies. However, current methods for disease association testing on rare variants cannot be applied directly to low-coverage sequencing data, as they require individual genotype data, which may not be called correctly due to low-coverage and inherent sequencing errors. In this article, we propose two novel methods for detecting association of rare variants with disease risk, using low coverage, error-prone sequencing. We show by simulation that our methods outperform previous methods under both low- and high-coverage sequencing and under different disease architectures. We use real data and simulation studies to demonstrate that to maximize the power to detect associations for a fixed budget, it is desirable to include more samples while lowering coverage and to perform an analysis using our suggested methods.
Incentives and Invention in Universities

Using data on U.S. universities, we show that universities that give higher royalty shares to faculty scientists generate greater license income, controlling for university size, academic quality, researchfunding and other factors. We use pre-sample data on university patenting to control for the potential endogeneity of royalty shares. We find that scientists respond both to cash royalties and to royalties used to support their research labs, suggesting both pecuniary and intrinsic (research) motivations. The incentive effects appear to be larger in private universities than in public ones, and we provide survey evidence indicating this may be related to differences in the use of performance pay, government constraints, and local development objectives of technology license offices. Royalty incentives work both by raising faculty effort and sorting scientists across universities. The effect of incentives works primarily by increasing the quality (value) rather than the quantity of inventions.
Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM

Recent progress in high-throughput data-production technologies pushes research toward systems biology, focusing on the global interaction between the components of biomolecular processes. In this article we present a formal modelling environment for network biology, called the Biochemical Abstract Machine (BIOCHAM). Biocham delivers precise semantics to biomolecular interaction maps. Based on this formal semantics, the Biocham system offers automated reasoning tools for querying the temporal properties of the system under all its possible behaviours. We present the main features of Biocham and report on our modelling experience with this language
DLTS Characterization of CIGS Cells

Deep Level Transient Spectroscopy (DLTS) and Capacitance-Voltage (C-V) measurements are employed to study deep- level electron and hole traps in CIGS solar cells fabricated at two different locations (EPV and NREL). The activation energy and trap density as well as suggested defect origins are given.
Relationship between metastatic ability and H-ras oncogene expression in rat mammary cancer cells transfected with the v-H-ras oncogene.

To study the relationship between metastatic ability and activated ras expression, a cloned, low metastatic, dimethylbenz(a)anthracene-induced rat mammary cancer cell line (RMC1) was transfected with the v-H-ras oncogene. Cloned transfectants were characterized as high, medium, or low expressors of the v-H-ras gene, on the basis of Southern, Northern, and Western blot analysis. Following s.c. inoculation in syngeneic rats, all transfectants produced tumors; however, the in vivo growth rate of cloned transfectants which expressed any level of v-H-ras oncogene was significantly higher (approximately 5-fold) than that observed in the untransfected RMC1 cells. Control (neo only) transfectants exhibited no change in growth rate and had a low metastatic ability comparable to that of the parental untransfected cells. Certain cloned v-H-ras expressing transfectants were highly metastatic to the lungs and lymph nodes. These highly metastatic H-ras transfectants differed widely however, in their level of H-ras expression. The lung colonization potential following i.v. inoculation was increased in all transfectants which expressed any level of v-H-ras gene. These studies suggest that while v-H-ras transfection can result in the development of metastatic ability in rat mammary cancer cells, there is no simple dose-response relationship between the level of v-H-ras expression in cloned rat mammary cancer cell transfectants and the development of experimental or spontaneous metastases.