gebhart/patrepeval huggingface dataset:
Identifying novel high-impact rare disease-causing mutations, genes and pathways in exomes of Ashkenazi Jewish inflammatory bowel disease patients (2020)

ABSTRACT Inflammatory bowel disease (IBD) is a group of chronic diseases, affecting different parts of the gastrointestinal tract, that mainly comprises Crohn’s Disease (CD) and Ulcerative Colitis (UC). Most IBD genomic research to date has involved genome-wide association studies (GWAS) of common genetic variants, mostly in Europeans, resulting in the identification of over 200 risk loci. The incidence of IBD in Ashkenazi Jews (AJ) is particularly high compared to other population groups and rare protein-coding variants are significantly enriched in AJ. These variants are expected to have a larger phenotypic effect and are hypothesized to complement the missing heritability that cannot be fully addressed by GWAS in IBD. Therefore, we genetically identified 4,974 AJs IBD cases and controls from whole exome sequencing (WES) data from the NIDDK IBD Genetics Consortium (IBDGC). We selected credible rare variants with high predicted impact, aggregated them into genes, and performed gene burden and pathway enrichment analyses to identify 7 novel plausible IBD-causing genes: NCF1, CES1, ICAM1, INPP5D, ABCB1, IL33 and TLR4 . We further perform bulk and single-cell RNA sequencing, demonstrating the likely relatedness of the novel genes to IBD. Importantly, we demonstrate that the rare and high impact genetic architecture of AJ adult IBD displays a significant overlap with very early onset IBD (VEOIBD) genetics. At the variant level, we performed Phenome-wide association studies (PheWAS) in the UK Biobank to replicate risk sites in IBD and reveal shared risk sites with other diseases. Finally, we showed that a polygenic risk score (PRS) has high power to differentiate AJ IBD cases from controls when using rare and high impact variants.
Automatic segmentation of all lower limb muscles from high-resolution magnetic resonance imaging using a cascaded three-dimensional deep convolutional neural network (2019)

High-resolution magnetic resonance imaging with fat suppression can obtain accurate anatomical information of all 35 lower limb muscles and individual segmentation can facilitate quantitative analysis. However, due to limited contrast and edge information, automatic segmentation of the muscles is very challenging, especially for athletes whose muscles are all well developed and more compact than the average population. Deep convolutional neural network (DCNN)-based segmentation methods showed great promise in many clinical applications, however, a direct adoption of DCNN to lower limb muscle segmentation is challenged by the large three-dimensional (3-D) image size and lack of the direct usage of muscle location information. We developed a cascaded 3-D DCNN model with the first step to localize each muscle using low-resolution images and the second step to segment it using cropped high-resolution images with individually trained networks. The workflow was optimized to account for different characteristics of each muscle for improved accuracy and reduced training and testing time. A testing augmentation technique was proposed to smooth the segmentation contours. The segmentation performance of 14 muscles was within interobserver variability and 21 were slightly worse than humans.
Corneal birefringence measured by spectrally resolved Mueller matrix ellipsometry and implications for non-invasive glucose monitoring (2016)

A good understanding of the corneal birefringence properties is essential for polarimetric glucose monitoring in the aqueous humor of the eye. Therefore, we have measured complete 16-element Mueller matrices of single-pass transitions through nine porcine corneas in-vitro, spectrally resolved in the range 300…1000 nm. These ellipsometric measurements have been performed at several angles of incidence at the apex and partially at the periphery of the corneas. The Mueller matrices have been decomposed into linear birefringence, circular birefringence (i.e. optical rotation), depolarization, and diattenuation. We found considerable circular birefringence, strongly increasing with decreasing wavelength, for most corneas. Furthermore, the decomposition revealed significant dependence of the linear retardance (in nm) on the wavelength below 500 nm. These findings suggest that uniaxial and biaxial crystals are insufficient models for a general description of the corneal birefringence, especially in the blue and in the UV spectral range. The implications on spectral-polarimetric approaches for glucose monitoring in the eye (for diabetics) are discussed.
Micro-optical Tandem Luminescent Solar Concentrators (2017)

Traditional concentrating photovoltaic (CPV) systems utilize multijunction cells to minimize thermalization losses, but cannot efficiently capture diffuse sunlight, which contributes to a high levelized cost of energy (LCOE) and limits their use to geographical regions with high direct sunlight insolation. Luminescent solar concentrators (LSCs) harness light generated by luminophores embedded in a light-trapping waveguide to concentrate light onto smaller cells. LSCs can absorb both direct and diffuse sunlight, and thus can operate as flat plate receivers at a fixed tilt and with a conventional module form factor. However, current LSCs experience significant power loss through parasitic luminophore absorption and incomplete light trapping by the optical waveguide. Here we introduce a tandem LSC device architecture that overcomes both of these limitations, consisting of a PLMA polymer layer with embedded CdSe/CdS quantum dot (QD) luminophores and InGaP micro-cells, which serve as a high bandgap absorber on top of a conventional Si photovoltaic. We experimentally synthesize CdSe/CdS QDs with exceptionally high quantum-yield (99%) and ultra-narrowband emission optimally matched to fabricated III-V InGaP micro-cells. Using a Monte Carlo ray-tracing model, we show the radiative limit power conversion efficiency for a module with these components to be 30.8% diffuse sunlight conditions. These results indicate that a tandem LSC-on-Si architecture could significantly improve upon the efficiency of a conventional Si photovoltaic module with simple and straightforward alterations of the module lamination steps of a Si photovoltaic manufacturing process, with promise for widespread module deployment across diverse geographical regions and energy markets.
A novel diagnostic test detects a low frequency of the hemicentin Gln5345Arg variant among Northern Irish age related macular degeneration patients. (2004)

We describe a rapid assay for the genotyping of the Gln5345Arg mutation using real-time fluorescence PCR to facilitate rapid processing of samples through combined amplification and detection steps. These characteristics are suitable for a clinical setting where high throughput diagnostic procedures are required. The frequency of this mutation within the Northern Ireland population has been estimated at 0.2%, concurring with previous findings that this mutation is a rare variant associated with AMD. A rapid diagnostic assay will facilitate a reliable and convenient evaluation of the frequency of the Gln5345Arg mutation and its association with AMD within other populations.
Vanadium doped Sb2Te3 material with modified crystallization mechanism for phase-change memory application (2015)

In this paper, V0.21Sb2Te3 (VST) has been proposed for phase-change memory applications. With vanadium incorporating, VST has better thermal stability than Sb2Te3 and can maintain in amorphous phase at room temperature. Two resistance steps were observed in temperature dependent resistance measurements. By real-time observing the temperature dependent lattice structure evolution, VST presents as a homogenous phase throughout the whole thermal process. Combining Hall measurement and transmission electron microscopy results, we can ascribe the two resistance steps to the unique crystallization mechanism of VST material. Then, the amorphous thermal stability enhancement can also be rooted in the suppression of the fast growth crystallization mechanism. Furthermore, the applicability of VST is demonstrated by resistance-voltage measurement, and the phase transition of VST can be triggered by a 15 ns electric pulse. In addition, endurance up to 2.7×104 cycles makes VST a promising candidate for phase-change memory applications.
Business process families using model-driven techniques (2011)

Traditionally, businesses have used IT systems as mechanical advantage for automating static a-priori-defined repetitive tasks. Increased business dynamics has placed greater demands of adaptation and agility on to IT systems. Service-oriented architecture is a step in this direction through separation of business process concerns from application functionality. There have been multiple attempts at improving adaptability of application services with varying degrees of success. But current business process modelling languages and execution platforms can at best support optimal point solutions that are not amenable for agile adaptation. Application services have benefited to some extent, from product-line architectures related to adaptation to a-priori known situations. We can apply the same idea to business processes. This paper presents an extension of essential BPMN meta model supporting business process families, and a set of adaptation operators are presented in this paper. We describe their realisation using model-driven techniques.
Electroless Deposition of Nanoscale MnO[sub 2] on Ultraporous Carbon Nanoarchitectures: Correlation of Evolving Pore-Solid Structure and Electrochemical Performance (2008)

The self-limiting redox reaction of carbon nanofoam substrates with permanganate at room temperature in neutral-pH solutions produces conformal nanoscale deposits throughout the macroscopic thickness of the nanofoam structure. The nanoscale morphology ranges from layered ribbons and rods for a 4 h deposition to polycrystalline nanoparticles that form at long deposition times (20 h). The through-connected pore network of the carbon nanofoam is maintained at all deposition times (5 min to 20 h), although the average pore size shifts to smaller values and the cumulative pore volume decreases as the coatings grow and thicken within the nanofoam structure. The electrochemical capacitance of the resulting hybrid electrode structure is dominated by the pseudocapacitance of the and increases with loading (a function of the exposure time in permanganate), particularly at low charge–discharge rates and at ac frequencies . The significant enhancement in mass-, volume-, and footprint-normalized capacitance at high mass loadings is accompanied by a modest increase in the Warburg resistance that develops as the pore size and void volume of the nanofoam substrate are reduced by internal deposition.
Automatic Generation of a Subject-Specific Model for Accurate Markerless Motion Capture and Biomechanical Applications (2008)

A novel approach for the automatic generation of a subject-specific model consisting of morphological and joint location information is described. The aim is to address the need for efficient and accurate model generation for markerless motion capture (MMC) and biomechanical studies. The algorithm applied and expanded on previous work on human shapes space by embedding location information for ten joint centers in a subject-specific free-form surface. The optimal locations of joint centers in the 3-D mesh were learned through linear regression over a set of nine subjects whose joint centers were known. The model was shown to be sufficiently accurate for both kinematic (joint centers) and morphological (shape of the body) information to allow accurate tracking with MMC systems. The automatic model generation algorithm was applied to 3-D meshes of different quality and resolution such as laser scans and visual hulls. The complete method was tested using nine subjects of different gender, body mass index (BMI), age, and ethnicity. Experimental training error and cross-validation errors were 19 and 25 mm, respectively, on average over the joints of the ten subjects analyzed in the study.
<title>Noise regeneration in compressed x-ray images</title> (1996)

Almost all present-day lossy image-compression methods are so-called waveform coders, i.e. they attempt to approximate the original image waveform as closely as possible with the available number of bits. At medium-to-low compression ratios this can usually be achieved quite well, but at high compression ratios clearly visible artefacts may be introduced into the coded images. During the compression of medical x-ray images we noticed that the data that suffer most from a high degree of compression are the noise-like components present in these images. The loss of these components is found to depreciate the perceived image quality. This paper proposes a method for modeling the noise components removed due to lossy compression and for regenerating these components during the decompression of the image.
Development and Initial Testing of a Magnetically Shielded Miniature Hall Thruster (2014)

The scaling of magnetically shielded Hall thrusters to low power is investigated through the development and fabrication of a 4-cm Hall thruster. During initial testing, the magnetically shielded miniature Hall thruster was operated at 275 V discharge voltage and 325-W discharge power. Inspection of the channel walls after testing suggests that the outer discharge channel wall was successfully shielded from high-energy ion erosion while the inner channel wall showed evidence of weaker shielding, likely due to magnetic circuit saturation. Scanning planar probe measurements taken at two locations downstream of the thruster face provided ion current density profiles. The ion current calculated by integrating these data was 1.04 A with a plume divergence half-angle of 30°. Swept retarding potential analyzer measurements taken 80-cm axially downstream of the thruster measured the most probable ion voltage to be 252 V. The total thruster efficiency was calculated from probe measurements to be 43% (anode efficiency of 59%) corresponding to a thrust of 19 mN at a specific impulse of 1870 s. Discharge channel erosion rates were found to be approximately three orders of magnitude less than unshielded Hall thrusters, suggesting the potential for a significant increase in operational life.
Concept of a novel fast neutron imaging detector based on THGEM for fan-beam tomography applications (2012)

The conceptual design and operational principle of a novel high-efficiency, fast neutron imaging detector based on THGEM, intended for future fan-beam transmission tomography applications, is described. We report on a feasibility study based on theoretical modeling and computer simulations of a possible detector configuration prototype. In particular we discuss results regarding the optimization of detector geometry, estimation of its general performance, and expected imaging quality: it has been estimated that detection efficiency of around 5-8% can be achieved for 2.5MeV neutrons; spatial resolution is around one millimeter with no substantial degradation due to scattering effects. The foreseen applications of the imaging system are neutron tomography in non-destructive testing for the nuclear energy industry, including examination of spent nuclear fuel bundles, detection of explosives or drugs, as well as investigation of thermal hydraulics phenomena (e.g., two-phase flow, heat transfer, phase change, coolant dynamics, and liquid metal flow).
Real-time Distribution System State Estimation (2010)

In this paper a new approach for a three-phase Distribution System State Estimator (DSSE) is presented. It utilizes the most types of analog real time measurements (including voltage and current magnitude, active and reactive power measurements). The correct utilization is supported by topology analysis and creation of measurement areas. Loads are modeled based on historical or AMR information. The estimation problem is solved by weighted least squares error method. Applying traditional state estimation on distribution networks, by using load data as pseudo measurement, causes state estimation formulations that have very large size. Approach presented in this paper is based on network reduction which reduces size of the problem. The approach is very fast and provides feasible results.
Single-stage single-switch input-current-shaping technique with reduced switching loss (2000)

In this paper, a new single-stage, single-switch input-current-shaping (S/sup 4/ICS) technique which features substantially reduced turn-on switching loss of the switch in a S/sup 4/ICS flyback topology is described. In the proposed technique, the turn-on switching loss due to the discharging of the output capacitance of the switch is reduced by turning on the switch when its voltage is minimum. To achieve the turn-on loss reduction for a wide range of line and load conditions, the flyback transformer is continuously operated at the boundary of the continuous conduction mode (CCM) and discontinuous conduction mode (DCM) by employing a variable-frequency control. The performance of the new S/sup 4/ICS flyback technique was evaluated on a 70-W (20-V/3.5-A) experimental prototype.
Research and Development of a Ventilation-Integrated Comfort System (2021)

From an indoor air quality perspective, the best residential ventilation strategies include filtering outdoor air and distributing that air to all occupied parts of a home. From an energy standpoint, it is desirable that energy be transferred from the exhaust air to the incoming outdoor air to limit heating and cooling impacts. Heat or energy recovery ventilators (HRVs or ERVs) can provide these functions, but researchers have seen many poor installations related to design, installation, and operation and maintenance. More robust ventilation systems may involve an ERV with a dedicated duct distribution system and controls. Such a duct system can be costly to install, and many builders reduce these costs by connecting an ERV to a central heating and cooling duct system. Although this can sometimes be done effectively, researchers have seen consistent challenges with low, inconsistent, or imbalanced flow rates; high electricity consumption; and—of greatest concern—outdoor air short-circuiting or not being delivered to occupied spaces at all. Most ERVs are designed to operate with their own duct system; they are not designed as an add-on to much larger heating, ventilating, and air-conditioning (HVAC) systems. The ventilation-integrated comfort system (VICS) is expressly designed to integrate with low-capacity, efficient, ducted heating and cooling systems. Overall, the latest VICS prototype consumed 40–75 watts (W), including the air handler power, to deliver 50–120 cfm of whole-dwelling ventilation. The large, cross-flow ERV core performed to match manufacturer values (73% winter sensible effectiveness, 64% summer total effectiveness), but further improvements are possible. The VICS system researched and tested during this project will provide efficient, controllable, balanced energy recovery ventilation that is integrated with heating and cooling systems. The integration reduces space and ductwork needed for separate ventilation systems, and there are no compromises to heating, cooling, or ventilation performance. The integrated nature of the device also reduces risks for improper installation and commissioning. Even when using the air handler blower to distribute outdoor air, the total power consumption is lower than that of most available ERV products in the same airflow range. This system has the potential to offer very high-performance ventilation with much smoother and simpler installation than conventional systems.
Optical switches based on semiconducting vanadium dioxide films prepared by the sol-gel process (1990)

Vanadium dioxide thin films have been grown from vanadium tetrakis (t-butoxide) by the sol-gel process. A new method for the synthesis of the vanadium precursor was also developed. Films were deposited by dipcoating glass slides from an isopropanol solution, followed by postdeposition annealing of the films at 600°C under nitrogen. The properties of these films, to a high degree, were a function of crystalline boundaries and crystalline grain size. These gel-derived V02 films undergo a reversible semiconductor-to-metal phase transition near 72°C, exhibiting characteristic resistive and spectral switching comparable with near stoichiometric V02 films prepared on non- crystalline substrates by other techniques. Paralleling the investigation of pure V02, films were doped with hexavalent transition metal oxides to demonstrate lowering of the transition of the transition temperature.
Real-time respiratory triggered four dimensional cone-beam CT halves imaging dose compared to conventional 4D CBCT (2019)

Four dimensional cone-beam computed tomography (4D CBCT) improves patient positioning and the accuracy of radiation therapy for patients with mobile tumours. Generally, 4D CBCT requires many hundreds of x-ray projections to measure target trajectories and the imaging frequency is not adapted to the patient's respiratory signal resulting in over-sampling. In contrast, respiratory triggered 4D CBCT (RT 4D CBCT) is an acquisition technique that has been experimentally implemented and has shown to reduce the number of x-ray projections and thus 4D CBCT dose with minimal impact on image quality. The aim of this work is to experimentally investigate RT 4D CBCT in situ and measure target trajectory mean position, image quality and imaging dose from this approach. A commercially available phantom with programmable target motion was programmed with nine target trajectories derived from patient-measured respiratory traces known to span the range of image quality when used for 4D CBCT reconstruction. 4D CBCT datasets were acquired for each target trajectory using the RT 4D CBCT acquisition technique and the conventional 4D CBCT acquisition technique. From the reconstructed 4D CBCT datasets, target trajectory mean positions, imaging dose and image quality metrics were calculated and compared between the two techniques. Target trajectory and mean position were measured by tracking the target's displacement in the phantom; imaging dose was measured by counting the total number of x-ray projections acquired; and image quality was assessed by calculating the contrast-to-noise ratio (CNR), signal-to-noise ration (SNR) and edge response width (ERW). For each of the nine cases, the target trajectory mean position as determined by RT 4D CBCT and conventional 4D CBCT varied from the reference source trajectory mean position by 0.7 mm or less except for one case where a conventional 4D CBCT mean position varied by 1.3 mm. On the average of these nine studies, RT 4D CBCT required half as many projections as conventional 4D CBCT giving a 50% reduction in imaging dose. Overall, the image quality metrics (CNR and SNR) were marginally worse for RT 4D CBCT; ERW metric showed no statistically significant difference between the RT 4D CBCT and conventional 4D CBCT reconstructed datasets. Respiratory triggered 4D CBCT couples the real-time respiratory signal to the 4D CBCT image acquisition system and requires less imaging dose than conventional 4D CBCT to determine target trajectory mean positions.