gebhart/patrepeval huggingface dataset:
Gene family information facilitates variant interpretation and identification of disease-associated genes (2017)

Abstract Differentiating risk-conferring from benign missense variants, and therefore optimal calculation of gene-variant burden, represent a major challenge in particular for rare and genetic heterogeneous disorders. While orthologous gene conservation is commonly employed in variant annotation, approximately 80% of known disease-associated genes are paralogs and belong to gene families. It has not been thoroughly investigated how gene family information can be utilized for disease gene discovery and variant interpretation. We developed a paralog conservation score to empirically evaluate whether paralog conserved or nonconserved sites of in-human paralogs are important for protein function. Using this score, we demonstrate that disease-associated missense variants are significantly enriched at paralog conserved sites across all disease groups and disease inheritance models tested. Next, we assessed whether gene family information could assist in discovering novel disease-associated genes. We subsequently developed a gene family de novo enrichment framework that identified 43 exome-wide enriched gene families including 98 de novo variant carrying genes in more than 10k neurodevelopmental disorder patients. 33 gene family enriched genes represent novel candidate genes which are brain expressed and variant constrained in neurodevelopmental disorders.
Reference Setup for Quantitative Comparison of Segmentation Techniques\n for Short Glass Fiber CT Data (2019)

Comparing different algorithms for segmenting glass fibers in industrial\ncomputed tomography (CT) scans is difficult due to the absence of a standard\nreference dataset. In this work, we introduce a set of annotated scans of\nshort-fiber reinforced polymers (SFRP) as well as synthetically created CT\nvolume data together with the evaluation metrics. We suggest both the metrics\nand this data set as a reference for studying the performance of different\nalgorithms. The real scans were acquired by a Nikon MCT225 X-ray CT system. The\nsimulated scans were created by the use of an in-house computational model and\nthird-party commercial software. For both types of data, corresponding ground\ntruth annotations have been prepared, including hand annotations for the real\nscans and STL models for the synthetic scans. Additionally, a Hessian-based\nFrangi vesselness filter for fiber segmentation has been implemented and\nopen-sourced to serve as a reference for comparisons.\n
User interfaces when and where they are needed (2002)

Users in ubiquitous computing environments need to be able to make serendipitous use of resources that they did not anticipate and of which they have no prior knowledge. The Speakeasy recombinant computing framework is designed to support such ad hoc use of resources on a network. In addition to other facilities, the framework provides an infrastructure through which device and service user interfaces can be made available to users on multiple platforms. The framework enables UIs to be provided for connections involving multiple entities, allows these UIs to be delivered asynchronously, and allows them to be injected by any party participating in a connection.
Instruction scheduling in the TOBEY compiler (1994)

The high performance of pipelined, superscalar processors such as the POWER2™ and PowerPC™ is achieved in large part through the parallel execution of instructions. This fine-grain parallelism cannot always be achieved by the processor alone, but relies to some extent on the ordering of the instructions in a program. This dependence implies that optimizing compilers for these processors must generate or schedule the instructions in an order that maximizes the possible parallelism. This paper describes the parts of the TOBEY compiler which address the instruction scheduling issue.
Supplementary Figure S4 from Pharmacological Inhibition of the Protein Kinase MRK/ZAK Radiosensitizes Medulloblastoma (2023)

&lt;p&gt;Animal weights during and after treatment. Color figure.&lt;/p&gt;
On multi-level exclusive caching: offline optimality and why promotions are better than demotions (2008)

Multi-level cache hierarchies have become very common; however, most cache management policies result in duplicating the same data redundantly on multiple levels. The state-of-the-art exclusive caching techniques used to mitigate this wastage in multi-level cache hierarchies are the DEMOTE technique and its variants. While these achieve good hit ratios, they suffer from significant I/O and computational overheads, making them unsuitable for deployment in real-life systems.

We propose a dramatically better performing alternative called PROMOTE, which provides exclusive caching in multi-level cache hierarchies without demotions or any of the overheads inherent in DEMOTE. PROMOTE uses an adaptive probabilistic filtering technique to decide which pages to promote to caches closer to the application. While both DEMOTE and PROMOTE provide the same aggregate hit ratios, PROMOTE achieves more hits in the highest cache levels leading to better response times. When inter-cache bandwidth is limited, PROMOTE convincingly outperforms DEMOTE by being 2x more efficient in bandwidth usage. For example, in a trace from a real-life scenario, PROMOTE provided an average response time of 3.42ms as compared to 5.05ms for DEMOTE on a two-level hierarchy of LRU caches, and 5.93ms as compared to 7.57ms on a three-level cache hierarchy.

We also discover theoretical bounds for optimal multi-level cache performance. We devise two offline policies, called OPT-UB and OPT-LB, that provably serve as upper and lower bounds on the theoretically optimal performance of multi-level cache hierarchies. For a series of experiments on a wide gamut of traces and cache sizes OPT-UB and OPTLB ran within 2.18% and 2.83% of each other for two-cache and three-cache hierarchies, respectively. These close bounds will help evaluate algorithms and guide future improvements in the field of multi-level caching.
Infrared plasmons on heavily-doped silicon (2011)

We examine the long-wave infrared (LWIR) optical characteristics of heavily-doped silicon and explore engineering of surface plasmons polaritons (SPP) in this spectral region. Both phosphorus (n-type Si) and boron (p-type Si) implants are evaluated and various cap layers and thermal annealing steps are examined. The optical properties are measured using ellipsometry and fit to a Drude model for the infrared (IR) permittivity. The predicted metallic behavior for Si in the thermal IR and its impact on the spatial confinement and dispersion for surface plasmons is studied. We find that the transverse spatial confinement for a surface plasmon on highly doped Si is strongly sub-wavelength near the plasma edge, and the confinement to the surface is enhanced to greater than 10× that of the metal confined SPP over the entire LWIR spectrum.
The sonochemical preparation of amorphous silver nanoparticles (1999)

Amorphous silver nanoparticles of ca. 20 nm size have been prepared by the sonochemical reduction of an aqueous silver nitrate solution in an atmosphere of argon-hydrogen. The silver nanoparticles have been characterized by TEM, X-ray diffraction, absorption spectroscopy, differential scanning calorimetry and EPR spectroscopy. The mechanism of the sonochemical reduction has been discussed, and occurs through the generation of hydrogen radicals during the sonication process.
Broadband optical studies of 1-D and 3-D photonic crystals (2005)

Supercontinuum based sources and measurement techniques are developed, enabling optical ultra-broadband studies of nano-scale photonic crystal devices and integrated photonic circuits over 1.2 – 2.0 µm wavelength range. Experiments involving 1-D periodic photonic crystal microcavity waveguides and 3-D periodic photonic crystals with embedded point defects are described. Experimental findings are compared with rigorous electromagnetic simulations.
ICA-fNORM: Spatial Normalization of fMRI Data Using Intrinsic Group-ICA Networks (2011)

A common pre-processing challenge associated with group level fMRI analysis is spatial registration of multiple subjects to a standard space. Spatial normalization, using a reference image such as the Montreal Neurological Institute brain template, is the most common technique currently in use to achieve spatial congruence across multiple subjects. This method corrects for global shape differences preserving regional asymmetries, but does not account for functional differences. We propose a novel approach to co-register task-based fMRI data using resting state group-ICA networks. We posit that these intrinsic networks (INs) can provide to the spatial normalization process with important information about how each individual's brain is organized functionally. The algorithm is initiated by the extraction of single subject representations of INs using group level independent component analysis (ICA) on resting state fMRI data. In this proof-of-concept work two of the robust, commonly identified, networks are chosen as functional templates. As an estimation step, the relevant INs are utilized to derive a set of normalization parameters for each subject. Finally, the normalization parameters are applied individually to a different set of fMRI data acquired while the subjects performed an auditory oddball task. These normalization parameters, although derived using rest data, generalize successfully to data obtained with a cognitive paradigm for each subject. The improvement in results is verified using two widely applied fMRI analysis methods: the general linear model and ICA. Resulting activation patterns from each analysis method show significant improvements in terms of detection sensitivity and statistical significance at the group level. The results presented in this article provide initial evidence to show that common functional domains from the resting state brain may be used to improve the group statistics of task-fMRI data.
Wafer topography modeling for ionic implantation mask correction dedicated to 2x nm FDSOI technologies (2013)

Reflection by wafer topography and underlying layers during optical lithography can cause unwanted exposure in the resist [1]. This wafer stack effect phenomenon which is neglected for larger nodes than 45nm, is becoming problematic for 32nm technology node and below at the ionic implantation process. This phenomenon is expected to be attenuated by the use of anti-reflecting coating but increases process complexity and adds cost and cycle time penalty. As a consequence, an OPC based solution is today under evaluation to cope with stack effects involved in ionic implantation patterning [2] [3]. For the source drain (SD) ionic implantation process step on 28nm Fully Depleted Silicon-on-Insulator (FDSOI) technology, active silicon areas, poly silicon patterns, Shallow Trench Isolation (STI), Silicon-on-Insulator (SOI) areas and the transitions between these different regions result in significant SD implant pattern critical dimension variations. The large number of stack variations involved in these effects implies a complex modeling to simulate pattern degradations. This paper deals with the characterization of stack effects on 28nm node using SOI substrates. The large number of measurements allows to highlight all individual and combined stack effects. A new modeling flow has been developed in order to generate wafer stack aware OPC model. The accuracy and the prediction of the model is presented in this paper.
High frequency electrical characterization of a high wiring density organic substrate ALIVH and a stud bump bonding SBB (1998)

High frequency electrical properties of a high wiring density organic substrate ALIVH , which has any layer inner via holes structure, and flip chip interconnection between pads on semiconductor chips and transmission lines using an SBB technique were characterized. The dielectric constant, loss tangent, transmission loss and via hole characteristics of the ALIVH substrate were measured from 1GHz to 4GHz frequency range. Flip chip interconnecting region using the SBB technique was also measured using resonant method and simulated using FEM method HFSS. The equivalent circuits of the via hole and the flip chip interconnection were evaluated. Both of the ALIVH substrate and the SBBflip chip interconnecting technique were found to be good enough to apply to high speed digital systems up to 1GHz.
Positioning and Location-Aware Communications for Modern Railways with\n 5G New Radio (2019)

Providing high-capacity radio connectivity for high-speed trains (HSTs) is\none of the most important use cases of emerging 5G New Radio (NR) networks. In\nthis article, we show that 5G NR technology can also facilitate high-accuracy\ncontinuous localization and tracking of HSTs. Furthermore, we describe and\ndemonstrate how the NR network can utilize the continuous location information\nfor efficient beam-management and beamforming, as well as for downlink Doppler\nprecompensation in the single-frequency network context. Additionally, with\nparticular focus on millimeter wave networks, novel concepts for low-latency\nintercarrier interference (ICI) estimation and compensation, due to residual\nDoppler and oscillator phase noise, are described and demonstrated. The\nprovided numerical results at 30 GHz operating band show that sub-meter\npositioning and sub-degree beam-direction accuracies can be obtained with very\nhigh probabilities in the order of 95-99%. The results also show that the\ndescribed Doppler precompensation and ICI estimation and cancellation methods\nsubstantially improve the throughput of the single-frequency HST network.\n
PSMA ADC monotherapy in patients with progressive metastatic castration‐resistant prostate cancer following abiraterone and/or enzalutamide: Efficacy and safety in open‐label single‐arm phase 2 study (2019)

PSMA ADC demonstrated some activity with respect to PSA declines, CTC conversions/reductions, and radiologic assessments in abi/enz treated mCRPC subjects. Clinically significant treatment-related AEs included neutropenia and neuropathy.
High-capacity undersea long-haul systems (2006)

This paper reviews technologies and techniques that have been used in deployed long-haul wavelength division multiplexing (WDM) systems and emerging technologies that could be used for the next generation of cost-reduced systems. The overview of current generation technologies starts with a discussion of modulation formats, focusing on the superior properties of the chirped return to zero on-off shift keying (CRZ-OOK) modulation format. The use of 10-Gb/s CRZ-OOK modulation format together with advanced fiber types, more powerful forward error correction (FEC), and broadband erbium-doped fiber amplifiers resulted in the deployment of dense WDM systems with capacities per fiber in terabits per second range and trans-Pacific reach. Demand for the systems with large design capacity led to further development of broadband optical amplifiers. Laboratory demonstrations successfully expanded transmission into the full C-band and later in the C and L transmission bands. The current market conditions dictate the need for reducing the first cost of an installed system rather than reaching record capacity per fiber. Reducing first cost can be achieved by reducing the amount of optical amplifiers in the cable by utilizing an excess performance margin provided by available RZ-OOK technology. Further improvements would be possible if more powerful FEC and modulation formats with better receiver sensitivity are used. For example, the RZ differential phase-shift keying (RZ-DPSK) modulation format with 3-dB better receiver sensitivity and better nonlinear tolerance to large amounts of accumulated dispersion is a very promising technology. This paper will review long-haul transmission results using RZ-DPSK and will compare the transmission properties of RZ-DPSK signals versus RZ-OOK signals. Due to superior receiver sensitivity, the RZ-DPSK modulation format can be an enabling technology for 40-Gb/s per channel transoceanic transmission
Optical network physical layer parameter optimization for digital backpropagation using Gaussian processes (2023)

Abstract We present a novel methodology for optimizing fiber optic network performance by determining the ideal values for attenuation, nonlinearity, and dispersion parameters in terms of achieved signal-to-noise ratio (SNR) gain from digital backpropagation (DBP). Our approach uses Gaussian process regression, a probabilistic machine learning technique, to create a computationally efficient model for mapping these parameters to the resulting SNR after applying DBP. We then use simplicial homology global optimization to find the parameter values that yield maximum SNR for the Gaussian process model within a set of a priori bounds. This approach optimizes the parameters in terms of the DBP gain at the receiver. We demonstrate the effectiveness of our method through simulation and experimental testing, achieving optimal estimates of the dispersion, nonlinearity, and attenuation parameters. Our approach also highlights the limitations of traditional one-at-a-time grid search methods and emphasizes the interpretability of the technique. This methodology has broad applications in engineering and can be used to optimize performance in various systems beyond optical networks.
Membrane changes in virus transformed cells. (1976)

Various aspects of membrane changes in cells transformed by oncogenic viruses are briefly described and discussed. Emphasis is made on changes recently observed in the hydrophobic portion of plasma membrane with the freeze-etching technique. The hypothesis is put forward that other changes seen at the surface of transformed cells are caused by a primary event occuring in proteins of the hydrophobic area.
Statistical analysis of dark count rate in Geiger-mode APD FPAs (2014)

We present a temporal statistical analysis of the array-level dark count behavior of Geiger-mode avalanche photodiode (GmAPD) focal plane arrays that distinguishes between Poissonian intrinsic dark count rate and non-Poissonian crosstalk counts by considering “inter-arrival” times between successive counts from the entire array. For 32 x 32 format sensors with 100 μm pixel pitch, we show the reduction of crosstalk for smaller active area sizes within the pixel. We also compare the inter-arrival time behavior for arrays with narrow band (900 - 1100 nm) and broad band (900 - 1600 nm) spectral response. We then consider a similar analysis of larger format 128 x 32 arrays. As a complement to the temporal analysis, we describe the results of a spatial analysis of crosstalk events. Finally, we propose a simple model for the impact of crosstalk events on the Poissonian statistics of intrinsic dark counts that provides a qualitative explanation for the results of the inter-arrival time analysis for arrays with varying degrees of crosstalk.
Kinematic Changes After Fusion and Total Replacement of the Ankle Part 1: Range of Motion (2003)

With respect to the ROM, total ankle replacement changes the natural ankle joint condition less than ankle arthrodesis, which reduces the ROM in all three planes and might increase stress in adjacent structures. The prosthesis that replicated the normal ankle joint ROM best was the one with the most anatomical design.
A 1.2–12 GHz Sliced Notch Antenna Array (2018)

Historically, Vivaldi arrays are known to suffer from high cross-polarization when scanning in the nonprincipal planes-a fault without a universal solution. In this paper, a solution to this issue is proposed in the form of a new Vivalditype array with low cross-polarization termed the Sliced Notch Antenna (SNA) array. For the first proof-of-concept demonstration, simulations and measurements are comparatively presented for two single-polarized 19 × 19 arrays-the proposed SNA and its Vivaldi counterpart-each operating over a 1.2-12 GHz (10:1) band. Both arrays are built using typical vertically integrated printed-circuit board cards, and are designed to exhibit VSWR <; 2.5 within a 60° scan cone over most of the 10:1 band as infinite arrays. Measurement results compare very favorably with full-wave finite array simulations that include array truncation effects. The SNA array element demonstrates well-behaved polarization performance versus frequency, with more than 20 dB of D-plane θ = 45° polarization purity improvement at the high frequency. Moreover, the SNA element also: 1) offers better suppression of classical Vivaldi E-plane scan blindnesses; 2) requires fewer plated through vias for striplinebased designs; and 3) allows relaxed adjacent element electrical contact requirements for dual-polarized arrangements.
False Positive Mononucleosis Screening Test Results Associated with Klebsiella Hepatic Abscess (1990)

False positive heterophile test results for infectious mononucleosis are rare but may lead to diagnostic confusion. A patient with Klebsiella hepatic abscess is described in whom a persistently false positive heterophile test resulted in delayed appropriate diagnosis and therapy.
Activity/Stability of Human Pepsin: Implications for Reflux Attributed Laryngeal Disease (2007)

Detectable levels of pepsin remain in laryngeal epithelia after a reflux event. Pepsin bound there would be enzymatically inactive because the mean pH of the laryngopharynx is pH 6.8. Significantly, pepsin could remain in a form that would be reactivated by a subsequent decrease in pH, such as would occur during an acidic reflux event or possibly after uptake into intracellular compartments of lower pH.
An efficient non-iterative smoothed particle hydrodynamics fluid simulation method with variable smoothing length (2023)

In classical smoothed particle hydrodynamics (SPH) fluid simulation approaches, the smoothing length of Lagrangian particles is typically constant. One major disadvantage is the lack of adaptiveness, which may compromise accuracy in fluid regions such as splashes and surfaces. Attempts to address this problem used variable smoothing lengths. Yet the existing methods are computationally complex and non-efficient, because the smoothing length is typically calculated using iterative optimization. Here, we propose an efficient non-iterative SPH fluid simulation method with variable smoothing length (VSLSPH). VSLSPH correlates the smoothing length to the density change, and adaptively adjusts the smoothing length of particles with high accuracy and low computational cost, enabling large time steps. Our experimental results demonstrate the advantages of the VSLSPH approach in terms of its simulation accuracy and efficiency.
Supplementary Figure S2 from Induction of Telomere Dysfunction Mediated by the Telomerase Substrate Precursor 6-Thio-2′-Deoxyguanosine (2023)

&lt;p&gt;Hematology.&lt;/p&gt;