gebhart/patrepeval huggingface dataset:
Fibroblast growth factor-2 (FGF2) and syndecan-1 (SDC1) are potential biomarkers for putative circulating CD15+/CD30+ cells in poor outcome Hodgkin lymphoma patients (2013)

The results suggest that small subsets of circulating CD30+/CD15+ cells expressing FGF2 and SDC1 represent biomarkers that identify NS-cHL patients who will experience a poor outcome (primary refractory and early relapsing).
0316 Evaluation of Axial Turbine Flow by a Viscous Throughflow Analysis (2012)

In the blade design process, flow pattern prediction tools have an essential role to create a highly efficient blade shape. A viscous throughflow code, which can take into account the effects of boundary layer and blade thickness, was developed to evaluate axial turbine flows. In the present paper, the throughflow code is validated by applying it to a concentric annular tube flow. In addition* axial turbine internal flows were evaluated by the throughflow code. The simulation results showed that the throughflow code can predict the flow patterns very well if the effects of secondary flow are marginal.
Functional properties of multispecific amino acid transporters and their implications to transporter-mediated toxicity. (2003)

The absorption, distribution and excretion of most of xenobiotics, drugs, environmental toxins and their metabolites are mediated by membrane transporters. Recent advances in the transporter molecular biology have made it possible to investigate the mechanisms of transport of those exogenous compounds and their transporter-mediated toxicity at the molecular level. Exogenous compounds including drugs and toxic substances occurring in the environment pass through the transporters with broad substrate selectivity, namely "multispecific" transporters, taking advantage of the multispecific nature to exert their toxic effects. The remarkable examples of such transporter-mediated toxicity are 1-methyl-4-phenyl-2,3-dihydropyridinium (MPP+)-neurotoxicity mediated by dopamine transporters, cephaloridine-nephrotoxicity mediated by organic anion transporters and methylmercury-toxicity mediated by system L amino acid transporters. The molecular identification of system L transporter LAT1 (L-type amino acid transporter 1) has lead to the understanding of the mechanisms of their multispecific substrate recognition and revealed their localization at the blood-brain barrier and placental barrier. LAT1 relies on the hydrophobic interaction between substrate amino acid side chains and the substrate binding site, so that many variations are possible for the substrate amino acid side chains, which is the basis of the broad substrate selectivity. System L transporters, thus, function as a path for the membrane permeation of drugs and toxic compounds occurring in the environment with amino acid-related structures. Beside methylmercury-cysteine conjugate, amino acid-related neurotoxins such as beta-N-methylamino-L-alanine, S-(1,2-dichlorovinyl)-L-cysteine and 3-hydroxykynurenine are proposed to pass through system L transporters to exert their toxicity. Because the presence of such transporters is crucial for the manifestation of the organ toxicity, the inhibition of the transporters would be expected to be beneficial to prevent the disorders caused by the transporter-mediated toxicity.
Single T Cell Sequencing Demonstrates the Functional Role of αβ TCR Pairing in Cell Lineage and Antigen Specificity (2019)

Although structural studies of individual T cell receptors (TCRs) have revealed important roles for both the α and β chain in directing MHC and antigen recognition, repertoire-level immunogenomic analyses have historically examined the β chain alone. To determine the amount of useful information about TCR repertoire function encoded within αβ pairings, we analyzed paired TCR sequences from nearly 100,000 unique CD4<sup>+</sup> and CD8<sup>+</sup> T cells captured using two different high-throughput, single-cell sequencing approaches. Our results demonstrate little overlap in the healthy CD4<sup>+</sup> and CD8<sup>+</sup> repertoires, with shared TCR sequences possessing significantly shorter CDR3 sequences corresponding to higher generation probabilities. We further utilized tools from information theory and machine learning to show that while α and β chains are only weakly associated with lineage, αβ pairings appear to synergistically drive TCR-MHC interactions. Vαβ gene pairings were found to be the TCR feature most informative of T cell lineage, supporting the existence of germline-encoded paired αβ TCR-MHC interaction motifs. Finally, annotating our TCR pairs using a database of sequences with known antigen specificities, we demonstrate that approximately a third of the T cells possess α and β chains that each recognize different known antigens, suggesting that αβ pairing is critical for the accurate inference of repertoire functionality. Together, these findings provide biological insight into the functional implications of αβ pairing and highlight the utility of single-cell sequencing in immunogenomics.
Human Mesenchymal Stem Cells Promote Human Osteoclast Differentiation from CD34+ Bone Marrow Hematopoietic Progenitors* (1999)

Interactions between osteoclast progenitors and stromal cells derived from mesenchymal stem cells (MSCs) within the bone marrow are important for osteoclast differentiation. In vitro models of osteoclastogenesis are well established in animal species; however, such assays do not necessarily reflect human osteoclastogenesis. We sought to establish a reproducible coculture model of human osteoclastogenesis using highly purified human marrow-derived MSCs (hMSCs) and CD34+ hematopoietic stem cells (HSCs). After 3 weeks, coculture of hMSCs and HSCs resulted in an increase in hematopoietic cell number with formation of multinucleated osteoclast-like cells (Ocls). Coculture of hMSCs with HSCs, transduced with a retroviral vector that expresses enhanced green fluorescent protein, produced enhanced green fluorescent protein+ Ocls, further demonstrating that Ocls arise from HSCs. These Ocls express calcitonin and vitronectin receptors and tartrate-resistant acid phosphatase and possess the ability to resorb bone. Ocl formation in this assay is cell contact dependent and is independent of added exogenous factors. Conditioned medium from the coculture contained high levels of interleukin (IL)-6, IL-11, leukemia inhibitory factor (LIF), and macrophage-colony stimulating factor. IL-6 and LIF were present at low levels in cultures of hMSCs but undetectable in cultures of HSCs alone. These data suggest that coculture with HSCs induce hMSCs to secrete cytokines involved in Ocl formation. Addition of neutralizing anti-IL-6, IL-11, LIF, or macrophage-colony stimulating factor antibodies to the coculture inhibited Ocl formation. hMSCs seem to support Ocl formation as undifferentiated progenitor cells, because treatment of hMSCs with dexamethasone, ascorbic acid, and β-glycerophosphate (to induce osteogenic differentiation) actually inhibited osteoclastogenesis in this coculture model. In conclusion, we have developed a simple and reproducible assay using culture-expanded hMSCs and purified HSCs with which to study the mechanisms of human osteoclastogenesis.
HistoQC: An Open-Source Quality Control Tool for Digital Pathology Slides (2019)

These results suggest that HistoQC could provide an automated, quantifiable, quality control process for identifying artefacts and measuring slide quality, in turn helping to improve both the repeatability and robustness of DP workflows.
Novd,Reffectarray.Antennas for Beam Steering (2005)

A class of novel reflectarray antenna topologies is proposed in this paper. The common features of these topologies are the presence of microstrip patches of similar size arranged into a regular lattice configuration on the top layer, and a periodic configuration of slots of variable size on the lower layer that are utilized to adjust the phase shift of the incoming wave. A novel method for generating a monfigurable reflectarray bzed on the creation of photo-induced plasma inside a semiconductor material is also presented. An . optically controlled variable slot located on the ground plane of a reflectarray antenna is . utilized in the suggested scheme to change the distribution of phase on the surface of the reflectamy. This property can be used for dynamic beam scanning and beam shaping.
Efficient and monolithic polarization conversion system based on a polarization grating (2012)

We introduce a new polarization conversion system (PCS) based on a liquid-crystal polarization grating (PG) and louvered wave plate. A simple arrangement of these elements laminated between two microlens arrays results in a compact and monolithic element, with the ability to nearly completely convert unpolarized input into linearly polarized output across most of the visible bandwidth. In our first prototypes, this PG-PCS approach manifests nearly 90% conversion efficiency of unpolarized to polarized for ±11° input light divergence, leading to an energy efficient picoprojector that presents high efficacy (12 lm/W) with good color uniformity.
Spin dice: A scalable truly random number generator based on spintronics (2014)

Generation of practical random numbers (RNs) by a spintronics-based, scalable truly RN generator called "spin dice" was demonstrated. The generator utilizes the stochastic nature of spin-torque switching in a magnetic tunnel junction (MTJ) to generate RNs. We fabricated eight perpendicularly magnetized MTJs on a single-board circuit and generated eight sequences of RNs simultaneously. The sequences of RNs of different MTJs were not correlated with each other, and performing an exclusive OR (XOR) operation among them improved the quality of the RNs. The RNs obtained by performing a nested XOR operation passed the statistical test of NIST SP-800 with the appropriate pass rate.
Secure candidate access router discovery (2004)

The candidate access router (CAR) discovery protocol is designed for use in wireless IP networks to dynamically collect information about neighboring access routers and their capabilities. This capability enables mobile nodes to dynamically execute low-latency hand-offs and to intelligently select a target access router. This paper presents possible approaches for CAR discovery, a security analysis of those approaches, and our novel security CAR discovery mechanisms.
Improved nutritional management of phenylketonuria by using a diet containing glycomacropeptide compared with amino acids [Erratum: 2010 Apr., v. 91, no. 4, p. 1072] (2009)

BACKGROUND: Phenylketonuria (PKU) requires a lifelong low-phenylalanine diet that provides the majority of protein from a phenylalanine-free amino acid (AA) formula. Glycomacropeptide (GMP), an intact protein formed during cheese production, contains minimal phenylalanine. OBJECTIVE: The objective was to investigate the effects of substituting GMP food products for the AA formula on acceptability, safety, plasma AA concentrations, and measures of protein utilization in subjects with PKU. DESIGN: Eleven subjects participated in an inpatient metabolic study with two 4-d treatments: a current AA diet (AA diet) followed by a diet that replaced the AA formula with GMP (GMP diet) supplemented with limiting AAs. Plasma concentrations of AAs, blood chemistries, and insulin were measured and compared in AA (day 4) and GMP diets (day 8). RESULTS: The GMP diet was preferred to the AA diet in 10 of 11 subjects with PKU, and there were no adverse reactions to GMP. There was no significant difference in phenylalanine concentration in postprandial plasma with the GMP diet compared with the AA diet. When comparing fasting with postprandial plasma, plasma phenalyalanine concentration increased significantly with the AA but not with the GMP diet. Blood urea nitrogen was significantly lower, which suggests decreased ureagenesis, and plasma insulin was higher with the GMP diet than with the AA diet. CONCLUSIONS: GMP, when supplemented with limiting AAs, is a safe and highly acceptable alternative to synthetic AAs as the primary protein source in the nutritional management of PKU. As an intact protein source, GMP improves protein retention and phenylalanine utilization compared with AAs.
Timing optimization in logic with interconnect (2008)

Timing optimization in logic paths with wires has become an important issue in the VLSI circuit design process. Existing techniques for minimizing delay treat only the relatively rare cases of logic without wires (logical effort) or logic with a long resistive wire (repeater insertion). The techniques described in this paper address the fundamental questions of optimal sizing, the number and location of the gates. The Unified Logical Effort (ULE) method supports fast and precise optimal sizing of gates in the presence of interconnect based on intuitive closed-form expressions. The optimal number of repeaters is determined by the Gate-terminated Sized Repeater Insertion (GSRI) technique, resulting in lower delay as compared to standard repeater insertion methodologies. The Logic Gates as Repeaters (LGR) method is used for optimal wire segmenting and gate location, suggesting a distribution of logic gates over interconnect rather than using logically-redundant repeaters. The combination of these techniques provides solution for a wide variety of design issues.
Reduced-Order Flux Observers With Stator-Resistance Adaptation for Speed-Sensorless Induction Motor Drives (2010)

This paper deals with reduced-order flux observers with stator-resistance adaptation for speed-sensorless induction motor (IM) drives. A general analytical solution for the stabilizing observer gain is given. The gain has two free positive parameters (which depend on the operating point), whose selection significantly affects the damping, convergence rate, robustness, and other properties of the observer. The general stability conditions for the stator-resistance adaptation are derived. An observer design is proposed that yields a robust and well-damped system and requires a minimal amount of tuning work. The proposed observer design is experimentally tested using a 45-kW IM drive; stable operation at very low speeds under different loading conditions is demonstrated.
Multidimensional Prognostic Risk Assessment Identifies Association Between IL12B Variation and Surgery in Crohn’s Disease (2013)

Progression to surgery is faster in patients with CD with both genetic and clinical risk factors. IL12B is independently associated with need and time to early surgery in CD patients and justifies the investigation of novel and existing therapies that affect this pathway.
Predicting Vehicular Travel Times by Modeling Heterogeneous Influences Between Arterial Roads (2018)

Predicting travel times of vehicles in urban settings is a useful and tangible quantity of interest in the context of intelligent transportation systems. We address the problem of travel time prediction in arterial roads using data sampled from probe vehicles. There is only a limited literature on methods using data input from probe vehicles. The spatio-temporal dependencies captured by existing data driven approaches are either too detailed or very simplistic. We strike a balance of the existing data driven approaches to account for varying degrees of influence a given road may experience from its neighbors, while controlling the number of parameters to be learnt. Specifically, we use a NoisyOR conditional probability distribution (CPD) in conjunction with a dynamic Bayesian network (DBN) to model state transitions of various roads. We propose an efficient algorithm to learn model parameters. We also propose an algorithm for predicting travel times on trips of arbitrary durations. Using synthetic and real world data traces we demonstrate the superior performance of the proposed method under different traffic conditions.
Time-division multiplexing for cable reduction in ultrasound imaging catheters (2015)

In ultrasound imaging catheter applications, gathering the data from multi-element transducer arrays is difficult as there is a restriction on cable count due to the diameter of the catheter. In such applications, CMUT-on-CMOS technology allows for 2D arrays with many elements to be designed and bonded directly onto CMOS circuitry. This allows for complex electronics to be placed at the tip of the catheter which leads to the possibility to include electronic multiplexing techniques to greatly reduce the cable count required for a large element array. Current approaches to cable reduction tend to rely on area and power hungry circuits to function, making them unsuitable for use in catheters. Furthermore the length requirement for catheters and lack of power available to on-chip cable drivers leads to limited signal strength at the receiver end. In this paper an alternative approach using Analogue Time Division Multiplexing (TDM) is presented, which addresses the cable restrictions of the catheter and, using a novel digital demultiplexing technique, allows for a reduction in the number of analogue signal processing stages required.
Detection, Tracking and 3D Modeling of Objects with Sparse RGB-D SLAM and Interactive Perception (2019)

We present an interactive perception system that enables an autonomous agent to deliberately interact with its environment and produce 3D object models. Our system verifies object hypotheses through interaction and simultaneously maintains 3D SLAM maps for each rigidly moving object hypothesis in the scene. We rely on depth-based segmentation and a multigroup registration scheme to classify features into various object maps. Our main contribution lies in the employment of a novel segment classification scheme that allows the system to handle incorrect object hypotheses, common in cluttered environments due to touching objects or occlusion. We start with a single map and initiate further object maps based on the outcome of depth segment classification. For each existing map, we select a segment to interact with and execute a manipulation primitive with the goal of disturbing it. If the resulting set of depth segments has at least one segment that did not follow the dominant motion pattern of its respective map, we split the map, thus yielding updated object hypotheses. We show qualitative results with a Fetch manipulator and objects of various shapes, which showcase the viability of the method for identifying and modelling multiple objects through repeated interactions.
Cheating attacks and resistance techniques in GeoGame design (2010)

The GeoGames Architecture (GGA) supports the implementation of electronic games that are to be played outdoors and that inherently incorporate vigorous physical activity. The basis of the GGA is to use geocast messaging within an ad hoc network of handheld devices, with game control implemented in a distributed fashion, without a central server and without requiring connection to the Internet cloud. This approach leads to several cheating attacks inherent to ad hoc networking, distributed control, and the open and uncontrolled nature of the play areas. This paper analyzes the threats, describes specific attacks, and gives several techniques that increase a GeoGame's resistance to these attacks. The threats, attacks, and resistance techniques are illustrated in the context of a case study focusing on two significantly different GeoGames, iTESS and iTron.
Neural network modeling for steering control of an autonomous vehicle (2017)

Model-based control of dynamical systems typically requires accurate domain-specific knowledge and specifications of possibly proprietary system components. In the context of autonomous driving, steering actuator dynamics can be difficult to model due to an integrated proprietary power steering control module. While first-principles models derived from physics laws can often approximate the system behavior, it remains generally difficult to capture non-physically derived behavior based on proprietary software algorithms in the power steering system. To overcome this limitation, this work instead employs a recurring neural network to model the steering dynamics of an autonomous vehicle. The resulting model is then integrated into a Nonlinear Model Predictive Control scheme to generate feedforward steering commands for embedded control. The proposed approach is compared to traditional first-principles steering modeling through on-vehicle experiments and statistical data validation. As a result, it is shown that the neural network model can be automatically generated with less domain-specific knowledge, can predict steering dynamics more accurately, and perform comparably to a high-fidelity first principles model when used for controlling the steering system of a self-driving vehicle.
Optical Alignment of Liquid Crystal Displays and Devices Via Polarized Light (1995)

The optical alignment of liquid crystals provides spatial and angular control of the local liquid crystal director. 1 - 3 This is achieved by properly designing photosensitive polymer alignment layers. These photosensitive alignment polymers are illuminated with polarized light which alters the bulk and surface properties of the polymer. The liquid crystal molecules adjacent to the alignment polymer interact with the altered polymer and align accordingly. The long range interaction of the liquid crystal molecules transfers the aligned state at the interface to the bulk of the liquid crystal layer. Since the alignment polymer itself is altered, the liquid crystal remains aligned after the illumination is terminated. With the proper design of the alignment material, the process is reversible allowing for the potential of real-time write/re-write control of the local liquid crystal director.
Towards Data-Efficient Modeling for Wake Word Spotting (2020)

Wake word (WW) spotting is challenging in far-field not only because of the interference in signal transmission but also the complexity in acoustic environment. Traditional WW model training requires large amount of in-domain WW-specific data with substantial human annotations. This prevents the model building in the situation of lacking such data. In this paper we present data-efficient solutions to address the challenges in WW modeling, such as domain-mismatch, noisy conditions, limited annotation, etc. Our proposed system is composed of a multi-condition training pipeline with stratified data augmentation, which improves the model robustness to a variety of predefined acoustic conditions, together with a semi-supervised learning pipeline to extract the WW and adversarial examples from untranscribed speech corpus. Starting from only 10 hours of domain-mismatched WW audio, we are able to enlarge and enrich the training dataset by 20-100 times to capture the complexity in acoustic environments. Our experiments on real user data show that the proposed solutions can achieve comparable performance of a production-grade model by saving 97% of the amount of WW-specific data to collect and 86% of the bandwidth for annotation.
Memory management during run generation in external sorting (1998)

If replacement selection is used in an external mergesort to generate initial runs, individual records are deleted and inserted in the sort operation's workspace. Variable-length records introduce the need for possibly complex memory management and extra copying of records. As a result, few systems employ replacement selection, even though it produces longer runs than commonly used algorithms. We experimentally compared several algorithms and variants for managing this workspace. We found that the simple best fit algorithm achieves memory utilization of 90% or better and run lengths over 1.8 times workspace size, with no extra copying of records and very little other overhead, for widely varying record sizes and for a wide range of memory sizes. Thus, replacement selection is a viable algorithm for commercial database systems, even for variable-length records.
HIGH-THROUGHPUT FABRICATION OF ADVANCED 3D MICROFLUIDIC DEVICES IN THERMOPLASTIC ELASTOMER FOR BIOLOGICAL PROBE IMMOBILIZATION (2011)

Peer reviewed: Yes