gebhart/patrepeval huggingface dataset:
Aberrant DOCK2, GRASP, HIF3A and PKFP Hypermethylation has Potential as a Prognostic Biomarker for Prostate Cancer (2019)

Prostate cancer (PCa) is a clinically heterogeneous disease and currently, accurate diagnostic and prognostic molecular biomarkers are lacking. This study aimed to identify novel DNA hypermethylation markers for PCa with future potential for blood-based testing. Accordingly, to search for genes specifically hypermethylated in PCa tissue samples and not in blood cells or other cancer tissue types, we performed a systematic analysis of genome-wide DNA methylation data (Infinium 450K array) available in the Marmal-aid database for 4072 malignant/normal tissue samples of various types. We identified eight top candidate markers (cg12799885, <i>DOCK2</i>, <i>FBXO30</i>, <i>GRASP</i>, <i>HIF3A</i>, <i>MOB3B</i>, <i>PFKP</i>, and <i>TPM4</i>) that were specifically hypermethylated in PCa tissue samples and hypomethylated in other benign and malignant tissue types, including in peripheral blood cells. Potential as diagnostic and prognostic biomarkers was further assessed by the quantitative methylation specific PCR (qMSP) analysis of 37 nonmalignant and 197 PCa tissue samples from an independent population. Here, all eight hypermethylated candidates showed high sensitivity (75⁻94%) and specificity (84⁻100%) for PCa. Furthermore, <i>DOCK2</i>, <i>GRASP</i>, <i>HIF3A</i> and <i>PKFP</i> hypermethylation was significantly associated with biochemical recurrence (BCR) after radical prostatectomy (RP; 197 patients), independent of the routine clinicopathological variables. <i>DOCK2</i> is the most promising single candidate marker (hazard ratio (HR) (95% confidence interval (CI)): 1.96 (1.24⁻3.10), adjusted <i>p</i> = 0.016; multivariate cox regression). Further validation studies are warranted and should investigate the potential value of these hypermethylation candidate markers for blood-based testing also.
Morphology of Human Embryonic and Induced Pluripotent Stem Cell Colonies Cultured with Feeders (2011)

To prolong the stage of undifferentiation, human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) have traditionally been isolated and cultured using feeder layers, such as mouse embryonic fibroblasts (MEFs) or foreskin fibroblasts, with medium supplemented by fetal bovine serum (FBS). For research purposes, these conditions are preferable and are often referred to as the gold standard. This chapter describes the colony morphology of undifferentiated hESCs and iPSCs cultured with MEFs or human foreskin fibroblasts.
Dynamic imaging microellipsometry: theory, system design, and feasibility demonstration (1988)

Dynamic imaging microellipsometry (DIM) is a new rapid full-field imaging technique for high spatial resolution studies of thin films. The DIM concept is based on radiometric polarizer, compensator, specimen, and analyzer ellipsometry combined with video and image processing techniques. The theoretical basis for this approach is developed using the Jones vector and matrix formalisms. Basic systems design is presented with error model predictions of ellipsometric accuracies better than 0.1 degrees for full-field Delta and psi images captured in a few seconds with spatial resolution under 10 microm. Initial feasibility tests have demonstrated interframe discriminations of 0.36 degrees for Delta and 0.082 degrees for psi.
An inter-residue network model to identify mutational-constrained regions on the Ebola coat glycoprotein (2017)

Recently, progress has been made in the development of vaccines and monoclonal antibody cocktails that target the Ebola coat glycoprotein (GP). Based on the mutation rates for Ebola virus given its natural sequence evolution, these treatment strategies are likely to impose additional selection pressure to drive acquisition of mutations in GP that escape neutralization. Given the high degree of sequence conservation among GP of Ebola viruses, it would be challenging to determine the propensity of acquiring mutations in response to vaccine or treatment with one or a cocktail of monoclonal antibodies. In this study, we analyzed the mutability of each residue using an approach that captures the structural constraints on mutability based on the extent of its inter-residue interaction network within the three-dimensional structure of the trimeric GP. This analysis showed two distinct clusters of highly networked residues along the GP<sub>1</sub>-GP<sub>2</sub> interface, part of which overlapped with epitope surfaces of known neutralizing antibodies. This network approach also permitted us to identify additional residues in the network of the known hotspot residues of different anti-Ebola antibodies that would impact antibody-epitope interactions.
Preliminary results from a stroke rehabilitation protocol utilizing a robotic BMI-exoskeleton system (2017)

Effective strategies for stimulating motor learning post-stroke involve large dosages of movement repetitions, during which patients are engaged both physically and mentally. While robots are inherently suitable for rehabilitation due to their ability to provide intensive movement training and precise measurement, it is less obvious how to ensure patient focus and mental engagement during therapy. To address this limitation, we have augmented an upper-limb robotic exoskeleton, the MAHI Exo-II, with a brain-machine interface (BMI) that monitors EEG signals to detect movement intention in real time. We present preliminary findings of a 12-session stroke rehabilitation protocol utilizing this BMI-Exo system for elbow flexion-extension training.
Molecular Mechanisms of Type III Hyperlipoproteinemia:  The Contribution of the Carboxy-Terminal Domain of ApoE Can Account for the Dyslipidemia That Is Associated with the E2/E2 Phenotype (2003)

Apolipoprotein E2, which has an R158 for C substitution, has reduced affinity for the LDL receptor and is associated with type III hyperlipoproteinemia in humans. Consistent with these observations, we have found that following adenovirus-mediated gene transfer, full-length apoE2 aggravates the hypercholesterolemia and induces hypertriglyceridemia in E-deficient mice and induces combined hyperlipidemia in C57BL/6 mice. Unexpectedly, the truncated apoE2-202 form that has an R158 for C substitution when expressed at levels similar to those of the full-length apoE2 normalized the cholesterol levels of E-deficient mice without induction of hypertriglyceridemia. The apoE2 truncation increased the affinity of POPC-apoE particles for the LDL receptor, and the full-length apoE2 had a dominant effect in VLDL triglyceride secretion. Hyperlipidemia in normal C57BL/6 mice was prevented by coinfection with equal doses of each, the apoE2 and the apoE2-202-expressing adenoviruses, indicating that truncated apoE forms have a dominant effect in remnant clearance. Hypertriglyceridemia was completely corrected by coinfection of mice with an adenovirus-expressing wild-type lipoprotein lipase, whereas an inactive lipoprotein lipase had a smaller effect. The findings suggest that the apoE2-induced dyslipidemia is not merely the result of substitution of R158 for C but results from increased secretion of a triglyceride-enriched VLDL that cannot undergo lipolysis, inhibition of LpL activity, and impaired clearance of chylomicron remnants. Infection of E(-)(/)(-)xLDLr(-)(/)(-) double-deficient mice with apoE2-202 did not affect the plasma cholesterol levels, and also did not induce hypertriglyceridemia. In contrast, apoE2 exacerbated the hypercholesterolemia and induced hypertriglyceridemia, suggesting that the LDL receptor is the predominant receptor in remnant clearance.
Golfomycin A, a Novel Designed Molecule with DNA‐Cleaving Properties and Antitumor Activity (1990)

Retroaldol reaction, propargyl–allenyl isomerization, and [4 + 2] cycloaddition are the steps involved in the reaction of the title compound 1 with 1,8-diazabi-cyclo[5.4.0]undec-7-ene at room temperature in THF. The product 2, like 1, reacts readily with nucleophiles such as methyl thioglycolate. The biological activity of these compounds is presumably due to this reactivity.
Underwater hyperspectral imaging for environmental mapping and monitoring of seabed habitats (2015)

Underwater hyperspectral imaging is a novel method for mapping and monitoring the seafloor. It uses the reflected light from objects under water to automatically identify them. This paper explains the basic technology and shows examples of use from two field missions in Norwegian waters. In the two cases, libraries of spectral signatures for the living organisms at the site were established, and subsequently used to automatically identify objects on the seafloor.
Recent advances in mechanical cardiopulmonary resuscitation devices (1999)

Over the past 40 years since standard closed-chest cardiopulmonary resuscitation was first described, several mechanical devices have been developed to increase vital organ perfusion in patients in cardiac arrest. The newer approaches aim to increase forward blood flow by increasing intrathoracic pressures and by direct cardiac compression during the “compression phase.” Equally important is the enhancement of venous return during the decompression phase of cardiopulmonary resuscitation. New approaches designed to increase venous return to the thorax during cardiopulmonary resuscitation include innovations that decrease “decompression phase” intrathoracic pressure and those that alternate abdominal compression with chest wall compression. The potential clinical value of these newer mechanical approaches is reviewed. In addition, some devices in the development stage are described.
Drug Delivery by the Intravaginal Route (2000)

The human vagina represents a potential, accessible space that offers a valuable route for drug delivery through the use of specifically designed carrier systems for both local and systemic applications. Intravaginal drug delivery is particularly appropriate for drugs associated with women's health issues but may also have applications in general drug delivery within the female population. A range of drug delivery platforms suitable for intravaginal administration are discussed in this review, including hydrogels, vaginal tablets, pessaries/suppositories, particulate systems, and intravaginal rings. Drug release mechanisms and absorption pathways are reviewed with respect to a range of therapeutic and prophylactic indications for intravaginal delivery.
Palladium-catalysed three-component coupling reactions of dimethylsilacyclobutane, carbon monoxide and organic halides: a convenient route to cyclic silyl enol ethers (1996)

A facile one pot synthesis of cyclic silyl enol ethers, 1-sila-2-oxacyclohex-3-enes has been achieved by coupling reactions of strained 1,1-dimethyl-1-silacyclobutane with organic halides in CO atmosphere (1 atm) in the presence of palladium catalysts.
Vehicle type classification from laser scans with global alignment kernels (2014)

This paper addresses the problem of vehicle classification using laser scanner profiles, which is usually found as a component of electronic tolling systems. Laser scanners obtain a 3D measurement of the vehicle surface. Previous approaches treated the laser scans as images. In addition to high-level features (such as width, height, length and other measurements) from the scanner profiles, feature descriptors have been used for supervised classification of laser scanner profiles. This allowed to deploy a generic approach to the image classification based on Fisher features. In this paper we adopt a different approach which extracts and analyses vehicle shapes from the laser scans. The method proceeds to finding typical vehicle shapes and classifying them through the global shape alignment.
Gain-enhanced LTCC system-on-package for automotive UMRR applications (2010)

A novel Low Temperature Co-fired Ceramic (LTCC) based SoP for automotive radar applications is presented. For the first time a combination of a relatively low dielectric constant LTCC substrate and a high dielectric constant LTCC superstrate has been incorporated to enhance the overall gain of the module. The superstrate can provide additional protection to the integrated circuits (IC) in the harsh automotive environment. A custom cavity in the LTCC substrate can accommodate the IC, which feeds an aperture coupled patch antenna array. The cavity is embedded below the ground plane that acts as a shield for the IC from antenna radiation. It is estimated that with mere 10 dBm of transmitted RF power the miniature SoP module (sized 2.0 cm × 2.0 cm × 0.22 cm) can communicate up to 67 m. The design's compactness, robustness, transmission power and resultant communication range are highly suitable for Universal Medium Range Radar (UMRR) applications.
WOAD: Weakly Supervised Online Action Detection in Untrimmed Videos (2021)

Online action detection in untrimmed videos aims to identify an action as it happens, which makes it very important for real-time applications. Previous methods rely on tedious annotations of temporal action boundaries for training, which hinders the scalability of online action detection systems. We propose WOAD, a weakly supervised framework that can be trained using only video-class labels. WOAD contains two jointly-trained modules, i.e., temporal proposal generator (TPG) and online action recognizer (OAR). Supervised by video-class labels, TPG works offline and targets at accurately mining pseudo frame-level labels for OAR. With the supervisory signals from TPG, OAR learns to conduct action detection in an online fashion. Experimental results on THUMOS’14, ActivityNet1.2 and ActivityNet1.3 show that our weakly-supervised method largely outperforms weakly-supervised baselines and achieves comparable performance to the previous strongly-supervised methods. Beyond that, WOAD is flexible to leverage strong supervision when it is available. When strongly supervised, our method obtains the state-of-the-art results in the tasks of both online per-frame action recognition and online detection of action start.
Discovery of Selective Small Molecule ROMK Inhibitors as Potential New Mechanism Diuretics (2012)

The renal outer medullary potassium channel (ROMK or Kir1.1) is a putative drug target for a novel class of diuretics that could be used for the treatment of hypertension and edematous states such as heart failure. An internal high-throughput screening campaign identified 1,4-bis(4-nitrophenethyl)piperazine (5) as a potent ROMK inhibitor. It is worth noting that this compound was identified as a minor impurity in a screening hit that was responsible for all of the initially observed ROMK activity. Structure-activity studies resulted in analogues with improved rat pharmacokinetic properties and selectivity over the hERG channel, providing tool compounds that can be used for in vivo pharmacological assessment. The featured ROMK inhibitors were also selective against other members of the inward rectifier family of potassium channels.
Visualization of mappings between schemas (2005)

In this paper we describe a novel approach to the visualization of the mapping between two schemas. Current approaches to visually defining such a mapping fail when the schemas or maps become large. The new approach uses various information visualization techniques to simplify the view, making it possible for users to effectively deal with much larger schemas and maps. A user study verifies that the new approach is useful, usable, and effective. The primary contribution is a demonstration of novel ways to effectively present highly complex information.
L-C Measurement Acquisition Method for Aerospace Systems (2003)

This paper describes a measurement acquisition method for aerospace systems that eliminates the need for sensors to have physical connection to a power source (i.e., no lead wires) or to data acquisition equipment. Furthermore, the method does not require the sensors to be in proximity to any form of acquisition hardware. Multiple sensors can be interrogated using this method. The sensors consist of a capacitor, C(p), whose capacitance changes with changes to a physical property, p, electrically connected to an inductor, L. The method uses an antenna to broadcast electromagnetic energy that electrically excites one or more inductive-capacitive sensors via Faraday induction. This method facilitates measurements that were not previously possible because there was no practical means of providing power and data acquisition electrical connections to a sensor. Unlike traditional sensors, which measure only a single physical property, the manner in which the sensing element is interrogated simultaneously allows measurement of at least two unrelated physical properties (e.g., displacement rate and fluid level) by using each constituent of the L-C element. The key to using the method for aerospace applications is to increase the distance between the L-C elements and interrogating antenna; develop all key components to be non-obtrusive and to develop sensing elements that can easily be implemented. Techniques that have resulted in increased distance between antenna and sensor will be presented. Fluid-level measurements and pressure measurements using the acquisition method are demonstrated in the paper.
New Quartz Resonators with Precision Frequency Linearity Over a Wide Temperature Range (1982)

Abstract : Quartz crystal resonators have been employed in a number of thermometer applications. We have recently discovered two new thermometric cuts; one exhibits a high degree of linearity over a wide temperature range; the other is located in the vicinity of the stress compensated locus. These doubly rotated cuts were found by calculations based on the thickness - vibration theory for ideal plates. This paper presents theoretical and experimental results concerning the frequency-temperature characteristics of these quartz resonators.
Rapid dual‐echo ramped hybrid encoding<scp>MR</scp>‐based attenuation correction (d<scp>RHE‐MRAC</scp>) for<scp>PET/MR</scp> (2017)

Dual-echo ramped hybrid encoding enables rapid and robust imaging for MRAC with a very rapid acquisition. Magn Reson Med 79:2912-2922, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Privacy-Preserving Predictive Models for Lung Cancer Survival Analysis (2008)

MAASTRO clinic, the Netherlands. Privacy-preserving data mining (PPDM) is a recent emergent research area that deals with the incorporation of privacy preserving concerns to data mining techniques. We consider a real clinical setting where the data is horizontally distributed among different institutions. Each one of the medical institutions involved in this work provides a database containing a subset of patients. There is recent work that shows the potential of the PPDM approach in medical applications. However, there is few work in developing/implementing PPDM for predictive personalized medicine. In this paper we use real data from several institutions across Europe to build models for survival prediction for non-small-cell lung cancer patients while addressing the potential privacy preserving issues that may arise when sharing data across institutions located in different countries. Our experiments in a real clinical setting show that the privacy preserving approach may result in improved models while avoiding the burdens of traditional data sharing (legal and/or anonymization expenses). 1
New developments in the design and generation of gear drives (2001)

Design, generation and simulation of the meshing and contact of gear drives with favourable bearing contact and reduced noise are considered. The proposed approach is based on replacement of the instantaneous line of contact of tooth surfaces by point contact and on application of a predesigned parabolic function of transmission errors that is able to absorb linear discontinuous functions of transmission errors caused by misalignment. Basic algorithms for analysis and synthesis of gear drives are presented. The developed theory is applied for design and generation of the following gear drives with modified geometry: (a) spur and helical gears, (b) a new version of Novikov-Wildhaber (N-W) helical gears, (c) asymmetric face gear drives with a spur pinion, (d) formate-cut spiral bevel gears. Generation of the tooth surface of a worm gear is presented as the formation of a two-branch envelope. The discussed topics are illustrated with examples.
Registration, calibration and blending in creating high quality panoramas (2002)

This paper presents a system for creating a full 360-degree panorama from rectilinear images captured from a single nodal position. The solution to the problem is divided into three steps. The first step registers all overlapping images projectively. A combination of a gradient-based optimization method and a correlation-based linear search is found to be robust even in cases of drastic exposure differences and small amount of parallax. The second step takes the projective matrices and their associated hessian matrices as inputs, and calibrates the internal and external parameters of every image through a global optimization. The objective is to minimize the overall image discrepancies in all overlap regions while converting projective matrices into camera parameters such as focal length, aspect ratio, image center, 3D orientation, etc. The third step re-projects all images onto a panorama by a Laplacian-pyramid-based blending. The purpose of blending is to provide a smooth transition between images and eliminate small residues of misalignments resulting from parallax or imperfect pairwise registrations. The blending masks are generated automatically through the grassfire transform. At the end, we briefly explain the necessary human interface for initialization, feedback and manual options.
Identification and Characterization of Functional Human Monoclonal Antibodies to <i>Plasmodium vivax</i> Duffy-Binding Protein (2019)

<i>Plasmodium vivax</i> invasion of reticulocytes relies on distinct receptor-ligand interactions between the parasite and host erythrocytes. Engagement of the highly polymorphic domain II of the <i>P. vivax</i> Duffy-binding protein (DBPII) with the erythrocyte's Duffy Ag receptor for chemokines (DARC) is essential. Some <i>P. vivax</i>-exposed individuals acquired Abs to DBPII that block DBPII-DARC interaction and inhibit <i>P. vivax</i> reticulocyte invasion, and Ab levels correlate with protection against <i>P. vivax</i> malaria. To better understand the functional characteristics and fine specificity of protective human Abs to DBPII, we sorted single DBPII-specific IgG<sup>+</sup> memory B cells from three individuals with high blocking activity to DBPII. We identified 12 DBPII-specific human mAbs from distinct lineages that blocked DBPII-DARC binding. All mAbs were <i>P. vivax</i> strain transcending and targeted known binding motifs of DBPII with DARC. Eleven mAbs competed with each other for binding, indicating recognition of the same or overlapping epitopes. Naturally acquired blocking Abs to DBPII from individuals with high levels residing in different <i>P. vivax-</i>endemic areas worldwide competed with mAbs, suggesting broadly shared recognition sites. We also found that mAbs inhibited <i>P. vivax</i> entry into reticulocytes in vitro. These findings suggest that IgG<sup>+</sup> memory B cell activity in individuals with <i>P. vivax</i> strain-transcending Abs to DBPII display a limited clonal response with inhibitory blocking directed against a distinct region of the molecule.