gebhart/patrepeval huggingface dataset:
Multitask Bioactivity Predictions Using Structural Chemical and Cell Morphology Information (2020)

The understanding of the Mechanism-of-Action (MoA) of compounds and the prediction of potential drug targets has an important role in small-molecule drug discovery. The aim of this work was to compare chemical and cell morphology information for bioactivity prediction. The comparison was performed by using bioactivity data from the ExCAPE database, image data from the Cell Painting data set (the largest publicly available data set of cell images with approximately ~30,000 compound perturbations) and Extended Connectivity Fingerprints (ECFPs) using the multitask Bayesian Matrix Factorisation (BMF) approach Macau. We found that the BMF Macau and Random Forest (RF) performance was overall similar when ECFP fingerprints were used as compounds descriptors. However, BMF Macau outperformed RF in 155 out of 224 target classes (69.20%) when image data was used as compounds information. By using BMF Macau 100 (corresponding to about 45%) and 90 ( about 40%) of the 224 targets were predicted with high predictive performance (AUC > 0.8) with ECFP data and image data as side information, respectively. There were targets better predicted by image data as side information, such as b-catenin, and others better predicted by fingerprint-based side information, like proteins belonging to the G-Protein Coupled Receptor 1 family, which could be rationalized from the underlying data distributions in each descriptor domain. In conclusion, both cell morphology changes and structural chemical information contain information about compound bioactivity, which is also partially complementary, and can hence contribute to in silico mechanism of action analysis.
Influence of current waveshape on motoring performance of the slotless permanent-magnet machine Torus (1993)

The Torus machine is a double-sided, axial-flux, disc-type, permanent-magnet, brushless machine which may be operated as either a generator or a motor. Its particularly short axial length and good power-to-weight ratio is being exploited in a number of generator applications and there is now fairly widespread activity in the study of this machine topology both as generator and as a motor. As the Torus machine is equipped with single or double layer, full pitch uniformly distributed windings its open circuit EMFs are far from sinusoidal. During these studies it was recognised that torque per ampere could be increased by matching the current waveshape to that of the trapezoidal EMF, adopting the principle of instantaneous current regulation which has been successfully exploited in field-oriented control of induction machines. An investigation of improved methods of current regulation is reported based upon a 2.5 kW, 24 V, 9-phase machine previously developed as a generator. >
Lab-on-a-chip: Continuous glucose monitoring antenna sensors (2014)

The development of a reliable continuous glucose monitoring technology, which would lessen the complications associated with diabetes through optimal glycemic control, is a key to improving the quality of lives of patients living with the disease. In recent years, considerable progress has been made in developing implantable biosensors that can continually monitor glucose levels. These biosensors rely on the interstitial fluid within the dermis to measure the interstitial glucose (IG) levels. However, to be truly beneficial, the implanted sensor must be able to function properly for an extended period of time. The biosensors developed thus far can only remain functional up several weeks after their implantation in the body. Contributing factors for this loss of functionality include the degradation and fouling of the sensor, and the changes in the tissue surrounding the sensor such as fibrosis and inflammation. While researchers explore potential solutions to improve the current implantable biosensors, there is an urgent need to investigate alternative technologies. Unless a reliable technology for long-term glucose monitoring is developed, continuous glucose monitoring is expected to remain problematic, and patients will continue to face the life-threatening complications associated with poor glycemic control. In order to provide a potential solution to this problem, in this study, we propose a lab-on-chip antenna sensor for continuous monitoring of the glucose concentration in the interstitial fluid. Unlike biosensors that require direct contact with the interstitial fluid in order to trigger necessary chemical reactions to operate, the new sensor works on an electromagnetic energy propagation principle. Thus, it does not need direct interface with the interstitial fluid and can be fabricated using biocompatible materials allowing it to remain functional in the body for years.
ME-GAN: Learning Panoptic Electrocardio Representations for Multi-view ECG Synthesis Conditioned on Heart Diseases (2022)

Electrocardiogram (ECG) is a widely used non-invasive diagnostic tool for heart diseases. Many studies have devised ECG analysis models (e.g., classifiers) to assist diagnosis. As an upstream task, researches have built generative models to synthesize ECG data, which are beneficial to providing training samples, privacy protection, and annotation reduction. However, previous generative methods for ECG often neither synthesized multi-view data, nor dealt with heart disease conditions. In this paper, we propose a novel disease-aware generative adversarial network for multi-view ECG synthesis called ME-GAN, which attains panoptic electrocardio representations conditioned on heart diseases and projects the representations onto multiple standard views to yield ECG signals. Since ECG manifestations of heart diseases are often localized in specific waveforms, we propose a new "mixup normalization" to inject disease information precisely into suitable locations. In addition, we propose a view discriminator to revert disordered ECG views into a pre-determined order, supervising the generator to obtain ECG representing correct view characteristics. Besides, a new metric, rFID, is presented to assess the quality of the synthesized ECG signals. Comprehensive experiments verify that our ME-GAN performs well on multi-view ECG signal synthesis with trusty morbid manifestations.
Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads (2019)

The sequence and assembly of human genomes using long-read sequencing technologies has revolutionized our understanding of structural variation and genome organization. We compared the accuracy, continuity, and gene annotation of genome assemblies generated from either high-fidelity (HiFi) or continuous long-read (CLR) datasets from the same complete hydatidiform mole human genome. We find that the HiFi sequence data assemble an additional 10% of duplicated regions and more accurately represent the structure of tandem repeats, as validated with orthogonal analyses. As a result, an additional 5 Mbp of pericentromeric sequences are recovered in the HiFi assembly, resulting in a 2.5-fold increase in the NG50 within 1 Mbp of the centromere (HiFi 480.6 kbp, CLR 191.5 kbp). Additionally, the HiFi genome assembly was generated in significantly less time with fewer computational resources than the CLR assembly. Although the HiFi assembly has significantly improved continuity and accuracy in many complex regions of the genome, it still falls short of the assembly of centromeric DNA and the largest regions of segmental duplication using existing assemblers. Despite these shortcomings, our results suggest that HiFi may be the most effective standalone technology for de novo assembly of human genomes.
Metabolomics Profiles of Smokers from Two Ethnic Groups with Differing Lung Cancer Risk (2020)

African American (AA) smokers are at a higher risk of developing lung cancer compared to whites. The variations in the metabolism of nicotine and tobacco-derived carcinogens in these groups were reported previously with the levels of nicotine metabolites and carcinogen-derived metabolites measured using targeted approaches. While useful, these targeted strategies are not able to detect global metabolic changes for use in predicting the detrimental effects of tobacco use and ultimately lung cancer susceptibility among smokers. To address this limitation, we have performed global untargeted metabolomics profiling in urine of AA and white smokers to characterize the pattern of metabolites, identify differentially regulated pathways, and correlate these profiles with the observed variations in lung cancer risk between these two populations. Urine samples from AA (<i>n</i> = 30) and white (<i>n</i> = 30) smokers were used for metabolomics analysis acquired in both positive and negative electrospray ionization modes. LC-MS data were uploaded onto the cloud-based XCMS online (http://xcmsonline.scripps.edu) platform for retention time correction, alignment, feature detection, annotation, statistical analysis, data visualization, and automated systems biology pathway analysis. The latter identified global differences in the metabolic pathways in the two groups including the metabolism of carbohydrates, amino acids, nucleotides, fatty acids, and nicotine. Significant differences in the nicotine degradation pathway (cotinine glucuronidation) in the two groups were observed and confirmed using a targeted LC-MS/MS approach. These results are consistent with previous studies demonstrating AA smokers with lower glucuronidation capacity compared to whites. Furthermore, the d-glucuronate degradation pathway was found to be significantly different between the two populations, with lower amounts of the putative metabolites detected in AA compared to whites. We hypothesize that the differential regulation of the d-glucuronate degradation pathway is a consequence of the variations in the glucuronidation capacity observed in the two groups. Other pathways including the metabolism of amino acids, nucleic acids, and fatty acids were also identified, however, the biological relevance and implications of these differences across ethnic groups need further investigation. Overall, the applied metabolomics approach revealed global differences in the metabolic networks and endogenous metabolites in AA and whites, which could be used and validated as a new potential panel of biomarkers that could be used to predict lung cancer susceptibility among smokers in population-based studies.
Absence of a single repeat from the coding region of the human involucrin gene leading to RFLP. (1989)

The human involucrin gene has been mapped to the region q21-q22 of chromosome 1. Three of six Utah families examined were polymorphic for a PstI fragment of the involucrin gene. In one individual, the variant PstI fragment was found by DNA sequencing to be missing one of the 39 repeats that make up two-thirds of the coding region.
No Shock That Biphasics Are Better for Cardioversion of AF (2000)

External defibrillators, which deliver up to 360 joules of energy using a monophasic waveform, are in widespread use for the cardioversion of atrial
Are ulcers a marker for invasive carcinoma in barrett's esophagus? data from a diagnostic variability study with clinical follow-up (2002)

OBJECTIVE: We correlated follow-up information from 138 patients with Barrett's esophagus and varying degrees of dysplasia with the presence of ulcers. METHODS: A group of pathologist participants were asked to contribute patients' initial biopsy slides showing Barrett's esophagus (BE) without dysplasia and with epithelial changes indefinite for dysplasia, low grade dysplasia (LGD), high grade dysplasia (HGD), and adenocarcinoma. From the initial 250 cases used for a diagnostic reproducibility study, follow-up information was available for 138 patients. RESULTS: There were 44 cases submitted as BE, 22 as BE with epithelial changes indefinite for dysplasia, 26 as BE with LGD, 33 as BE with HGD, and 13 as BE with adenocarcinoma. Ulcers were present in 35/138 cases (25%), including 3/44 cases of BE without dysplasia (7%), 2/22 cases of BE with epithelial changes indefinite for dysplasia (9%), 0/26 cases of BE with LGD (0%), 10/33 cases of BE with HGD (30%), and 7/13 cases of BE with adenocarcinoma (54%). On follow-up, there were no invasive carcinomas detected among the BE without dysplasia group (median follow-up = 38.5 months). Adenocarcinomas were detected in 4/22 cases (18%) submitted as BE with epithelial changes indefinite for dysplasia at 19, 55, 60, and 62 months and in 4/26 cases (15%) of BE with LGD at 9, 9, 11, and 60 months. None of these carcinomas occurred in cases in which an ulcer was present in the initial biopsy specimen. Among the 33 HGD cases, 20 (60%) were found to have adenocarcinoma on subsequent resection specimens. The presence of an ulcer with HGD increased the likelihood of finding carcinoma in the resection specimen, as 8/10 biopsies (80%) of HGD patients with ulcers had carcinoma, compared to 12/23 biopsies (52%) of HGD patients without ulcers. All of the cases interpreted as adenocarcinomas on biopsy were found either to have invasive carcinoma on esophageal resection or to have metastases that were demonstrated in unresectable patients. CONCLUSION: If an ulcer accompanies HGD in a biopsy specimen from a patient with BE, it is likely that invasive carcinoma is also present at that time.
Organocatalytic Asymmetric Synthesis of 1,2-Dihydronaphthalenes (2015)

Key words isobenzopyrylium - dihydronaphthalenes - boronic acids - oxocarbenium
Abstract 13446: Use of Sodium-Glucose Cotransporter 2 Inhibitors for Diuretic Resistance in Acute Decompensated Heart Failure Are Associated With Improved Diuretic Response (2019)

Introduction: Sodium glucose cotransporter 2 inhibitors (SGLT-2is), originally developed as antihyperglycemics, have shown promising signals for decreasing heart failure hospitalization. This effec...
Relay-aided interference alignment for the quasi-static X channel (2009)

In this paper, we first introduce a simple procedure for aligning interference directions in an M×N user MIMO X channel. The scheme is then modified for an M×2 user X channel in which each user is equipped with M + 1 antennas. Next we investigate the degrees of freedom (DOF) for a single antenna X channel in slow fading environments with the help of a simple relay. The relay stores all the received signals and sends their linear combination in subsequent transmissions. Using this scheme, it is shown that adding a relay can help the system to achieve all the available DOF. It is also proved that if the relay's output power scales with P/(log P) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sup> , there is no loss in the achieved DOF as long as s > 0. In other words, in a network with quasi-static channels, it is possible to achieve a higher DOF through the use of randomizing relays whose powers grow at a much slower rate than the main transmitters. Similarly, when there are stricter constraints on the output power scaling of the transmitters, all the DOF can still be utilized, if the relay power can grow with P/(log P) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sup> for any t > 0. These results suggest that adding relays to a network can be beneficial in terms of simultaneously acquiring higher DOF.
Validation of a Fully Anechoic Chamber (2016)

This paper describes a technique to characterize the performance of a Fully Anechoic Chamber (FAC) from 500 MHz to 3 GHz based on S-Parameter analysis with antennas and a Vector Network Analyzer (VNA. The measurements have been performed by placing one antenna inside the chamber and performing S11 reflection analyses in the frequency domain. Via Inverse Fast Fourier Transformation (IFFT) the reflections in the time domain have been analyzed. Also, experiments where S21 transmission loss is measured by putting 2 antennas at different locations have been performed. One antenna is omnidirectional while the other is directional and measurements have been performed in the frequency domain using the VNA. The results are transformed to time domain using the IFFT and time gating is applied to identify the direct and reflected signals, resulting in the so-called site-Voltage Standing Wave Ratio (sVSWR). This sVSWR method enables the analysis of the reflected wave, or imperfection of the chamber. The measurement results show that the chamber has good performance.
DEPRESSIVE SYMPTOMS AFTER ACUTE MYOCARDIAL INFARCTION (2006)

PULMONARY REHABILITATION: Literature Update: Selected Abstracts From Recent Publications in Exercise Physiology, Cardiopulmonary Prevention, and Rehabilitation
ThUnderVolt: Enabling Aggressive Voltage Underscaling and Timing Error Resilience for Energy Efficient Deep Learning Accelerators (2018)

Hardware accelerators are being increasingly deployed to boost the performance and energy efficiency of deep neural network (DNN) inference. In this paper we propose Thundervolt, a new framework that enables aggressive voltage underscaling of high-performance DNN accelerators without compromising classification accuracy even in the presence of high timing error rates. Using post-synthesis timing simulations of a DNN accelerator modeled on the Google TPU, we show that Thundervolt enables between 34%-57% energy savings on state-of-the-art speech and image recognition benchmarks with less than 1% loss in classification accuracy and no performance loss. Further, we show that Thundervolt is synergistic with and can further increase the energy efficiency of commonly used run-time DNN pruning techniques like Zero-Skip.
Assessing the Instantaneous Risk of Direct Laser Impingement (2003)

Covers advancements in spacecraft and tactical and strategic missile systems, including subsystem design and application, mission design and analysis, materials and structures, developments in space sciences, space processing and manufacturing, space operations, and applications of space technologies to other fields.
A label-free approach to detect ligand binding to cell surface proteins in real time (2018)

Electrophysiological recordings allow for monitoring the operation of proteins with high temporal resolution down to the single molecule level. This technique has been exploited to track either ion flow arising from channel opening or the synchronized movement of charged residues and/or ions within the membrane electric field. Here, we describe a novel type of current by using the serotonin transporter (SERT) as a model. We examined transient currents elicited on rapid application of specific SERT inhibitors. Our analysis shows that these currents originate from ligand binding and not from a long-range conformational change. The Gouy-Chapman model predicts that adsorption of charged ligands to surface proteins must produce displacement currents and related apparent changes in membrane capacitance. Here we verified these predictions with SERT. Our observations demonstrate that ligand binding to a protein can be monitored in real time and in a label-free manner by recording the membrane capacitance.
Reversible Transformations of Gold Nanoparticle Morphology (2005)

Herein is reported a metamorphosis taking place in a gold nanosized system. The observed phenomenon of shape and size transformations was found to be completely reversible. Unlike most procedures in the literature where shape and size control occur in the synthetic step by adding growth- and shape-controlling agents such as surfactants or polymers, in this system postsynthetic changes in shape and size can be carried out simply by changing the ratio of reactive, competing reagents, more specifically, alkylthiols versus tetralkylammonium salts. Interestingly, the transfer of gold metal occurs (large prismatic particles to small particles and vice versa) under the influence of reagents that do not cause such interactions with bulk gold. All intermediate steps of the morphology change were observed using HRTEM and electron diffraction. The processes of breaking down and "welding back" solid metal nanoparticles occur under mild conditions and are remarkable examples of the unique chemical properties of nanomaterials. The described process is expected to be relevant to other nanoscale systems where similar structural circumstances could occur.
Human activity detection by combining motion descriptors with boosting (2007)

A new, combined human activity detection method is proposed. Our method is based on Efros et al.’s motion descriptors and Ke et al.’s event detectors. Since both methods use optical flow, it is easy to combine them. However, the computational cost of the training increases considerably because of the increased number of weak classifiers. We reduce this computational cost by extending Ke et al.’s weak classifiers to incorporate multi-dimensional features. We also introduce a Look Up Table for further high-speed computation. The proposed method is applied to off-air tennis video data, and its performance is evaluated by comparison with the original two methods. Experimental results show that the performance of the proposed method is a good compromise in terms of detection rate and computation time of testing and training.
An expert system for the design of input shapers (2003)

Input shaping is a command generation technique that reduces vibration by convolving a sequence of impulses, known as the input shaper, with any desired system command. The success of the approach depends on the characteristics of the input shaper. Numerous shapers have been proposed, each with unique properties. The selection of an input shaper for any given system has generally relied to some degree on the knowledge of an expert. An expert system has been developed in an attempt to capture the expertise involved in input shaper design. Furthermore, the design of the input shaper can be refined if the system response is fed back into the expert system.
Layer-by-Layer Deposition with Polymers Containing Nitrilotriacetate, A Convenient Route to Fabricate Metal- and Protein-Binding Films (2016)

This paper describes a convenient synthesis of nitrilotriacetate (NTA)-containing polymers and subsequent layer-by-layer adsorption of these polymers on flat surfaces and in membrane pores. The resulting films form NTA-metal-ion complexes and capture 2-3 mmol of metal ions per mL of film. Moreover, these coatings bind multilayers of polyhistidine-tagged proteins through association with NTA-metal-ion complexes. Inclusion of acrylic acid repeat units in NTA-containing copolymers promotes swelling to increase protein binding in films on Au-coated wafers. Adsorption of NTA-containing films in porous nylon membranes gives materials that capture ∼46 mg of His-tagged ubiquitin per mL. However, the binding capacity decreases with the protein molecular weight. Due to the high affinity of NTA for metal ions, the modified membranes show modest leaching of Ni(2+) in binding and rinsing buffers. Adsorption of NTA-containing polymers is a simple method to create metal- and protein-binding films and may, with future enhancement of stability, facilitate development of disposable membranes that rapidly purify tagged proteins.