gebhart/patrepeval huggingface dataset:
Designing Feature-Controlled Humanoid Antibody Discovery Libraries Using Generative Adversarial Networks (2020)

ABSTRACT We demonstrate the use of a Generative Adversarial Network (GAN), trained from a set of over 400,000 light and heavy chain human antibody sequences, to learn the rules of human antibody formation. The resulting model surpasses common in silico techniques by capturing residue diversity throughout the variable region, and is capable of generating extremely large, diverse libraries of novel antibodies that mimic somatically hypermutated human repertoire response. This method permits us to rationally design de novo humanoid antibody libraries with explicit control over various properties of our discovery library. Through transfer learning, we are able to bias the GAN to generate molecules with key properties of interest such as improved stability and developability, lower predicted MHC Class II binding, and specific complementarity-determining region (CDR) characteristics. These approaches also provide a mechanism to better study the complex relationships between antibody sequence and molecular behavior, both in vitro and in vivo . We validate our method by successfully expressing a proof-of-concept library of nearly 100,000 GAN-generated antibodies via phage display. We present the sequences and homology-model structures of example generated antibodies expressed in stable CHO pools and evaluated across multiple biophysical properties. The creation of discovery libraries using our in silico approach allows for the control of pharmaceutical properties such that these therapeutic antibodies can provide a more rapid and cost-effective response to biological threats.
Development of a Unipolar Converter for Variable Reluctance Motor Drives (1987)

A new converter concept for driving the switched reluctance motor has been developed. This converter has only one switching device per phase, uses a unipolar dc supply, returns all the trapped energy to the source, and does not require bifilar windings; it is called a C-dump converter because the trapped energy is dumped in a capacitor and then returned to the dc source. The topology for several different C-dump converters is presented. In addition, the design and experimental results for a C-dump converter using a chopper to recover the energy dumped on the capacitor are presented.
Miniature and Low-cost Wireless Sensor Platform for Environmental Monitoring (2007)

Abstract : A sensor platform with DO, pH, and turbidity sensors was developed. It was equipped with pH and oxygen sensitive fluorescent foils. The foils were attached outside of the waterproof case and read through optical window. They had also antibiofouling protection, which allowed them to operate for extended period of time. A microcontroller switched the channels and collected the reading of O2, pH, and turbidity every 15 minutes, than transmitted it through wires interface to a base station. The platform operates from 4 AA size alkaline batteries. The transmitter has a range of approximately 1 kilometer, depending on the terrain, with transmission rate of 10 kbps The sensor platform is miniature in size (3x3x3 sensing head, electronics and battery pack) and low-cost (~$450/unit).
Tunable self-injection locked green laser diode (2018)

We report, to the best of our knowledge, the first employment of a self-injection locking scheme for the demonstration of a tunable InGaN/GaN semiconductor laser diode. We have achieved a 7.11 nm (521.10-528.21 nm) tunability in a green color with different injection currents and temperatures. The system exhibited mode spectral linewidth as narrow as ∼69 pm and a side mode suppression ratio as high as ∼28 dB, with a maximum optical power of ∼16.7 mW. In the entire tuning window, extending beyond 520 nm, a spectral linewidth of ≤100 pm, high power, and stable performance were consistently achieved, making this, to the best of our knowledge, the first-of-its-kind compact tunable laser system attractive for spectroscopy, imaging, sensing systems, and visible light communication.
Gate-Level Simulation with GPU Computing (2011)

Functional verification of modern digital designs is a crucial, time-consuming task impacting not only the correctness of the final product, but also its time to market. At the heart of most of today’s verification efforts is logic simulation, used heavily to verify the functional correctness of a design for a broad range of abstraction levels. In mainstream industry verification methodologies, typical setups coordinate the validation effort of a complex digital system by distributing logic simulation tasks among vast server farms for months at a time. Yet, the performance of logic simulation is not sufficient to satisfy the demand, leading to incomplete validation processes, escaped functional bugs, and continuous pressure on the EDA industry to develop faster simulation solutions. In this work we propose GCS, a solution to boost the performance of logic simulation, gate-level simulation in particular, by more than a factor of 10 using recent hardware advances in Graphic Processing Unit (GPU) technology. Noting the vast available parallelism in the hardware of modern GPUs and the inherently parallel structures of gate-level netlists, we propose novel algorithms for the efficient mapping of complex designs to parallel hardware. Our novel simulation architecture maximizes the utilization of concurrent hardware resources while minimizing expensive communication overhead. The experimental results show that our GPU-based simulator is capable of handling the validation of industrial-size designs while delivering more than an order-of-magnitude performance improvements on average, over the fastest multithreaded simulators commercially available.
Topical Retinoic Acid (Tretinoin) for Melasma in Black Patients (1994)

This controlled study demonstrates that topical 0.1% tretinoin lightens melasma in black patients, with only mild side effects.
Obstructive Sleep Apnea Screening Using Spectral and Bispectral Features of Breathing Sounds in Wakefulness (2012)

The goal of this study was to investigate the potential of tracheal breathing sounds recorded during wakefulness for screening of obstructive sleep apnea (OSA) patients. Breathing sounds were recorded from 189 subjects during nose and mouth deep breathing in supine and sitting postures. Characteristic features, were extracted from the power spectrum density and bispectrum of the signal. The subjects were divided into three groups based on their apnea hypopnea index (AHI): non-OSA group (AHI 20; n=52). The data from 35 non-OSA and 35 OSA subjects were used to select the best subsets of the features. Classification was based on building a minimum-distance classifier for each feature and a majority vote approach to decide the class prediction. A leave-one-out scheme was used for evaluating the classification performance. For the nonOSA and OSA subjects in the testing dataset, the highest classification accuracy, specificity, and sensitivity were 78%, 77%, and 82%, respectively. The classification accuracy for the subjects in the middle group with a threshold of AHI=15 was 61%. In addition, an approach for classification based on six risk OSA factors, including age, gender, body mass index (BMI), neck circumference, Mallampati score, and smoking history, was investigated. For non-OSA and OSA groups, the accuracy, specificity, and sensitivity of this approach were 68%, 76%, and 35%, respectively. Parallel classification by both methods resulted in a highly sensitive (>90%) screening of OSA subjects at the cost of low specificity (~60%). The proposed wakefulness screening method can lead to significant improvement in efficient use of expensive resources such as overnight sleep laboratories.
Future prospects for adjunctive therapy (1990)

An increasingly large number of dietary components have been found to alter immune system function and, therefore, may be considered to have a pharmacologic effect (pharmacologic nutrition). Those dietary factors which have already been shown to influence outcome by producing a pharmacologic effect rather than correcting or preventing a simple deficiency include proteins (both type and amount), arginine, glutamine, omega-6 and omega-3 fatty acids, short-chain fatty acids, the metals iron and zinc, and the vitamins E, C, and A. Therapeutic outcome has already been influenced by dietary therapy (pharmacologic nutrition) in patients after burn injury or who have vascular diseases, and in experimental animals for the prevention of gut origin sepsis, the prevention and treatment of infection, prevention and development of secondary lesions in autoimmune diseases, augmentation of immunosuppression in transplantation, and in the treatment of cancer. Nutritional therapy using disease-specific formulations or supplements is an old idea now undergoing rapid evolution to increasing importance for successful therapeutic outcome.
A New View of Earthquake Ground Motion Data: The Hilbert Spectral Analysis (2000)

A brief description of the newly developed Empirical Mode Decomposition (ENID) and Hilbert Spectral Analysis (HSA) method will be given. The decomposition is adaptive and can be applied to both nonlinear and nonstationary data. Example of the method applied to a sample earthquake record will be given. The results indicate those low frequency components, totally missed by the Fourier analysis, are clearly identified by the new method. Comparisons with Wavelet and window Fourier analysis show the new method offers much better temporal and frequency resolutions.
Massive storage of wind power to reduce CO<inf>2</inf> emissions to produce wind-clean fuels (2010)

Wind power is being curtailed because large scale electrical energy storage systems are not available. However, a practical, large-scale, electro-thermal in situ energy storage system has been designed. Wind energy via the grid is transferred into unconventional oil deposits, such as the oil shale, tar sand or heavy oil deposits in the USA. This stored heat eventually converts the hydrocarbons into recoverable oil and gas products without generating CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> emissions or needing much water. The energy in these wind clean fuels greatly exceeds the applied electrical energy. These wind-clean fuels can be used to offset use of foreign oil or to regenerate electrical power into back into the grid. The grid is stabilized by electronically controlling the system load. It can be used for smart grid functions. Fuel production can be sustained for over 100 years by the massive oil shale and tar sand deposits in the USA.
The effect of a miR-96-5p inhibitor delivery to brain using microbubbles and ultrasound technology on neuroprotection and autophagy activation (2022)

Glutathione (GSH) is an important antioxidant that plays a critical role in neuroprotection. GSH depletion in neuron induces oxidative stress promoting neuronal damage, which is regarded as a hallmark of the early stage in some neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease. The neuronal GSH levels are mainly regulated by excitatory amino acid carrier 1 (EAAC1) and its inhibitory protein, glutamate transporter-associated protein 3-18 (GTRAP3-18). In this study, we found that GTRAP3-18 levels were increased by the up-regulation of the microRNA miR-96-5p, which has been reported to decrease EAAC1 levels in our previous study. We also discovered that neuro-oncological ventral antigen 1 (NOVA1) is an intermediate protein for GTRAP3-18 expression via miR-96-5p. Moreover, we show that the intra arterial administration of a miR-96-5p-inhibiting nucleic acid to living mice by a drug delivery system using microbubbles and ultrasound decreased the levels of GTRAP3-18 via NOVA1, while increased the levels of both EAAC1 and GSH in the mouse brain. Moreover, we found that the administration of a miR-96-5p inhibitor increased autophagy activation in the mouse hippocampus. These findings suggest that the delivery of a miR-96-5p inhibitor to the brain would efficiently increase the neuroprotective activity by increasing GSH levels via EAAC1, GTRAP3-18 and NOVA1.
On measuring the change in size of pulmonary nodules (2006)

The pulmonary nodule is the most common manifestation of lung cancer, the most deadly of all cancers. Most small pulmonary nodules are benign, however, and currently the growth rate of the nodule provides for one of the most accurate noninvasive methods of determining malignancy. In this paper, we present methods for measuring the change in nodule size from two computed tomography image scans recorded at different times; from this size change the growth rate may be established. The impact of partial voxels for small nodules is evaluated and isotropic resampling is shown to improve measurement accuracy. Methods for nodule location and sizing, pleural segmentation, adaptive thresholding, image registration, and knowledge-based shape matching are presented. The latter three techniques provide for a significant improvement in volume change measurement accuracy by considering both image scans simultaneously. Improvements in segmentation are evaluated by measuring volume changes in benign or slow growing nodules. In the analysis of 50 nodules, the variance in percent volume change was reduced from 11.54% to 9.35% (p = 0.03) through the use of registration, adaptive thresholding, and knowledge-based shape matching.
A Cryogenic Linear Paul Trap for Quantum Simulation (2015)

statistics. We present progress towards the construction of a cryogenic ion trap apparatus, designed to cryopump background gas within the 4K chamber. The resulting reduction in pressure will allow robust trapping of up to 100 ions in a single chain. Cooling is provided by a closed cycle cryostat with a gas mediated thermal linkage which mechanically decouples the ion trap from the vibrating cold head. A spherical octagon surrounding the ion trap allows optical access for global and individual addressing beams and high numerical aperture uorescence collection.
Highly integrated CO<sub>2</sub>capture and conversion: direct synthesis of cyclic carbonates from industrial flue gas (2016)

The ability of early transition metal halides to capture and convert CO<sub>2</sub>from diluted gas flows has been exploited in the cycloaddition of CO<sub>2</sub>to epoxides using industrial flue gas as an impure source of CO<sub>2</sub>.
Microfluidic point-of-care blood panel based on a novel technique: Reversible electroosmotic flow (2015)

A wide range of diseases and conditions are monitored or diagnosed from blood plasma, but the ability to analyze a whole blood sample with the requirements for a point-of-care device, such as robustness, user-friendliness, and simple handling, remains unmet. Microfluidics technology offers the possibility not only to work fresh thumb-pricked whole blood but also to maximize the amount of the obtained plasma from the initial sample and therefore the possibility to implement multiple tests in a single cartridge. The microfluidic design presented in this paper is a combination of cross-flow filtration with a reversible electroosmotic flow that prevents clogging at the filter entrance and maximizes the amount of separated plasma. The main advantage of this design is its efficiency, since from a small amount of sample (a single droplet [Formula: see text]10 μl) almost 10% of this (approx 1 μl) is extracted and collected with high purity (more than 99%) in a reasonable time (5-8 min). To validate the quality and quantity of the separated plasma and to show its potential as a clinical tool, the microfluidic chip has been combined with lateral flow immunochromatography technology to perform a qualitative detection of the thyroid-stimulating hormone and a blood panel for measuring cardiac Troponin and Creatine Kinase MB. The results from the microfluidic system are comparable to previous commercial lateral flow assays that required more sample for implementing fewer tests.
Cloning and Evaluation of the Role of Rat GALR‐2, a Novel Subtype of Galanin Receptor, in the Control of Pain Perception (1998)

We have identified a novel subtype of galanin receptor (GALR-2) in rat dorsal root ganglia and spinal cord. The open reading frame of GALR-2 is 1116 nucleotides long, encoding a protein of 372 amino acids with a theoretical molecular mass of 40.7 kD. Membranes prepared from stable pools of 293 cells expressing GALR-2, but not wild-type 293 cells, demonstrated high affinity galanin binding sites. Rat galanin and galanin-related peptides M40, C7, M15, and galanin effectively competed for binding; peptide C7 demonstrated a lower affinity for rGALR-2, and all these peptides were agonists at rGALR-2 when assessed on a microphysiometer. Studies on the expression of GALR-2 in various tissues by Northern and in situ hybridization analyses suggest a low abundance but wide distribution of GALR-2 mRNA, including several discrete areas in brain and spinal cord and a high abundance in the dorsal root ganglia.
Prevalence of Antibodies to the Core Protein P17, <i>a</i> Serological Marker During HIV-1 Infection (1990)

Studies on monitoring the immune response to viral structural proteins during human immunodeficiency virus (HIV-1) infection have established the significance of antibodies to the core protein p24 during the progression of the disease. We have studied the prevalence of antibodies to the core protein p17 in order to study their diagnostic and prognostic significance in the pathogenesis of HIV-1. Full-length HIV-1 p17, molecularly cloned and expressed in Escherichia coli was purified by immunoaffinity chromatography using an HIV-1 p17-specific monoclonal antibody. A highly sensitive enzyme-linked immunoassay was developed using the purified recombinant p17 as the serological target to detect antibodies to p17. The results indicated that antibodies to p17 decline during progression of disease, with the decline being more dramatic as patients moved from asymptomatic to AIDS-related complex (ARC). Patient specimens deficient in p24 antibody, but having detectable levels of antibody to p17 were almost always positive for p24 antigen. Under these conditions, p17 antibody is an important serological marker because it provides a more consistent marker for core antigens during HIV-1 infection.
Total Syntheses and Initial Evaluation of [Ψ[C(═S)NH]Tpg<sup>4</sup>]vancomycin, [Ψ[C(═NH)NH]Tpg<sup>4</sup>]vancomycin, [Ψ[CH<sub>2</sub>NH]Tpg<sup>4</sup>]vancomycin, and Their (4-Chlorobiphenyl)methyl Derivatives: Synergistic Binding Pocket and Peripheral Modifications for the Glycopeptide Antibiotics (2015)

Full details of studies are disclosed on the total syntheses of binding pocket analogues of vancomycin bearing the peripheral L-vancosaminyl-1,2-D-glucosyl disaccharide that contain changes to a key single atom in the residue-4 amide (residue-4 carbonyl O → S, NH, H2) designed to directly address the underlying molecular basis of resistance to vancomycin. Also disclosed are studies piloting the late-stage transformations conducted on the synthetically more accessible C-terminus hydroxymethyl aglycon derivatives and full details of the peripheral chlorobiphenyl functionalization of all of the binding-pocket-modified vancomycin analogues designed for dual D-Ala-D-Ala/D-Ala-D-Lac binding. Their collective assessment indicates that combined binding pocket and chlorobiphenyl peripherally modified analogues exhibit a remarkable spectrum of antimicrobial activity (VSSA, MRSA, and VanA and VanB VRE) and impressive potencies against both vancomycin-sensitive and vancomycin-resistant bacteria (MICs = 0.06-0.005 and 0.5-0.06 μg/mL for the amidine and methylene analogues, respectively) and likely benefit from two independent and synergistic mechanisms of action, only one of which is dependent on D-Ala-D-Ala/D-Ala-D-Lac binding. Such analogues are likely to display especially durable antibiotic activity that is not prone to rapidly acquired clinical resistance.
Synthesis of a Transition State Analogue Inhibitor of Purine Nucleoside Phosphorylase via the Mannich Reaction (2003)

[reaction: see text] The expeditious convergent synthesis of the potent human purine nucleoside phosphorylase inhibitor DADMe-Immucillin-G (3) was achieved via the Mannich reaction. The Mannich chemistry of a series of deazapurines and amine hydrochlorides was also investigated.
pneuRIPTM: A Novel Respiratory Inductance Plethysmography Monitor (2016)

Objective pulmonary function (PF) evaluation is essential for the diagnosis, monitoring, and management of many pediatric respiratory diseases as seen in the emergency room, intensive care, and outpatient settings. In this paper, the development and testing of a new noninvasive PF instrument, pneuRIP<sup>TM</sup>, which utilizes respiratory inductance plethysmography (RIP) are discussed. The pneuRIP<sup>TM</sup> hardware includes a small circuit board that connects to the RIP bands and measures and wirelessly transmits the band inductance data to any designated wirelessly connected tablet. The software provides indices of respiratory work presented instantaneously in a user-friendly graphical user interface on the tablet. The system was tested with ten normal children and compared with an existing system, Respitrace (Sensormedics, Yorba Linda, CA), under normal and loaded breathing conditions. Under normal breathing, the percentage differences between the two systems were 2.9% for labored breathing index (LBI), 31.8% for phase angle (Φ), 4.8% for percentage rib cage (RC%), and 26.7% for respiratory rate (BPM). Under loaded breathing, the percentage differences between the two systems were 1.6% for LBI, 4.1% for Φ, 8.5% for RC%, and 52.7% for BPM. For LBI, Φ, and RC%, the two systems were in general agreement. For BPM the pneuRIP<sup>TM</sup> is shown to be more accurate than the respitrace when compared to manually counting the breaths: 13.2% versus 36.4% accuracy for normal breathing and 16.9% versus 60.7% accuracy for breathing under load, respectively.
Structure–Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease (2018)

Metalloenzymes represent an important target space for drug discovery. A limitation to the early development of metalloenzyme inhibitors has been the lack of established structure-activity relationships (SARs) for molecules that bind the metal ion cofactor(s) of a metalloenzyme. Herein, we employed a bioinorganic perspective to develop an SAR for inhibition of the metalloenzyme influenza RNA polymerase PA<sub>N</sub> endonuclease. The identified trends highlight the importance of the electronics of the metal-binding pharmacophore (MBP), in addition to MBP sterics, for achieving improved inhibition and selectivity. By optimization of the MBPs for PA<sub>N</sub> endonuclease, a class of highly active and selective fragments was developed that displays IC<sub>50</sub> values <50 nM. This SAR led to structurally distinct molecules that also displayed IC<sub>50</sub> values of ∼10 nM, illustrating the utility of a metal-centric development campaign in generating highly active and selective metalloenzyme inhibitors.
Serum Pro Prostate Specific Antigen Improves Cancer Detection Compared to Free and Complexed Prostate Specific Antigen in Men With Prostate Specific Antigen 2 to 4 Ng/Ml (2003)

The %pPSA significantly improved specificity for cancer detection and decreased the number of unnecessary biopsies in the PSA 2 to 4 ng/ml range. This relative improvement of %pPSA compared to % free PSA and complexed PSA was maintained throughout the PSA range of 2 to 10 ng/ml.
Multiple‐Interaction Ligands Inspired by Mussel Adhesive Protein: Synthesis of Highly Stable and Biocompatible Nanoparticles (2011)

Fest verklebt: Ein auf Poly(L-3,4-dihydroxyphenylalanin) basierender Ligand verwandelt hydrophobe Nanopartikel in hydrophile und biokompatible Spezies. Nanopartikel, die mit diesem Liganden funktionalisiert wurden (siehe Bild), sind hoch stabil in wässrigen Lösungen. Eine erfolgreiche Anwendung funktionalisierter Fe3O4-Nanopartikel in der In-vivo-Tomographie bestätigt die Eignung für biomedizinische Anwendungen.