gebhart/patrepeval huggingface dataset:
Design of Novel Amphipathic α-Helical Antimicrobial Peptides with No Toxicity as Therapeutics against the Antibiotic-Resistant Gram-Negative Bacterial Pathogen, Acinetobacter Baumannii (2021)

We designed <i>de novo</i> and synthesized two series of five 26-residue amphipathic α-helical cationic antimicrobial peptides (AMPs) with five or six positively charged residues (D-Lys, L-Dab (2,4-diaminobutyric acid) or L-Dap (2,3-diaminopropionic acid)) on the polar face where all other residues are in the D-conformation. Hemolytic activity against human red blood cells was determined using the most stringent conditions for the hemolysis assay, 18h at 37°C, 1% human erythrocytes and peptide concentrations up to 1000 μg/mL (~380 μM). Antimicrobial activity was determined against 7 <i>Acinetobacter baumannii</i> strains, resistant to polymyxin B and colistin (antibiotics of last resort) to show the effect of positively charged residues in two different locations on the polar face (positions 3, 7, 11, 18, 22 and 26 <i>versus</i> positions 3, 7, 14, 15, 22 and 26). All 10 peptides had two D-Lys residues in the center of the non-polar face as "specificity determinants" at positions 13 and 16 which provide specificity for prokaryotic cells over eukaryotic cells. Specificity determinants also maintain excellent antimicrobial activity in the presence of human sera. This study shows that the location and type of positively charged residue (Dab and Dap) on the polar face are critical to obtain the best therapeutic indices.
ChemInform Abstract: 6‐HYDROXYCHROMAN‐2‐CARBOXYLIC ACIDS, NOVEL ANTIOXIDANTS (1974)

Abstract Durch Umsetzung von Trimethylhydrochinon (I) mit Orthoameisensäuretrimethylester und anschließend mit Methylvinylketon entsteht 2‐Methoxy‐ ‐hydroxy‐2,5 ,7,8‐ tetramethylchroman (II), aus dem durch Erhitzen in wäßrigem Aceton in Gegenwart von etwas Salzsäure das 2,6‐Dihydroxychroman (III) erhalten wird.
Preparation of a drug-eluting stent using a TiO2 film deposited by plasma enhanced chemical vapour deposition as a drug-combining matrix (2010)

A TiO2 thin film was deposited onto a bare metal stent by the plasma enhanced chemical vapour deposition (PECVD) process and its potential as a drug-combining matrix was investigated. When deposited at a discharge power of 5 W, the film showed a highly smooth surface with a surface roughness of 9.4 nm, mechanical stability with good adhesion, and good blood compatibility. The film was surface-modified with water plasma to introduce hydroxyl groups on the TiO2 surface. Then, drugs could be chemically grafted to the modified surface through the formation of ester bonds between hydroxyl groups on the modified TiO2 film and carboxyl groups in the drugs. When heparin, α-lipoic acid, and abciximab were grafted onto the TiO2-deposited and surface-modified stents, the grafted amount was measured to be 106.1 μg for α-lipoic acid, 32.5 μg for abciximab, and 53.9 μg for heparin on average. In the in vitro drug-release test, heparin and abciximab were released continuously for 4 weeks but ALA showed a burst release within 6 days.
Plasmon-Enhanced below Bandgap Photoconductive Terahertz Generation and Detection (2015)

We use plasmon enhancement to achieve terahertz (THz) photoconductive switches that combine the benefits of low-temperature grown GaAs with mature 1.5 μm femtosecond lasers operating below the bandgap. These below bandgap plasmon-enhanced photoconductive receivers and sources significantly outperform commercial devices based on InGaAs, both in terms of bandwidth and power, even though they operate well below saturation. This paves the way for high-performance low-cost portable systems to enable emerging THz applications in spectroscopy, security, medical imaging, and communication.
Dual Grid Method for Aquifer Acceleration in Parallel Implicit Field-Scale Reservoir Simulation (2017)

Abstract For many field-scale reservoir simulation models, aquifer regions (both peripheral and bottom) can represent a large percentage of total active grid blocks. The objective of this work is to build an accurate method respecting the fine-scale heterogeneities, but significantly reduce the computational cost of keeping the aquifer grids in the model, where they are deemed necessary to better describe the variable strength of water influx. The present method can be considered a specialized two-level grid coarsening or upscaling method. Within the aquifer regions, each column of fine cells are coarsened vertically based on fine-scale z-transmissibility. A coarsened column may consist of a single amalgamated aquifer cell or multiple vertically disconnected aquifer cells separated by flow barriers. The pore volume (PV), compressibility, and lateral flow terms of the coarse cell are restricted from the fine-grid cell. The lateral connectivities within the aquifer regions and between the aquifer and the reservoir are honored, inclusive of the fine-scale description of faults, pinchouts, and null cells. Reservoir regions are not coarsened. Two alternatives exist for the fine-scale pressure reconstruction from the coarse-grid solution. The first method uses the vertical equilibrium concept. The second method performs a 1D solution for the fine-scale pressure. A spatially variable multi-porosity permeability model can also be accommodated. In parallel implementation, besides the load balancing method, the memory balancing method is also necessary. All these aspects will be explained in the paper. The method has been applied successfully to several complex full-field simulation models where the transient aquifer water influx has been identified as a key factor. These models include dual porosity, dual permeability models with a complex geologic description. We compare simulation results using the accelerated aquifer calculation method against the original fine-grid simulation model without acceleration and demonstrate the efficacy of the new method. For the models tested, the actual speedup factors achieved are also compared against the theoretically computed improvement factors. The dual grid method strives to significantly reduce computational cost but retain the fine-scale heterogeneity data to accurately represent the water movement within the water zones of the simulation model. The method differs from the standard upscaling and grid coarsening method where the coarse-grid properties are computed a priori. Instead, the fine-scale information is restricted to the coarse grid during Newton's iteration to represent the fine-scale flow behavior. This is analogous to the multiscale method, but we apply this only vertically within the aquifer regions.
Detecting and Tracking the Rise of DGA-Based Malware. (2012)

When bots go in search of their command and control (C&C) servers, they often
use algorithmically generated domain names (DGAs). We have created a system
(Pleiades) that watches unsuccessful DNS resolution requests (NXDomain) from
recursive DNS servers in large networks. Pleiades can reliably identify new clusters
of NXDomains generated by DGAs, the newly infected hosts, and often, the
actual C&C servers the DGA malware employs. In this article, we explain how our
system works, as well as the most interesting information about current bot infections
and C&C structures
<title>Estimation of accuracy in localizing externally attached markers in multimodal volume head images</title> (1993)

We recently examined the registration of multimodal volume head images using extrinsic markers. We analyzed the problem into the three separate problems of finding the positions of at least three non-collinear markers in the two images, matching corresponding markers in the two image spaces, and estimating the translation and rotation parameters of the rigid body transformation that maps one space into the other. We call the calculation of the geometric centers fiducial localization. Knowing the fiducial localization error is important since it is an important determinant of target registration error, and because it provides a useful way to compare localization algorithms. In the present work we present a technique for experimentally estimating the error associated with localizing a fiducial in a tomographic image. Our method involves acquiring a volume image of a large number of markers with precisely known positions in the physical space of a phantom containing the markers, localizing the fiducials in the image, and registering the localized fiducial positions in image space to the precisely known positions in physical space. Fiducial localization error is estimated from the fiducial registration error, i.e. the distance between corresponding fiducial positions after registration.
<title>Image retrieval in the industrial environment</title> (1999)

The ability to manage large image databases has been a topic of growing research over the past several years. Imagery is being generated and maintained for a large variety of applications including remote sensing, art galleries, architectural and engineering design, geographic information systems, weather forecasting, medical diagnostics, and law enforcement. Content-based image retrieval (CBIR) represents a promising and cutting-edge technology that is being developed to address these needs. To date, little work has been accomplished to apply these technologies to the manufacturing environment. Imagery collected from manufacturing processes have unique characteristics that can be used in developing a manufacturing-specific CBIR approach. For example, a product image typically has an expected structure that can be characterized in terms of its redundancy, texture, geometry, or a mixture of these. Defect objects in product imagery share a number of common traits across product types and imaging modalities as well. For example, defects tend to be contiguous, randomly textured, irregularly shaped, and they disrupt the background and the expected pattern. We will present the initial results of the development of a new capability for manufacturing-specific CBIR that addresses defect analysis, product quality control, and process understanding in the manufacturing environment. Image data from the semiconductor-manufacturing environment will be presented.
Abstract 3259: Giant obscurins: Novel tumor and metastasis suppressors in breast cancer (2015)

Abstract Obscurins, encoded by the single OBSCN gene, are giant cytoskeletal proteins containing tandem adhesion and signaling domains, including an active RhoGEF motif that directly binds and activates RhoA. The OBSCN gene is highly mutated in breast cancer resulting in a 2-fold reduction of its mRNA levels. Consistent with this, obscurin proteins are nearly lost from breast cancer cell lines and human biopsies, independently of their hormonal status or molecular differentiation. Loss of giant obscurins from breast epithelial cells confers them with a survival and growth advantage, following exposure to current chemotherapies. Moreover, obscurin-depleted breast epithelial cells fail to form adhesion junctions, undergo epithelial-to-mesenchymal transition and generate primary and secondary mammospheres bearing markers of cancer-initiating cells. In line with these phenotypic alterations, obscurin-deficient cells display markedly increased motility as a sheet in 2-dimensional (2D) substrata and individually in confined spaces, and invasion in 3D matrices. More importantly, loss of giant obscurins from breast epithelial cells promotes primary tumor formation and lung colonization in vivo. Obscurin depletion leads to &gt;50% reduction in RhoA activity, as well as decreased phosphorylation of RhoA effectors, including myosin light chain phosphatase, myosin light chain, lim kinase, and cofilin, in both attached and suspended cells. These molecular alterations manifest as decreased actomyosin contractility, allowing suspended cells to escape detachment-induced apoptosis. Moreover, ∼40% of obscurin-depleted cells extend microtentacles, tubulin-based projections that mediate the attachment of circulating tumor cells to endothelium, an advantage that persists even after paclitaxel exposure. Collectively, our findings reveal that loss of giant obscurins from breast epithelium results in disruption of cell-cell contacts and acquisition of a mesenchymal phenotype that leads to enhanced tumorigenesis, migration and invasiveness in vitro and in vivo by affecting RhoA-mediated processes. Moreover, our data suggest that loss of obscurins may represent a substantial selective advantage for breast epithelial cells during metastasis, and that treatment with paclitaxel may exacerbate this advantage by preferentially allowing obscurin-deficient, stem-like cells to attach to the endothelium of distant sites, a first step towards colonizing metastatic tumors. Citation Format: Aikaterini Kontrogianni-Konstantopoulos, Marey Shriver, Nicole Perry, Kimberly Stroka, Michele Vitole, David Huso, Stuart Martin, Konstantinos Konstantopoulos. Giant obscurins: Novel tumor and metastasis suppressors in breast cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3259. doi:10.1158/1538-7445.AM2015-3259
Bulk heterojunction perovskite hybrid solar cells with large fill factor (2015)

A bulk heterojunction device structure was developed to address the unbalanced charge carrier extraction efficiencies in perovskite hybrid solar cells.
Routine clinical brain MRI sequences for use at 3.0 Tesla (2005)

When parameters are adjusted for changes in relaxation rates, routine clinical scans at 3.0 T can provide similar image appearance as 1.5 T, but with superior image quality and/or increased speed.
A High-temperature, High-efficiency Solar Thermoelectric Generator Prototype (2014)

Solar thermoelectric generators (STEGs) have the potential to convert solar energy at greater than 15% efficiency. This project investigates the system design, the necessary thermoelectric and optical technologies, and the economic feasibility of the STEG approach. A STEG is a solid-state heat engine that converts sunlight directly into DC electricity through the thermoelectric effect. STEGs consist of three subsystems: the solar absorber, the thermoelectric generator (TEG), and the heat management system (insulation, heat exchanger, vacuum enclosure, etc.). This project will integrate several state-of-the-art technologies to achieve high efficiency, including next- generation materials for TEGs, high-temperature solar-selective absorbers, and thermal cavities. We will test STEGs at NREL's high flux solar furnace (HFSF) and perform analysis of parasitic losses and lifetime analysis to optimize prototype operation. Equally important for this technology is the development of a cost model to determine the economic competitiveness and possible application niches for STEG technologies. We report on first-order economic analysis to identify the most promising pathways for advancing the technology.
Cardiogoniometry (1983)

Cardiogoniometry is a new method to test heart function. It consists of a simple computerized vectorcardiography with a system of leads derived for the construction of three orthogonal projections. With the aid of these three-dimensional projections the cardiogoniometer, a microprocessor system, measures and computes the maximal vectors of depolarization (QRS) and repolarization (T). It also fixes the orientation of these two spatial vectors by projection on two planes (frontal and oblique sagittal) and determines the solid angle phi between them. Every third heart beat these five parameters and the preceding beat interval are printed out. In this way, a series of measurements is obtained in which only little disturbances of the signals of cardiac de- and repolarization occur. In patients with latent coronary insufficiency an abnormal position of the T vector can be detected long before the standard ECG shows a pathological pattern. Cardiogoniometry can be performed in the consulting room or at the bedside. It is noninvasive, painless, and free of risk. The value and limits of this new method are to be tested in comparison with the ECG and invasive methods in cardiology laboratories.
Measurement of platelet aggregation functions using whole blood migration ratio in a microfluidic chip (2016)

Platelets play a major role in maintaining endothelial integrity and hemostasis. Of the various soluble agonists, ADP is an important in vivo stimulus for inducing platelet aggregation. In this study, a simple, rapid, and affordable method was designed for testing bleeding time (BT) and platelet aggregation with a two-channel microfluidic chip. Whole blood migration ratio (MR) from a microchip system was evaluated in comparison to the closure time (CT) from PFA-100 assays (Siemens, Germany) and CD62P expression on platelets. To induce platelet aggregation, a combination of collagen (1.84 mg/ml) and ADP (37.5 mg/ml) were used as agonists. After adding the agonists to samples, whole blood MR from the microchip system was measured. The outcome of the assessment depended on reaction time and agonist concentration. MR of whole blood from the microchip system was significantly correlated with CT from PFA-100 (r = 0.61, p < 0.05, n = 60). In addition, MR was negatively correlated with CD62P expression (r =-0.95, p < 0.05, n = 60). These results suggest that the measurement of MR using agonists is an easy, simple and efficient method for monitoring platelet aggregation in normal and ADP-receptors defective samples, along with the BT test. Thus, usage of the current microfluidic method could expand to diverse applications, including efficacy assessments in platelet therapy.
Spill-Detector-and-Shutoff Device (1985)

Overflow in liquid chromatography systems rapidly detected and stopped. Spill-detector-and-shutoff device incorporated into liquid-chromatography system. When liquid from output nozzle spills on liquid sensor, device automatically shuts off pump and releases solenoid to pinch off flow in tube. Device uses common type of alarm circuit reset manually before normal operation resumes.
Optimal cuts of langasite, La/sub 3/Ga/sub 5/SiO/sub 14/ for SAW devices (2001)

The results of a theoretical and experimental investigation of the SAW propagation characteristics in an optimal region of langasite defined by the Euler angles phi from -15 degrees to +10 degrees, theta from 120 degrees to 165 degrees, and psi from 20 degrees to 45 degrees are presented. Based on temperature coefficients of the elastic constants derived from experimental data, some optimal orientations of langasite characterized by high electromechanical coupling factor (k2), zero power flow angle (PFA) and low or zero temperature coefficient of frequency (TCF) were found. The SAW velocity in the region of interest is highly anisotropic; this results in a significant amount of diffraction, which must be taken into account in the search for orientations useful for SAW devices. An orientation having simultaneously zero PFA, zero TCF, negligible diffraction, and relatively high piezoelectric coupling has been found and verified experimentally. The experimental results are in excellent agreement with the calculated SAW characteristics. The frequency response of a SAW device fabricated on the optimal cut of langasite is presented and demonstrates that high performance SAW filters can be realized on this optimal cut of langasite.
Decision-Level Fusion of EEG and Pupil Features for Single-Trial Visual Detection Analysis (2009)

Several recent studies have reported success in applying EEG-based signal analysis to achieve accurate single-trial classification of responses to visual target detection. Pupil responses are proposed as a complementary modality that can support improved accuracy of single-trial signal analysis. We develop a pupillary response feature-extraction and -selection procedure that helps to improve the classification performance of a system based only on EEG signal analysis. We apply a two-level linear classifier to obtain cognitive-task-related analysis of EEG and pupil responses. The classification results based on the two modalities are then fused at the decision level. Here, the goal is to support increased classification confidence through the inherent modality complementarities. The fusion results show significant improvement over classification performance based on a single modality.
Transport properties of minority carriers in mid-wavelength InAs/InAsSb superlattice infrared detectors (2022)

A variety of mid-, long - and very long– wavelength infrared (MWIR, LWIR and VLWIR) detectors and focal plane arrays utilizing InAs/InAsSb superlattices have been demonstrated in the last decade. At the same time, the transport properties of minority carriers in these structures became an area of active investigation after initial observations of hole localization at low temperatures attributed to the nonuniformity of superlattice layers thickness. In this work we study the dependence of minority carrier (hole) transport, absorption coefficient and quantum efficiency (QE) of a 5.6 µm cut-off wavelength MWIR InAs/InAsSb detector on temperatures and applied bias
Abstract 239: A novel multimeric protein scaffold stimulates apoptotic signaling through TRAILR2 (2012)

Abstract TRAILR2 (DR5, TNFRSF10B) is a member of the TNF-receptor superfamily that mediates programmed cell death following stimulation with its ligand. Binding of homotrimeric ligand TRAIL to TRAILR2 induces oligomerization of the receptors and triggers the apoptotic pathway through induction of caspases. Although TRAILR2 is found to be expressed in a number of normal cell types it is routinely found at high levels in many cancer types. Since TRAIL has been shown to preferentially induce apoptosis in cancer cells versus normal cells, several TRAIL receptor agonists including monoclonal antibodies as well as the ligand itself, are currently in clinical development. Here, we describe a novel protein scaffold (Tn3) based on a fibronectin type-III domain from the protein Tenascin that was engineered to specifically agonize TRAILR2. Connecting TRAILR2-binding Tn3 domains together significantly improved the in vitro potency of the molecule in several cancer cell models. For example, a hexameric TRAILR2-binding Tn3 construct has an EC50 of 0.5 pM in a 72 hour cell viability assay with Colo-205 cells. This is approximately 2 logs better than TRAIL. Furthermore, a subset of TRAIL-resistant cancer cell lines derived from multiple tissues of origin is sensitive to the multimeric Tn3. The improved potency over TRAIL was demonstrated in colorectal cancer xenograft models. In addition, tumor regression was also observed at doses as low as 0.3 mg/kg. These results suggest that a multimeric Tn3 protein scaffold targeting TRAILR2 has more potent anti-tumor activity in vitro and in vivo compared than the natural ligand. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 239. doi:1538-7445.AM2012-239