gebhart/patrepeval huggingface dataset:
A Multiplexed Fluorescent Assay for Independent Second-Messenger Systems: Decoding GPCR Activation in Living Cells (2013)

There is a growing need in drug discovery and basic research to measure multiple second-messenger components of cell signaling pathways in real time and in relevant tissues and cell types. Many G-protein-coupled receptors activate the heterotrimeric protein, Gq, which in turn activates phospholipase C (PLC). PLC cleaves phosphatidylinositol 4,5-bisphosphate (PIP2) to produce two second messengers: diacylglycerol (DAG), which remains in the plasma membrane, and inositol triphosphate (IP3), which diffuses through the cytosol to release stores of intracellular calcium ions (Ca(2+)). Our goal was to create a series of multiplex sensors that would make it possible to simultaneously measure two different components of the Gq pathway in living cells. Here we describe new fluorescent sensors for DAG and PIP2 that produce robust changes in green or red fluorescence and can be combined with one another, or with existing Ca(2+) sensors, in a live-cell assay. These assays can detect multiple components of Gq signaling, simultaneously in real time, on standard fluorescent plate readers or live-cell imaging systems.
Synthesis of well defined polymers by controlled radical polymerization (1995)

Abstract Controlled radical polymerizations can be achieved by using either unimolecular or bimolecular exchange between growing radicals and dormant chains. Dormant chains can be represented as either covalent species or organometallic compounds. Systems based on alkoxyamines, organochromium, organoaluminum compounds, and alkyl iodides are discussed in detail. In many systems, straight semilogarithmic plots indicate a constant number of growing radicals. A linear increase of molecular weights with conversion indicates a constant number of chains capable of growth but being predominantly in the dormant state. Some of these systems can be used in the synthesis of block copolymers and for end‐functionalization.
Effect of amino acid changes in the V1/V2 region of the human immunodeficiency virus type 1 gp120 glycoprotein on subunit association, syncytium formation, and recognition by a neutralizing antibody (1993)

The contributions of the first and second variable regions of the human immunodeficiency virus type 1 gp120 glycoprotein to envelope glycoprotein structure, function, and recognition by a neutralizing antibody were studied. Several mutants with substitutions in the V2 loop demonstrated complete dissociation of the gp120 and gp41 glycoproteins, suggesting that inappropriate changes in V2 conformation can affect subunit assembly. Some glycoproteins with changes in V1 or V2 were efficiently expressed on the cell surface and were able to bind CD4 but were deficient in syncytium formation and/or virus entry. Recognition of gp120 by the neutralizing monoclonal antibody G3-4 was affected by particular substitutions affecting residues 176 to 184 in the V2 loop. These results suggest that the V1/V2 variable regions of the human immunodeficiency virus type 1 gp120 glycoprotein play a role in postreceptor binding events in the membrane fusion process and can act as a target for neutralizing antibodies.
Urinary Vitamin D Binding Protein and KIM-1 Are Potent New Biomarkers of Major Adverse Renal Events in Patients Undergoing Coronary Angiography (2016)

Urinary VDBP is a promising novel biomarker of major contrast induced nephropathy-associated events 90 days after contrast media exposure.
Randomized Language Models via Perfect Hash Functions (2008)

We propose a succinct randomized language model which employs a perfect hash function to encode fingerprints of n-grams and their associated probabilities, backoff weights, or other parameters. The scheme can represent any standard n-gram model and is easily combined with existing model reduction techniques such as entropy-pruning. We demonstrate the space-savings of the scheme via machine translation experiments within a distributed language modeling framework. 1
2D Surface Roughness Quantification for Enhanced Petrophysical Applications (2022)

Abstract Surface roughness is an essential rock parameter affecting petrophysical properties that are surface sensitive such as characterization of pore structure and wettability. For instance, Wenzel's contact angle formula for rough surfaces requires knowledge of the surface roughness, and surface roughness is expected to speed up aging of cores in crude oil for wettability restoration. In addition, proper quantification of surface roughness is critical for obtaining representative, roughness-independent, pore sizes for applications such as prediction of permeability and interpretation of capillary pressure curves. Intuitively, a surface is better characterized in 2D than in 1D. This 2D study is a continuation and enhancement of the previous 1D work, recently published in the SPE Journal (Ma et al., 2021). In this current paper, a comprehensive investigation of 1D versus 2D surface roughness measurements is conducted to evaluate and cross validate the two approaches. In this study, surface roughness is measured on 26 carbonate rock samples by laser scanning confocal microscopy (LSCM), where both the 1D absolute increment surface roughness, Sr, as well as 2D interfacial area ratio of surface roughness, Sdr, are reported. As expected, results indicate that surface roughness characterized by 2D Sdr has a greater dynamic range than the 1D Sr measurement, i.e., the 2D Sdr provides a more representative characterization of surface roughness. A detailed account of methodologies, assumptions, limitations, validation and applications of the 1D and 2D surface roughness characterization is documented in this paper. To extract the roughness features present on rock grain surfaces, effects of de-spiking and filter length, used to eliminate pore size effects, are investigated. For specific applications of surface roughness corrected pore size estimation from nuclear magnetic resonance (NMR) measurements, differences in length-scales of surface roughness are compared between LSCM measurement and that derived from NMR diffusion-T2 plus BET surface area. The surface roughness-corrected NMR pore-size distribution is also validated against the pore-size distribution obtained from measurement of micro-CT scanning.
Gene expression-based prediction of myeloma cell sensitivity to histone deacetylase inhibitors (2013)

In conclusion, the HA Score allows identification of MM patients with poor survival, who could benefit from HDACi treatment.
Real-Time, Transcranial Monitoring of Safe Blood-Brain Barrier Opening in Non-Human Primates (2014)

The delivery of drugs to specific neural targets faces two fundamental problems: (1) most drugs do not cross the blood-brain barrier, and (2) those that do, spread to the entire brain. To date, there exists only one non-invasive methodology with the potential to solve these problems: selective blood-brain barrier (BBB) opening using micro-bubble enhanced focused ultrasound. We have recently developed a single-element 500-kHz spherical transducer ultrasound setup for targeted BBB opening in the non-human primate that does not require simultaneous MRI monitoring. So far, however, the targeting accuracy that can be achieved with this system has not been quantified systematically. In this paper, the accuracy of this system was tested by targeting caudate nucleus and putamen of the basal ganglia in two macaque monkeys. The average lateral targeting error of the system was ∼2.5 mm while the axial targeting error, i.e., along the ultrasound path, was ∼1.5 mm. We have also developed a real-time treatment monitoring technique based on cavitation spectral analysis. This technique also allowed for delineation of a safe and reliable acoustic parameter window for BBB opening. In summary, the targeting accuracy of the system was deemed to be suitable to reliably open the BBB in specific sub-structures of the basal ganglia even in the absence of MRI-based verification of opening volume and position. This establishes the method and the system as a potentially highly useful tool for brain drug delivery.
Generating k-best solutions to auction winner determination problems (2006)

Auction participants cannot always articulate their requirements and preferences. Sometimes, for instance, the buyer in a procurement auction cannot quantify the value of non-price solution attributes or delineate between hard and soft constraints. This precludes formulating the winner determination problem (WDP) as an optimization problem. Existing decision-support aids for such situations extend an optimization framework. We present an approach that frames the decision problem as one of exploration rather than optimization. Our method relies on an algorithm that generates k -best solutions to auction WDPs. Our algorithm can incorporate hard constraints into the generation process and can scale to practical procurement auctions. We show how to extract useful guidance from k -best WDP solutions, and we evaluate our method using real bids submitted by real suppliers in an HP material parts procurement auction.
Traffic profiling for mobile video streaming (2017)

This paper describes a novel system that provides key parameters of HTTP Adaptive Streaming (HAS) sessions to the lower layers of the protocol stack. A non-intrusive traffic profiling solution is proposed that observes packet flows at the transmit queue of base stations, edge-routers, or gateways. By analyzing IP flows in real time, the presented scheme identifies different phases of an HAS session and estimates important application-layer parameters, such as play-back buffer state and video encoding rate. The introduced estimators only use IP-layer information, do not require standardization and work even with traffic that is encrypted via Transport Layer Security (TLS). Experimental results for a popular video streaming service clearly verify the high accuracy of the proposed solution. Traffic profiling, thus, provides a valuable alternative to cross-layer signaling and Deep Packet Inspection (DPI) in order to perform efficient network optimization for video streaming.
Identification of a Crohn’s disease specific transcript with potential as a diagnostic marker (1998)

This finding of a 3.1 kb RNA species permits the discrimination of Crohn's disease manifestations. Although further clinical work is required, this transcript appears to have definite potential as a diagnostic marker.
Isolation and characterisation of milk growth factor, a transforming‐growth‐factor‐<i>β</i>2‐related polypeptide, from bovine milk (1991)

A strategy was developed for the purification of a biologically active polypeptide growth and migration factor from skimmed bovine milk. This 25-kDa dimeric molecule, termed milk growth factor (MGF), was isolated by a method consisting of a combination of strong cation-exchange chromatography, low-pressure hydrophobic-interaction chromatography, hydrophobic-interaction HPLC and size-exclusion HPLC steps, which separated the protein according to its properties of charge, hydrophobicity and size, respectively. On average, a total purification of 10(6)-10(7)-fold and a yield of approximately 115 +/- 78 ng/MGF/milk was obtained using the method described. All purification steps were performed with novel combinations of ethanol and volatile acidic salt (ammonium acetate) solutions in order to retain biological activity of the protein. These conditions, together with the easy removal of salt by lyophilization, facilitated the detection of biological activity in fractions collected at each step of the purification by means of a sensitive in vitro fibroblast-migration assay in which the half-maximal activity was obtained at a concentration of approximately 17 +/- 4 pg/ml (i.e. approximately 1 pM) of the pure protein. Biological activity of the dimeric protein was unaffected by heat treatment or exposure to acid (pH 2.0), but was lost upon reduction to its monomeric form. Amino acid composition and sequence analyses demonstrate that MGF is related to transforming growth factor type beta 2.
Applying a dynamic method to the measurement of ion mobility (2009)

A dynamic method is applied to measure the mobility of gas-phase ions in the dual ion funnel interface of the electrospray source of a quadrupole orthogonal time-of-flight mass spectrometer. In a new operational mode, a potential barrier was formed in the second ion funnel of the mass spectrometer and then progressively increased. In this region, a flow of gas drags the ions into the mass spectrometer while the electric force applied by the potential barrier decelerates them. Ions with lower mobility can be carried by the gas flow more easily than those with high mobility. Thus, electrical forces can block the more mobile ions more easily. Hence, the electric barrier formed in the ion funnel permits only ions below a certain mobility threshold to enter the mass spectrometer. When the barrier voltage is increased, this threshold moves from high to low mobilities. Ions with mobilities above the threshold cannot enter the mass spectrometer, and their signal decreases to zero. Thus, in a barrier voltage scan, mass spectrometric signals of ions sequentially disappear. Differentiation of these decreasing ion signal curves produces peaks from which an ion mobility spectrum can be reconstructed. Blocking voltages, i.e., the positions of the peaks on the barrier voltage scale are directly related to the mobility of these ions. An internal calibration using ions with known mobility values helps determine the unknown ion mobilities and allows calculation of ionic cross sections.
Container-Based Cloud Platform for Mobile Computation Offloading (2017)

With the explosive growth of smartphones and cloud computing, mobile cloud, which leverages cloud resource to boost the performance of mobile applications, becomes attrac- tive. Many efforts have been made to improve the performance and reduce energy consumption of mobile devices by offloading computational codes to the cloud. However, the offloading cost caused by the cloud platform has been ignored for many years. In this paper, we propose Rattrap, a lightweight cloud platform which improves the offloading performance from cloud side. To achieve such goals, we analyze the characteristics of typical of- floading workloads and design our platform solution accordingly. Rattrap develops a new runtime environment, Cloud Android Container, for mobile computation offloading, replacing heavy- weight virtual machines (VMs). Our design exploits the idea of running operating systems with differential kernel features inside containers with driver extensions, which partially breaks the limitation of OS-level virtualization. With proposed resource sharing and code cache mechanism, Rattrap fundamentally improves the offloading performance. Our evaluation shows that Rattrap not only reduces the startup time of runtime environments and shows an average speedup of 16x, but also saves a large amount of system resources such as 75% memory footprint and at least 79% disk capacity. Moreover, Rattrap improves offloading response by as high as 63% over the cloud platform based on VM, and thus saving the battery life.
Mechanisms and Responses of a Dielectric Barrier Plasma Actuator: Geometric Effects (2004)

The single dielectric barrier discharge plasma, a plasma sustainable at atmospheric pressure, has shown considerable promise as a flow control device operating at modest (tens of watts) power levels. Measurements are presented of the development of the plasma during the course of the discharge cycle, and the relevance of these measurements to the modeling of the actuator's electrical properties is discussed. Experimental evidence is presented strongly pointing to the electric field enhancement near the leading edge of the actuator as a dominant factor determining the effectiveness of momentum coupling into the surrounding air
Corneal epithelial cell growth over tethered‐protein/peptide surface‐modified hydrogels (2004)

In this study, we investigated the corneal epithelial cell growth rate and adhesion to novel hydrogels with (1) extracellular matrix proteins [fibronectin, laminin, substance P, and insulin-like growth factor-1 (IGF-1)] and (2) peptide sequences [RGD and fibronectin adhesion-promoting peptide (FAP)] tethered to their surface on poly(ethylene glycol) (PEG) chains. The growth rate to confluence of primary rabbit cornea epithelial cells was compared for plain polymethacrylic acid-co-hydroxyethyl methacrylate (PHEMA/MAA) hydrogels, PHEMA/MAA hydrogels coated with extracellular matrix proteins or peptides, and PHEMA/MAA hydrogels with tethered extracellular matrix proteins or peptides on the surface. The development of focal adhesions by the epithelial cells grown on the surfaces was determined by F-actin staining. Little to no epithelial cell growth occurred on the plain hydrogel surfaces throughout the 15-day culture period. Of the coated hydrogels, only the fibronectin-coated surfaces showed a significant increase in cell growth compared to plain hydrogels (p < 0.009). However, even these surfaces reached a maximum of only 20% confluence. Laminin, fibronectin adhesion-promoting peptide (FAP), and fibronectin/laminin (1:1) tether-modified hydrogels all achieved 100% confluence by the end of the culture period, although the rates at which confluence was reached differed. F-actin staining showed that focal adhesions were formed for the laminin, FAP, and fibronectin/laminin tether-modified surfaces. The results support the hypothesis that tethering certain extracellular matrix proteins and/or peptides to the hydrogel surface enhances epithelial cell growth and adhesion, compared with that seen for protein-coated or plain hydrogel surfaces.
Development of an Unmanned Aerial Vehicle-Borne Crop-Growth Monitoring System (2017)

In view of the demand for a low-cost, high-throughput method for the continuous acquisition of crop growth information, this study describes a crop-growth monitoring system which uses an unmanned aerial vehicle (UAV) as an operating platform. The system is capable of real-time online acquisition of various major indexes, e.g., the normalized difference vegetation index (NDVI) of the crop canopy, ratio vegetation index (RVI), leaf nitrogen accumulation (LNA), leaf area index (LAI), and leaf dry weight (LDW). By carrying out three-dimensional numerical simulations based on computational fluid dynamics, spatial distributions were obtained for the UAV down-wash flow fields on the surface of the crop canopy. Based on the flow-field characteristics and geometrical dimensions, a UAV-borne crop-growth sensor was designed. Our field experiments show that the monitoring system has good dynamic stability and measurement accuracy over the range of operating altitudes of the sensor. The linear fitting determination coefficients (R²) for the output RVI value with respect to LNA, LAI, and LDW are 0.63, 0.69, and 0.66, respectively, and the Root-mean-square errors (RMSEs) are 1.42, 1.02 and 3.09, respectively. The equivalent figures for the output NDVI value are 0.60, 0.65, and 0.62 (LNA, LAI, and LDW, respectively) and the RMSEs are 1.44, 1.01 and 3.01, respectively.
Prostate-targeted radiosensitization via aptamer-shRNA chimeras in human tumor xenografts (2011)

Dose-escalated radiation therapy for localized prostate cancer (PCa) has a clear therapeutic benefit; however, escalated doses may also increase injury to noncancerous tissues. Radiosensitizing agents can improve ionizing radiation (IR) potency, but without targeted delivery, these agents will also sensitize surrounding normal tissues. Here we describe the development of prostate-targeted RNAi agents that selectively sensitized prostate-specific membrane antigen-positive (PSMA-positive) cells to IR. siRNA library screens identified DNA-activated protein kinase, catalytic polypeptide (DNAPK) as an ideal radiosensitization target. DNAPK shRNAs, delivered by PSMA-targeting RNA aptamers, selectively reduced DNAPK in PCa cells, xenografts, and human prostate tissues. Aptamer-targeted DNAPK shRNAs, combined with IR, dramatically and specifically enhanced PSMA-positive tumor response to IR. These findings support aptamer-shRNA chimeras as selective sensitizing agents for the improved treatment of high-risk localized PCa.
The reactive bed plasma system for contamination control (1990)

The contamination control capabilities of the Reactive Bed Plasma (RBP) system is described by delineating the results of toxic chemical composition studies, aerosol filtration work, and other testing. The RBP system has demonstrated its capabilities to decompose toxic materials and process hazardous aerosols. The post-treatment requirements for the reaction products have possible solutions. Although additional work is required to meet NASA requirements, the RBP may be able to meet contamination control problems aboard the Space Station.
Mode Tracker for Mode-Hop-Free Operation of a Laser (2010)

A mode-tracking system that includes a mode-controlling subsystem has been incorporated into an external-cavity (EC) quantum cascade laser that operates in a mid-infrared wavelength range. The mode-tracking system makes it possible to perform mode-hop-free wavelength scans, as needed for high-resolution spectroscopy and detection of trace gases. The laser includes a gain chip, a beam-collimating lens, and a diffraction grating. The grating is mounted on a platform, the position of which can be varied to effect independent control of the EC length and the grating angle. The position actuators include a piezoelectric stage for translation control and a motorized stage for coarse rotation control equipped with a piezoelectric actuator for fine rotation control. Together, these actuators enable control of the EC length over a range of about 90 m with a resolution of 0.9 nm, and control of the grating angle over a coarse-tuning range of +/-6.3deg and a fine-tuning range of +/-520 microrad with a resolution of 10 nrad. A mirror mounted on the platform with the grating assures always the same direction of the output laser beam.
Strategies for enhancing viral-based gene therapy using ionizing radiation (1999)

Many gene-therapy strategies under investigation aim to increase the efficacy of current cancer-treatment regimens. Promising results have been obtained in the laboratory and early clinical trials using viral-based motifs specifically designed to enhance the efficacy of ionizing radiation or chemotherapy. These strategies fall into two general categories: replication-incompetent viral shuttle vectors for the delivery of specific genes encoding a chemo/radiation modulator and attenuated replication-competent viruses with proposed replicative advantages in tumor cells. In this review, we discuss the rational, molecular mechanisms, and clinical application of these strategies with particular focus on recent research applying these viral-based strategies to improve the therapeutic index of ionizing radiation.
An efficient synthesis of 6‐fluoronalidixic acid and its conversion to enoxacin (1987)

Abstract 1‐Ethyl‐6‐fluoro‐1,4‐dihydro‐7‐methyl‐4‐oxo‐1,8‐naphthyridine‐3‐carboxylic acid ( 8 ) has been prepared in large quantities by a highly efficient process. It has in turn been degraded to give 7‐chloro‐1‐ethyl‐6‐fluoro‐1,4‐dihydro‐4‐oxo‐1,8‐naphthyridine‐3‐carboxylic acid ( 11 ). This intermediate has been reacted with piperazine to give the known antibacterial agent, enoxacin ( 12 ).