gebhart/patrepeval huggingface dataset:
Determination of the Molecular Basis for a Limited Dimorphism, N417K, in the Plasmodium vivax Duffy-Binding Protein (2011)

Invasion of human red blood cells by Plasmodium merozoites is vital for replication and survival of the parasite and, as such, is an attractive target for therapeutic intervention. Merozoite invasion is mediated by specific interactions between parasite ligands and host erythrocyte receptors. The P. vivax Duffy-binding protein (PvDBP) is heavily dependent on the interaction with the human Duffy blood group antigen/receptor for chemokines (DARC) for invasion. Region II of PvDBP contains many allelic polymorphisms likely to have arisen by host immune selection. Successful vaccine development necessitates a deeper understanding of the role of these polymorphisms in both parasite function and evasion of host immunity. A 3D structure of the homologous P. knowlesi DBP predicts that most variant residues are surface-exposed, including N417K, which is a dimorphic residue change that has previously been shown to be part of a linked haplotype that alters DBP sensitivity to inhibitory antibody. In natural isolates only two residues are found at this site, asparagine (N) and lysine (K). Site-directed mutagenesis of residue 417 was used to create a panel of 20 amino acid variants that were then examined for their binding phenotype and response to immune sera. Our results suggest that the observed dimorphism likely arose due to both structural requirements and immune selection pressure. To our knowledge, this is the first exhaustive examination of this kind of the role of a single amino acid residue in antigenic character and binding ability. Our results demonstrate that a single amino acid substitution can dramatically alter both the ability of the PvDBP to bind to human erythrocytes and its antigenic character.
THE SEPARATION OF m-DIISOPROPYLBENZENE FROM p-DIISOPROPYLBENZENE BY AZEOTROPIC DISTILLATION (1990)

Abstract m-Diisopropylbenzene can be separated from p-diisopropyl-benzene by azeotropic distillation when the azeotrope forming agent is selected from certain ketones, e.g. acetophenone; alcohols, e.g. o-isopropyl-phenol; esters, e.g. methyl benzoate; ethers, e.g. dipropylene glycol dimethyl ether or nitrogeneous compounds, e.g. 2-nitrotoluene. KEYWORDS: DiisopropylbenzeneAzeotropic distillation.
Track geometry defect rectification based on track deterioration modelling and derailment risk assessment (2014)

Analysing track geometry defects is critical for safe and effective railway transportation. Rectifying the appropriate number, types and combinations of geo-defects can effectively reduce the probability of derailments. In this paper, we propose an analytical framework to assist geo-defect rectification decision making. Our major contributions lie in formulating and integrating the following three data-driven models: (1) A track deterioration model to capture the degradation process of different types of geo-defects; (2) A survival model to assess the dynamic derailment risk as a function of track defect and traffic conditions; (3) An optimization model to plan track rectification activities with two different objectives: a cost-based formulation (CF) and a risk-based formulation (RF). We apply these approaches to solve the optimal rectification planning problem for a real-world railway application. We show that the proposed formulations are efficient as well as effective, as compared with existing strategies currently in practice.
Conversion of urodynamic pressures measured simultaneously by air-charged and water-filled catheter systems (2014)

The developed algorithm can be used to convert rapidly changing urodynamic pressures, such as cough leak point pressure, obtained using ACC systems to corresponding values expected from WFC systems.
Electrophoretic Immunoassays for Oral Diagnostics (2005)

Analysis of oral fluid (e.g., saliva) has the potential to aid diagnosis of both oral and systemic diseases. Oral fluids offer advantages over other bodily fluids, including quick, non-invasive, and inexpensive collection in both clinical and non-clinical settings. Nevertheless, current assay techniques using saliva are time-consuming, require large sample volumes, and are not amenable to automation or portability. We report on a robust microfluidic platform that performs rapid immunoassay-based analysis (<3 minutes) of saliva with low sample volume requirements (10 /spl mu/L) and appreciable sensitivity (10/sup -12/ M) with a high-degree of autonomy. Immunoassays for the detection of the systemic disease biomarker, C-reactive protein, and the cytokines interleukin-6 and tumor necrosis factor-/spl alpha/ were conducted in spiked human saliva using a microfluidic chip. The immunoassay developed is based on binding of fluorescently-labeled reporter antibodies to analytes followed by electrophoretic separation and quantitation of bound and unbound reporter. The separation selectivity was achieved using native polyacrylamide gel electrophoresis in a microchip containing in situ photolithographically patterned cross-linked polyacrylamide. Native electrophoresis conditions maintained the integrity of fragile immune complexes and provided rapid separations of complex samples. On-going work focuses on integration of the on-chip immunoassay with miniaturized hardware towards developing a portable prototype.
Optimizing total power of many-core processors considering voltage scaling limit and process variations (2009)

Recently, processor manufacturers have integrated more than a hundred cores in a single die to deliver extremely high throughput for highly-parallel, data-intensive applications like physics simulations, 3D-graphics, etc. Meanwhile, excessive power consumption rather than silicon area will limit the performance of many-core processors running the aforementioned applications. In this paper, to optimize the total power of many-core processors, we analyze the impact of 1) the number of cores, 2) parallelism in applications, and 3) supply voltage scaling limit due to on-die memory failure at low supply voltage. Our analysis shows that doubling the number of cores with lower than nominal supply voltage offers the most cost-effective power reduction, resulting in up to 65% less power consumption for highly-parallel applications even when supply voltage scaling is limited to 0.7V. The reduced power, in turn, can be used to improve throughput at higher voltage in power-constrained many-core processors. Furthermore, we extend our analysis to consider within-die core-to-core frequency and leakage variations. When only a subset of cores in a many-core processor are to be chosen to achieve a demanded throughput, moderately fast and leaky cores always provide optimal power consumption. In addition, frequency-island clocking, which allows independent frequency for each core, leads to 7% less power consumption than global clocking, and it prefers the fastest core (among the chosen ones) to process the totally sequential portion of workload.
Nanoporous Tin with a Granular Hierarchical Ligament Morphology as a Highly Stable Li-Ion Battery Anode (2016)

Next generation Li-ion batteries will require negative electrode materials with energy densities many-fold higher than that found in the graphitic carbon currently used in commercial Li-ion batteries. While various nanostructured alloying-type anode materials may satisfy that requirement, such materials do not always exhibit long cycle lifetimes and/or their processing routes are not always suitable for large-scale synthesis. Here, we report on a high-performance anode material for next generation Li-ion batteries made of nanoporous Sn powders with hierarchical ligament morphology. This material system combines both long cycle lifetimes (more than 72% capacity retention after 350 cycles), high capacity (693 mAh/g, nearly twice that of commercial graphitic carbon), good charging/discharging capabilities (545 mAh/g at 1 A/g, 1.5C), and a scalable processing route that involves selective alloy corrosion. The good cycling performance of this system is attributed to its nanoporous architecture and its unique hierarchical ligament morphology, which accommodates the large volume changes taking place during lithiation, as confirmed by synchrotron-based ex-situ X-ray 3D tomography analysis. Our findings are an important step for the development of high-performance Li-ion batteries.
Quinones. Part 2. General synthetic routes to quinone derivatives with modified polyprenyl side chains and the inhibitory effects of these quinones on the generation of the slow reacting substance of anaphylaxis (SRS-A) (1982)

General synthetic routes to quinone acids (8), quinone amides (9), quinone alcohols (10), and quinone methylketones (11) with polyprenyl side chains, in which allylic alcohols (3) are employed as the key intermediates, are described. The Claisen rearrangements and the Carrot reactions of the allylic alcohols (3) with ethyl orthoacetate and diketen produced the ethyl esters (4) and the methylketones (5), respectively. Quinone products (8), (10), and (11) were recovered by oxidative demethylation of hydroquinone dimethyl ethers (4), (5), and (7) or by acid hydrolysis of hydroquinone bis(methoxymethyl) ethers (4) and (5) followed by ferric chloride oxidation. Amidation of quinone acids (8) led to the formation of quinone amides (9). Inhibitory effects of these quinone derivatives on the generation of the slow reacting substance of anaphylaxis (SRS-A) in the lungs of sensitised guinea pigs are evaluated.
MOMBAT: Heart Rate Monitoring from Face Video using Pulse Modeling and Bayesian Tracking (2020)

A non-invasive yet inexpensive method for heart rate (HR) monitoring is of great importance in many real-world applications including healthcare, psychology understanding, affective computing and biometrics. Face videos are currently utilized for such HR monitoring, but unfortunately this can lead to errors due to the noise introduced by facial expressions, out-of-plane movements, camera parameters (like focus change) and environmental factors. We alleviate these issues by proposing a novel face video based HR monitoring method MOMBAT, that is, MOnitoring using Modeling and BAyesian Tracking. We utilize out-of-plane face movements to define a novel quality estimation mechanism. Subsequently, we introduce a Fourier basis based modeling to reconstruct the cardiovascular pulse signal at the locations containing the poor quality, that is, the locations affected by out-of-plane face movements. Furthermore, we design a Bayesian decision theory based HR tracking mechanism to rectify the spurious HR estimates. Experimental results reveal that our proposed method, MOMBAT outperforms state-of-the-art HR monitoring methods and performs HR monitoring with an average absolute error of 1.329 beats per minute and the Pearson correlation between estimated and actual heart rate is 0.9746. Moreover, it demonstrates that HR monitoring is significantly
Studies on antitumor-active 2,3-dioxopiperazine derivatives. II. Synthesis and structure-antitumor activity relationship of 1-benzyl-2,3-dioxopiperazine derivatives. (1981)

2, 3-Dioxopiperazine derivatives, which are antitumor agents of a new type, were synthesized and the structure-activity relationship was investigated from the viewpoint of lipophilic-hydrophilic balance. It was found that 1-(4-diethylaminobenzyl)-4-n-hexyl-2, 3-dioxopiperazine (12n) possessed significant in vitro cytotoxicity and in vivo antitumor activity against transplanted tumor, but this in vivo antitumor activity did not reflect the in vitro cytotoxicity. The metabolism of 12n in rats and mice was then studied. It was found that the Et2N-group of 12n was easily metabolized to an AcNH-group in vivo.
Multi-band quantum well infrared photodetectors (2002)

The GaAs/AlGaAs based Quantum Well Infrared Photodetectors (QWIPs) afford greater flexibility than the usual extrinsically doped semiconductor IR detectors because the wavelength of the peak response and cutoff can be continuously tailored over any wavelength between 6-20 mu m.
Multivariate Analysis Applied to the Study of Spatial Distributions Found in Drug-Eluting Stent Coatings by Confocal Raman Microscopy (2008)

Multivariate data analysis was applied to confocal Raman measurements on stents coated with the polymers and drug used in the CYPHER Sirolimus-eluting Coronary Stents. Partial least-squares (PLS) regression was used to establish three independent calibration curves for the coating constituents: sirolimus, poly(n-butyl methacrylate) [PBMA], and poly(ethylene-co-vinyl acetate) [PEVA]. The PLS calibrations were based on average spectra generated from each spatial location profiled. The PLS models were tested on six unknown stent samples to assess accuracy and precision. The wt % difference between PLS predictions and laboratory assay values for sirolimus was less than 1 wt % for the composite of the six unknowns, while the polymer models were estimated to be less than 0.5 wt % difference for the combined samples. The linearity and specificity of the three PLS models were also demonstrated with the three PLS models. In contrast to earlier univariate models, the PLS models achieved mass balance with better accuracy. This analysis was extended to evaluate the spatial distribution of the three constituents. Quantitative bitmap images of drug-eluting stent coatings are presented for the first time to assess the local distribution of components.
An improved synthesis of the radiolabeled prostate‐specific membrane antigen inhibitor, [<sup>18</sup>F]DCFPyL (2016)

The radiosynthesis of [(18) F]DCFPyL on 2 distinct automated platforms with full regulatory compliant quality control specifications is described. The radiotracer synthesis was performed on a custom-made radiofluorination module and the Sofie Biosciences ELIXYS. The radiofluorination module synthesis was accomplished in an average of 66 minutes from end of bombardment with an average specific activity at end of synthesis (EOS) of 4.4 TBq/μmol (120 Ci/μmol) and an average radiochemical yield of 30.9% at EOS. The ELIXYS synthesis was completed in an average of 87 minutes with an average specific activity of 2.2 TBq/μmol (59.3 Ci/μmol) and an average radiochemical yield of 19% at EOS. Both synthesis modules produced large millicurie quantities of [(18) F]DCFPyL while conforming to all standard US Pharmacopeia Chapter <823> acceptance testing criteria.
Adaptive Spatio-Temporal Video Noise Filtering for High Quality Applications (2007)

High-quality digital video filtering applications pose interesting challenges. Noise reduction cannot come at the expense of losing picture detail or introducing post-filtering artifacts. We address these issues by proposing an adaptive spatio-temporal method for reducing noise in digital video. The novelty of this method is that it aims to achieve an "even" amount of noise reduction at each pixel while preserving picture detail. The emphasis on even noise reduction helps reduce post-filtering artifacts arising from uneven filtering. We further propose an algorithm for automatically estimating the key filtering parameters, given two intuitive high-level inputs, filtering strength and a tolerance value. The high-level inputs provide user-friendly "knobs" that could be adjusted to obtain the desired filtering performance.
Evaluation of each electron beam and exposure results with four column cells in multicolumn e-beam exposure system (2009)

In the Mask D2I project at ASET, the authors assembled an electron beam exposure system to prove the concept of the multicolumn cell with character projection capability. They performed beam calibrations in individual column cell to evaluate beams after character deflections. They measured the impacts on beam positions in one column cell caused by deflections in other column cells and concluded that there were no deflection impacts on beam positions from neighboring column cells in the multicolumn cell system. They also evaluated stitching errors of the patterns exposed by different column cells. Present stitching errors of the patterns between the different column cells were estimated to be less than 20nm.
Synthesis and Dual D<sub>2</sub> and 5-HT<sub>1A</sub> Receptor Binding Affinities of 7-piperazinyl and 7-piperidinyl-3,4-dihydroquinazolin-2(1H)-ones (2013)

A series of new 7-piperazinyl and 7-piperidinyl-3,4-dihydroquinazolin-2(1H)-ones has been synthesized. The described compounds are structurally related to adoprazine, a potential atypical antipsychotic bearing potent D2 receptor antagonist and 5-HT1A receptor agonist properties. Suitably modified aryl bromides were prepared and condensed with tert-butyl piperazine-1-carboxylate to afford the advanced intermediate piperazinyl-3,4-dihydroquinazolin-2(1H)-one. Likewise Suzuki-Miyaura cross-coupling reaction of cyclic vinyl boronate with appropriate aryl bromides rendered piperidinyl-3,4-dihydroquinazolin-2(1H)-one. The reductive amination of the piperazinyl and piperidinyl-3,4- dihydroquinazolin-2(1H)-ones with suitably designed biarylaldehydes accomplished the synthesis of these title compounds. The described compounds were screened for D2 and 5-HT1A receptors binding affinities. The structure-activity relationship studies revealed that cyclopentenylpyridine and cyclopentenylbenzyl groups contribute significantly to the dual D2 and 5-HT1A receptor binding affinities of these compounds.
A new antibody label 5-10 times smaller than previous ones (1987)

By covalently coupling an undecagold complex to an Fab’ fragment, the smallest gold-conjugated antibody label yet devised has been synthesized. Its overall dimension is 50 x 30 x 20 Å and when bound to an antigen, the gold cluster is 40-50 Å from the antigen surface. The preparation procedure does not alter the activity and specificity of the antibody since coupling of the gold cluster is at a crystallographically known position at the opposite end of the Fab’ fragment from the antigen combining site. One significance of this new label is that with a smaller E.M. antibody label, higher resolution of labeling is possible. In fact, if monoclonals are used, specific sites on a single macromolecule, or subunits of a protein complex could be mapped.
<i>PIK3CA</i> Mutational Status in Circulating Tumor Cells Can Change During Disease Recurrence or Progression in Patients with Breast Cancer (2014)

PIK3CA hotspot mutations are present at a relatively high frequency in CTCs and their presence is associated with worse survival in patients with breast cancer with metastasis. Evaluation of PIK3CA mutational status in CTCs is a strategy with potential clinical application.
A simple edge termination for silicon carbide devices with nearly ideal breakdown voltage (1994)

In this paper, a simple edge termination is described which can achieve near ideal parallel plane breakdown for silicon carbide devices. This novel edge termination involves self aligned implantation of a neutral species on the edges of devices to form an amorphous layer. With this termination formed using argon implantation, the breakdown voltage of Schottky barrier diodes was measured to be very close to ideal plane parallel breakdown voltage.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Phenotypic Re-expression of Near Quiescent Chondrocytes: The Effects of Type II Collagen and Growth Factors (2009)

After extensively expanding in monolayer culture, the cultured chondrocytes become quiescent. The aim of this study was to establish the hypothesis that the phenotypic function of extensively expanded primary chondrocytes may be restored with extracellular matrix (ECM) compositions with or without growth factors. The restoring effects of these microenvironmental factors on the near quiescent passage 9 (P9) chondrocyte were investigated. The data showed that exogenous type I collagen and type II collagen at 1:1 ratio stimulate cell proliferation greatly while type II collagen alone was enough to revive most of cartilaginous functions of near quiescent P9 chondrocytes. Exogenous type II collagen by itself was more effective in restoring cell proliferation rate, elevating glycosaminoglycan (GAG) accumulation and promoting the re-expression of type II collagen mRNAs in the near quiescent chondrocytes. The supplement of P9 chondrocytes with type II collagen plus TGF-beta1 and IGF-I appeared essential for the re-expression of aggrecan and type II collagen mRNA in monolayer culture. In 3D type II collagen construct, P9 chondrocytes appeared healthy as chondrocytes and showed clear lacuna. However, in 3D type I collagen matrix, only some P9 chondrocytes exhibited lacuna. The cartilaginous microenvironments are crucial to restoring chondrocyte-phenotypic features of the quiescent or 'dedifferentiated' chondrocytes, implicating the potential of expanding a scarcity of healthy chondrocytes for cartilage repair or regeneration.
Multi-objective particle swarm optimization for postoperative deep brain stimulation targeting of subthalamic nucleus pathways (2018)

These results suggest that pathway targeting with patient-specific model-based optimization algorithms can efficiently identify non-trivial electrode configurations for enhancing activation of clinically relevant pathways. However, the results also indicate that inter-pathway correlations can limit selectivity for certain pathways even with directional DBS leads.
Simultaneous multi-frequency switchable oscillator and FSK modulator based on a capacitive-gap MEMS disk array (2015)

An electromechanical circuit constructed from array-composites of capacitive-gap micromechanical resonators with differing frequencies, wired in closed-loop feedback with a single ASIC amplifier, provides a first MEMS-based multi-frequency oscillator generating simultaneous oscillation outputs in the vicinity of 61 MHz. The use of only one amplifier for all frequencies (as opposed to one for each frequency) saves substantial power and is made possible by exploiting softening and damping non-linearities in the MEMS resonators, often considered a limitation, but here providing amplitude limiting that prevents amplifier desensitization to other frequencies. Furthermore, electrical stiffness-based frequency tuning enables Frequency-Shift Keyed (FSK) modulation of the output waveform, offering a space and power-efficient multichannel transmitter, as desired for mobile applications requiring long battery life, such as wireless sensor nodes. Indeed, while capable of multiple simultaneous and independent frequency outputs, this oscillator consumes only 137 μW, which is one-third that of previous multi-frequency efforts that only produce one frequency at a time [1].
Status and Use of the Rocky Flats Environmental Technology Site Pipe Overpack Container for TRU Waste Storage and Shipments (1998)

The Pipe Overpack Container was designed to optimize shipments of high plutonium content transuranic waste from Rocky Flats Environmental Technology Site (RFETS) to Waste Isolation Pilot Plant (WIPP). The container was approved for use in the TRUPACT-II shipping container by the Nuclear Regulatory Commission in February 1997. The container optimizes shipments to WIPP by increasing the TRUPACT-II criticality limit from 325 fissile grams equivalent (FGE) to 2,800 FGE and provides additional shielding for handling wastes with high americium-241 (Am-241) content. The container was subsequently evaluated and approved for storage of highly dispersible TRU wastes and residues at RFETS. Thermal evaluation of the container shows that the container will mitigate the impact of a worst case thermal event from reactive or potentially pyrophoric materials. These materials contain hazards postulated by the Defense Nuclear Facilities Safety Board for interim storage. Packaging these reactive or potentially pyrophoric residues in the container without stabilizing the materials is under consideration at RFETS. The design, testing, and evaluations used in the approvals, and the current status of the container usage, will be discussed.