gebhart/patrepeval huggingface dataset:
Ultra-thin layer packaging for implantable electronic devices (2013)

State of the art packaging for long-term implantable electronic devices generally uses reliable metal and glass housings; however, these are limited in the miniaturization potential and cost reduction. This paper focuses on the development of biocompatible hermetic thin-film packaging based on poly-para-xylylene (Parylene-C) and silicon oxide (SiOx) multilayers for smart implantable microelectromechanical systems (MEMS) devices. For the fabrication, a combined Parylene/SiOx single-chamber deposition system was developed. Topological aspects of multilayers were characterized by atomic force microscopy and scanning electron microscopy. Material compositions and layer interfaces were analyzed by Fourier transform infrared spectrometry and x-ray photoelectron spectroscopy. To evaluate the multilayer corrosion protection, water vapor permeation was investigated using a calcium mirror test. The calcium mirror test shows very low water permeation rates of 2 × 10−3 g m−2 day−1 (23 °C, 45% RH) for a 4.7 µm multilayer, which is equivalent to a 1.9 mm pure Parylene-C coating. According to the packaging standard MIL-STD-883, the helium gas tightness was investigated. These helium permeation measurements predict that a multilayer of 10 µm achieves the hermeticity acceptance criterion required for long-term implantable medical devices.
The C-Terminal SH2 Domain of p85 Accounts for the High Affinity and Specificity of the Binding of Phosphatidylinositol 3-Kinase to Phosphorylated Platelet-Derived Growth Factor β Receptor (1992)

Upon stimulation by its ligand, the platelet-derived growth factor (PDGF) receptor associates with the 85-kDa subunit of phosphatidylinositol (PI) 3-kinase. The 85-kDa protein (p85) contains two Src homology 2 (SH2) domains and one SH3 domain. To define the part of p85 that interacts with the PDGF receptor, a series of truncated p85 mutants was analyzed for association with immobilized PDGF receptor in vitro. We found that a fragment of p85 that contains a single Src homology domain, the C-terminal SH2 domain (SH2-C), was sufficient for directing the high-affinity interaction with the receptor. Half-maximal binding of SH2-C to the receptor was observed at an SH2-C concentration of 0.06 nM. SH2-C, like full-length p85, was able to distinguish between wild-type PDGF receptor and a mutant receptor lacking the PI 3-kinase binding site. An excess of SH2-C blocked binding of full-length p85 and PI 3-kinase to the receptor but did not interfere with the binding of two other SH2-containing proteins, phospholipase C-gamma and GTPase-activating protein. These results demonstrate that a region of p85 containing a single SH2 domain accounts both for the high affinity and specificity of binding of PI 3-kinase to the PDGF receptor.
Novel Synthesis of 3,4-Diarylisoxazole Analogues of Valdecoxib:  Reversal Cyclooxygenase-2 Selectivity by Sulfonamide Group Removal (2004)

3,4-Diarylisoxazole analogues of valdecoxib [4-(5-methyl-3-phenylisoxazol-4-yl)-benzensulfonamide], a selective cyclooxygenase-2 (COX-2) inhibitor, were synthesized by 1,3-dipolar cycloaddition of arylnitrile oxides to the enolate ion of phenylacetone regioselectively prepared in situ with lithium diisopropylamide at 0 degrees C. The corresponding 3-aryl-5-methyl-4-phenylisoxazoles were easily generated by a dehydration/aromatization reaction under basic conditions of 3-aryl-5-hydroxy-5-methyl-4-phenyl-2-isoxazolines and further transformed into their benzenesulfonamide derivatives. The biochemical COX-1/COX-2 selectivity was evaluated in vitro by using the human whole blood assays of COX isozyme activity. Three compounds not bearing the sulfonamide group present in valdecoxib were selective COX-1 inhibitors.
<title>Effect of surfaces on the performance of CdZnTe detectors</title> (2001)

Surface processing plays a major role in manufacturing CdZnTe semiconductor devices used for radiation detection. We are conducting a thorough, systematic study of surfaces and contacts and their effect on charge transport and signal formation in CdZnTe devices. We are investigating wet chemical processing techniques as well as treatment of surfaces with energetic neutral atoms. Our goal is to develop and implement improved surface treatment methods and device manufacturing techniques for large-volume CdZnTe detectors. In addition, we will determine how surfaces and electrical contacts affect the performance of CdZnTe devices used for radiation detection. In this paper, we will show how surface electronic properties influence carrier transport and signal formation in devices designed to simulate coplanar grid detectors. By altering the surface using a wet chemical process, we will show that charge collection is significantly effected by the conductivity of the surface.
Maximum core capacity of heterogeneous uncoupled multi-core fibers (2010)

The maximum capacity of cores in heterogeneous uncoupled multi-core fibers is analytically derived for the number of different index profiles and different arrangement topologies. An approximate formula is derived using the least-squares fit.
Development of a modular configurable multi-megawatt power amplifier (2013)

This paper details the design and development work for fabricating a modular and configurable multi-megawatt power amplifier. The impetus for creating the amplifier was to enable electric grid code standards testing for interconnection of large wind turbines. However, the flexible nature of the amplifier topology and control readily enables its use as a multipurpose power interconnect converter.
<title>Occlusion spectroscopy as a new paradigm for noninvasive blood measurements</title> (2001)

We prove experimentally that RBC aggregation is among the major factors affecting time evolution of light transmission in both the normal situation of pulsatile blood flow and the situation of over-systolic vessel occlusion. Optical transmissions of tissue in vivo have been measured in red/near-infrared region. Sudden blood flow cessation causes the light transmission rising. For certain wavelengths range this growth becomes non-monotonic. The correspondence between in vivo measurements and the theoretical simulations is reached if we attribute the transmission growth to the change of average size of scatterers. The most important blood parameters such as hemoglobin, glucose, oxygen saturation, etc., influence the transmission growth following over-systolic occlusion and, therefore, may be extracted from the detailed analysis of the time evolution of optical transmission. It forms a basis for new kind of non-invasive measurements, i.e., occlusion spectroscopy. The results of in vivo clinical trials are presented for glucose and hemoglobin.
Object recognition speed improvement using BITMAP-HoG (2016)

Commonly, HoG/SVM classifier uses rectangular images for HoG feature descriptor extraction and training. This means significant additional work has to be done to process irrelevant pixels belonging to the background surrounding the object of interest. While some objects may indeed be square or rectangular, most of objects are not easily representable by simple geometric shapes. In Bitmap-HoG approach we propose in this paper, the irregular shape of object is represented by a bitmap to avoid processing of extra background pixels. Bitmap, derived from the training dataset, encodes those portions of an image to be used to train a classifier. Experimental results show that not only the proposed algorithm decreases the workload associated with HoG/SVM classifiers by 75% compared to the state-of-the-art, but also it shows an average increase about 5% in recall and a decrease about 2% in precision in comparison with standard HoG.
<i>Cryptococcus neoformans</i> Chitin Synthase 3 (Chs3) Plays a Critical Role in Dampening Host Inflammatory Responses (2019)

ABSTRACT Cryptococcus neoformans infections are significant causes of morbidity and mortality among AIDS patients and the third most common invasive fungal infection in organ transplant recipients. One of the main interfaces between the fungus and the host is the fungal cell wall. The cryptococcal cell wall is unusual among human pathogenic fungi in that the chitin is predominantly deacetylated to chitosan. Chitosan deficient strains of C. neoformans were found to be avirulent and rapidly cleared from the murine lung. Moreover, infection with a chitosan deficient C. neoformans lacking three chitin deacetylases ( cda1Δ2Δ3Δ ) was found to confer protective immunity to a subsequent challenge with a virulent wild type counterpart. In addition to the chitin deacetylases, it was previously shown that chitin synthase 3 (Chs3) is also essential for chitin deacetylase mediated formation of chitosan. Mice inoculated with chs3Δ at a dose previously shown to induce protection with cda 1Δ2Δ3Δ die within 36 hours after installation of the organism. Mortality was not dependent on viable fungi as mice inoculated with heat-killed preparation of chs3Δ died at the same rate as mice inoculated with live chs3Δ , suggesting the rapid onset of death was host mediated likely caused by an over exuberant immune response. Histology, cytokine profiling, and flow cytometry indicates a massive neutrophil influx in the mice inoculated with chs3Δ . Mice depleted of neutrophils survived chs3Δ inoculation indicating that death was neutrophil mediated. Altogether, these studies lead us to conclude that Chs3, along with chitosan, plays critical roles in dampening cryptococcal induced host inflammatory responses. IMPORTANCE Cryptococcus neoformans is the most common disseminated fungal pathogen in AIDS patients, resulting in ∼200,000 deaths each year. There is a pressing need for new treatments for this infection, as current antifungal therapy is hampered by toxicity and/or the inability of the host’s immune system to aid in resolution of the disease. An ideal target for new therapies is the fungal cell wall. The cryptococcal cell wall is different than many other pathogenic fungi in that it contains chitosan. Strains that have decreased chitosan are less pathogenic and strains that are deficient in chitosan are avirulent and can induce protective responses. In this study we investigated the host responses to chs3 Δ, a chitosan-deficient strain, and found mice inoculated with chs3 Δ all died within 36 hours and death was associated with an aberrant hyperinflammatory immune response driven by neutrophils, indicating that chitosan is critical in modulating the immune response to Cryptococcus .
Increasing Traffic Flows with DSRC Technology: Field Trials and Performance Evaluation (2018)

As traffic congestion becomes a huge problem for most developing and developed countries across the world, intelligent transportation systems (ITS) are becoming a hot topic that is attracting attention of researchers and the general public alike. In this paper, we demonstrate a specific implementation of an ITS system whereby traffic lights are actuated by DSRC radios installed in vehicles. More specifically, we report the design of prototype of a DSRC-Actuated Traffic Lights (DSRC-ATL) system. It is shown that this system can reduce the travel time and commute time significantly, especially during rush hours. Furthermore, the results reported in this paper do NOT assume or require all vehicles to be equipped with DSCR radios. Even with low penetration ratios, e.g., when only 20% of all vehicles in a city are equipped with DSRC radios, the overall performance of the designed system is superior to the current traffic control systems.
Hypomorphic Apolipoprotein E Mice (2002)

In creating an allelic variant of mouse Apoe designed to resemble human apolipoprotein E4 (apoE4), we generated hypomorphic apoE (hypoE) mice that express only approximately 5% of normal apoE mRNA levels in all tissues. Insertion of a neo cassette flanked by loxP sites in the third intron of Apoe reduced expression of the Arg-61 allelic variant in hypoE mice and resulted in plasma apoE levels that were approximately 2-5% of normal. Unlike other mouse models with low levels of circulating apoE, hypoE mice had a nearly normal lipoprotein cholesterol profile when fed a chow diet. Further reduction of apoE expression in hypoE/Apoe(-/-) heterozygous mice led to an increase in remnant lipoprotein-associated cholesterol levels, demonstrating that hypoE mice express close to the threshold level of Arg-61 apoE required for a normal lipoprotein profile. Unlike wild type mice, hypoE mice were susceptible to diet-induced hypercholesterolemia, which was fully reversed within 3 weeks after resumption of a chow diet. In Mx1-Cre transgenic hypoE mice, plasma apoE levels returned to normal within 10 days after gene repair and removal of the neo cassette following induction of Cre recombinase. HypoE mice provide the opportunity for conditional gene repair by crossing with inducible or lineage/cell type-specific Cre transgenic mice, generating new models to dissect the roles of apoE in atherosclerosis regression, immunoregulation, and neurodegeneration.
Detection of 5-fluorouracil surface contamination in near real time (2015)

The 5-FU monitor is capable of detecting 10 ng/100 cm(2) (0.1 ng/cm(2)) using the electronic reader and 25 ng/100 cm(2) (0.25 ng/cm(2)) using the visual comparison method for the surfaces studied. The response of the monitors was compared to LC-MS/MS results for the same samples for validation and there was good correlation of the two methods but some differences in absolute response, especially at higher spiking levels for the surface samples.
Isolation of Gamma and Delta Tocotrienols from Rice Bran Oil Deodorizer Distillate Using Flash Chromatography (2015)

Abstract Gamma (γ‐T3) and delta (δ‐T3) tocotrienols are the most potent natural protective agents against harmful effects of radiation exposure and there is substantial interest in advancing these tocols toward Food and Drug Administration approval. However, co‐administration with alpha tocopherol is reported to interfere with the radioprotective properties of the tocotrienols. The objective of this study was to test various flash chromatography conditions for the purification of fractions with a high proportion of γ‐T3 or δ‐T3 and a minimal amount of alpha isomers from tocol extract obtained from rice bran oil deodorizer distillate (RBODD). Load size (0.125, 0.250, 0.500 and 1.000 g), sample cartridge type (pre‐packed silica cartridge, empty cartridge+Celite 545) and mobile phase gradient [varying proportions of hexane–acetic acid (99.1:0.9 v/v) and ethyl acetate–acetic acid (99.1:0.9 v/v)] were evaluated. Peak resolution was best with a load size of ~1 % column capacity and a 5‐g silica sample cartridge coupled with a 12‐g silica column. A linear gradient of 0.8 % ethyl acetate–acetic acid (99.1:0.9 v/v) to hexane–acetic acid (99.1:0.9 v/v) (50 min ) → 100 % ethyl acetate–acetic acid (99.1:0.9 v/v) (5 min) resulted in the best separation of tocols. The method developed was used to isolate tocols from samples of crude RBODD, tocol concentrate and tocol‐rich extract. The use of these conditions with a tocol‐rich extract resulted in several fractions containing 100 % purities of both γ‐T3 and δ‐T3.
Disabling Cas9 by an anti-CRISPR DNA mimic (2017)

CRISPR-Cas9 gene editing technology is derived from a microbial adaptive immune system, where bacteriophages are often the intended target. Natural inhibitors of CRISPR-Cas9 enable phages to evade immunity and show promise in controlling Cas9-mediated gene editing in human cells. However, the mechanism of CRISPR-Cas9 inhibition is not known and the potential applications for Cas9 inhibitor proteins in mammalian cells has not fully been established. We show here that the anti-CRISPR protein AcrIIA4 binds only to assembled Cas9-single guide RNA (sgRNA) complexes and not to Cas9 protein alone. A 3.9 Å resolution cryo-EM structure of the Cas9-sgRNA-AcrIIA4 complex revealed that the surface of AcrIIA4 is highly acidic and binds with 1:1 stoichiometry to a region of Cas9 that normally engages the DNA protospacer adjacent motif (PAM). Consistent with this binding mode, order-of-addition experiments showed that AcrIIA4 interferes with DNA recognition but has no effect on pre-formed Cas9-sgRNA-DNA complexes. Timed delivery of AcrIIA4 into human cells as either protein or expression plasmid allows on-target Cas9-mediated gene editing while reducing off-target edits. These results provide a mechanistic understanding of AcrIIA4 function and demonstrate that inhibitors can modulate the extent and outcomes of Cas9-mediated gene editing.
Ensnaring microbes: the components of plant disease resistance (1996)

SUMMARY Plants activate an array of co‐ordinated defence responses to restrict microbial attack. Timely perception of foreign molecules appears to be critical for the success of these defences. However, the nature of the molecular events required for resistance is largely unknown. Recent isolation of disease resistance (R) genes, has revealed that R gene products have several features in common. This finding suggests that plants have evolved several common or similar signal transduction pathways to activate resistance to a range of unrelated microbes. R gene isolation and the genetic identification of other loci required for R function permits analysis of the structure and evolution of microbe‐perception mechanisms. Numerous types of activated defence responses are recognized. A requirement for salicylic acid in resistance has been established in some systems. Roles for other events, like reactive oxygen species and the hypersensitive (host cell death) response, remain enigmatic. A thorough understanding of the components leading to pathogen recognition and the expression of resistance should permit the design of novel strategies to engineer broad‐spectrum and durable plant disease control.
Microstructure and Mechanical Properties of Austempered Medium Carbon Steels (2011)

Microstructures and mechanical properties for medium carbon steels including practical spring steels austempered at 400°C and 300°C were investigated. The larger strain was applied, the larger the fraction of retained austenite became martensite through strain induced transformation. 0.2% proof stress was increased by the increase of the fraction of bainitic ferrite. Uniform elongation was increased by increasing the fraction of retained austenite. Good strength–ductility balance with tensile stress over 1800 MPa for high strength spring was achieved in austempered SUP12 at 300°C composed of three phases of retained austenite, martensite and lower bainite.
Parallel Accumulation–Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device (2015)

In liquid chromatography-mass spectrometry (LC-MS)-based proteomics, many precursors elute from the column simultaneously. In data-dependent analyses, these precursors are fragmented one at a time, whereas the others are discarded entirely. Here we employ trapped ion mobility spectrometry (TIMS) on an orthogonal quadrupole time-of-flight (QTOF) mass spectrometer to remove this limitation. In TIMS, all precursor ions are accumulated in parallel and released sequentially as a function of their ion mobility. Instead of selecting a single precursor mass with the quadrupole mass filter, we here implement synchronized scans in which the quadrupole is mass positioned with sub-millisecond switching times at the m/z values of appropriate precursors, such as those derived from a topN precursor list. We demonstrate serial selection and fragmentation of multiple precursors in single 50 ms TIMS scans. Parallel accumulation-serial fragmentation (PASEF) enables hundreds of MS/MS events per second at full sensitivity. Modeling the effect of such synchronized scans for shotgun proteomics, we estimate that about a 10-fold gain in sequencing speed should be achievable by PASEF without a decrease in sensitivity.
Compound Metaoptics for Lossless Amplitude and Phase Control of Wavefronts (2019)

Summary form only given. Lossless and reflectionless metasurfaces reported to date control radiation by imposing phase discontinuities onto a wavefront. As a result, a single metasurface of this type can control either the phase or the amplitude profile of a field at a particular plane. In this talk, compound metaoptics will be described that can independently manipulate the amplitude and phase profiles of a wavefront. The compound metaoptic consists of two passive metasurfaces that are lossless and reflectionless, and separated by a wavelength-scale distance. As shown in Figure 1, the first metasurface projects the correct power density onto the second metasurface, allowing beam shaping. The second metasurface provides a phase correction that allows beam steering. The proposed approach allows amplitude control without relying on loss (reflection, absorption, or polarization loss), as in earlier works. In designing the compound metaoptic, a phase retrieval/optimization algorithm is used to determine the field distribution between the metasurfaces, region II in Figure 1. This field links the power density of the incident wavefront (incident from region I) to the power density of the desired wavefront (transmitted to region III) at the metasurface boundaries. The field in region II, along with the incident and desired (overall transmitted) wavefronts determine the surface parameters of each transparent metasurface comprising the metaoptic. The two metasurfaces are, in general, bianisotropic and can be implemented as cascades of three electric impedance sheets: patterned metallic or dielectric surfaces. A metaoptic design will be presented at the conference that provides the amplitude and phase control needed to convert an incident Gaussian beam to a Dolph-Tchebyscheff radiation pattern. In addition, a second metaoptic design will be shown that forms a simple complex-valued hologram. Specifically, it recreates the field scattered by a collection of line scatterers. More recent efforts to implement polarization preserving, non-bianisotropic compound metaoptics at near infrared wavelengths will also be described. In this case, arrays of silicon pillars, embedded in a PDMS medium, are used to provide phase shifts and implement each metasurface.