gebhart/patrepeval huggingface dataset:
Progress in InAs/InAsSb superlattice barrier infrared detectors (2022)

The InAs/InAsSb (Gallium-free) type-II strained-layer superlattice (T2SLS) has emerged in recent years as a viable infrared detector material. In particular, mid-wavelength InAs/InAsSb T2SLS focal plane array (FPA) based on the nBn detector architecture exhibits good operating characteristics at 160 K, demonstrating a considerably operating temperature advantage over InSb FPAs. In the long and very long cutoff wavelengths, InAs/InAsSb T2SLS detectors with n-type absorbers are limited in their attainable quantum efficiency (QE) due to short hole diffusion lengths and relatively modest absorption coefficients. We have explored long and very long wavelength InAs/InAsSb T2SLS complementary barrier infrared detectors (CBIRDs) that contain p-type absorber layers in order to take advantage of the longer electron diffusion length for QE enhancement. We also discuss recent development of the InAs/InAsSb T2SLS infrared detectors at the Jet Propulsion Laboratory for NASA Earth Science applications, including long-wavelength infrared FPAs for land imaging, and mid-wavelength infrared FPAs for CubeSat hyperspectral imaging.
Feedback control of mammalian Hedgehog signaling by the Hedgehog-binding protein, Hip1, modulates Fgf signaling during branching morphogenesis of the lung (2003)

Hedgehog (Hh) signaling plays a major role in multiple aspects of embryonic development. A key issue is how negative regulation of Hh signaling might contribute to generating differential responses over tens of cell diameters. In cells that respond to Hh, two proteins that are up-regulated are Patched1 (Ptch1), the Hh receptor, a general target in both invertebrate and vertebrate organisms, and Hip1, a Hh-binding protein that is vertebrate specific. To address the developmental role of Hip1 in the context of Hh signaling, we generated Hip1 mutants in the mouse. Loss of Hip1 function results in specific defects in two Hh target issues, the lung, a target of Sonic hedgehog (Shh) signaling, and the endochondral skeleton, a target of Indian hedgehog (Ihh) signaling. Hh signaling was up-regulated in Hip1 mutants, substantiating Hip1's general role in negatively regulating Hh signaling. Our studies focused on Hip1 in the lung. Here, a dynamic interaction between Hh and fibroblast growth factor (Fgf) signaling, modulated at least in part by Hip1, controls early lung branching.
Hardware/Software Co-Exploration of Neural Architectures (2020)

We propose a novel hardware and software co-exploration framework for efficient neural architecture search (NAS). Different from existing hardware-aware NAS which assumes a fixed hardware design and explores the <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">NAS space</i> only, our framework simultaneously explores both the architecture search space and the <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">hardware design space</i> to identify the best neural architecture and hardware pairs that maximize both test accuracy and hardware efficiency. Such a practice greatly opens up the design freedom and pushes forward the Pareto frontier between hardware efficiency and test accuracy for better design tradeoffs. The framework iteratively performs a two-level (fast and slow) exploration. Without lengthy training, the fast exploration can effectively fine-tune hyperparameters and prune inferior architectures in terms of hardware specifications, which significantly accelerates the NAS process. Then, the slow exploration trains candidates on a validation set and updates a controller using the reinforcement learning to maximize the expected accuracy together with the hardware efficiency. In this article, we demonstrate that the co-exploration framework can effectively expand the search space to incorporate models with high accuracy, and we theoretically show that the proposed two-level optimization can efficiently prune inferior solutions to better explore the search space. The experimental results on ImageNet show that the co-exploration NAS can find solutions with the same accuracy, 35.24% higher throughput, 54.05% higher energy efficiency, compared with the hardware-aware NAS.
Parallel power grid analysis using distributed direct linear solver (2014)

Accurate and efficient power grid analysis has become increasingly important in semiconductors chip design and verification. It is one of the most computationally challenging tasks in high performance processor design analysis. Due to the extremely large memory required to store and manipulate the design data, it is no longer possible to accommodate the analysis using one or more serial processes on a single computer. The proposed method of large scale power grid analysis with sparse linear solver effectively distributes the computing tasks across multiple processes running on different computers within the network. It provides a stable, accurate, and scalable solution for the future process technology and design generations. The implementation incorporates advanced packages for matrix ordering, matrix factorization and solution, and message passing interface (MPI) integrated into the software tool capable of simulating extremely large scale design with billions of devices. The method can be applied to the power grid of arbitrary size and configuration, and produces results with SPICE-like accuracy. The benchmark analysis runs applied to the largest blocks of the latest Sparc processor design using 16 distributed processes demonstrate more than 6X memory utilization improvement and 9X performance improvement over a state-of-the-art serial solution currently employed in semiconductor industry.
A modeling and analysis methodology for modular logic controllers of machining systems with auto, hand, and manual control modes (2000)

Logic controllers for machining systems typically have three control modes: auto, hand, and manual. Hand and manual modes are designed for various fault recovery operations in machining systems. In this paper, a unified formal representation of logic controllers with three control modes is provided using Petri nets. A modular logic controller structure is introduced and formalized for reconfigurable high-volume transfer lines. The modular logic controller consists of a control module for mode decision and control modules for station logic controllers. Each station control module is represented by connecting operation modules which are designed with respect to the fault recovery processes of operations; their connection algorithm is also provided. In our formal representation, each control module is represented by a live, safe, and reversible Petri net. A condition for the modular logic controller to generate a correct control logic is provided.
Modified Spot Welder Solders Flat Cables (1992)

Soldering device, essentially modified spot welder, melts high-melting-temperature solders without damaging plastic insulation on flat electrical cables. Solder preform rests on exposed conductor of cable, under connector pin. Electrodes press pin/preform/conductor sandwich together and supply pulse of current to melt preform, bonding pin to conductor. Anvil acts as support and heat sink. Device used to solder flexible ribbon cables to subminiature pin connectors.
Adjoint optimization of polarization-splitting grating couplers (2023)

We have designed a polarization-splitting grating coupler (PSGC) in silicon-on-insulator (SOI) that has 1.2 dB peak loss in numerical simulations, which is the best simulated performance of PSGCs without a bottom reflector to the best of our knowledge. Adjoint method-based shape optimization enables us to explore complex geometries that are intractable with conventional design approaches. Physics-based process-independent knowledge of PSGCs is extracted from the adjoint optimization and can be transferred to other platforms with a minimum of effort.
Co-occurring gland tensors in localized cluster graphs: Quantitative histomorphometry for predicting biochemical recurrence for intermediate grade prostate cancer (2013)

Quantitative histomorphometry (QH), computational tools to analyze digitized tissue histology, has become increasingly important for aiding pathologists in assessing cancer severity. In this study, we introduce a novel set of QH features utilizing co-occurring gland tensors (CGT) in localized cluster graphs to quantitatively evaluate prostate cancer (CaP) histology. CGTs offer three main advantages over previous QH features: 1) gland tensors represent a novel measurement that has been anecdotally described as one of interest, but never quantitatively modeled, 2) CGTs extract measurements based on local rather than global glandular networks, constructed using cluster graphs, and 3) second order statistical features (energy, homogeneity, energy, and correlation) obtained from a co-occurrence matrix capture the spatial interactions of gland tensors in the image. We extract 4 CGT features from 56 regions across 40 intermediate grade CaP patients and evaluated the ability of CGT features to predict biochemical recurrence (BCR) within 5 years of radical prostatectomy. Intermediate Gleason score 7 cancers represent the predictive borderline for BCR cases, where 50% of cases develop BCR. We found that CGT features outperformed 5 different sets of QH features, previously shown to be effective in CaP grading, when evaluated via a Random Forest classifier (66% accuracy for CGT features versus 55% for the next closest QH feature set), all comparisons being statistically significant.
A selective video encryption for the region of interest in scalable video coding (2007)

In this paper, we propose an encryption method to protect the region of interest (ROI) which is standard element in the scalable video coding (SVC). The proposed video encryption method provides secured SVC contents with the selective encryption scheme. In order to confine the encryption into the ROI, three encoding schemes are also proposed, which include the constrained motion estimation, exceptional handlings for the half-pel interpolation and Intra_BL mode in the boundary of a ROI. Experiments were performed to verify the proposed methods using the joint scalable video model (JSVM), and the experimental results showed that the proposed methods protect the ROI in SVC effectively.
Molecular Cloning of Mouse Collectin Liver 1 (2002)

Collectins are members of the superfamily of vertebrate C-type lectins that contain a collagen-like region, and are involved in first-line host defense. We earlier cloned and characterized a new kind of collectin, collectin liver 1 (CL-L1). In this study, we isolated the mouse homologue of CL-L1 encoding 277 amino acid residues; its deduced protein sequence was 88% identical with human CL-L1. Mouse CL-L1 mRNA was expressed mainly in the liver and stomach, but was found also in muscles, testes, intestines, and embryos. In mouse embryos, the level of CL-L1 mRNA gradually increased with embryonic age. In 16-day-old mouse embryos, CL-L1 mRNA was expressed in the liver, amnion, and visceral yolk sac. The mouse CL-L1 gene, Cll1 was found on chromosome 15 in a region syntenic with human chromosome 8q. CL-L1 was a highly conserved protein in mammals, birds, and fish.
Use of Genetic Algorithms to Optimize Fiber Optic Probe Design for the Extraction of Tissue Optical Properties (2007)

This paper outlines a framework by which the optimal illumination/collection geometry can be identified for a particular biomedical application. In this paper, this framework was used to identify the optimal probe geometry for the accurate determination of tissue optical properties representative of that in the ultraviolet-visible (UV-VIS) spectral range. An optimal probe geometry was identified which consisted of a single illumination and two collection fibers, one of which is insensitive to changes in scattering properties, and the other is insensitive to changes in the attenuation coefficient. Using this probe geometry in conjunction with a neural network algorithm, the optical properties could be extracted with root-mean-square errors of 0.30 cm(-1) for the reduced scattering coefficient (tested range of 3-40 cm(-1)), and 0.41 cm(-1) for the absorption coefficient (tested range of 0-80 cm(-1)).
Toward Compact High-Performance Ion Mobility Spectrometers: Ion Gating in Ion Mobility Spectrometry (2021)

Printed circuit board (PCB) based drift tube ion mobility spectrometers enable the use of state-of-the-art production techniques to manufacture compact devices with excellent performance at minimum cost. The new PCB ion mobility spectrometer (PCB-IMS) presented here is equipped with either a 140 MBq tritium or a 95 MBq nickel-63 ionization source and consists of a combination of horizontally arranged 6-layer PCBs for the drift and reaction regions and vertically arranged PCBs for interfacing the ionization source, ion shutter, and detector. The design allows the reproducible manufacturing and thus comparison of different IMS topologies. Here, we investigate different ion shutters, field-switching, Bradbury-Nielsen, and tristate and their effects on resolving power and limits of detection considering two different ionization region geometries and ionization sources, tritium and nickel-63. It is shown that the high resolving power of <i>R</i><sub>P</sub> > 80 at low drift voltage of 3 kV and short drift length of 50 mm can be achieved independent of the used ion shutter mechanism and reaction region geometry. While the resolving power of all ion shutters is excellent, the Bradbury-Nielsen shutter shows a pronounced discrimination of slow ion species when using short shutter opening times for small initial ion cloud widths, as required for high resolving power. Thus, the intensity of the proton-bound dimer of 2-pentanone is reduced by 30% compared to the signal intensity obtained with both the field-switching and tristate shutter. The detection limits employing the Bradbury-Nielsen shutter and a 50 mm reaction region as required for nickel-63 are 58 ppt<sub>v</sub> for the protonated monomer and 3.4 ppb<sub>v</sub> for the proton-bound dimer of 2-pentanone. The detection limits achieved with the tristate shutter utilizing the same reaction region are slightly higher for the protonated monomer at 68 ppt<sub>v</sub>, but lower for the proton-bound dimer at 2 ppb<sub>v</sub> due to the advanced ion shutter principle not discriminating slow ions. However, the lowest detection limits of 13 ppt<sub>v</sub> and 301 ppt<sub>v</sub> can be achieved with the field-switching shutter and a 2 mm reaction region, sufficient for a tritium ionization source.
Intravitreal Crystalline Drug Delivery for Intraocular Proliferation Diseases (2010)

The intravitreous injectable lipid prodrugs of AraG and 5-fluoro-2'-deoxyuridine could be long-lasting, slow-release, antiproliferative compounds to treat unwanted intraocular proliferation.
Brain-enriched microRNAs circulating in plasma as novel biomarkers for Rett syndrome (2019)

Rett syndrome (RTT) is a severe neurodevelopmental disorder caused by mutations in the X-linked gene MECP2 (methyl-CpG-binding protein 2). Minimally invasive and accurate biomarkers of disease progression and treatment response could facilitate screening of therapeutic compounds in animal models, enrollment of better-defined participants into clinical trials, and treatment monitoring. In this study, we used a targeted approach based on analysis of brain-enriched microRNAs (miRNAs) circulating in plasma to identify miRNA biomarkers of RTT using Mecp2-mutant mice as a model system and human plasma samples. An "miRNA pair" approach, i.e. the ratio between two miRNAs, was used for data normalization. Specific miRNA pairs and their combinations (classifiers) analyzed in plasma differentiated wild-type from Mecp2 male and female mice with >90% accuracy. Individual miRNA pairs were more effective in distinguishing male (homozygous) animals than female (heterozygous) animals, suggesting that disease severity correlated with the levels of the miRNA biomarkers. In the human study, 30 RTT patients were compared with age-matched controls. The results of this study showed that miRNA classifiers were able to differentiate RTT patients from controls with 85-100% sensitivity. In addition, a comparison of various age groups demonstrated that the dynamics in levels of miRNAs appear to be associated with disease development (involvement of liver, muscle and lipid metabolism in the pathology). Importantly, certain miRNA biomarker pairs were common to both the animal models and human subjects, indicating the similarity between the underlying pathological processes. The data generated in this feasibility study suggest that circulating miRNAs have the potential to be developed as markers of RTT progression and treatment response. Larger clinical studies are needed to further evaluate the findings presented here.
Adipogenic potential of multiple human adenoviruses in vivo and in vitro in animals (2005)

Human adenovirus-36 (Ad-36) increases adiposity in chickens, mice, and nonhuman primates and is associated with human obesity. Ad-36 paradoxically reduces serum cholesterol and triglycerides in animal models. Ad-36 increases adipocyte differentiation and triglyceride accumulation in 3T3-L1 cells in vitro. This study evaluated whether three other human adenoviruses increase adiposity in chickens and in 3T3-L1 cells in vitro. We inoculated chickens with human Ad-2, Ad-31, Ad-37, or media at age 3 wk. Food intake and weights were recorded for 3.5 wk, and then chickens were killed and visceral fat, body composition, serum lipids, and viral antibody status were determined. Visceral fat and total body fat were significantly elevated (P < 0.001) in the Ad-37 group compared with all other groups. Final body weights were higher in chickens inoculated with Ad-37 compared with Ad-2, but not significantly higher than in control or Ad-31 groups. Food intake did not differ among groups. Serum cholesterol was elevated in Ad-37 chickens compared with control (P < 0.01) but was not affected by other viruses. Triglycerides were reduced in Ad-37 chickens (P < 0.0001) but were not affected by other viruses. In 3T3-L1 cells in vitro, Ad-31, Ad-36, and Ad-37, but not Ad-2, increased adipocyte differentiation and triglycerides accumulation. In summary, Ad-37 is another human adenovirus that increases adiposity and reduces serum triglycerides in an animal model. However, the response of serum cholesterol is opposite that of Ad-36. Evaluation of other human adenoviruses to determine their effects on adiposity and serum lipids is warranted, but in vitro assays may not be definitive for this purpose.
Synthesis of Colloidal Upconverting NaYF<sub>4</sub>:  Er<sup>3+</sup>/Yb<sup>3+</sup> and Tm<sup>3+</sup>/Yb<sup>3+</sup> Monodisperse Nanocrystals (2007)

The synthesis, characterization, and spectroscopy of upconverting lanthanide-doped NaYF4 nanocrystals (NCs) is presented. The monodisperse cubic NaYF4 NCs were synthesized via a thermal decomposition reaction of trifluoroacetate precusors in a mixture of technical grade chemicals, octadecene and the coordinating ligand oleic acid. In this straightforward method, the dissolved precursors are added slowly to the reaction solution through a stainless-steel canula resulting in highly luminescent nanocrystals with an almost monodisperse particle size distribution. The NCs were characterized through the use of transmission electron microscopy, selected area electron diffraction, 1H NMR, powder X-ray diffraction, and high-resolution luminescence spectroscopy. The NaYF4 NCs are capable of being of dispersed in nonpolar organic solvents thus forming colloidally stable solutions. The colloids of the Er3+, Yb3+ and Tm3+, Yb3+ doped NCs exhibit green/red and blue upconversion luminescence, respectively, under 980 nm laser diode excitation with low power densities.
ChemInform Abstract: Asymmetric Dihydroxylation Via Ligand‐Accelerated Catalysis. (1988)

Abstract A new catalytic process for asym.
Broad-spectrum monoclonal antibodies against chikungunya virus structural proteins: Promising candidates for antibody-based rapid diagnostic test development (2018)

In response to the aggressive global spread of the mosquito-borne chikungunya virus (CHIKV), an accurate and accessible diagnostic tool is of high importance. CHIKV, an arthritogenic alphavirus, comprises three genotypes: East/Central/South African (ECSA), West African (WA), and Asian. A previous rapid immunochromatographic (IC) test detecting CHIKV E1 protein showed promising performance for detection of the ECSA genotype. Unfortunately, this kit exhibited lower capacity for detection of the Asian genotype, currently in circulation in the Americas, reflecting the low avidity of one of the monoclonal antibodies (mAbs) in this IC kit for the E1 protein of the Asian-genotype because of a variant amino acid sequence. To address this shortcoming, we set out to generate a new panel of broad-spectrum mouse anti-CHIKV mAbs using hybridoma technology. We report here the successful generation of mouse anti-CHIKV mAbs targeting CHIKV E1 and capsid proteins. These mAbs possessed broad reactivity to all three CHIKV genotypes, while most of the mAbs lacked cross-reactivity towards Sindbis, dengue, and Zika viruses. Two of the mAbs also lacked cross-reactivity towards other alphaviruses, including O'nyong-nyong, Ross River, Mayaro, Western Equine Encephalitis, Eastern Equine Encephalitis, and Venezuelan Equine Encephalitis viruses. In addition, another two mAbs cross-reacted weakly only with most closely related O'nyong-nyong virus. Effective diagnosis is one of the keys to disease control but to date, no antibody-based rapid IC platform for CHIKV is commercially available. Thus, the application of the mAbs characterized here in the rapid diagnostic IC kit for CHIKV detection is expected to be of great value for clinical diagnosis and surveillance purposes.
Cyclic carbamate analogs of pilocarpine (1989)

A number of pilocarpine analogues containing the (S)-3-ethyl-4-[(4'-imidazolyl)methyl]-2-oxazolidinone (9) structural feature were synthesized from L-histidine. With 1-benzyl-L-histidine as the key intermediate, a regiospecific synthetic route was developed to the N pi-methyl derivative 8. The regiochemistry of the alkylation of the imidazole nucleus was determined by measuring proton cross-ring coupling constants in the high-field 1H NMR. The effects on muscarinic receptors of these variously alkylated derivatives 6-10 were studied on isolated guinea pig ileum. The derivatives in which the imidazole nitrogen was unsubstituted (9), N tau-methylated (10), and N pi-methylated (8) were cholinergic muscarinic agonists with an increasing order of potency; compounds 6 and 7 were inactive. Analogue 8 with the same substitution pattern as pilocarpine was equipotent with pilocarpine, making these hydrolytically stable carbamate derivatives potentially useful drugs.
Thermotropic Poly(ester-<i>co</i>-carbonate) (1990)

A number of thermotropic polyester-carbonates were prepared through melt-polymerization of substituted hydroquinones and diphenyl terephthalate and diphenyl carbonate to have high molecular weight, with reduced viscosity in the range of 2-3. The molecular weights of the polymers can be advanced further by solid state heat-treatment, with the rate of postpolymerization depending on temperature and Concentration of catalyst. Samples of some compositions can be spun into high performance fibers and processed into self-reinforced plastics. The properties of thermotropic polyester-carbonates and polyesters were compared as fibers and plastics.