gebhart/patrepeval huggingface dataset:
Bayesian image estimation of digital chest radiography: Interdependence of noise, resolution, and scatter fraction (1995)

Previously, it has been shown that Bayesian image estimation (BIE) can reduce the effects of scattered radiation and improve contrast-to-noise ratios (CNR) in digital radiographs of anthropomorphic chest phantoms by improving contrast while constraining noise. Here, the use of BIE as a noise reduction technique is reported. An anthropomorphic phantom was imaged with a previously calibrated photostimulable phosphor system using standard bedside chest radiography protocols. The Bayesian technique was then used to process this image. BIE incorporates a radial exponential convolution scatter model with two adjustable parameters. In previous reports, these parameters were optimized to reduce the residual fraction of scattered radiation in the processed image. Here, the parameters were adjusted to evaluate the potential of BIE to reduce image noise. While the full width at half maximum of the scatter model was held constant, the magnitude was varied. Evaluation was based on residual scatter fractions and CNR. The magnitude of the kernel in the scatter model was varied from 0.0 to 2.5 in steps of 0.5. Previously, it was found that an "ideal" scatter kernel magnitude of 2.33 provided a minimum residual scatter fraction. This magnitude corresponds to the average scatter-to-primary ratio in the chest radiograph. As the magnitude was increased, the residual scatter fraction decreased and the CNR increased in both the lungs and the mediastinum. However, as the magnitude was decreased, the percent noise also decreased; therefore, a lower magnitude kernel reduces noise. By varying the magnitude of the kernel used, differing amounts of noise reduction and contrast enhancement can be obtained.(ABSTRACT TRUNCATED AT 250 WORDS)
LLAMA (2013)

LLAMA is a subsystem designed for new hardware environments that supports an API for page-oriented access methods, providing both cache and storage management. Caching (CL) and storage (SL) layers use a common mapping table that separates a page's logical and physical location. CL supports data updates and management updates (e.g., for index re-organization) via latch-free compare-and-swap atomic state changes on its mapping table. SL uses the same mapping table to cope with page location changes produced by log structuring on every page flush. To demonstrate LLAMA's suitability, we tailored our latch-free Bw-tree implementation to use LLAMA. The Bw-tree is a B-tree style index. Layered on LLAMA, it has higher performance and scalability using real workloads compared with BerkeleyDB's B-tree, which is known for good performance.
Raman Spectroscopy as a Versatile Tool for Investigating Thermochemical Processing of Coal, Biomass, and Wastes: Recent Advances and Future Perspectives (2020)

Raman spectroscopy, as a rapid, high-precision, and nondestructive tool, can be used for analyzing the samples from gas to solid, from ex situ to in situ, from organic macromolecule to minerals. It has been demonstrated as a powerful tool for characterizing carbonaceous solid fuels and their thermal conversion products. This review provides a systematic overview of the application of Raman spectroscopy for investigating the entire thermochemical processing of coal, biomass, and wastes. After introducing the fundamentals of Raman spectroscopy, its application for characterizing the feedstock (raw coals, biomass, and wastes) is reviewed. Then, using the Raman spectroscopy for ex situ characterization of the products (char and ash) after reactions and in situ diagnostic during reactions are discussed. Besides, some potential advanced Raman spectroscopy techniques are further briefly introduced. Lastly, the challenges and prospects of using Raman spectroscopy to study thermochemical processes are discussed.
INHA promoter polymorphisms are associated with premature ovarian failure (2005)

Inhibin is an important glycoprotein that is involved in folliculogenesis. INHA, the gene encoding the inhibin alpha subunit, was recently proposed as a candidate for premature ovarian failure (POF), a syndrome that leads to the cessation of ovarian function under the age of 40 years. 70 POF patients and 70 controls were screened for the previously identified INHA -16C>T transition mutation. The T allele was found in 31/70 (44.3%) of controls, but only 18/70 (25.7%) of POF patients. This result indicates that the T allele is significantly underrepresented in the POF patient population (Fisher's exact test, two-tail: P = 0.033). Sequence analysis of the INHA promoter in 50 POF patients and 50 controls identified a highly polymorphic imperfect TG repeat at approximately -300 bp, that consisted of four common haplotypes (A, B, C and D). The -16T allele is linked to the shortest repeat haplotype (haplotype C). Despite the association between haplotype C and POF, no significant difference was found between the promoter activity of a luciferase reporter construct containing haplotype C, and most of the other haplotypes tested. Interestingly, haplotype B failed to show any promoter activity. We conclude that the inheritance of specific INHA promoter haplotypes predispose to the development of premature ovarian failure.
Catalytic Transamidation under Moderate Conditions (2003)

The carboxamide group is generally inert, except under harsh conditions or in the presence of highly evolved enzymes. We have identified several metal complexes that efficiently catalyze transamidation reactions of amide/amine mixtures under moderate conditions. This unprecedented reactivity represents an important step toward our long-term goal of using dynamic combinatorial chemistry to generate new amide-based molecules with interesting structures and functions.
Micromagnetics of a soft underlayer (2000)

The micromagnetic properties of a soft underlayer in perpendicular media are studied. It is shown that stray fields from a recording layer can substantially modify magnetic properties of soft underlayer material. The degree of modification is determined by the characteristic bit size in the recording layer and by the soft underlayer material magnetic characteristics. It is found that there exists a thin layer within a soft underlayer with reduced permeability. The effects of the presence of such a reduced permeability region within a soft underlayer on both reading and writing processes are discussed.
Method for catalyzing a fuel cell electrode and an electrode so produced. [using electric potential with catalyst compound in solution with electrolyte] (1974)

A process for catalyzing an inert, porous conducting particle, hydrophobic bonded, substrate supported electrochemical cell electrode is described which comprises contacting the inert, porous conducting particle, hydrophobic-bonded portion of said electrode with the electrolyte composition applying a non-alternating electrical potential across the electrode between the substrate and the electrolyte, the electrical potential being of sufficient magnitude to increase the rate at which the electrolyte enters and fills the porous conducting particles, then causing a soluble catalyst-containing compound to enter into solution in the electrolyte within the electrode structure and depositing insoluble catalyst from said electrolyte solution onto the conducting particles.
Abstract 2939: Canonical and noncanonical survivin isoforms translocate to the plasma membrane and are secreted in exosomes (2020)

Abstract Background: Previously we found that survivin is expressed on the surface of cancer cells in vitro, and is targetable using certain survivin-specific antibodies. The survivin gene is alternatively spliced into two alternative isoforms, ΔEX3 and 2B, which diverge structurally from the canonical isoform in their C-termini but retain a conserved BIR (Baculovirus IAP Repeat) domain. Methods: In order to characterize plasma membrane survivin (PM-SVN), tagged proteins representing canonical survivin (isoform 1), Δex3 and 2B were transiently expressed in multiple cancer cell line backgrounds. Relative surface expression was measured by flow cytometry staining of intact cells. Mutant constructs were used to determine the structural requirements for translocation. Imaging flow cytometry (Imagestream) was used to visualize survivin isoform localization, and to detect co-localization on the cell surface. Secreted exosomes were examined for expression of survivin isoforms. Results: Isoforms 1, Δex3 and 2B could be detected on the surface of HEK293T embryonic kidney, HeLa cervical adenocarcinoma, U87 glioblastoma, and A1207 glioblastoma cells. PM-SVN expression was variable, however Δex3 showed robust membrane expression across all cell lines. Deletion of a predicted transmembrane sequence in Δex3's unique C-terminus did not impair its translocation, and deletion of the first 10 amino acids, thought to be required for dimerization, disrupted surface expression only in HEK293T cells. Imaging flow cytometry analysis of cells revealed polar localization of PM-SVN, with specific punctate areas seen in 13-20% of cells. Staining with antibodies targeting both isoform 1 and Δex3 showed co-immunofluorescence in cell membrane puncta, indicating the formation of heterodimers. Stressing cells by heat shock increased the proportion of PM-SVN in 293T and A1207 cells; in 293T, this was accompanied by enrichment of survivin protein in secreted exosomes. Conclusions: In addition to canonical survivin, isoforms Δex3 and 2B are displayed on the surface of cancer cells, and can be secreted as exosomal cargo. Membrane translocation may be stress-induced and appears to require the conserved BIR domain. PM-SVN shows a polar distribution on the cell membrane, and isoforms 1 and Δex3 heterodimerize within these puncta. Citation Format: Sheila Figel, Meaghan Birkemeier, Sanam Dharma, Emma Steinmetz, Michael Ciesielski, Robert Fenstermaker. Canonical and noncanonical survivin isoforms translocate to the plasma membrane and are secreted in exosomes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2939.
Gabor domain optical coherence microscopy (2010)

Optical Coherence Microscopy (OCM) utilizes a higher NA microscope objective in the sample arm of a low coherence interferometer than in Optical Coherence Tomography (OCT) to achieve axially and laterally high-resolution optical tomographic images. An increase in NA, however, leads to a dramatically decreased depth of focus (DOF), and hence shortens the imaging depth range so that high lateral resolution is maintained only within a small depth region around the focal plane. One solution to increase the depth of imaging while keeping a high lateral resolution is dynamic-focusing. Utilizing the voltage controlled refocus capability of a liquid lens, we have recently presented a solution for invariant high-resolution imaging using the liquid lens embedded within a fixed optics hand-held custom microscope. An implementation of the microscope for optical imaging using a broadband light source centered at 800 nm has been completed. Subsequently, we have developed Gabor-Domain Optical Coherence Microscopy (GD-OCM) that utilizes the high speed imaging of spectral domain OCT, the high lateral resolution of OCM, and the ability of real time refocusing of our custom design variable focus objective. In this paper, we provide an overview of the technology developed and highlight resent results. We also provide linkages to current related research in our group all directed at finding expedient pathways to the clinical settings.
Three-Dimensional Noninvasive Imaging of Ventricular Arrhythmias in Patients With Premature Ventricular Contractions (2017)

The present results demonstrate the excellent performance of the 3-D cardiac activation imaging technique in imaging the activation sequence associated with PVC, and localizing the initial sites of focal ventricular arrhythmias in patients. These promising results suggest that the 3-D cardiac activation imaging technique may become a useful tool for aiding clinical diagnosis and management of ventricular arrhythmias.
Micromachined Hot-Wire Thermal Conductivity Probe for Biomedical Applications (2009)

This paper presents the design, fabrication, numerical simulation, and experimental validation of a micromachined probe that measures thermal conductivity of biological tissues. The probe consists of a pair of resistive line heating elements and resistance temperature detector sensors, which were fabricated by using planar photolithography on a glass substrate. The numerical analysis revealed that the thermal conductivity and diffusivity can be determined by the temperature response induced by the uniform heat flux in the heating elements. After calibrating the probe using a material (agar gel) of known thermal conductivity, the probe was deployed to calculate the thermal conductivity of Crisco. The measured value is in agreement with that determined by the macro-hot-wire probe method to within 3%. Finally, the micro thermal probe was used to investigate the change of thermal conductivity of pig liver before and after RF ablation treatment. The results show an increase in thermal conductivity of liver after the RF ablation.
PANDA: Pose Aligned Networks for Deep Attribute Modeling (2014)

We propose a method for inferring human attributes (such as gender, hair style, clothes style, expression, action) from images of people under large variation of viewpoint, pose, appearance, articulation and occlusion. Convolutional Neural Nets (CNN) have been shown to perform very well on large scale object recognition problems. In the context of attribute classification, however, the signal is often subtle and it may cover only a small part of the image, while the image is dominated by the effects of pose and viewpoint. Discounting for pose variation would require training on very large labeled datasets which are not presently available. Part-based models, such as poselets [4] and DPM [12] have been shown to perform well for this problem but they are limited by shallow low-level features. We propose a new method which combines part-based models and deep learning by training pose-normalized CNNs. We show substantial improvement vs. state-of-the-art methods on challenging attribute classification tasks in unconstrained settings. Experiments confirm that our method outperforms both the best part-based methods on this problem and conventional CNNs trained on the full bounding box of the person.
Superconductors. [Nb/sub 3/Ge] (1977)

The structural quality of niobium germanide as a high-transition-temperature superconducting material is substantially improved by the presence of about 5 at. percent oxygen. Niobium germanide having this oxygen content may readily be prepared as a bulk coating bonded to a metallic substrate by chemical vapor deposition techniques. 2 figures, 1 table.
All-solid-state lock-in imaging for wide-field fluorescence lifetime sensing (2005)

Fluorescence Lifetime Imaging Microscopy (FLIM) is a powerful technique that is increasingly being used in the life sciences during the past decades. However, a broader application of FLIM requires more cost-effective and user-friendly solutions. We demonstrate the use of a simple CCD/CMOS lock-in imager for fluorescence lifetime detection. The SwissRanger SR-2 time-of-flight detector, originally developed for 3D vision, embeds all the functionalities required for FLIM in a compact system. The further development of this technology and its combination with light-emitting-and laser diodes could drive a wider spreading of thuse of FLIM including high-throughput applications.
Investigating the Effect of Garbage Collection on Service Level Objectives of Clouds (2017)

Platform as a Service (PaaS) clouds abstract large parts of the hardware/software stack to its tenant clients and provide it as a service. In this paper, we highlight the lack of scientific literature on the problem of Service Level Objective (SLO) satisfaction effects on clouds due to Garbage Collection (GC). To this end, we propose and implement CloudGC, a configurable PaaS application framework that aims in stressing the GC component of the underlying runtime. We use our CloudGC to experimentally evaluate the performance of the four GC policies (Gencon, Balanced, Optavgpause and Optthroughput) available in the IBM J9 Java Runtime, running on top of a local and isolated installation of the PaaS software Cloud Foundry.
AlGaN-GaN Double-Channel HEMTs (2005)

We present the design, fabrication, and characterization of AlGaN-GaN double-channel HEMTs. Two carrier channels are formed in an AlGaN-GaN-AlGaN-GaN multilayer structure grown on a sapphire substrate. Polarization field in the lower AlGaN layer fosters formation of a second carrier channel at the lower AlGaN-GaN interface, without creating any parasitic conduction path in the AlGaN barrier layer. Unambiguous double-channel behaviors are observed at both dc and RF. Bias dependent RF small-signal characterization and parameter extraction were performed. Gain compression at a high current level was attributed to electron velocity degradation induced by interface scattering. Dynamic IV measurement was carried out to analyze large-signal behaviors of the double-channel high-electron mobility transistors. It was found that current collapse mainly occurs in the channel closer to device surface, while the lower channel suffers minimal current collapse, suggesting that trapping/detrapping of surface states is mainly responsible for current collapse. This argument is supported by RF large-signal measurement results.
Sapphire: A Configurable Crypto-Processor for Post-Quantum Lattice-based Protocols (2019)

Public key cryptography protocols, such as RSA and elliptic curve cryptography, will be rendered insecure by Shor’s algorithm when large-scale quantum computers are built. Cryptographers are working on quantum-resistant algorithms, and lattice-based cryptography has emerged as a prime candidate. However, high computational complexity of these algorithms makes it challenging to implement lattice-based protocols on low-power embedded devices. To address this challenge, we present Sapphire – a lattice cryptography processor with configurable parameters. Efficient sampling, with a SHA-3-based PRNG, provides two orders of magnitude energy savings; a single-port RAM-based number theoretic transform memory architecture is proposed, which provides 124k-gate area savings; while a low-power modular arithmetic unit accelerates polynomial computations. Our test chip was fabricated in TSMC 40nm low-power CMOS process, with the Sapphire cryptographic core occupying 0.28 mm2 area consisting of 106k logic gates and 40.25 KB SRAM. Sapphire can be programmed with custom instructions for polynomial arithmetic and sampling, and it is coupled with a low-power RISC-V micro-processor to demonstrate NIST Round 2 lattice-based CCA-secure key encapsulation and signature protocols Frodo, NewHope, qTESLA, CRYSTALS-Kyber and CRYSTALS-Dilithium, achieving up to an order of magnitude improvement in performance and energy-efficiency compared to state-of-the-art hardware implementations. All key building blocks of Sapphire are constant-time and secure against timing and simple power analysis side-channel attacks. We also discuss how masking-based DPA countermeasures can be implemented on the Sapphire core without any changes to the hardware.
Synthesis and In Vitro Opioid Receptor Functional Antagonism of Methyl-Substituted Analogues of (3<i>R</i>)-7-Hydroxy-<i>N</i>-[(1<i>S</i>)-1-{[(3<i>R</i>,4<i>R</i>)-4-(3-hydroxyphenyl)-3,4-dimethyl-1-piperidinyl]methyl}-2-methylpropyl]-1,2,3,4-tetrahydro-3-isoquinolinecarboxamide (JDTic) (2009)

In previous structure−activity relationship (SAR) studies, (3R)-7-hydroxy-N-[(1S)-1-{[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethyl-1-piperidinyl]methyl}-2-methylpropyl]-1,2,3,4-tetrahydro-3-isoquinolinecarboxamide (JDTic, 3) was identified as the first potent and selective κ-opioid receptor antagonist from the trans-3,4-dimethyl-4-(3-hydroxyphenyl)piperidine class of opioid antagonists. In the present study, we report the synthesis of analogues 8a−p of 3 and present their in vitro opioid receptor functional antagonism using a [35S]GTPγS binding assay. Compounds 8a−p are analogues of 3 containing one, two, or three methyl groups connected to the JDTic structure at five different positions. All the analogues with one and two added methyl groups with the exception of 8k had subnanomolar Ke values at the κ receptor. The three most potent analogues were the monomethylated (3R)-7-hydroxy-N-[(1S,2S)-1-{[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidine-1-yl]methyl}-2-methylbutyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxamide (8a) and (3R)-7-hydroxy-N-[(1S)-1-{[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]methyl}-(2-methylpropyl)]-3-methyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide (8e) with Ke values of 0.03 nM at the κ receptor and (3R)-7-hydroxy-N-[(1S)-1-{[(3R,4R)-4-(3-methoxyphenyl)-3,4-dimethylpiperidin-1-yl]methyl}-2-methylpropyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxamide (8d) with Ke = 0.037 nM at the κ receptor. All three compounds were selective for the κ receptor relative to the μ and δ receptors. Overall, the results from this study highlight those areas that are tolerant to substitution on 3.
Robust and Persistent Replication of the Genotype 6a Hepatitis C Virus Replicon in Cell Culture (2014)

Genotype 6 (GT6) hepatitis C virus (HCV) is prevalent in Southeast Asia and southern China, where it can constitute up to 50% of HCV infections. Despite this, no direct-acting antivirals are approved to treat GT6 HCV infection, and no cell culture systems have been described. In this study, we aimed to develop a GT6 HCV subgenomic replicon to facilitate the identification and development of new HCV therapies with pan-genotype activity. A subgenomic replicon cDNA encoding a GT6a consensus sequence plus an NS5A amino acid substitution (S232I) was synthesized. Electroporation of RNA encoding the GT6a replicon into Huh-7-derived cells consistently yielded 20 to 100 stable replicon colonies. Genotypic analyses of individual replicon colonies revealed new adaptive mutations across multiple viral nonstructural proteins. The E30V and K272R mutations in NS3 and the K34R mutation in NS4A were observed most frequently and were confirmed to enhance GT6a replicon replication in the presence of the NS5A amino acid substitution S232I. These new adaptive mutations allowed establishment of robust luciferase-encoding GT6a replicons for reproducible quantification of HCV replication, and the luciferase-encoding replicons enabled efficient determinations of antiviral activity for HCV inhibitors in a 384-well assay format. While nucleoside/nucleotide NS5B inhibitors and cyclophilin A inhibitors had similar antiviral activities against both GT6a and GT1b replicons, some nonnucleoside NS5B inhibitors, NS3 protease inhibitors, and NS5A inhibitors had less antiviral activity against GT6a replicons. In conjunction with other genotype replicons, this robust GT6a replicon system will aid in the development of pan-genotypic HCV regimens.