gebhart/patrepeval huggingface dataset:
Proteins in aqueous humor from cataract patients with and without pseudoexfoliation syndrome : A quantitative investigation using isobaric tags and mass spectrometry (2008)

Development and improvement of analytical techniques are vital in analytical chemistry research. This thesis describes the development and use of tailored surfaces for bioanalytical applications. In sample preparation, solid phase extraction is often used and the development of a protocol for extraction on a molecular imprinted polymer (MISPE) directly from plasma sample is presented. Molecular imprinted polymers (MIP) offer selective sorbents for the imprinted analyte. MISPE has mainly been used in organic phase but in this thesis the development of a protocol for direct extraction of the analyte form an aqueous phase is described. For analysis of complex samples a separation step is often needed. The growing interest in analysis of biological samples and analysis of the human proteome and potential biomarkers has increased the interest in developing new separation techniques. Capillary electrophoresis (CE) has evolved into an important technique for use in analysis of body fluids. In this thesis a novel polyamine coating named PolyE 323 tailored for minimizing the adsorption of basic proteins to the surface is introduced. A straightforward coating protocol, with four simple rinsing steps, was developed. The coating was highly reproducible and useable over a wide pH range. Successful protein separations on PolyE-323-coated capillaries coupled to electrospray ionization mass spectrometry (ESI-MS) were demonstrated. The coated capillaries were also used in studies of protein content of aqueous humor samples from cataract patients as a complement to capillary liquid chromatography. In the studies presented the protein content of aqueous humor samples from two clinical groups was compared. By using capillary liquid separation techniques coupled to matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and MS/MS in combination with isobaric tags for relative and absolute quantitation (iTRAQ) the identity and relative concentrations of proteins in the samples were evaluated. Earlier studies of the proteins in these kinds of samples have mainly been done with techniques using immunological detection where the proteins of interest were chosen in advance. In this thesis it was shown that liquid-based separation techniques are a good complement and by using the mass spectrometry approach presented the protein content of the samples could be evaluated without bias.
2D free‐breathing dual navigator‐gated cardiac function validated against the 2D breath‐hold acquisition (2008)

The FB cine acquisition provided results qualitatively and quantitatively similar to 2D BH methods with improved slice registration.
Geometric Sampling of Images, Vector Quantization and Zador’s Theorem (2013)

We present several consequences of the geometric approach to image sampling and reconstruction we have previously introduced. We single out the relevance of the geometric method to the vector quantization of images and, more important, we give a concrete and candidate for the optimal embedding dimension in Zador’s Thorem. An additional advantage of our approach is that that this provides a constructive proof of the aforementioned theorem, at least in the case of images. Further applications are also briefly discussed. 1.
Electron-optical-phonon interaction in the In0.73Ga0.27As–AlAs intersubband laser (2005)

The magnetic-field dependence of the operation of a quantum-cascade intersubband laser (QCL) is used to investigate the energetic relaxation of injected electrons through phonon emission. The QCL emits at 3.8μm and incorporates a strain-compensated active region with a large degree of internal strain. Energies of the relevant electron-phonon scattering responsible for the depopulation of the upper laser level are determined from the analysis of the Landau-level spectra. A comparison of those energies with the Raman spectrum of the active region is used to identify which phonon is primarily involved in the electron-phonon scattering. In spite of the low Ga-content in the (In,Ga)As quantum wells and high Al-content in the AlAs∕(In,Al)As composite barriers, the depopulation of the upper laser level appears to be dominated by the resonant electron-GaAs-like-longitudinal-phonon intersubband scattering. In particular, the contribution due to AlAs-like modes is negligible.
The effect of fan operating point and location on temperature distribution in electronic systems (2003)

This paper investigates the effects of fan operating point and location on the temperature distribution in a simple test electronic system. First the investigation is performed with the fan mounted at the system outlet and drawing air through the system. Then the investigation is performed with the fan mounted at system inlet, pushing air through the system. Both cases were investigated at three flow rates within the fan's recommended operating range. In each case, Particle Image Velocimetry (PIV) was used to measure system air flow and infra red thermography was used to measure PCB surface temperature. At each flow rate examined, PIV showed the air velocity to be uniform in direction and magnitude in the system with the fan mounted at system outlet, with local velocities changing in proportion to the flow rate. PCB temperature increased with reduced flow rate. In the system with the fan mounted at inlet, flow had large tangential components, impingement onto the PCB and reverse flow. Mean PCB temperature was found to be unchanged by flow rate, due to the increased thermal mixing which occurred at lower flow rates. This paper illustrates the gains, which can be made through correct fan placement, and discusses how heat transfer coefficients within fan cooled electronic systems can be optimised throughout the fan operating range.
Surface plasmon enhanced bright light emission from InGaN/GaN (2007)

Abstract Surface plasmon (SP) coupling technique was used to enhance blue and green light emissions from InGaN/GaN quantum wells (QWs). Large enhancement of photoluminescence (PL) of both blue and green emissions was observed with silver coated samples, whereas the enhancements were not so effective for the gold coated samples. We could obtain well enhanced green emission by tuning the matching condition of QW‐SP coupling with nano‐grating structures at gold layers. This method should be useful to design even more efficient structures and to fabricate super bright light emitting devices. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Verification column (2015)

In this issue of the SIGLOG newsletter, the technical column on verification presents an invited contribution on "Algorithmic Logic-Based Verification" by Arie Gurfinkel (Software Engineering Institute / Carnegie Mellon University), Temesghen Kahsai (NASA Ames / Carnegie Mellon University), and Jorge Navas (NASA Ames / SGT Inc.). The increasing number of programming languages and intermediate representations poses an obstacle in the development of a unified verification framework. The article presents a case for the use of Constrained Horn Clauses (CHC) as a universal representation for transition systems to overcome this obstacle. This article should be of special interest to the readers of this newsletter as CHCs have been used in various logic-based application domains, but are relatively new to the domain of verification. I would like to thank the authors for submitting the article.
Multi-view Image-based Hand Geometry Refinement using Differentiable Monte Carlo Ray Tracing (2021)

The amount and quality of datasets and tools available in the research field of hand pose and shape estimation act as evidence to the significant progress that has been made. We find that there is still room for improvement in both fronts, and even beyond. Even the datasets of the highest quality, reported to date, have shortcomings in annotation. There are tools in the literature that can assist in that direction and yet they have not been considered, so far. To demonstrate how these gaps can be bridged, we employ such a publicly available, multi-camera dataset of hands (InterHand2.6M), and perform effective image-based refinement to improve on the imperfect ground truth annotations, yielding a better dataset. The image-based refinement is achieved through raytracing, a method that has not been employed so far to relevant problems and is hereby shown to be superior to the approximative alternatives that have been employed in the past. To tackle the lack of reliable ground truth, we resort to realistic synthetic data, to show that the improvement we induce is indeed significant, qualitatively, and quantitatively, too.
Supplementary Table 4 from Transcriptional Profiling Identifies Cyclin D1 as a Critical Downstream Effector of Mutant Epidermal Growth Factor Receptor Signaling (2023)

Supplementary Table 4 from Transcriptional Profiling Identifies Cyclin D1 as a Critical Downstream Effector of Mutant Epidermal Growth Factor Receptor Signaling
A Decade of HIV-1 Drug Resistance in the United States: Trends and Characteristics in a Large Protease/Reverse Transcriptase and Co-Receptor Tropism Database from 2003 to 2012 (2013)

Decreased prevalence of three-class resistance and increased prevalence of one-class resistance was observed within samples reported between 2003 and 2012. The fraction of CXCR4-tropic viruses has decreased over time; however, CXCR4 usage was more prevalent among multi-class-resistant samples, which may be due to the more advanced disease stage of treatment-experienced patients. These trends have important implications for clinical practice and future drug discovery and development.
Enhancement of beta-catenin in cardiomyocytes suppresses survival protein expression but promotes apoptosis and fibrosis (2016)

Taken together, these results revealed that altered Wnt/b-catenin signaling might provoke heart failure. (Cardiol J 2017; 24, 2: 195-205).
Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits (2020)

Red blood cell (RBC) traits are important heritable clinical biomarkers and modifiers of disease severity. To identify coding genetic variants associated with these traits, we conducted meta-analys ...
SRv6 BGP based Overlay services (2019)

This draft defines procedures and messages for SRv6-based services
including L3VPN, EVPN and Internet services. It builds on RFC4364
BGP/MPLS IP Virtual Private Networks (VPNs) and RFC7432 BGP MPLS-
Based Ethernet VPN.
56. Foretinib Enhances Myelination of Neurons in Vitro (2023)

BACKGROUND: Nerve injuries cause significant functional impairment. Despite advanced diagnostic methods and microsurgical procedures, recovery after peripheral nerve repair is often disappointing. Therefore, new therapeutics are needed to promote recovery after nerve injury. Schwann cells play a crucial role in nerve repair and regeneration, including remyelination post-injury. Our group previously discovered that Foretinib, a pan-kinase inhibitor, is neuroprotective (Feinberg et al., 2017). In the present study, we ask whether foretinib affects myelination in vitro. METHODS: To test the effect of foretinib on myelination in vitro, we extracted dorsal root ganglia from E14 rats and co-cultured them with Schwann cells. After three days, we induced myelination with ascorbic acid or ascorbic acid plus foretinib. After ten days in culture, we performed immunohistochemistry using the myelination marker myelin basic protein (MBP) to assess the extent of myelination. RESULTS: Co-cultures with neuronal cells and Schwann cells ten days after inducing myelination demonstrated a significant increase (more than six-fold) in myelination with foretinib in vitro CONCLUSION: Foretinib increases myelination in vitro, possibly by virtue of the mechanism of mitochondrial preservation as noted in our previous studies, or perhaps by a new, as yet unidentified molecular pathway. Given these intriguing findings, our group is interested in conducting studies of this agent in vivo as a potential agent for future clinical application.
THE CELL AGAR PLATE SCREENING FOR ANTITUMOR CELL EFFECT I. SCREENING RESULTS OF 1300 ORGANIC COMPOUNDS (1959)

The cell agar plate screening method for antitumor cell effect (Yamazaki et al., 1956) was applied to 1300 organic compounds. The method is based on the inhibition of the dehydrogenase activity (on 2, 6-dichlorophenol indophenol) of cancer cells mixed in the agar containing Hanks' solution. The inhibitory activity against dehydrogenase system of cancer cell is arbitrarily expressed by mm in diameter of non-reduced zone on the agar surface around the cylinder containing a drug suspension, in a way analogous to the cylinder plate assay for antibacterial substances. The preliminary report was already published (Mizuno et al., 1957) .
How thin barrier metal can be used to prevent Co diffusion in the modern integrated circuits? (2017)

In modern integrated circuits (ICs), billions of transistors are connected to each other via thin metal layers (e.g. copper, cobalt, etc) known as interconnects. At elevated process temperatures, inter-diffusion of atomic species can occur among these metal layers, causing sub-optimal performance of interconnects, which may lead to the failure of an IC. Thus, typically a thin barrier metal layer is used to prevent the inter-diffusion of atomic species within interconnects. For ICs with sub-10 nm transistors (10 nm technology node), the design rule (thickness scaling) demands the thinnest possible barrier layer. Therefore, here we investigate the critical thickness of a titanium–nitride (TiN) barrier that can prevent the cobalt diffusion using multi-scale modeling and simulations. First, we compute the Co diffusion barrier in crystalline and amorphous TiN with the nudged elastic band method within first-principles density functional theory simulations. Later, using the calculated activation energy barriers, we quantify the Co diffusion length in the TiN metal layer with the help of kinetic Monte Carlo simulations. Such a multi-scale modelling approach yields an exact critical thickness of the metal layer sufficient to prevent the Co diffusion in IC interconnects. We obtain a diffusion length of a maximum of 2 nm for a typical process of thermal annealing at 400 °C for 30 min. Our study thus provides useful physical insights for the Co diffusion in the TiN layer and further quantifies the critical thickness (~2 nm) to which the metal barrier layer can be thinned down for sub-10 nm ICs.
ENDOSCOPIC ESOPHAGEAL VARICEAL BAND LIGATION: HOW INTENSIVELY SHOULD WE LIGATE? (1998)

American Journal of Gastroenterology: February 1998 - Volume 93 - Issue 2 - p 135-137 doi: 10.1111/j.1572-0241.1998.135_1.x
A Benchmark for Generalizable and Interpretable Temporal Question Answering over Knowledge Bases (2022)

Knowledge Base Question Answering (KBQA) tasks that involve complex reasoning are emerging as an important research direction. However, most existing KBQA datasets focus primarily on generic multi-hop reasoning over explicit facts, largely ignoring other reasoning types such as temporal, spatial, and taxonomic reasoning. In this paper, we present a benchmark dataset for temporal reasoning, TempQA-WD, to encourage research in extending the present approaches to target a more challenging set of complex reasoning tasks. Specifically, our benchmark is a temporal question answering dataset with the following advantages: (a) it is based on Wikidata, which is the most frequently curated, openly available knowledge base, (b) it includes intermediate sparql queries to facilitate the evaluation of semantic parsing based approaches for KBQA, and (c) it generalizes to multiple knowledge bases: Freebase and Wikidata. The TempQA-WD dataset is available at https://github.com/IBM/tempqa-wd.
Platforms for GHz Microplasma-Material Studies (2017)

Split-ring resonators and a dielectric-loaded, double-ridge waveguide are developed as platforms for studying plasmamaterial interactions when igniting and sustaining plasmas using microwaves. Split-ring resonators have been studied extensively in the past as devices for microplasma formation using microwaves <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> . Here, we utilize simulations to inform the design of rings. In order to expedite materials studies, we study screen-printing as a method for producing split-ring resonators which resonate at 2.7GHz. The effects of different materials on plasma generation and plasma damage are explored in Ar and air plasmas.
Progress toward an Antibody Glycosidase (1994)

The piperidine-based hapten 1 generates monoclonal antibodies that catalyze the hydrolysis of substrate 2 at pH5.5 (kcal = 0.904 h−1, KM = 324 μM). Hapten 1 is a competitive inhibitor of the antibody-catalyzed reaction. These results are significant for the development of antibodies for the sequence-specific hydrolysis of oligosaccharides.
Molecular Modeling of the Human P2Y2 Receptor and Design of a Selective Agonist, 2′-Amino-2′-deoxy-2-thio-UTP (2020)

A rhodopsin-based homology model of the nucleotide-activated human P2Y2 receptor, including loops, termini, and phospholipids, was optimized with Monte Carlo Multiple Minimum. Docked UTP formed a nucleobase π–π complex with conserved Phe3.32. Selectivity-enhancing 2′-amino-2′-deoxy substitution interacted through π-hydrogen bonding with aromatic Phe6.51 and Tyr3.33. A “sequential ligand composition” approach for docking the flexible dinucleotide agonist Up4U demonstrated a shift of conserved cationic Arg3.29 from the UTP γ position to δ position of Up4U and Up4ribose. Sysnthesized nucleotides were tested as agonists at human P2Y receptors expressed in 1321N1 astrocytoma cells. 2′-Amino and 2-thio modifications synergized to enhance potency and selectivity; compound 8 (8 nM EC50) was 300-fold P2Y2-selective versus P2Y4. 2′-Amine acetylation reduced potency, and trifluoroacetylation produced intermediate potency. 5-Amino nucleobase substitution did not enhance potency through a predicted hydrophilic interaction, possibly because of destabilization of the receptor-favored (N)-ribose conformation. This detailed view of P2Y2 receptor recognition suggests mutations for model validation.
Device Channel Temperature Measurement Using NIR Emission (2017)

Abstract In this paper, we present a technique for device temperature measurement using spontaneous near infrared (NIR) emission from an Integrated Circuit (IC). By leveraging modeling and data analysis, time-integrated emission measurements are used to estimate the temperature increase due to switching activity inside the channel of CMOS transistors. The non-invasive nature of the technique allows one to reliably monitor the temperature of any device on-chip without the need for circuit modifications or dedicated on-chip sensors and with a higher spatial resolution than thermal cameras. This method has important applications for modeling heat dissipation during early process development, localizing hot spots, calibrating on-chip sensors, etc. In this paper, temperature is estimated by fitting empirical emission data to an emission model that can be solved for device channel temperature.
Organization of Motor Proteins into Functional Micropatterns Fabricated by a Photoinduced Fenton Reaction (2009)

Walking the line: Selective photodestruction of nitrilotriacetic acid moieties on a poly(ethylene glycol) polymer brush by a light-induced Fenton reaction enabled the functional organization of motor proteins into micropatterns (see schematic illustration). Microtubules were selectively captured on the structures, and adenosine triphosphate dependent transport along lines was observed.
Inverse Global Illumination using a Neural Radiometric Prior (2023)

Inverse rendering methods that account for global illumination are becoming more popular, but current methods require evaluating and automatically differentiating millions of path integrals by tracing multiple light bounces, which remains expensive and prone to noise. Instead, this paper proposes a radiometric prior as a simple alternative to building complete path integrals in a traditional differentiable path tracer, while still correctly accounting for global illumination. Inspired by the Neural Radiosity technique, we use a neural network as a radiance function, and we introduce a prior consisting of the norm of the residual of the rendering equation in the inverse rendering loss. We train our radiance network and optimize scene parameters simultaneously using a loss consisting of both a photometric term between renderings and the multi-view input images, and our radiometric prior (the residual term). This residual term enforces a physical constraint on the optimization that ensures that the radiance field accounts for global illumination. We compare our method to a vanilla differentiable path tracer, and more advanced techniques such as Path Replay Backpropagation. Despite the simplicity of our approach, we can recover scene parameters with comparable and in some cases better quality, at considerably lower computation times.
Supplementary Table 5 from Androgen Receptor Gene Aberrations in Circulating Cell-Free DNA: Biomarkers of Therapeutic Resistance in Castration-Resistant Prostate Cancer (2023)

&lt;p&gt;Supplementary Table 5. Univariate and multivariate analysis examining association between pre-treatment clinico-pathological factors and progression-free survival (radiographic and/or clinical) in patients switched onto enzalutamide after collection of circulating cell-free DNA (n = 39)&lt;/p&gt;
Response to the Letter by Pfutzner and Forst (2002)

Pfutzner and Forst (1) report that they found no significant blood glucose (BG) differences between the arm and finger during 1 ) BG decrease induced by intravenous insulin injection, and 2 ) BG increase and decrease induced by a standardized meal in combination with subcutaneous insulin injection.

As previously suggested by Pfutzner and Forst, the observed differences between our data and their observations are caused by differences in experimental design. Our study protocol aimed at rapid BG decreases and achieved a mean BG change at the finger (averaged over total decline) of 3 mg · dl−1 · min−1. Hypoglycemic values at the finger were reached faster after insulin injection. This velocity has not been repeated by Pfutzner and Forst, as their mean rate of BG decline did not exceed 2 mg · dl− · min−1 during the first hour after insulin injection and fell below 1 mg · dl−1 · min …
Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants (2021)

Neutralizing antibodies (nAbs) elicited against the receptor binding site (RBS) of the spike protein of wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are generally less effective against recent variants of concern. RBS residues Glu<sup>484</sup>, Lys<sup>417</sup>, and Asn<sup>501</sup> are mutated in variants first described in South Africa (B.1.351) and Brazil (P.1). We analyzed their effects on angiotensin-converting enzyme 2 binding, as well as the effects of two of these mutations (K417N and E484K) on nAbs isolated from COVID-19 patients. Binding and neutralization of the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2), which can both bind the RBS in alternative binding modes, are abrogated by K417N, E484K, or both. These effects can be structurally explained by their extensive interactions with RBS nAbs. However, nAbs to the more conserved, cross-neutralizing CR3022 and S309 sites were largely unaffected. The results have implications for next-generation vaccines and antibody therapies.