gebhart/patrepeval huggingface dataset:
Lipocalin-type Prostaglandin D Synthase (β-Trace) Is a Newly Recognized Type of Retinoid Transporter (1997)

Lipocalin-type prostaglandin D synthase is responsible for the biosynthesis of prostaglandin D2 in the central nervous system and the genital organs and is secreted into the cerebrospinal fluid and the seminal plasma as beta-trace. Here we analyzed retinoids binding of the enzyme by monitoring the fluorescence quenching of an intrinsic tryptophan residue, and appearance of circular dichroism around 330 nm, and a red shift of the UV absorption spectra of retinoids. We found that the enzyme binds all-trans- or 9-cis-retinoic acid and all-trans- or 13-cis-retinal, but not all-trans-retinol, with affinities (Kd of 70-80 nM) sufficient for function as a retinoid transporter. All-trans-retinoic acid inhibited the enzyme activity in a noncompetitive manner, suggesting that it binds to the same hydrophobic pocket as prostaglandin H2, the substrate for prostaglandin D synthase, but at a different site in this pocket. It is likely that this enzyme is a bifunctional protein that acts as both retinoid transporter and prostaglandin D2-producing enzyme.
Proenkephalin for the early detection of acute kidney injury in hospitalized patients with chronic kidney disease (2018)

Delta PENK levels improve the early detection of contrast-induced AKI in CKD patients over serial creatinine sampling. Delta PENK accelerates the detection of creatinine-blind AKI by 24 hours.
Investigation of the Exometabolomic Profiles of Rat Islets of Langerhans Cultured in Microfluidic Biochip (2022)

Diabetes mellitus (DM) is a complex disease with high prevalence of comorbidity and mortality. DM is predicted to reach more than 700 million people by 2045. In recent years, several advanced in vitro models and analytical tools were developed to investigate the pancreatic tissue response to pathological situations and identify therapeutic solutions. Of all the in vitro promising models, cell culture in microfluidic biochip allows the reproduction of in-vivo-like micro-environments. Here, we cultured rat islets of Langerhans using dynamic cultures in microfluidic biochips. The dynamic cultures were compared to static islets cultures in Petri. The islets' exometabolomic signatures, with and without GLP1 and isradipine treatments, were characterized by GC-MS. Compared to Petri, biochip culture contributes to maintaining high secretions of insulin, C-peptide and glucagon. The exometabolomic profiling revealed 22 and 18 metabolites differentially expressed between Petri and biochip on Day 3 and 5. These metabolites illustrated the increase in lipid metabolism, the perturbation of the pentose phosphate pathway and the TCA cycle in biochip. After drug stimulations, the exometabolome of biochip culture appeared more perturbed than the Petri exometabolome. The GLP1 contributed to the increase in the levels of glycolysis, pentose phosphate and glutathione pathways intermediates, whereas isradipine led to reduced levels of lipids and carbohydrates.
Composite nanoparticles for defectivity reduction during CMP (2004)

The synthesis and characterization of nanoparticles comprising a polymer core and a silica shell, with and without a silane-coupling agent between the core and the shell, is presented in this paper. The first step in the nanoparticle synthesis is a “surfactant free” radical suspension polymerization in water of monomeric units of methylmethacrylate in the presence of methoxypolyethilene glycol methacrylate, as a comonomer, and 4-vynilpyridine. Vynilpyridine provides electrostatic stabilization in the form of functional basic amino groups located at the polymer surface, as confirmed by FTIR analysis. In the second step of the procedure, the Polymethyl Methacrylate (PMMA) spheres were mixed with silica spheres. Dynamic Light Scattering (DLS) measurements were used to correlate particle size to pH or ionic strength, while Electrophoretic Light Scattering (ELS) measurements revealed the dependency of the zeta potential on pH or ionic strength (I). Since the interaction between the abrasives and the wafer surface in the CMP process is expected to be dependent also on the particle morphology and structure of the polymer core, N2 adsorption isotherms on PMMA were taken to evaluate porosity and total surface area using the Brunauer-Emmett-Teller (BET) method.
P1B-8 Experimental Investigation of the Effects of Gas Pockets on HIFU Field (2007)

The paper describes experimental and numerical studies of the effects of gas pockets on HIFU filed. Spherical air bubbles ranging from 1.5 to 5.0 mm diameter were produced in transparent polyacrylamide tissue mimicking gels. A single element 3.5 MHz HIFU transducer was used for sonication of the gel phantoms. Diffused backlight visualization technique was used to observe lesion formation in the tissue models. The changes in the HIFU beam pattern for air bubbles at different positions were visualized by schlieren method. Quantitative measurement of pressure at the HIFU focus by a calibrated needle hydrophone showed considerable reduction in the focal pressure with the presence of a pre-focal air pocket. The effects were simulated numerically and good agreement with experiments was obtained. The results provide guidelines for evaluation of potential safety concerns produced by trapped gas- pockets in various HIFU therapies.
SiGe-Driven Hybrid-Integrated Silicon Photonic Link Using Optical-Domain Equalization (2018)

We report 50- and 60-Gb/s hybrid-integrated optical links in the O-band with CMOS photonic components driven by silicon-germanium ICs using optical-domain feed-forward equalization. The link includes a segmented-electrode Mach-Zehnder modulator and a Ge photodetector that provide high bandwidths and the potential for tight integration with control and monitoring electronics. The combination of these features enables the demonstration of a 60-Gb/s AC-coupled link and a 50-Gb/s DC-coupled link with bit error rates below 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-12</sup> without the use of forward-error correction codes. This result provides a promising path toward extending speeds in latency sensitive optical links.
Supplementary Figure 2 from Antigen Shedding May Improve Efficiencies for Delivery of Antibody-Based Anticancer Agents in Solid Tumors (2023)

&lt;p&gt;PDF file - 66K, Kinetic steps that control the surface receptor concentration&lt;/p&gt;
Efficient sparse-to-dense optical flow estimation using a learned basis and layers (2015)

We address the elusive goal of estimating optical flow both accurately and efficiently by adopting a sparse-to-dense approach. Given a set of sparse matches, we regress to dense optical flow using a learned set of full-frame basis flow fields. We learn the principal components of natural flow fields using flow computed from four Hollywood movies. Optical flow fields are then compactly approximated as a weighted sum of the basis flow fields. Our new PCA-Flow algorithm robustly estimates these weights from sparse feature matches. The method runs in under 200ms/frame on the MPI-Sintel dataset using a single CPU and is more accurate and significantly faster than popular methods such as LDOF and Classic+NL. For some applications, however, the results are too smooth. Consequently, we develop a novel sparse layered flow method in which each layer is represented by PCA-Flow. Unlike existing layered methods, estimation is fast because it uses only sparse matches. We combine information from different layers into a dense flow field using an image-aware MRF. The resulting PCA-Layers method runs in 3.2s/frame, is significantly more accurate than PCA-Flow, and achieves state-of-the-art performance in occluded regions on MPI-Sintel.
Synthesis and characterization of ionic conducting sulfonated polybenzimidazoles Part A Polymer chemistry (2010)

By copolymerization of the disodium-2,2′-disulfonate-4,4′-oxydibenzoic acid (SODBA), the 4,4′-oxybis(benzoic acid) (OBBA) with the bis 3,4-(diaminophenyl)sulfone (BDAPS), a series of high molecular weight sulfonated polybenzimidazoles (sPBI) were prepared by varying the ratio of monomers SODBA/OBBA. Polymers with ion exchange capacity (IEC) ranging from 0 to 3.2 meqH⁺/g were obtained. The chemical structure of the sPBI was confirmed by NMR, Fourier-transform infra-red (FTIR). Although the sPBI display a very poor solubility in organic solvents, they are, in the ammonium salt form, soluble in polar aprotic solvents such as DMF, NMP, or DMSO. Tough and ductile membranes from solution casting method were prepared. The water uptake and the ionic conductivity were determined at 30 and 90 °C.
Substrate temperature measurements using ultrasonically bonded Platinel II thermocouples (1992)

The accurate measurement of substrate temperature is important for thin-film deposition processes. In this paper, we report a simple and reproducible method to bond thermocouples directly to a substrate, thus circumventing many difficulties of other temperature measurement techniques. We have ultrasonically bonded 25-μm-diam wires of two different Au-Pt-Pd alloys (14%-31%-55% and 65%-0%-35%), commercially known as Platinel II, to gold bonding pads evaporated onto several surfaces: stainless steel, LaAlO3, Al2O3, and YBa2Cu3O7−x (YBCO) thin films. The ultrasonic bonding process does not change the thermal emf of the thermocouple from the bulk value, and the resultant bond is able to withstand temperature cycling from room temperature to at least 800 °C without detachment of the thermocouple from the surface or change in its thermal emf. We have used these thermocouples to measure the surface temperature of a LaAlO3 substrate and a 2000-Å YBCO film on a LaAlO3 substrate in order to evaluate the effectiveness of silver paste as a thermal contact to anchor substrates to a heater block during the sputter deposition of YBCO thin films. Silver paste is found to provide an excellent contact. At a heater temperature of 750 °C, the temperature difference between the surface of the LaAlO3 substrate and the surface of the heater was 348 °C without silver paste and only 2 °C with silver paste.
Gas separation membranes: needs for combined materials science and processing approaches (2002)

Huge markets would exist for high volume gas separation membranes if more robust and higher selectivity membranes were economically available. Many of these markets include totally new paradigms, such as fuel cell driven vehicles and membrane reactors for hydrocarbon production. Other markets involve displacing entrenched large scale separations processes with more advanced versions of first generation “conventional” membranes. Existing materials and formation processes cannot exploit most of these opportunities, so basic research is needed. This research must occur with an awareness that competition to displace highly optimized conventional technologies such as absorption, cryogenic distillation and adsorption must consider economic as well as technical efficacy. Next generation membrane processes should, therefore, maintain attractive economics associated with current polymer-based membranes, while greatly extending performance properties. Several “contender” strategies based largely on polymers and specialized polymer processing approaches for achieving this ambitious goal will be considered in more detail.
A Proximity Measure using Blink Model (2016)

This paper proposes a new graph proximity measure. This measure is a derivative of network reliability. By analyzing its properties and comparing it against other proximity measures through graph examples, we demonstrate that it is more consistent with human intuition than competitors. A new deterministic algorithm is developed to approximate this measure with practical complexity. Empirical evaluation by two link prediction benchmarks, one in coauthorship networks and one in Wikipedia, shows promising results. For example, a single parameterization of this measure achieves accuracies that are 14-35% above the best accuracy for each graph of all predictors reported in the 2007 Liben-Nowell and Kleinberg survey.
Choroidal Thickness in Birdshot Retinochoroiditis Over a 2-Year Period (2018)

In patients with BRC, foveal choroidal thinning and increase of SCF at 2-year follow-up can be observed, even in the absence of visual loss.
The Novel Clostridial Neurotoxin Produced by Strain IBCA10-7060 Is Immunologically Equivalent to BoNT/HA (2019)

The results, combined with the chimeric structure and neutralization by anti-A, but not anti-F antitoxin indicate that immunologically the novel BoNT is BoNT/HA. This determination has significant implications for existing countermeasures and potential vulnerabilities.
Bioactive Azo- and Azoxyformamides From Lycoperdon Pyriforme (Schaeff. Ex Pers.)1 (1999)

Abstract Extracts of the basidiomycete Lycoperdon pyriforme yielded 4-methoxy-benzene-1-azoformamide (1) and 4-methoxybenzene-1-ONN-azoxyformamide (2), which posses namaticidal activity against the parasitic nematode Meloidogyne incognita but not against the saprophytic nematode Caenorhabditis elegans, and the chlorinated derivative 3,5-dichloro-4-methoxybenzene-1-ONN-azoxyformide (3). Compound 3, which is less active towards nematodes but more cytotoxic compared to 1 and 2, is new and its structure was elucidated by spectroscopic techniques.
Numerical Study on the Performance of a Microchannel Heat Exchanger with a Novel Channel Array (2011)

기존 마이크로채널 열교환기는 한 플레이트에 고온 또는 저온, 한 종류의 유체만이 흐르고 있다. 채널 내부를 흐르는 유체의 수직 방향으로는 다른 종류의 유체가 존재하지만, 수평 방향으로는 같은 종류의 유체가 존재한다. 그로 인해 수평 방향의 열전달률은 수직 방향에 비하여 낮게 나타나게 된다. 열교환기 성능 향상을 위하여 한 플레이트에서 고온, 저온 유동이 번갈아가며 존재하는 새로운 채널 배열을 제안하였다. 새로운 채널 배열을 위해서는 특별한 입구 및 출구 설계가 필요하다. 제안된 채널 배열을 통하여 기존 열교환기보다 높은 열전달률을 얻을 수 있다. Reynolds 수와 Prandtl수가 증가할수록 새로운 채널 배열로 인한 열 성능 향상이 증가하고, 고체와 유체의 열전도계수 비가 증가할수록 열 성능 향상은 감소한다.
Enhanced Activation of Memory, but Not Naïve, B Cells in Chronic Hepatitis C Virus-Infected Patients with Cryoglobulinemia and Advanced Liver Fibrosis (2013)

Mixed cryoglobulinemia is the most common extrahepatic disease manifestation of chronic hepatitis C virus (HCV) infection, where immunoglobulins precipitate at low temperatures and cause symptoms such as vasculitis, glomerulonephritis and arthralgia. HCV-associated cryoglobulinemia is also strongly linked with the development of B cell non-Hodgkin lymphoma. Abnormal B cell function in HCV infections can lead to the formation of HCV cryoglobulin complexes that usually comprise monoclonal rheumatoid factor and HCV-specific immune complexes. The aim of this study was to characterize the activation phenotype of B cells from patients with chronic HCV infection in comparison to healthy controls using flow cytometry. In addition, we determined how the activation status varies depending on the presence of cryoglobulinemia and advanced liver fibrosis. We found that only memory B cells, not naïve cells, were significantly activated in chronic HCV infection when compared with healthy controls. We also identified markers of memory B cell activation that were specific for HCV patients with cryoglobulinemia (CD86, CD71, HLA-DR) and advanced liver disease (CD86). Our results demonstrate that HCV infection has differential effects on B cells depending on the severity of hepatic and extrahepatic disease.
Spinal GABAA receptors for pain control—lost in translation? (2018)

aInstitute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland bInstitute of Pharmaceutical Sciences, ETH Zurich, Zürich, Switzerland cDepartment of Anesthesiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany dDepartment of Neurology, Danish Headache Center, Glostrup Research Institute, Glostrup, Denmark Sponsorships or competing interests that may be relevant to content are disclosed at the end of this article.
Determination of uncertainty in parameters extracted from single spectroscopic measurements (2007)

The ability to quantify uncertainty in information extracted from spectroscopic measurements is important in numerous fields. The traditional approach of repetitive measurements may be impractical or impossible in some measurements scenarios, while chi-squared analysis does not provide insight into the sources of uncertainty. As such, a need exists for analytical expressions for estimating uncertainty and, by extension, minimum detectable concentrations or diagnostic parameters, that can be applied to a single noisy measurement. This work builds on established concepts from estimation theory, such as the Cramer-Rao lower bound on estimator covariance, to present an analytical formula for estimating uncertainty expressed as a simple function of measurement noise, signal strength, and spectral overlap. This formalism can be used to evaluate and improve instrument performance, particularly important for rapid-acquisition biomedical spectroscopy systems. We demonstrate the experimental utility of this expression in assessing concentration uncertainties from spectral measurements of aqueous solutions and diagnostic parameter uncertainties extracted from spectral measurements of human artery tissue. The measured uncertainty, calculated from many independent measurements, is found to be in good agreement with the analytical formula applied to a single spectrum. These results are intended to encourage the widespread use of uncertainty analysis in the biomedical optics community.
Adult T cell leukemia aggressivenness correlates with loss of both 5-hydroxymethylcytosine and TET2 expression (2016)

Mutations in <i>TET2</i>, encoding one of the TET members responsible for the conversion of DNA cytosine methylation to hydroxymethylation (5-hmc), have been recently described in Human T-lymphotropic virus type 1-associated adult T-cell leukemia/lymphoma (ATLL). However, neither the amount of genomic 5-hmc in ATLL tumor cells nor TET2 expression has been studied yet. In this study, we analyzed these two parameters as well as the mutational status of <i>TET2</i> in ATLL patients. By employing a direct <i>in situ</i> approach, we documented that tumor T cells infiltrating lymph nodes exhibit low level of 5-hmc compared to residual normal T cells. Furthermore, this 5-hmc defect was more pronounced in tumor T cells from acute patients than from chronic ones and correlated with reduced expression of TET2 protein. <i>TET2</i> variations were found in 14 patients (20%), including 13 with aggressive forms. Strikingly, 9 of the 14 patients showed the same variation (SNP rs72963007), whose frequency in ATLL patients was significantly higher than that of an ethnically matched control population (13% vs. 5%). However, no reduction of 5-hmc was found in PBMC from individuals possessing the variant rs72963007 <i>TET2</i> allele, as compared to wild-type individuals. In contrast, a robust correlation was observed between 5-hmc and the levels of <i>TET2</i> mRNA. Finally, loss of 5-hmc and TET2 downregulation both correlated with poor survival. These findings demonstrate that ATLL progression coincides with loss of genomic 5-hmc and indicate that downregulation of <i>TET2</i>, rather than <i>TET2</i> mutations, is the key mechanism involved in 5-hmc modulation during ATLL progression.
A Hardware-Based Longest Prefix Matching Scheme for TCAMs (2005)

Ternary content addressable memory (TCAM) is a popular device for hardware based lookup table solutions due to its high speed. However TCAM devices suffer from slow updates, high power consumption and low density. In this paper, we present a novel hardware-based longest prefix matching (HLPM) technique for pipelined TCAMs to increase TCAM efficiency. Our HLPM provides very simple and fast table updates, with no TCAM management requirements, as well as potentially decreasing the power consumption and area requirements for a TCAM. Up to 30% power savings for matching entries, compared to previously designed TCAMs, is reported.
FDG-SPECT: correlation with FDG-PET. (1995)

FDG-SPECT with 511-keV collimation is less expensive, more available and technically simpler than PET. We believe that FDG-SPECT has achieved sufficient sensitivity and resolution to detect myocardial viability and diagnose malignant tumors > or = 2 cm in diameter.
Novel large cross-section single-mode AlGaAs/GaAs asymmetric optical switch based on carrier injection effect (2004)

A novel AlGaAs/GaAs asymmetric Y-junction optical switch, with 1.7um-thick core layer for single-mode operation at 1.55um, has been designed and fabricated. The switch is based on total internal reflection (TIR) from a carrier-induced index barrier. At the TIR interface inside the Y-junction, a small tapered gap is introduced to obtain a sharp carrier gradient profile for improved switching efficiency. A double masking technique, suitable for monolithic circuit integration, is used to achieve a nearly perfect gap vertex. The switch's strip-loaded waveguide design has a five-layer-heterostructure with a W-shaped index profile, and can provide high coupling efficiency to a single-mode fiber. We have obtained a low optical loss of 1.0dB/cm on 5um-wide waveguides. The asymmetric Y-junction design is carried out by simulating two-dimensional carrier-induced index change based on the calculated carrier concentration and self-heating temperature profile using finite element method (FEM). Preliminary experimental results indicate that optical switches with small size, low loss, fast switching speed and high extinction ratio can be obtained. Switching times of a few nanoseconds have been obtained.
Systems Biology and Genomics (2017)

Overview Cancers are complex, adaptive systems comprised of cancer cells, the proximal and distal cells, and soluble and insoluble proteins that influence the behavior of the cancer cells. Features pertaining to the cancer are referred to as intrinsic to the cancer and those comprising the proximal and distal microenvironments are referred to as extrinsic to the cancer. Genomics studies seek to develop comprehensive cellular and molecular profiles of cancers and cancer systems biology studies seek to develop the experimental and theoretical methods needed to understand how the components work together to determine cancer function. The overall goal of these efforts is to develop the ability to predict the behavior of cancers—including progression and response to therapy—from measurements of the intrinsic and extrinsic molecular and cellular components of the cancers. Here, we review recent progress in international efforts to measure the genomic, epigenomic, and proteomic features (aka omic features) of major tumor types. We summarize work on establishing associations between omic features and cancer behavior. Finally, we summarize the computational and experimental models that are currently being used to understand and manipulate the behavior of complex cancer systems.
Self‐reported therapy adherence and predictors for nonadherence in patients who switched from vitamin K antagonists to direct oral anticoagulants (2020)

Self-reported treatment persistence and adherence were high in our study population, and several predictors of nonadherence were identified. Factors that can be influenced (low consult frequency with medical specialist, daily dosing regimen) may be used to improve therapy adherence.