gebhart/patrepeval huggingface dataset:
Harmonization guidelines for HLA-peptide multimer assays derived from results of a large scale international proficiency panel of the Cancer Vaccine Consortium (2009)

Three key recommendations emerged that would likely reduce assay variability and thus move toward harmonizing of this assay. (1) Use of more than two colors for the staining (2) collect at least 100,000 CD8 T cells, and (3) use of a background control sample to appropriately set the analytical gates. We also provide more insight into the limitations of the assay and identified additional protocol steps that potentially impact the quality of data generated and therefore should serve as primary targets for systematic analysis in future panels. Finally, we propose initial guidelines for harmonizing assay performance which include the introduction of standard operating protocols to allow for adequate training of technical staff and auditing of test analysis procedures.
Methods and Tools for Policy Analysis (2019)

Policy-based management of computer systems, computer networks and devices is a critical technology especially for present and future systems characterized by large-scale systems with autonomous devices, such as robots and drones. Maintaining reliable policy systems requires efficient and effective analysis approaches to ensure that the policies verify critical properties, such as correctness and consistency. In this paper, we present an extensive overview of methods for policy analysis. Then, we survey policy analysis systems and frameworks that have been proposed and compare them under various dimensions. We conclude the paper by outlining novel research directions in the area of policy analysis.
Prevalence and Predictors of Nonalcoholic Steatohepatitis Using Multiple Non-Invasive Methods: Data from NHANES III. (2020)

We conclude that the combined non-invasive methods can help identify candidates with a high likelihood of being diagnosed with NASH. Health care providers can screen people with the combined non-invasive methods for the risk factors and identify candidates for interventions, including exercise and/or referral to biopsy.
Implementation of colonoscopy quality monitoring in a Belgian university hospital with integrated computer-based extraction of adenoma detection rate (2021)

<b>Background and study aims </b> Quality in colonoscopy has been promoted in last decade with definition of different quality indicators (QI) as benchmarks. Currently, automatized monitoring systems are lacking, especially for merging pathologic and endoscopic data, which limits quality monitoring implementation in daily practice. We describe an adapted endoscopy reporting system that allows continuous QI recording, with automatic pathological data inclusion. <b>Material and methods </b> We locally adapted a reporting system for colonoscopy by adding and structuring in a dedicated tab selected key QI. Endoscopic data from a reporting system and pathological results were extracted and merged in a separate database. During the initial period of use, performing physicians were encouraged to complete the dedicated tab on a voluntary basis. In a second stage, completing of the tab was made mandatory. The completeness of QI recording was evaluated across both periods. Performance measures for all endoscopists were compared to global results for the department and published targets. <b>Results</b> During the second semester of 2017, a total of 1827 colonoscopies were performed with a QI tab completed in 100 % of cases. Among key QI, the cecal intubation rate was 93.8 %, the rate of colonoscopies with adequate preparation was 90.7 %, and the adenoma detection rate was 29.8 % considering all colonoscopies, irrespective of indication; 28.8 % considering screening procedures; and 36.6 % in colonoscopies performed in people older than age 50 years. <b>Conclusion</b> This study shows that quality monitoring for colonoscopy can be easily implemented with limited human resources by adapting a reporting system and linking it to a pathology database.
Electrochemical conversion of pressurized CO2 at simple silver-based cathodes in undivided cells: study of the effect of pressure and other operative parameters (2020)

Abstract Electrochemical reduction of pressurized CO 2 is proposed as an interesting approach to overcome the main hurdle of the CO 2 electrochemical conversion in aqueous solution, its low solubility (ca. 0.033 M), and to achieve good faradaic efficiency in CO using simple sheet silver cathodes and undivided cells, thus lowering the overall costs of the process. The effect on the process of CO 2 pressure (1–30 bar), current density, nature of the supporting electrolyte and other operative conditions, such as the surface of the cathode or the mixing rate, was studied to enhance the production of CO. It was shown that pressurized conditions allow to improve drastically the current efficiency of CO (CE CO ). Furthermore, at relatively high pressure (20 bars), the utilization of simple sheet silver cathodes and silver electrodes with high surfaces gave similar CE CO . The stability of the system was monitored for 10 h; it was shown that at a relatively high pressure (15 bar) in aqueous electrolyte of KOH using a simple plate silver cathode a constant current efficiency of CO close to 70% was obtained. Graphic abstract
In vivo visualization of single native pancreatic islets in the mouse (2013)

The purpose of this study was to investigate the potential of a novel targeted contrast agent (CA) for the in vivo visualization of single native pancreatic islets, the sites of insulin production, in the pancreas of mice using magnetic resonance imaging (MRI). The CA for intravenous administration was composed of the β-cell-specific single-chain antibody fragment, SCA B1, and ferromagnetic carbon-coated cobalt nanoparticles. MRI experiments were performed at 7, 9.4 and 16.4 T in excised organs (pancreas, liver, kidney, spleen), at 7 T in mice fixed in formalin and at 9.4 and 16.4 T in living mice. Image contrast in untreated control animals was compared with images from mice treated with unspecific and specific CA. For the validation of MRI results, selected pancreases were subjected to immunohistochemical staining and numerical contrast simulations were performed. Ex vivo results and the outcome of immunohistochemistry suggest that islets are marked only by the CA containing SCA B1. Strong accumulation of particles was found also in other investigated organs owing to the uptake by the reticuloendothelial system, but the contrast in the MR images is clearly distinguishable from the islet specific contrast in pancreases and numerical predictions. In vivo experiments based on averaged dynamic sampling with 66 × 66 × 100 µm³ and triggered acquisition with 90 × 90 × 200 µm³ nominal resolution resulted in similar particle contrast to in in vitro measurements. The newly developed CA and MRI strategies have the potential to be used for studying mouse diabetes models by visualizing single native pancreatic islets.
Role of Zinc Oxide in the Compounding Formulation on the Growth of Nonstoichiometric Copper Sulfide Nanostructures at the Brass–Rubber Interface (2022)

Tire technology has evolved substantially by the introduction of brass-coated steel cords (BCSCs) in radial tires. The durability of radial tires is dependent on the integrity of the brass-rubber interface composed predominantly of nonstoichiometric copper sulfide (Cu<sub>2-<i>x</i></sub> S, where <i>x</i> = 1 to 2) nanostructures whose morphology and characteristics are dependent upon the crucial rubber additive, ZnO. Its higher concentration impacts environmental sustainability, while at lower levels, there is insufficient bonding between steel and the rubber thus affecting tire's safety. This brings in the need for an optimum ZnO concentration to be used in radial tires and is thus the theme of the present work. The changes in the properties of interfacial nanostructures such as morphology, thickness, crystallinity, and chemical composition were studied at various ZnO concentrations. We adopted our previously reported methodology, the "brass mesh experiment", to investigate the thickness of nanostructures at varied ZnO concentrations using transmission electron microscopy (TEM). Significant results were obtained from field-emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), Raman imaging and X-ray photoelectron spectroscopy (XPS). In conjunction with a more practical experimental technique, namely the measurement of pull-out force (POF), it has been concluded that 9 parts per hundred rubber (PHR) ZnO is essential for the optimum growth of nanostructures and is considered to be the optimum for the composition studied. We believe that the scientific approach outlined in the manuscript would help the tire- and the material science communities to widen the knowledge of understanding sustainability in tire industries. It is estimated that the optimization presented here can save $400-450 million for the tire industry and 2.4 million tons of ZnO per year.
High refractive index nanoparticle-loaded encapsulants for light-emitting diodes (2007)

TiO<sub>2</sub> nanoparticle-loaded epoxy for light-emitting diode (LED) encapsulation is demonstrated to have a refractive index of n = 1.68, higher than that of pure epoxy (n = 1.53). The dispersion of surfactant-coated TiO<sub>2</sub> nanoparticles into epoxy is shown to reduce the number and size of TiO<sub>2</sub> agglomerates compared to uncoated TiO<sub>2</sub> nanoparticle-loaded epoxy. The scattering of nanoparticle-loaded media is highly dependent on nanoparticle size and loading factor. A multilayer graded refractive index structure for LED encapsulants with layer thicknesses less than the calculated mean optical scattering length is therefore proposed. The graded-index structure shows increasing optical transmittance as the number of layers increases.
Serum blocking factors in bovine ocular squamous cell carcinoma demonstrated by inhibition of erythrocyte rosette augmentation. (1983)

Blood leukocytes from cattle with bovine ocular squamous cell carcinoma (BOSCC) react with extracts of BOSCC, and blood leukocytes from cattle with cutaneous papillomas react with extracts of papillomas in the erythrocyte rosette (E-rosette) augmentation test. Sera from cattle with BOSCC, with cutaneous papillomas, and with ocular papillomas and sera from lesion-free cattle were tested for their ability to block antigen-induced E-rosette augmentation and E-rosette augmentation induced by phytohemagglutinin. Autologous serum from 16 BOSCC-affected cattle blocked E-rosette augmentation induced by BOSCC extract, and autologous sera from three cattle with cutaneous papillomas blocked E-rosette augmentation induced by papilloma extract. Sera from cattle with BOSCC did not block E-rosette augmentation induced by papilloma extract, nor did sera from cattle with cutaneous papillomas block BOSCC extract-induced E-rosette augmentation. Sera from cattle with BOSCC blocked BOSCC extract-induced E-rosette augmentation in some but not all allogeneic combinations. E-rosette augmentation was observed when blood leukocytes from all 12 BOSCC-affected and six control cattle were exposed to phytohemagglutinin. This reaction was blocked by autologous sera from 11 of the 12 BOSCC-affected cattle, from one of the three cattle with cutaneous papillomas, but from none of the three other cattle. Sera from BOSCC-affected cattle also blocked phytohemagglutinin-induced E-rosette augmentation in allogeneic combination, regardless of the tumor status of the donor of the leukocytes.
Interspersion of sequences in avian myeloblastosis virus rna that rapidly hybridize with leukemic chicken cell DNA (1975)

Liquid hybridization of progressively smaller fragments (35S, 27S, 15.5S, 12.5S, and 8S) of poly(A)-selected avian myeloblastosis virus RNA with excess DNA from leukemic chicken myeloblasts revealed that all sizes of RNA contained sequences complementary to both slowly and rapidly hybridizing cellular DNA sequences. Apparently, the RNA sequences which hybridize rapidly with excesses of cellular DNA are not restricted to any one region of the avian myeloblastosis virus 35S RNA. Instead, they appear to be randomly distributed over the entire 35S avian myeloblastosis virus RNA molecule with some positioned within 200 nucleotides of the poly(A) tract at the 3' end of the RNA.
CENTRALLY ACTING ACETYLCHOLINESTERASE INHIBITORS IMPROVE SURVIVAL IN A MURINE MODEL OF SEPSIS (2004)

Pavlov, V. A.; Ochani, M.; Gallowitsch, M.; Ochani, K.; Amella, C. A.; Huston, J.; Czura, C. J.; Al-Abed, Y.; Tracey, K. J. Author Information
Fully Integrated Voltage Regulators with Package-Embedded Inductors for Heterogeneous 3D-TSV-Stacked System-in-Package with 22nm CMOS Active Silicon Interposer Featuring Self-Trimmed, Digitally Controlled ON-Time Discontinuous Conduction Mode (DCM) Operation (2022)

A 10-tile buck IVR using 0.9nH-1.4nH 3D-TSV-based package-embedded inductors demonstrates up to 37.6% higher efficiency than LDO. Communication-free inter-tile ganging is achieved with flat efficiency over a 10mA-1A load range. Stability-aware interleaving of IVR tiles in DCM shows up to 34% reduction in output ripple compared to zero interleaving.
In vivo SPECT imaging of 5-HT1A receptors with [123I]p-MPPI in nonhuman primates (1996)

The in vivo imaging of a novel iodinated phenylpiperazine derivative for 5-HT1A receptors, [123I]p-MPPI (4-(2'-methoxy-)phenyl-1-[2'-(n-2"-pyridinyl)-p-iodobenzamido-] ethyl-piperazine), using single photon emission computed tomography (SPECT), was evaluated in nonhuman primates. After an i.v. injection, [123I]p-MPPI penetrated the blood-brain barrier quickly and localized in brain regions where 5-HT1A receptor density is high (hippocampus, frontal cortex, cingulate gyrus, entorhinal cortex). Maximum ratio of hippocampus to cerebellum was 3 to 1 at 50 min postinjection. The specific binding of the radioligand in the hippocampal region, an area rich in 5-HT1A receptor density, was blocked by a chasing dose of (+/-) 8-OH-DPAT (2 mg/kg, i.v.) or non-radioactive p-MPPI (1 mg/kg, i.v.), whereas the regional distribution of [123I]p-MPPI was unaffected by treatment with non 5-HT1A agents, such as ketanserin. Ex vivo and in vitro autoradiographic studies using monkey brain further confirmed that the specific binding of [123I]p-MPPI is associated with 5-HT1A receptor sites. However, the initial attempt at [123I]p-MPPI human imaging studies did not display specific localization of 5-HT1A receptors. This discrepancy observed for [123I]p-MPPI may be due to a dramatic difference in metabolic pathways between humans and monkeys.
Mixed-signal neuromorphic platform design for streaming biomedical signal processing (2020)

This chapter presents the mixed -signal design approach for the design of neuromorphic platforms for the biomedical signal processing. The proposed approach combines algorithmic, architectural and circuit design concepts to offer a low -power neuromorphic platform for streaming biomedical signal processing. The platform employs liquid state machines using spiking neurons (implemented on analog neuron circuits) and support vector machine (SVM) (implemented as software running on advanced RISC machine (ARM) processor). A dynamic global synaptic communication network realized using the ultralow leakage IGZO thin film transistor (TFT) technology circuit switch is also presented. The proposed architectural technique offers a scalable low -power neuromorphic platform design approach suitable for processing real-time biomedical signals.
Functional glass slides for in vitro evaluation of interactions between osteosarcoma TE85 cells and mineral-binding ligands (2004)

Primary amine-functionalized glass slides obtained through a multi-step plasma treatment were conjugated with anionic amino acids that are frequently found as mineral binding elements in acidic extracellular matrix components of natural bone. The modified glass surfaces were characterized by X-ray photoelectron spectroscopy (XPS) and contact angle measurements. Human osteosarcoma TE85 cells were cultured on these functionalized slides and analyses on both protein and gene expression levels were performed to probe the “biocompatibility” of the surface ligands. Cell attachment and proliferation on anionic surfaces were either better than or comparable to those of cells cultured on tissue culture polystyrene (TCPS). The modified glass surfaces promoted the expression of osteocalcin, alkaline phosphatase activity and ECM proteins such as fibronectin and vitronectin under differentiation culture conditions. Transcript analysis using gene chip microarrays confirmed that culturing TE85 cells on anionic surfaces did not activate apoptotic pathways. Collectively, these results suggest that the potential mineral-binding anionic ligands examined here do not exert significant adverse effects on the expression of important osteogenic markers of TE85 cells. This work paves the way for the incorporation of these ligands into 3-dimensional artificial bone-like scaffolds.
Controlled Crystallization in Self‐Reinforced Silicon Nitride with Y 2 O 3 , SrO, and CaO: Crystallization Behavior (1995)

The controlled crystallization of the amorphous grain boundary phase has been examined in a series of self‐reinforced Si 3 N 4 materials with added Y 2 O 3 , SrO, and CaO. The effects of time, temperature, atmosphere, glass content, glass chemistry, and matrix Si 3 N 4 on the crystallization have been investigated. The stability of the crystallized product, the crystallization kinetics ( T‐T‐T curve), and crystallization mechanisms have also been examined. Crystallization produced an oxynitroapatite containing Y, Sr, and Ca over a broad range of heat‐treatment conditions and glass compositions. The oxynitroapatite was compatible with Si 3 N 4 and remained stable up to 1600°C. At low temperatures (&lt;1350°C), the rate‐limiting crystallization mechanism was oxygen diffuson in the glass, and at higher temperatures (&gt;1350°C) the rate‐limiting crystallization step changed to either the formation of new Si 3 N 4 grains or solute diffusion in the glass.
Predictive value of flow cytometric DNA‐analysis on fresh retinoblastoma tissue (1988)

The cellular DNA content and the distribution of tumour cells in different phases of the cell cycles has been analysed in 8 consecutive enucleated eyes with retinoblastoma. All tumours had abnormal ploidy levels. The analysis did not reveal any specific pattern in 2 tumours which had metastasized compared to 6 local tumours. The flow cytometric analysis alone or in combination with histopathology appeared not to improve the classification of large retinoblastomas.
A Real-Time Video Stitching Algorithm in H.264/AVC Compressed Domain (2014)

본 논문에서는 사용자가 하나의 화면을 가진 장치에서 원하는 여러 비디오 콘텐츠를 동시에 볼 수 있도록 하는 새로운 실시간 H.264/AVC 압축 영역에서의 영상 합성 알고리즘을 제안한다. 본 논문에서 제안하는 알고리즘은 사용자의 요청에 따른 다수 비트스트림들을 압축 영역에서의 하나의 비트열으로 합성한다. 즉, 압축 영역에 있는 다수 영상들의 경계면에 있는 매크로블록들에 대해서 화면 내 예측 모드와 화면 간 예측 MVD를 다시 계산하고 변환 오차 계수 테이블을 수정 하여 경계 매크로블록 확정하는 방법, 영상의 나머지 부분에서 매크로블록 데이터를 단순히 복사하는 방법으로 이뤄진다. 실험 결과, 제안 알고리즘은 480p 크기의 4개 영상을 1초에 103장 이상 합성할 수 있어, 실시간 적용의 가능함을 보여주고 있다. In this paper, a novel, real-time video stitching algorithm in an H.264/AVC compressed domain is proposed. This enables viewers to watch multiple video contents using a single device. The basic concept of this paper is that the server is asked to combine multiple streams into one bit-stream based in a compressed domain. In other words, this paper presents a new compressed domain combiner that works in boundary macroblocks of input videos with re-calculating intra prediction mode, intra prediction MVD, a re-allocation of the coefficient table, and border extension methods. The rest of the macroblocks of the input video data are achieved simply by copying them. Simulation experiments have demonstrated the possibility and effectiveness of the proposed algorithm by showing that it is able to generate more than 103 frames per second, stitching four 480p-sized images into each frame.
Salt-Dependent Structure in Methylcellulose Fibrillar Gels (2021)

Methylcellulose (MC) is a commercially important, water-soluble polysaccharide. Many food applications exploit the thermoreversible gelation behavior of MC in aqueous media. The mechanism of MC gelation upon heating has been debated for decades; however, recent work has demonstrated that gelation is concurrent with the formation of ca. 15 nm diameter fibrils, which percolate into a network. The fibrillar network dictates the properties and mechanical behavior of the resulting hydrogel. The addition of salt to MC gels has also been an area of academic and commercial interest. It has been reported that MC solutions containing salts exhibit an increase or decrease in the gelation temperature, which generally follows the Hofmeister series. To build upon these investigations, we study the effect of salt on the MC fibril structure. We demonstrate the effect of salt (NaCl, NaI, NaBr, NaNO3, KCl, NH4Cl, LiCl, and CaCl2) on the gelation and dissolution temperatures using rheology and cloud point measurements. From small-angle X-ray scattering (SAXS) and high contrast cryogenic transmission electron microscopy (cryo-TEM) we show that salty MC gels are also composed of fibrils. Fitting the SAXS curves to a semiflexible cylinder model, we demonstrate that the fibril diameter decreases monotonically with increasing salt molarity, largely independent of the salt anion or cation type.
Peroxisome Proliferator-Activated Receptor γ B Cell-Specific–Deficient Mice Have an Impaired Antibody Response (2012)

Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear hormone receptor superfamily. PPARγ, a ligand-activated transcription factor, has important anti-inflammatory and antiproliferative functions, and it has been associated with diseases including diabetes, scarring, and atherosclerosis, among others. PPARγ is expressed in most bone marrow-derived cells and influences their function. PPARγ ligands can stimulate human B cell differentiation and promote Ab production. A knowledge gap is that the role of PPARγ in B cells under physiological conditions is not known. We developed a new B cell-specific PPARγ (B-PPARγ) knockout mouse and explored the role of PPARγ during both the primary and secondary immune response. In this article, we show that PPARγ deficiency in B cells decreases germinal center B cells and plasma cell development, as well as the levels of circulating Ag-specific Abs during a primary challenge. Inability to generate germinal center B cells and plasma cells is correlated to decreased MHC class II expression and decreased Bcl-6 and Blimp-1 levels. Furthermore, B-PPARγ-deficient mice have an impaired memory response, characterized by low titers of Ag-specific Abs and low numbers of Ag-experienced, Ab-secreting cells. However, B-PPARγ-deficient mice have no differences in B cell population distribution within primary or secondary lymphoid organs during development. This is the first report, to our knowledge, to show that, under physiological conditions, PPARγ expression in B cells is required for an efficient B cell-mediated immune response as it regulates B cell differentiation and Ab production.
Nonlinear compressed sensing with application to phase retrieval (2013)

We extend the ideas of compressed sensing to nonlinear measurement systems. In particular, we treat the problem of minimizing a general continuously differentiable function subject to sparsity constraints. We derive several different optimality criteria which are based on the notions of stationarity and coordinate-wise optimality. These conditions are then used to derive three numerical algorithms aimed at finding points satisfying the resulting optimality criteria: the iterative hard thresholding method and the greedy and partial sparse-simplex methods. The theoretical convergence of these methods and their relations to the derived optimality conditions are studied. We then specialize our algorithms to the problem of phase retrieval and develop an efficient method for retrieving a signal from its magnitude only measurements.