gebhart/patrepeval huggingface dataset:
Multi-target immunofluorescence using spectral FLIM-FRET for separation of undesirable antibody cross-labeling and autofluorescence (Conference Presentation) (2020)

To overcome limitations of indirect immunofluorescence, a new method is presented to employ the ostensible disadvantage of cross-labeling secondary antibodies by separation of the fluorescence signals via spectral FLIM-FRET. The undesirable cross-labeling among secondary antibodies leads to the generation of new characteristic FRET emission spectra including a change in the donor lifetime. We used a spectrally resolved FLIM detection system with pulse interleaved excitation. The combined spectral FLIM-FRET and pattern-matching analysis forms an excellent tool for use in indirect immunofluorescence that overcomes the undesirable effect of secondary antibody cross-labeling by assigning separate color channels to cross-labeled fluorescent antibodies.
Supplementary Fig. S1 from Epigenetic mechanisms of irinotecan sensitivity in colorectal cancer cell lines (2023)

Supplementary Fig. S1 from Epigenetic mechanisms of irinotecan sensitivity in colorectal cancer cell lines
The PV fibre project: a PV concentrator for indoor operation of 1000X MJ solar cells by fibre transmission (2003)

S.2135-2138
Radial Analysis of Fine Sprays Using Phase Doppler Anemometry (PDA) (2010)

A mobile fine spray unit, utilising a Spill Return Atomiser (SRA) has been developed for the purpose of decontamination within healthcare environments. The unit must be able to spray uniformly onto any given surface,&#13;\nproviding ‘mist like’ coverage. Any uneven coating would jeopardise the efficiency of delivering the decontaminant fluid. Thus it is pertinent to understand and analyse the characteristics of the spray at various radial and&#13;\ndownstream locations within the full cone patternation produced by the SRA.&#13;\nPDA equipment was used to acquire Sauter Mean Diameter (SMD), droplet velocity and mass flux data at set radial positions across the spray and at various distances downstream of the atomiser. The results provided a comprehensive analysis of the spray and were used to determine the most effective coating distance to achieve ‘mist&#13;\nlike’ coverage for delivering a decontaminant fluid.
Encapsulation of Fe Particles in Carbon Cages using Both Surface Wave Plasma and Arc Discharge Techniques (2008)

Fine Fe particles encapsulated in carbon cages were synthesized by employing both arc and surface wave plasma discharge techniques. The size of synthesized nanocapsules ranged from several 10s nm to 10 μm in diameter, which was approximately one order of magnitude larger than that of nanocapsules synthesized by the arc discharge method. The transmission electron micrographs revealed that the Fe particles were encapsulated in graphite shells. The selected-area electron diffraction patterns indicated that the Fe particles were single crystals. The fraction of a-Fe, g-Fe and Fe3C components in the nanocapsules synthesized under the total gas pressure of 1.0 kPa were estimated to be 83, 6, 11 wt%, respectively.
Structural Behavior Of Precast Foamed Concrete Sandwich Panel Subjected To Vertical In-Plane Shear Loading (2016)

Experimental and analytical studies were accomplished to examine the structural behavior of precast foamed concrete sandwich panel (PFCSP) under vertical in-plane shear load. PFCSP full-scale specimens with total number of six were developed with varying heights to study an important parameter slenderness ratio (H/t). The production technique of PFCSP and the procedure of test setup were described. The results obtained from the experimental tests were analysed in the context of in-plane shear strength capacity, load-deflection profile, load-strain relationship, slenderness ratio, shear cracking patterns and mode of failure. Analytical study of finite element analysis was implemented and the theoretical calculations of the ultimate in-plane shear strengths using the adopted ACI318 equation for reinforced concrete wall were determined aimed at predicting the in-plane shear strength of PFCSP. The decrease in slenderness ratio from 24 to 14 showed an increase of 26.51% and 21.91% on the ultimate in-plane shear strength capacity as obtained experimentally and in FEA models, respectively. The experimental test results, FEA models data and theoretical calculation values were compared and provided a significant agreement with high degree of accuracy. Therefore, on the basis of the results obtained, PFCSP wall has the potential use as an alternative to the conventional load-bearing wall system.
Sarco/endoplasmic reticulum Ca2+-ATPase isoforms: diverse responses to acidosis (1997)

The effects of acidic pH on the kinetics of Ca2+-ATPase isoforms from intracellular membranes of skeletal muscle, cardiac muscle, cerebellum and blood platelets were studied. At neutral pH, all four Ca2+-ATPase isoforms exhibited similar Ca2+-concentration requirements for half-maximal rates of Ca2+ uptake and ATP hydrolysis. A decrease in the pH from 7.0 to 6.0 promoted a decrease in both the apparent affinity for Ca2+ [increasing half-maximal activation (K0.5)] and the maximal velocity (Vmax) of Ca2+ uptake. With skeletal muscle vesicles these effect were 5 to 10 times smaller than those observed with all the other isoforms. Acidification of the medium from pH 7.0 to 6.5 caused the release of Ca2+ from loaded vesicles and a decrease in the amount of Ca2+ retained by the vesicles at the steady state. With the vesicles derived from skeletal muscle these effects were smaller than for vesicles derived from other tissues. The rate of passive Ca2+ efflux from skeletal and cardiac muscle vesicles, loaded with Ca2+ and diluted in a medium containing none of the ligands of Ca2+-ATPase, was the same at pH 7.0 and 6.0. In contrast, the rate of Ca2+ efflux from cerebellar and platelet vesicles increased 2-fold after acidification of the medium. The effects of DMSO, Mg2+ with Pi and arsenate on the rate of Ca2+ efflux varied among the different preparations tested. The differences became more pronounced when the pH of the medium was decreased from 7.0 to 6.0. It is proposed that the kinetic differences among the Ca2+-ATPase isoforms may reflect different adaptations to cellular acidosis, such as that which occurs during ischaemia.
Post Plasma Etch Residue Removal Using Carbon Dioxide Based Fluids (2004)

As feature sizes in semiconductor devices become smaller and newer materials are incorporated, current methods for photoresist and post plasma etch residue removal face several challenges. A cleaning process should be environmentally benign, compatible with dielectric materials and copper, and provide residue removal from narrow and high aspect ratio features. In this work, sub-critical CO2 based mixtures have been developed to remove the etch residues; these mixtures satisfy the above requirements and can potentially replace the two step residue removal process currently used in the integrated circuit (IC) industry.\n\nBased on the chemical nature of the residue being removed, additives or co-solvents to CO2 have been identified that can remove the residues without damaging the dielectric layers. Using the phase behavior of these additives as a guide, the composition of the co-solvent was altered to achieve a single liquid phase at moderate pressures without compromising cleaning ability. The extent of residue removal has been analyzed primarily by x-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). Various techniques such as attenuated total reflection - Fourier transform infrared (ATR-FTIR) spectroscopy, angle-resolved XPS (ARXPS), and interferometry were used to probe the interaction of cleaning fluids with residues. Model films of photoresists and plasma deposited residues were used to assist in understanding the mechanism of residue removal. From these studies, it was concluded that residue removal takes place primarily by attack of the interface between the residue and the substrate; a solvent rinse then lifts these residues from the wafer. It has been shown that transport of the additives to the interface is enhanced in the presence of CO2. From positronium annihilation lifetime spectroscopy (PALS) studies on a porous dielectric film, it has been shown that these high pressure fluids do not cause significant changes to the pore sizes or the bonding structure of the film. Hence, this method can be used to remove post etch residues from low-k dielectric films.
Measles virus and rinderpest virus divergence dated to the sixth century BCE (2020)

Many infectious diseases are thought to have emerged in humans after the Neolithic revolution. Although it is broadly accepted that this also applies to measles, the exact date of emergence for this disease is controversial. We sequenced the genome of a 1912 measles virus and used selection-aware molecular clock modeling to determine the divergence date of measles virus and rinderpest virus. This divergence date represents the earliest possible date for the establishment of measles in human populations. Our analyses show that the measles virus potentially arose as early as the sixth century BCE, possibly coinciding with the rise of large cities.
ChemInform Abstract: Stereoselective Synthesis of Skipped Polyols by Substrate‐Directed Asymmetric Induction. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Disk-Based Indexing of Recent Trajectories (2018)

The plethora of location-aware devices has led to countless location-based services in which huge amounts of spatiotemporal data get created every day. Several applications require efficient processing of queries on the locations of moving objects over time, i.e., the moving object trajectories. This calls for efficient trajectory-based indexing methods that capture both the spatial and temporal dimensions of the data in a way that minimizes the number of disk I/Os required for both updating and querying. Most existing spatiotemporal index structures capture either the current locations of the moving objects or the entire history of the moving objects. Historical spatiotemporal indexing methods require multiple disk I/Os to process new updates and use a discrete trajectory representation that may result in incomplete query results. In this article, we introduce the trails-tree, a disk-based data structure for indexing recent trajectories. The trails-tree requires half the number of disk I/Os needed by other historical spatiotemporal indexing methods for the insertion and querying operations. We give a detailed description of the trails-tree, and we mathematically analyze its performance. Moreover, we present a novel query processing algorithm that ensures the completeness of the query result set. We experimentally verify the performance of the trails-tree using various real and synthetic datasets.
Building web applications without a database system (2008)

Publishing data on the Web has become a commodity. Building, deploying, and operating a Web application, however, are still difficult tasks. This talk argues that one of the reasons is the use of database systems. While such database systems provide a great deal of features, they are hard to deploy and manage, do not scale, and dictate the architecture of the whole application. This talk proposes a new data management architecture and shows how XQuery can be used as a programming language in order to build applications on such a data management infrastructure.
&lt;title&gt;Pulse-length dependence of absorptance and degradation rate of fused silica at 248 nm&lt;/title&gt; (1997)

Optical components for industrial excimer laser applications such as semiconductor lithography steppers have to withstand more than 10<SUP>10</SUP> laser pulses without suffering from significant cumulative absorption increase due to color center formation. Lithography lasers are now approaching pulse durations of 10 ns and repetition rates of 1000 Hz, a domain unexplored in previous degradation studies. With the aid of an optical pulse-extension unit and a modified laser resonator, we measured absorptance and absorption changes in Suprasil 312 UV-grade fused silica calorimetrically at pulse lengths of 7-73 ns. At 100 mJ/cm<SUP>2</SUP>, no degradation was detectable even after 500,000 pulses, but there was slight evidence of an absorption decrease due to laser cleaning. At 400 mJ/cm<SUP>2</SUP>, both absorptance and degradation rate increased towards shorter pulses and hence higher intensities, but even over the full pulse-length range, the changes remained moderate. Furthermore, degradation at 300 Hz was lower than at 150 Hz, indicating that a simultaneous bleaching effect might be involved which favors future high- repetition rate applications.
Rate of Ethylene Polymerization with the Catalyst System (η<sup>5</sup>-RC<sub>5</sub>H<sub>4</sub>)<sub>2</sub>ZrCl<sub>2</sub>—Methylaluminoxane (1992)

Ethylene was polymerized, at 60°C, using the homogeneous catalyst system (η5-RC5H4)2ZrCl2-methylaluminoxane (where R = H, Me, n-Pr, i-Pr and t-Bu). A modest increase in the maximum rate of ethylene polymerization according to the order t-Bu < H < i-Pr < n-Pr < Me was observed. However active centre studies carried out using a 14CO radio-tagging method demonstrated that active centre concentrations, C*, remained more or less constant for all the catalysts systems, leading to the conclusion that there is some variation in the propagation rate constant, kp, for the different catalyst systems investigated. Possible explanations are given in terms of the opposing influences of the electronic and the steric effects of the ring substituents.
Oropharyngeal samples versus lesion specimens at diagnosis in patients infected with monkeypox virus in Northern France (2022)

The ongoing outbreak of monkeypox virus (MPXV) is the largest one in historically non-endemic countries. Early reports described atypical epidemiological and clinical presentations. We investigated MPXV DNA detection in oropharyngeal samples (OPS), and compared the viral load to that in lesion samples at diagnosis in patients infected with MPXV. We retrospectively included patients suspected to have monkeypox in Northern France, who underwent a MPXV PCR in the Virology Laboratory, University Hospital of Lille, from May 23 to August 18, 2022. Overall, a total of 228 patients (376 samples) were included. A positive result in at least one sample was found in 138 patients (60.5%). We compared PCR results between OPS and lesion samples (i.e., cutaneous or anal/rectal samples) in patients with both samples. A positive result in OPS was observed in 54 out of 60 patients (90%). The viral load in OPS (median C<sub>t</sub> value = 29.5; interquartile range [IQR] = 24.7-34) was significantly lower than that in lesion samples (median C<sub>t</sub> value = 17.8; IQR = 16.3 and 19.7) (p < 0.0001). This report shows that pharyngeal sampling does not bring additional information for the initial diagnosis in patients presenting with typical lesions.
Simultaneous imaging of <sup>13</sup>C metabolism and <sup>1</sup>H structure: technical considerations and potential applications (2015)

Real-time imaging of (13)C metabolism in vivo has been enabled by recent advances in hyperpolarization. As a result of the inherently low natural abundance of endogenous (13)C nuclei, hyperpolarized (13)C images lack structural information that could be used to aid in motion detection and anatomical registration. Motion before or during the (13)C acquisition can therefore result in artifacts and misregistration that may obscure measures of metabolism. In this work, we demonstrate a method to simultaneously image both (1)H and (13)C nuclei using a dual-nucleus spectral-spatial radiofrequency excitation and a fully coincident readout for rapid multinuclear spectroscopic imaging. With the appropriate multinuclear hardware, and the means to simultaneously excite and receive on both channels, this technique is straightforward to implement requiring little to no increase in scan time. Phantom and in vivo experiments were performed with both Cartesian and spiral trajectories to validate and illustrate the utility of simultaneous acquisitions. Motion compensation of dynamic metabolic measurements acquired during free breathing was demonstrated using motion tracking derived from (1)H data. Simultaneous multinuclear imaging provides structural (1)H and metabolic (13)C images that are correlated both spatially and temporally, and are therefore amenable to joint (1)H and (13)C analysis and correction of structure-function images.
SC-52151, a novel inhibitor of the human immunodeficiency virus protease (1995)

SC-52151 is a potent, selective, tight-binding human immunodeficiency virus (HIV) protease inhibitor containing the novel (R)-(hydroxyethyl) urea isostere. The mean 50% effective concentration for lymphotropic, monocytotropic strains and field isolates of HIV type 1 (HIV-1), HIV-2, and simian immunodeficiency virus is 26 ng/ml (43 nM). The combination of SC-52151 and nucleoside reverse transcriptase inhibitors synergistically inhibited HIV-1 replication without additive toxicity. An extended postantiviral effect correlates with inhibition of gag and gag-pol polyprotein processing. SC-52151 is highly protein bound ( >90%) in human plasma, and the level of partitioning into erythrocytes is low. Physiological concentrations of alpha-1-acid glycoprotein, but not albumin, substantially affect the antiviral potency of SC-52151. The oral bioavailability of [14C]SC-52151 is 17% when it is administered as an elixir to the rat, dog, or monkey. Oxidation of the t-butyl moiety is the major route of biotransformation, and elimination is mainly by biliary excretion. No toxicologically significant effects have been observed in animals. Pharmacokinetic and metabolism studies in multiple animal species predict 20 to 30% systemic bioavailability, an elimination half-life of 1 to 2 h, and a volume of distribution of greater than 3 liters/kg in humans.
Lopinavir/ritonavir for treatment of non-hospitalized patients with COVID-19: a randomized clinical trial (2022)

ClinicalTrials.gov Identifier: NCT04372628.
IDH1/2 Mutations in Patients With Diffuse Gliomas: A Single Centre Retrospective Massively Parallel Sequencing Analysis (2021)

Patients below 55 years were genetically studied because the prevalence of isocitrate dehydrogenase 1 (IDH1) decreases in older patients and on grounds of cost-effectiveness, as suggested by the World Health Organization (WHO) in 2016. The aim of our study was to use novel massively parallel sequencing (MPS) approaches to examine rare variants of IDH1/2 in Czech diffuse astrocytic and oligodendroglial tumors (gliomas) patients below 55 years of age who had been immunohistochemically (IHC) diagnosed as IDH1 R132H negative. The IHC IDH1 status (wild type or mutant) of 275 tissue samples was analyzed using antibodies against the IDH1 R132H protein. Sixty-three samples of 55 years old patients with IHC IDH1 WT status were genotyped using two different MPS technologies to detect rare IDH1 and IDH2 variants. The tiered IHC (60 positive) and molecular (10 positive) approach thus revealed that 70 of the 275 samples (25%) bore IDH1/IDH2 mutations. The combined molecular and IHC approach thus revealed that 70 of the 275 samples (25%) considered in the study bore IDH1/IDH2 mutations. IHC detection of the IDH1 R132H variant should be routinely complemented with MPS to detect rare IDH1/2 variants in glioma patients below 55 years of age with negative IHC result of IDH R132H variant.
Low Valent Magnesium Chemistry with a Super Bulky β‐Diketiminate Ligand (2018)

Abstract The steric bulk of the well‐known DIPP BDI ligand (CH[C(CH 3 )N‐DIPP] 2 , DIPP=2,6‐diisopropylphenyl) was increased by replacing isopropyl for isopentyl groups. This very bulky DIPeP BDI ligand could not stabilize the radical species ( DIPeP BDI)Mg . : reduction of ( DIPeP BDI)MgI with Na gave ( DIPeP BDI) 2 Mg 2 with a rather long Mg‐Mg bond of 3.0513(8) Å. Addition of TMEDA prior to reduction gave complex ( DIPeP BDI) 2 Mg 2 (C 6 H 6 ), which could also be obtained as its THF adduct. It is speculated that combination of a bulky spectator ligand and TMEDA prevents dimerization of the intermediate Mg I radical, which then reacts with the benzene solvent. Complex ( DIPeP BDI) 2 Mg 2 (C 6 H 6 ), which formally contains the anti ‐aromatic anion C 6 H 6 2− , reacted with t BuOH as a Brønsted base to 1,3‐ and 1,4‐cyclohexadiene and with H 2 as a two electron donor to ( DIPeP BDI) 2 Mg 2 H 2 and C 6 H 6 . It also reductively cleaved the C−F bond in fluorobenzene and gave ( DIPeP BDI)MgPh, ( DIPeP BDI)MgF, and C 6 H 6 .
Precise Fault Location on Transmission Lines Using Ensemble Kalman Filter (2018)

Accurate pin-pointing of faults on transmission lines minimizes outage time, labor, and costs. This letter proposes a simple yet effective ensemble Kalman filter (EnKF) approach to accurately locating the faults on transmission lines within half-cycle time. The approach is easy to implement and does not require foreknowledge of either the fault type or an approximate guess of the fault location. Extensive results validate the effectiveness and accuracy of the EnKF-based fault location approach.
Ligand-free Palladium-Catalyzed Direct Arylation of Heteroaromatics using Low Catalyst Loading: An Economically and Environmentally attractive Procedure (2008)

International audience
Deciphering the tumor-specific immunopeptidome <i>in vivo</i> with genetically engineered mouse models (2021)

Abstract Effective immunosurveillance of cancer requires the presentation of peptide antigens on major histocompatibility complex Class I (MHC-I). Recent developments in proteomics have improved the identification of peptides that are naturally presented by MHC-I, collectively known as the “immunopeptidome”. Current approaches to profile tumor immunopeptidomes have been limited to in vitro investigation, which fails to capture the in vivo repertoire of MHC-I peptides, or bulk tumor lysates, which are obscured by the lack of tumor-specific MHC-I isolation. To overcome these limitations, we report here the engineering of a Cre recombinase-inducible affinity tag into the endogenous mouse MHC-I gene and targeting of this allele to the Kras LSL-G12D/+ ; p53 fl/fl (KP) mouse model (KP; K b Strep). This novel approach has allowed us to isolate tumor-specific MHC-I peptides from autochthonous pancreatic ductal adenocarcinoma (PDAC) and lung adenocarcinoma (LUAD) in vivo . With this powerful analytical tool, we were able to profile the evolution of the LUAD immunopeptidome through tumor progression and show that in vivo MHC-I presentation is shaped by post-translational mechanisms. We also uncovered novel, putative LUAD tumor associated antigens (TAAs). Many peptides that were recurrently presented in vivo exhibited very low expression of the cognate mRNA, provoking reconsideration of antigen prediction pipelines that triage peptides according to transcript abundance. Beyond cancer, the K b Strep allele is compatible with a broad range of Cre-driver lines to explore antigen presentation in vivo in the pursuit of understanding basic immunology, infectious disease, and autoimmunity.