gebhart/patrepeval huggingface dataset:
Comprehensive Data Integration Approach to Assess Immune Responses and Correlates of RTS,S/AS01-Mediated Protection From Malaria Infection in Controlled Human Malaria Infection Trials (2021)

RTS,S/AS01 (GSK) is the world's first malaria vaccine. However, despite initial efficacy of almost 70% over the first 6 months of follow-up, efficacy waned over time. A deeper understanding of the immune features that contribute to RTS,S/AS01-mediated protection could be beneficial for further vaccine development. In two recent controlled human malaria infection (CHMI) trials of the RTS,S/AS01 vaccine in malaria-naïve adults, MAL068 and MAL071, vaccine efficacy against patent parasitemia ranged from 44% to 87% across studies and arms (each study included a standard RTS,S/AS01 arm with three vaccine doses delivered in four-week-intervals, as well as an alternative arm with a modified version of this regimen). In each trial, RTS,S/AS01 immunogenicity was interrogated using a broad range of immunological assays, assessing cellular and humoral immune parameters as well as gene expression. Here, we used a predictive modeling framework to identify immune biomarkers measured at day-of-challenge that could predict sterile protection against malaria infection. Using cross-validation on MAL068 data (either the standard RTS,S/AS01 arm alone, or across both the standard RTS,S/AS01 arm and the alternative arm), top-performing univariate models identified variables related to Fc effector functions and titer of antibodies that bind to the central repeat region (NANP6) of CSP as the most predictive variables; all NANP6-related variables consistently associated with protection. In cross-study prediction analyses of MAL071 outcomes (the standard RTS,S/AS01 arm), top-performing univariate models again identified variables related to Fc effector functions of NANP6-targeting antibodies as highly predictive. We found little benefit-with this dataset-in terms of improved prediction accuracy in bivariate models vs. univariate models. These findings await validation in children living in malaria-endemic regions, and in vaccinees administered a fourth RTS,S/AS01 dose. Our findings support a "quality as well as quantity" hypothesis for RTS,S/AS01-elicited antibodies against NANP6, implying that malaria vaccine clinical trials should assess both titer and Fc effector functions of anti-NANP6 antibodies.
Oxadiazole: A biologically important heterocycle (2009)

Oxadiazole, a heterocyclic nucleus has attracted a wide attention of the chemist in search for the new therapeutic molecules. Out of its four poss ible isomers, 1, 3, 4-oxadiazole is widely exploited for various applications. A numbers of th erapeutic agents such as HIV-integrase inhibitor raltagravir, a nitrofuran antibacterial furamizole , a potent PDF inhibitor BB-83698 , antihypertensive agents tiodazosin and nesapidil are based on 1,3,4-oxadiazole moiety. The 1, 3, 4-oxadiazole undergoes number of reactions in cluding electrophillic substitution, nucleophilic substitution, thermal and photochemica l. The present review attempts to summarize the various routes of synthesis and the r eactions of 1, 3, 4-oxadiazole and its derivatives and focus on their biological potential .
Scanned laser-induced fluorescence reproducibility (1993)

Laser-induced fluorescence has potential for both caries research and diagnosis. However, research has shown that precise control is necessary for accurate enamel comparisons. Such factors as focus, number of sampling points, scan matrix size and reproducible placement of the scan matrix can all have substantial effects on results. Five noncarious third molars were mounted in acrylic and ground so that a flat Bu enamel surface was created. Each enamel area was covered with acid-resistant varnish except for a window approximately 1.0 mm<SUP>2</SUP>. Each specimen was mounted in the fluorometer for scanned laser fluorescence analysis using a 1.0 mm<SUP>2</SUP> scan matrix. Readings were taken at 50 micrometers intervals for a total of 400 readings per matrix. Each specimen was remounted and reanalyzed in the fluorometer. Each specimen was lased (1.5 W, 1.5 mm f.s., 0.15 sec.) and reanalyzed as per above by fluorometer. Running-sums of line means were calculated for each scan and graphed. In all samples, the curves for nonlased enamel were lower and widely separated from those for lased enamel. In each specimen, the nonlased curves were either coincident or nearly so. The results indicate that ensuring constant focus, repeatable orientation of scan matrices and high sampling frequency collectively can lead to a high degree of scanned laser fluorescence reproducibility.
Macromol. Rapid Commun. 23–24/2013 (2013)

Back Cover: A heterotritopic copillar[5]arene monomer is prepared by introducing effective neutral guest moieties to a pillar[5]arene macrocycle. This well-designed AB2-type copillar[5]arene contains strong recognition sites and relatively flexible and long linkers between the host and guest unimers, and thus efficiently assembles to form supramolecular hyperbranched polymer in chloroform solution. Particularly, this supramolecular polymer can be effectively depolymerized by adding a competitive butanedinitrile guest. Further details can be found in the article by X. Wang, H. Deng, J. Li, K. Zheng, X. Jia, and C. Li* on page 1856.
High levels of soluble CD25 in COVID‐19 severity suggest a divergence between anti‐viral and pro‐inflammatory T‐cell responses (2021)

These results suggest that high levels of sCD25 in COVID-19 patients probably result from insufficient anti-viral immunity and indicate an expansion of pro-inflammatory T cells that contribute to disease severity.
Virus-activated CD8 T cells and lymphokine-activated NK cells express the mast cell function-associated antigen, an inhibitory C-type lectin. (1998)

The mast cell function-associated Ag (MAFA) is an inhibitory C-type lectin that was originally identified on the cell surface of a rat mucosal mast cell line, RBL-2H3. We have cloned the mouse homologue of the rat MAFA gene, and Northern blot analysis revealed that mouse MAFA (mMAFA) gene expression was strongly induced in effector CD8 T cells and lymphokine-activated NK cells but not in effector CD4 T cells and in mouse mast cells. Moreover, mMAFA gene expression was only found in effector CD8 T cells that had been primed in vivo with live virus because in vitro activated CD8 T cells did not express mMAFA. Primary sequence comparison revealed a high degree of conservation (89% similarity) between rat MAFA and mMAFA. Thus, the MAFA molecule in the mouse is a putative inhibitory receptor on anti-viral CD8 T cells induced in vivo and on NK cells.
Synthesis and Crystal Structure of a Phospholyl Anion (1989)

A simple and efficient synthesis of the phospholyl anion 3 was achieved by reaction of zirconacyclopentadiene 1 with PCl3 and Li/TMEDA (TMEDA = tetramethylethylenediamine). The structural parameters obtained by X-ray analysis confirm that 3 is aromatic. This procedure for the preparation of 3 appears to be applicable to other precursors.
One-pot synthesis of silica core–shell particles with double shells and different pore orientations from their nonporous counterparts (2012)

Silica core–shell particles (CSPs) have been successfully synthesized from their nonporous counterparts under basic conditions in the presence of the cationic surfactant cetyltrimethylammonium chloride and NH4F using a new one-pot templated dissolution and templated redeposition hybrid method. This method leads to high yield (∼85%) CSPs with an extremely narrow particle size distribution (no particle aggregation or fine particles) and allows us to vary reaction time to rapidly and conveniently control shell thickness up to the radius of the core particles. The resultant porous shells possess a unique double ordered pore arrangement with the inner and outer shells consisting of wormhole-like and radially oriented pores, respectively. To the best of our knowledge, this is the first report describing the fabrication of double shells in one step with the ability to manipulate the shell thickness from preformed silica particles in the presence of a surfactant. A mechanism to account for the formation of porous shells with different pore morphologies is presented. The resultant CSP particles have the combined characteristics of narrow particle distribution, narrow pore size distribution, unique double shells, and controlled shell thickness, surface area, and pore volume. These properties make them ideal candidates for fast and highly efficient chromatographic separation applications. The ability to control shell thickness while not dissolving the entire nonporous silica protective layer is particularly important to prepare functional core–shell particles (e.g., quantum dot core–nonporous silica shell–porous silica shell) for biomedical applications while avoiding toxic nanoparticles being directly exposed to the body. It is expected that this new hybrid synthesis method could be extended to generate a superficially porous silica layer with a controlled shell thickness and dual mesopore structure from any materials with a sol–gel silica coating.
A Rapid Method for Generating Infectious SARS-CoV-2 and Variants Using Mutagenesis and Circular Polymerase Extension Cloning (2023)

The appearance of SARS-CoV-2 variants in late 2020 raised alarming global public health concerns. Despite continued scientific progress, the genetic profiles of these variants bring changes in viral properties that threaten vaccine efficacy. Thus, it is critically important to investigate the biologic profiles and significance of these evolving variants. In this study, we demonstrate the application of circular polymerase extension cloning (CPEC) to the generation of full-length clones of SARS-CoV-2. We report that, combined with a specific primer design scheme, this yields a simpler, uncomplicated, and versatile approach for engineering SARS-CoV-2 variants with high viral recovery efficiency. This new strategy for genomic engineering of SARS-CoV-2 variants was implemented and evaluated for its efficiency in generating point mutations (K417N, L452R, E484K, N501Y, D614G, P681H, P681R, Δ69-70, Δ157-158, E484K+N501Y, and Ins-38F) and multiple mutations (N501Y/D614G and E484K/N501Y/D614G), as well as a large truncation (ΔORF7A) and insertion (GFP). The application of CPEC to mutagenesis also allows the inclusion of a confirmatory step prior to assembly and transfection. This method could be of value in the molecular characterization of emerging SARS-CoV-2 variants as well as the development and testing of vaccines, therapeutic antibodies, and antivirals. <b>IMPORTANCE</b> Since the first emergence of the SARS-CoV-2 variant in late 2020, novel variants have been continuously introduced to the human population, causing severe public health threats. In general, because these variants acquire new genetic mutation/s, it is critical to analyze the biological function of viruses that such mutations can confer. Therefore, we devised a method that can construct SARS-CoV-2 infectious clones and their variants rapidly and efficiently. The method was developed based on a PCR-based circular polymerase extension cloning (CPEC) combined with a specific primer design scheme. The efficiency of the newly designed method was evaluated by generating SARS-CoV-2 variants with single point mutations, multiple point mutations, and a large truncation and insertion. This method could be of value for the molecular characterization of emerging SARS-CoV-2 variants and the development and testing of vaccines and antiviral agents.
High levels of osteopontin associated with polymorphisms in its gene are a risk factor for development of autoimmunity/lymphoproliferation (2003)

The autoimmune/lymphoproliferative syndrome (ALPS) displays defective function of Fas, autoimmunities, lymphadenopathy/splenomegaly, and expansion of CD4/CD8 double-negative (DN) T cells. Dianzani autoimmune/lymphoproliferative disease (DALD) is an ALPS variant lacking DN cells. Both forms have been ascribed to inherited mutations hitting the Fas system but other factors may be involved. A pilot cDNA array analysis on a DALD patient detected overexpression of the cytokine osteopontin (OPN). This observation was confirmed by enzyme-linked immunosorbent assay (ELISA) detection of higher OPN serum levels in DALD patients (n = 25) than in controls (n = 50). Analysis of the OPN cDNA identified 4 polymorphisms forming 3 haplotypes (A, B, and C). Their overall distribution and genotypic combinations were different in patients (N = 26) and controls (N = 158) (P <.01). Subjects carrying haplotype B and/or C had an 8-fold higher risk of developing DALD than haplotype A homozygotes. Several data suggest that these haplotypes influence OPN levels: (1) in DALD families, high levels cosegregated with haplotype B or C; (2) in healthy controls, haplotype B or C carriers displayed higher levels than haplotype A homozygotes; and (3) in AB and AC heterozygotes, mRNA for haplotype B or C was more abundant than that for haplotype A. In vitro, exogenous OPN decreased activation-induced T-cell death, which suggests that high OPN levels are involved in the apoptosis defect.
Differential Evolution with adaptive population size (2014)

Differential Evolution (DE) is one of the evolutionary algorithms under active research. It has been successfully applied to many real-world problems. The performance of DE highly depends on the population size Np. An improper selection of Np may result in premature convergence or waste of computational resources. In this paper, we proposed a novel method to adaptively control the population size of DE. With this method users do not need to set the Np parameter for DE. The proposed algorithm DEAPS is compared with the conventional DE with different population sizes. DEAPS demonstrates encouraging results on its capability of adaption for seven problems of benchmark test functions.
INTERIM REPORT: MOISTURE MOVEMENT AND MOISTURE EQUILIBRIA IN PAVEMENT SYSTEMS (1976)

The primary purpose of IHR-604 is to develop a satisfactory and realistic procedure for determining moisture movement and moisture equilibria in pavement systems and to develop procedures for utilizing this information in pavement design. The specific objectives of this interim report were to fulfill the requirements of Phase I (Development of Working Moisture Model), as follows: 1. Part 1.1 - Develop, based on environmental factors, a theoretical model for predicting moisture movement and moisture equilibria in pavement systems. 2. Part 1.2 - Validate the moisture model and if necessary refine the moisture model by means of controlled laboratory studies. 3. Part 1.3 - Prepare the interim report concerning the development of the moisture model and its validation by using laboratory data and available field data. It is expected that the findings from this research project will be helpful to those who must make decisions relating to moisture problems in pavement systems. The moisture model can be used to determine how various design modifications influence the moisture regime in a pavement system. It is anticipated that the model and related field and laboratory studies will lead to a less empirical approach for incorporating moisture effects into pavement design, construction, behavior, and performance. /FHWA/
Investigation of four phantoms for PET normalization (2012)

Normalization in Positron Emission Tomography (PET) is essential to correct for sensitivity variation across detector elements and produce uniform images. Currently, the standard normalization protocol for General Electric (GE) systems requires a 20 minute scan of a 20 cm diameter cylindrical phantom filled with 2 mCi of 18F Fluorodeoxyglucose (FDG). This process calculates the single detector efficiency factors (e) from the component based normalization factors (NF). We have investigated the feasibility of using smaller phantoms for normalization, including sensitivity to positioning and radioactivity concentration. Four new test phantoms were used for normalization on a GE Discovery 690 PET/CT scanner. The test phantoms included 4.5 cm, 7.5 cm and IOcm diameter cylinders, and a 16-20 cm diameter cylindrical shell. Normalization scans were also taken using the 7.5 cm and 10 cm cylinder phantoms over a range of FDG activities and at transaxially off-center positions. Image quality was assessed by reconstructing a 4 hr high count, uniform activity image quality (IQ) phantom scan using each normalization data set. All test phantoms produced similarly uniform reconstructions of the IQ phantom scan. Upon examining subtractions from the standard, high frequency ring artifacts with ±1 % peak intensity were present in images reconstructed using the 4.5cm, 7.5cm, and 10cm normalization phantoms. FFT analysis quantified the spatial period of ring artifacts as T = 2.15 ± 0.1 cm, one half of the detector block width of the GE 690 system. Simulation confirmed that ring artifacts result from periodic detector sensitivity decrease, which points to incident photo obliquity being the cause of said artifact. ROIs across anterior/posterior direction of the central slice were used to quantify low frequency uniformity. Low frequency non-uniformities were found to be produced by off-center normalization phantom positioning, as expected. In addition, an 8 minute Hoffman brain phantom scan was reconstructed using each a centered normalization data set from each phantom. Grey matter was isolated and statistically assessed using mean and max intensity difference from the standard. When subtracted from the standard reconstruction, all four test phantom images displayed ~0.5% standard deviation of pixel intensity variation, which did not create a visibly noticeable difference in the reconstructed images.
Eucaryotic replication origin binding proteins (2004)

Initiation of eukaryotic DNA replication is a tightly controlled process. Replication initiates at multiple specific sites (replication origins) that have been licensed for replication, following the cell cycle-dependent, multi-step assembly of specific factors. Thus, replication origins occur in two chromatin states: a replication-competent pre-replicative (pre-RC) state, when a number of replication proteins assemble on the origin in a stepwise fashion, and a replication-incompetent post-replicative (post-RC) state, in which the origin (or elements of it) is bound only by the origin recognition complex (ORC) (or subunits of it). This review summarizes the origin binding proteins that have been have been identified to date.
Prostate Cancer: Correlation of MR Imaging and MR Spectroscopy with Pathologic Findings after Radiation Therapy–Initial Experience (2005)

In summary, MR imaging and MR spectroscopy may be more sensitive than sextant biopsy and digital rectal examination for sextant localization of cancer recurrence after external-beam radiation therapy.
Studies of interaction of plasma jets generated in a plasma focus facility with an ambient plasma in external magnetic field (2001)

The aim of the present experiments was to reproduce and to study in laboratory quasi-perpendicular supercritical collisionless shocks similar to the Earth-Solar Wind shock, by using a plasma focus facility as the plasma source. The experi- ments were performed on the PF-3 facility (Filippov-type plasma focus) at a level of energy supply of about 1 MJ. Directed plasma jets are produced with axial velocities ~10 7 cm/s after compression of a plasma-current sheath in the initial stage of plasma focus formation. These jets then travel through an ambient plasma resulting in early gas ionization by X-ray radiation from the plasma focus, and at an angle of 90° to the 2500 G external magnetic field applied by a system based on rear-earth magnets. Our experimental conditions allowed us to reach a range MA ~ 5÷ 10.
A User-Centric QoS Management Approach for Digital Home (2007)

Modern home networking technologies provide great possibilities for distributing digital content throughout the home. However, media distribution is not ready yet to satisfy users' quality expectations, especially in wireless networks. That is why a number of quality of service (QoS) mechanisms have to be deployed in the network in order to guarantee a certain level of quality. We propose a user-centric QoS management approach based on user preferences. Unlike traditional QoS approaches that always give multimedia applications a pre-determined high priority due to their strict latency and loss requirements, the proposed approach classifies traffic according to user preferences, thus, ensuring a certain quality regardless of the application requirements. The application priorities are assigned according to user profiles and automatically updated in case of changes in the network or user environment. The paper suggests that the introduced management approach will significantly contribute to the overall user experience in digital home.
Über Actinomycetenfarbstoffe, IX1) Konformation und absolute Konfiguration des Actinorhodins (1969)

Abstract Die Konformation der Dihydropyran‐Ringe des Actinorhodins läßt sich aus dem NMR‐Spektrum seines Dimethyl‐Derivates 7a oder 7b ableiten: Die C‐9‐Methyl‐Gruppe *) steht quasi‐axial, der CH 2 –CO 2 H‐Rest äquatorial. – Für die schon beschriebene Abbausäure 14a , die die Chiralitätszentren C‐9 bzw. C‐9′ *) des Actinorhodins enthält, sichert das ORD‐Spektrum (R)‐Konfiguration. – Damit fällt die Entscheidung zwischen vier zur Wahl stehenden Stereoformeln zugunsten von (+)‐(7S, 7′S, 9 R, 9′ R)‐Actinorhodin *) (15) .
Demonstration of Package Level 3D-printed Direct Jet Impingement Cooling applied to High power, Large Die Applications (2020)

This work presents, for the first time, a package- level, bare die liquid jet impingement 3D polymer microfluidics heatsink fabricated using 3D printing, or additive manufacturing for large die size and high-power applications. The heatsink achieves a chip temperature increase of 17.5°C at a chip power of 285 W for a coolant flow rate of 3.25 LPM, demonstrating that 3D printing enables the design for low-cost, high efficiency direct on-chip microfluidic heatsink with complex internal 3D manifold liquid delivery channels. The measurement results show that the jet impingement cooling performance can be successfully described using a unit cell approach, allowing an easy scaling of the thermal performance for arbitrary die size applications. Long term thermal tests of 1000h show a constant thermal performance and no degradation of the cooler material.
Pyrethroid insecticidesChapter IVa. Reactivity of chrysanthemic acid and its lower esters (2021)

The reactivity of chrysanthemic acid and of its "lower esters" (methyl, ethyl, isopropyl and t-butyl) has played a crucial role in their structure elucidation, the discovery of new insecticides and in the understanding of their environmental fate.
Analysis and Testing of Notifications in Android Wear Applications (2017)

Android Wear (AW) is Google's platform for developing applications for wearable devices. Our goal is to make a first step toward a foundation for analysis and testing of AW apps. We focus on a core feature of such apps: notifications issued by a handheld device (e.g., a smartphone) and displayed on a wearable device (e.g., a smartwatch). We first define a formal semantics of AW notifications in order to capture the core features and behavior of the notification mechanism. Next, we describe a constraint-based static analysis to build a model of this run-time behavior. We then use this model to develop a novel testing tool for AW apps. The tool contains a testing framework together with components to support AW-specific coverage criteria and to automate the generation of GUI events on the wearable. These contributions advance the state of the art in the increasingly important area of software for wearable devices.