gebhart/patrepeval huggingface dataset:
Immunostaining of PD-1/PD-Ls in liver tissues of patients with hepatitis and hepatocellular carcinoma (2011)

PD-L1 may contribute to negative regulation of the immune response in chronic hepatitis B. PD-1 and PD-Ls may play a role in immune evasion of tumors.
Recovery from Acute SARS-CoV-2 Infection and Development of Anamnestic Immune Responses in T Cell-Depleted Rhesus Macaques (2021)

Severe coronavirus disease 2019 (COVID-19) has been associated with T cell lymphopenia, but no causal effect of T cell deficiency on disease severity has been established. To investigate the specific role of T cells in recovery from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, we studied rhesus macaques that were depleted of either CD4<sup>+</sup>, CD8<sup>+</sup>, or both T cell subsets prior to infection. Peak virus loads were similar in all groups, but the resolution of virus in the T cell-depleted animals was slightly delayed compared to that in controls. The T cell-depleted groups developed virus-neutralizing antibody responses and class switched to IgG. When reinfected 6 weeks later, the T cell-depleted animals showed anamnestic immune responses characterized by rapid induction of high-titer virus-neutralizing antibodies, faster control of virus loads, and reduced clinical signs. These results indicate that while T cells play a role in the recovery of rhesus macaques from acute SARS-CoV-2 infections, their depletion does not induce severe disease, and T cells do not account for the natural resistance of rhesus macaques to severe COVID-19. Neither primed CD4<sup>+</sup> nor CD8<sup>+</sup> T cells appeared critical for immunoglobulin class switching, the development of immunological memory, or protection from a second infection. <b>IMPORTANCE</b> Patients with severe COVID-19 often have decreased numbers of T cells, a cell type important in fighting most viral infections. However, it is not known whether the loss of T cells contributes to severe COVID-19 or is a consequence of it. We studied rhesus macaques, which develop only mild COVID-19, similar to most humans. Experimental depletion of T cells slightly prolonged their clearance of virus, but there was no increase in disease severity. Furthermore, they were able to develop protection from a second infection and produced antibodies capable of neutralizing the virus. They also developed immunological memory, which allows a much stronger and more rapid response upon a second infection. These results suggest that T cells are not critical for recovery from acute SARS-CoV-2 infections in this model and point toward B cell responses and antibodies as the essential mediators of protection from re-exposure.
An improvement to the adaptive Kalman filter with the feedback of estimation error (2005)

This paper presents a new novel technique for implementation of the adaptive Kalman filter. The algorithm is based on Kalman filtering tracking method with the addition of feedback estimation error. The performance of the algorithm is compared with that of a standard Kalman filter and also with that of an IMM algorithm. This proposed filter is simple to implement and requires less computational load while produce better estimates than the standard Kalman filter algorithm and closely to the IMM algorithm.
Etching mechanisms of HfO2, SiO2, and poly-Si substrates in BCl3 plasmas (2007)

B Cl 3 based plasmas exhibit promising plasma chemistries to etch high-k materials and, in particular, HfO2, with a high selectivity over SiO2 and Si substrates. The authors report on the mechanisms involved in the etching of HfO2, SiO2, and poly-Si substrates in BCl3 plasmas. X-ray photoelectron spectroscopy analyses help in understanding the mechanism driving the high etch selectivity between HfO2 and silicon-containing substrates. The ion energy plays an important role in the etching mechanisms since it controls a transition between a BCl-like deposition on the substrate and its etching by ionic bombardment. The ion energy threshold above which etching occurs is different from one substrate to another, being lower for HfO2 than for Si substrates. Indeed, BClx deposition forms more easily on poly-Si or SiO2 rather than on HfO2 surfaces, because boron reacts with Si atoms to form Si–B bonds initiating the growth of BClx polymer on Si-containing surfaces, while on HfO2 surfaces, boron is directly involved in the etching and reacts with oxygen to form volatile BOCl etch products.
In Vitro and In Vivo Comparison of Selected Ga-68 and Zr-89 Labelled Siderophores (2015)

Zr-89 and [(68)Ga]siderophores showed analogous in vitro and in vivo behaviour. Tested [(89)Zr]siderophores could be applied for longitudinal positron emission tomography (PET) studies of fungal infections and especially TAFC for the development of novel bioconjugates.
Functional interaction of constant and variable domains of human immunodeficiency virus type 1 gp120 (1989)

A previously reported amino acid substitution within the second conserved domain of the human immunodeficiency virus type 1 (HIV-1) gp120 envelope results in the production of noninfectious particles. Molecular characterization of spontaneous revertant viruses, which arose during long-term cocultures of this env mutant, revealed that an amino acid change within another region of gp120 could functionally compensate for the mutation and restore infectivity. In the current study, we have introduced a conservative amino acid substitution at this second-site revertant codon and observed a marked reduction in HIV-1 infectivity. During the passage of this defective virus in cocultures, yet another revertant appeared which contained an amino acid change within a variable region of gp120 which restored infectivity to near wild-type levels. These results, in combination with other point mutations that have been introduced into the HIV-1 envelope, suggest that at least three discrete regions of gp120 may interact during the establishment of a productive viral infection. This critical step occurs subsequent to the adsorption of virions to the cell surface and either prior to or concomitant with the fusion of viral and cellular membranes.
<title>Characterization of passive polymer optical waveguides</title> (1999)

The characterization of monomode passive polymer optical devices fabricated according to the POPCORN technology by methods originated from electron, ion and optical spectroscopy is summarized. Impacts of observed waveguide perturbations on the optical characteristics of the waveguide are evaluated. In the POPCORN approach optical components for telecommunication applications are fabricated by photo-curing of liquid halogenated (meth)acrylates which have been applied on moulded thermoplastic substrates. For tuning of waveguide material refractive indices with respect to the substrate refractive index frequently comonomer mixtures are used. The polymerization characteristics, especially the polymerization kinetics of individual monomers, determine the formation of copolymers. Therefore the unsaturation as function of UV-illumination time in the formation of halogenated homo- and copolymers has been examined. From different suitable copolymer system, after characterization of their glass transition temperatures, their curing behavior and their refractive indices as function of the monomer ratios, monomode waveguides applying PMMA substrates have been fabricated. To examine the materials composition also in the 6 X 6 micrometers <SUP>2</SUP> waveguides they have been visualized by transmission electron microscopy. With this method e.g. segregation phenomena could be observed in the waveguide cross section characterization as well. The optical losses in monomode waveguides caused by segregation and other materials induce defects like micro bubbles formed as a result of shrinkage have been quantized by return loss measurements. Defects causing scattering could be observed by convocal laser scanning microscopy and by conventional light microscopy.
Green synthesis of densely dispersed and stable silver nanoparticles using myrrh extract and evaluation of their antibacterial activity (2013)

In the present study, green synthesis of densely dispersed and stable silver nanoparticles (Ag NPs) using myrrh extract as green-reducing and stabilizing agent was investigated. The Ag NPs were synthesized by exposing a mixture of AgNO3 and myrrh extract to UV irradiation for different time intervals. The effects of parameters such as concentration of AgNO3 and reaction time onto the physicochemical characteristics of the developed Ag NPs were studied. Formation of the Ag NPs was noted upon changing the solution color from pale yellow into brown and was confirmed by the appearance of surface plasmon resonance peaks at about 445 nm. The resulting Ag NPs were characterized by UV-vis spectrophotometry, transmission electron microscopy, Fourier transform infrared spectroscopy, and X-ray diffraction. The developed NPs demonstrated a relatively high antibacterial activity against Bacillus thuringiensis and Pseudomonas aeruginosa bacteria as compared to that of myrrh extract. The antibacterial activity increased with increasing the Ag NP concentration.
Two translocating hydrophilic segments of a nascent chain span the ER membrane during multispanning protein topogenesis (2007)

During protein integration into the endoplasmic reticulum, the N-terminal domain preceding the type I signal-anchor sequence is translocated through a translocon. By fusing a streptavidin-binding peptide tag to the N terminus, we created integration intermediates of multispanning membrane proteins. In a cell-free system, N-terminal domain (N-domain) translocation was arrested by streptavidin and resumed by biotin. Even when N-domain translocation was arrested, the second hydrophobic segment mediated translocation of the downstream hydrophilic segment. In one of the defined intermediates, two hydrophilic segments and two hydrophobic segments formed a transmembrane disposition in a productive state. Both of the translocating hydrophilic segments were crosslinked with a translocon subunit, Sec61alpha. We conclude that two translocating hydrophilic segment in a single membrane protein can span the membrane during multispanning topogenesis flanking the translocon. Furthermore, even after six successive hydrophobic segments entered the translocon, N-domain translocation could be induced to restart from an arrested state. These observations indicate the remarkably flexible nature of the translocon.
Glycemic index: overview of implications in health and disease,,, (2002)

The glycemic index concept is an extension of the fiber hypothesis, suggesting that fiber consumption reduces the rate of nutrient influx from the gut. The glycemic index has particular relevance to those chronic Western diseases associated with central obesity and insulin resistance. Early studies showed that starchy carbohydrate foods have very different effects on postprandial blood glucose and insulin responses in healthy and diabetic subjects, depending on the rate of digestion. A range of factors associated with food consumption was later shown to alter the rate of glucose absorption and subsequent glycemia and insulinemia. At this stage, systematic documentation of the differences that exist among carbohydrate foods was considered essential. The resulting glycemic index classification of foods provided a numeric physiologic classification of relevant carbohydrate foods in the prevention and treatment of diseases such as diabetes. Since then, low-glycemic-index diets have been shown to lower urinary C-peptide excretion in healthy subjects, improve glycemic control in diabetic subjects, and reduce serum lipids in hyperlipidemic subjects. Furthermore, consumption of low-glycemicindex diets has been associated with higher HDL-cholesterol concentrations and, in large cohort studies, with decreased risk of developing diabetes and cardiovascular disease. Case-control studies have also shown positive associations between dietary glycemic index and the risk of colon and breast cancers. Despite inconsistencies in the data, sufficient, positive findings have emerged to suggest that the dietary glycemic index is of potential importance in the treatment and prevention of chronic diseases.
Neutron reflection as a probe of surface magnetism (1981)

Polarized neutrons reflected from the surface of a ferromagnet are sensitive to the magnetization close to the surface as well as to the bulk magnetization. In a calculation using parameters appropriate to nickel it is shown how the two contributions can be separated. Neutron measurements can determine the first moment of the magnetic disturbances at the surface, with a sensitivity corresponding to one magnetic dead layer.
Taming Dinitramide Anions within an Energetic Metal–Organic Framework: A New Strategy for Synthesis and Tunable Properties of High Energy Materials (2016)

Energetic polynitro anions, such as dinitramide ion [N(NO2)2–], have attracted significant interest in the field of energetic materials due to their high densities and rich oxygen contents; however, most of them usually suffer from low stability. Conveniently stabilizing energetic polynitro anions to develop new high energy materials as well as tuning their energetic properties still represent significant challenges. To address these challenges, we herein propose a novel strategy that energetic polynitro anions are encapsulated within energetic cationic metal–organic frameworks (MOFs). We present N(NO2)2– encapsulated within a three-dimensional (3D) energetic cationic MOF through simple anion exchange. The resultant inclusion complex exhibits a remarkable thermal stability with the onset decomposition temperature of 221 °C, which is, to our knowledge, the highest value known for all dinitramide-based compounds. In addition, it possesses good energetic properties, which can be conveniently tuned by changing the mole ratio of the starting materials. The encapsulated anion can also be released in a controlled fashion without disrupting the framework. This work may shed new insights into the stabilization, storage, and release of labile energetic anions under ambient conditions, while providing a simple and convenient approach for the preparation of new energetic MOFs and the modulation of their energetic properties.
A Yeast Mutant Showing Diagnostic Markers of Early and Late Apoptosis (1997)

A Saccharomyces cerevisiae mutant in cell division cycle gene CDC48 shows typical markers of apoptosis: membrane staining with annexin V, indicating an exposure of phosphatidylserine at the outer layer of the cytoplasmic membrane; intense staining, using the terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling method, indicating DNA fragmentation; and chromatin condensation and fragmentation. The coordinate occurrence of these events at different locations in the cell, which have no obvious connection except their relation to apoptosis, implies the presence of the molecular machinery performing the basic steps of apoptosis already in yeast. Saccharomyces cerevisiae may prove a suitable model to trace the roots of apoptosis.
Carbohydrates and soluble lectins in the regulation of cell adhesion and proliferation. (1994)

There is a large body of suggestions that complex carbohydrates play a role in the regulation of cell adhesion and cell proliferation. Many reports have emphasized that proteoglycans, glycoproteins or glycolipids are participating to cell adhesion mechanisms. The use of polyvalent anti-carbohydrate antibodies and plant lectins as well as the use of glycosylation inhibitors suggested that cell proliferation can be modulated by surface carbohydrates. The dating experiment of Burger and Noonan (1970) showing restoration of contact inhibition of malignant cells by monovalent concanavalin A was a determining experiment. However, in the latter as in the others, no precise mechanism was demonstrated how carbohydrates can be involved in adhesion and proliferation. New insights were opened with the discovery of vertebrate membrane-bound and soluble lectins. The latter generally display agglutinating activities in in vitro systems, suggesting that they were potential cell adhesion molecules, by forming bridges between cell surface carbohydrates. These polyvalent molecules may be also considered as clustering agents for their cell surface ligands, consequently generating signals for cell proliferation and/or differentiation.
DEPTH IMAGE BASED VIEW SYNTHESIS WITH MULTIPLE REFERENCE VIEWS FOR VIRTUAL REALITY (2018)

This paper presents a method for view synthesis from multiple views and their depth maps for free navigation in Virtual Reality with six degrees of freedom (6DoF) and 360 video (3DoF+), including synthesizing views corresponding to stepping in or out of the scene. Such scenarios should support large baseline view synthesis, typically going beyond the view synthesis involved in light field displays [1]. Our method allows to input an unlimited number of reference views, instead of the usual left and right reference views. Increasing the number of reference views overcomes problems such as occlusions, tangential surfaces to the cameras axis and artifacts in low quality depth maps. We outperform MPEG's reference software, VSRS [2], with a gain of up to 2.5 dB in PSNR when using four reference views.
A geographical routing protocol for highly-dynamic aeronautical networks (2011)

Emerging networked systems require domain-specific routing protocols to cope with the challenges faced by the aeronautical environment. We present a geographic routing protocol AeroRP for multihop routing in highly dynamic MANETs. The AeroRP algorithm uses velocity-based heuristics to deliver the packets to destinations in a multi-Mach speed environment. Furthermore, we present the decision metrics used to forward the packets by the various AeroRP operational modes. The analysis of the ns-3 simulations shows AeroRP has several advantages over other MANET routing protocols in terms of PDR, accuracy, delay, and overhead. Moreover, AeroRP offers performance tradeoffs in the form of different AeroRP modes.
Asynchronous FIFO Interfaces for GALS On-Chip Switched Networks (2005)

In this paper we present a novel design approach that combines the advantages of on-chip switched networks (OCSNs) and the globally asynchronous, locally synchronous (GALS) design methodology using the mechanism of asynchronous FIFO buffers. Our proposed two GALS OCSN models were synthesized with 0.25μm Chip Express structured ASIC library. Comparative simulations were performed for these two platforms using three different mixed-clock test scenarios to show functional verification. Performance results are given.
Rare Sesquiterpenoids from the Shed Trunk Barks of the Critically Endangered Plant <i>Abies beshanzuensis</i> and Their Bioactivities (2016)

Abstract Two rare rearranged cuparane‐type sesquiterpenoid C‐10 epimers [beshanzuenones A ( 1 ) and B ( 2 )] and two bisabolane‐type sesquiterpenoid spirolactones [beshanzuenones C ( 3 ) and D ( 4 )] featuring an unusual [6/6/5]‐fused tricyclic ring system were isolated from the shed trunk barks of Abies beshanzuensis , one of the critically endangered plant species in the world. The structures of these four new enone‐containing sesquiterpenoids were determined by spectroscopic analyses and single‐crystal X‐ray diffraction or electronic circular dichroism (ECD) calculations. Compounds 1 and 2 showed considerable activity against the H3N2 virus, whereas 3 and 4 exhibited significant inhibition on PTP1B.
Crisis management: The role of command, control and communications (1983)

Click to increase image sizeClick to decrease image size Additional informationNotes on contributorsPhil Williamshas held a term of Research Fellow at the Royal Institute of International Affairs from July 1982 to June 1983.
An Internet-Scale Service for Publishing and Locating XML Documents (2009)

In recent years, there has been a growing interest for peer-to-peer (P2P) based computing and applications. One of the most important challenges in P2P environments is to quickly locate relevant data across many participating peers. In this demonstration, we present psiX, which is an Internet-scale service for publishing and locating XML documents. This service runs on several PlanetLab nodes geographically spread across the globe. The psiX system adopts a suite of new techniques for XML indexing and pattern matching in a P2P network, namely, (a) representing XML documents and XPath queries compactly via algebraic signatures, (b) searching signatures of documents and value summaries indexed using distributed hierarchical indexes built over a distributed hash table (DHT), and (c) gracefully adapting to failures while running on the Internet, where failures are a norm rather than an exception.
69. New trypanocides. Part I. Quaternary salts derived from 2 : 7-diaminophenanthridine and the attempted preparation of quaternary salts from 2 : 7-diamino-9-anilinophenanthridine (1956)

M. Davis, J. Chem. Soc., 1956, 337 DOI: 10.1039/JR9560000337
Investigations on Drug Release Systems Using Cmc Crosslinked with Ferric Ions (1999)

A drug delivery system with controlled release capability was developed by crosslinking carboxymethylcellulose with ferric ions. Erythromycin was used as model drug throughout the research. It was aimed to transport model drug through gastro intestinal track with minimal release up to intestines. Different techniques were applied to obtain a suitable delivery system and finally minimal release (10% of the total) in stomach (simulated by pH 2.0) and a high release (90% of the total) in intestinal systems (simulated by pH 7.5) was obtained by applying a combination of wet and dry coating, drying and secondary crosslinking.
Glutamine‐fueled mitochondrial metabolism is decoupled from glycolysis in melanoma (2012)

In this perspective, we revise the historic notion that cancer is a disease of mitochondria. We summarize recent findings on the function and rewiring of central carbon metabolism in melanoma. Metabolic profiling studies using stable isotope tracers show that glycolysis is decoupled from the tricarboxylic acid (TCA) cycle. This decoupling is not 'dysfunction' but rather an alternate wiring required by tumor cells to remain metabolically versatile. In large part, this requirement is met by glutamine feeding the TCA cycle as an alternative source of carbon. Glutamine is also used in non-conventional ways, like traveling in reverse through the TCA flux to feed fatty acid biosynthesis. Biosynthetic networks linked with non-essential amino acids alanine, serine, arginine, and proline are also significantly impacted by the use of glutamine as an alternate carbon source.
On-chip screening for prostate cancer: an EIS microfluidic platform for contemporary detection of free and total PSA (2013)

Prostate cancer affects a large part of the western male population. The need for an early and accurate detection is thus a great challenge in common clinical practice, but the lack of specificity of the serum marker PSA (Prostate Specific Antigen) is a serious problem since its increased concentration can be related to several abnormalities. PSA, however, is found in serum in both a free and a complexed form with other proteins and the percentage amount of unbound PSA (the free-to-total PSA ratio) can be employed to distinguish prostate cancer from benign prostatic conditions, and also to predict the future risk of prostate cancer. To improve the operating characteristics of current PSA tests and to provide a clinical tool able to run label-free and sensitive analysis, we thus developed a biosensing platform based on Electrochemical Impedance Spectroscopy (EIS), which allows the contemporary detection of free and total PSA on a single biochip, enabling a quick screening for the risk of prostate cancer thanks to the presence of two different immobilized antibodies specific for the different antigens researched.