gebhart/patrepeval huggingface dataset:
Mechanisms of Oxidative Glutamate Toxicity: The Glutamate/Cystine Antiporter System xc&#175; as a Neuroprotective Drug Target (2010)

The glutamate/cystine antiporter system x(c)- transports cystine into cells in exchange for the important neurotransmitter glutamate at a ratio of 1:1. It is composed of a specific light chain, xCT, and a heavy chain, 4F2, linked by a disulfide bridge. Both subunits are localized prominently in the mouse and human brain especially in border areas between the brain and periphery including vascular endothelial cells, ependymal cells, choroid plexus, and leptomeninges. Glutamate exported by system x(c)- is largely responsible for the extracellular glutamate concentration in the brain, whereas the imported cystine is required for the synthesis of the major endogenous antioxidant, glutathione. System x(c)- thus connects the antioxidant defense with neurotransmission and behavior. Disturbances in the function of system x(c)- have been implicated in nerve cell death due to increased extracellular glutamate and reduced intracellular glutathione. In vitro, inhibition of cystine import through system x(c)- leads to cell death by a mechanism called oxidative glutamate toxicity or oxytosis, which includes depletion of intracellular glutathione, activation of 12-lipoxygenase, accumulation of intracellular peroxides, and the activation of a cyclic guanosine monophosphate (cGMP)-dependent calcium channel towards the end of the death cascade. Cell death caused by oxytosis is distinct from classical apoptosis. In this contribution, we discuss the function of system x(c)- in vitro and in vivo, the role of xCT as an important but due to its dual role probably ambivalent drug target, and the relevance of oxytosis as an in vitro assay for the identification of novel neuroprotective proteins and signaling pathways.
Dietzia, New Genus Including Dietzia maris comb. nov., Formerly Rhodococcus maris (1995)

Sequencing of the 16S ribosomal DNAs (rDNA) of two strains of Rhodococcus maris was performed to determine the relationship of this species to other mycolic acid-containing actinomycetes. For this purpose we also determined the 16S rDNA sequences for the type species of the genus Rhodococcus, Rhodococcus rhodochrous, and for Mycobacterium chlorophenolicum (formerly Rhodococcus chlorophenolicus), Rhodococcus erythropolis, Gordona bronchialis, and Gordona terrae, for which only partial sequence data have been available previously. The sequences of the two strains of R. maris were identical. The results of a distance matrix analysis indicated that R. maris is not a member of the genus Rhodococcus but is located between members of the genus Corynebacterium and members of the Rhodococcus-Nocardia-Mycobacterium-Gordona-Tsukamurella cluster. The finding that R. maris is phylogenetically isolated is supported by the presence of N-acetyl residues in the glycan moiety of the peptidoglycan and the lack of phosphatidylinositol and phosphatidylinositol mannosides, characteristics which distinguish this taxon from related taxa. On the basis of our results and previous findings, we propose that R. maris should be reclassified in a new genus, Dietzia. The type species is Dietzia maris comb. nov.
Enumerating Immunoglobulin-Secreting Cells Among Peripheral Human Lymphocytes. A Hemolytic Plaque Assay for A B Cell Function (1975)

Cells bearing immunoglobulin (Ig) can be enumerated by current methods, but cells secreting Ig (with unknown antibody specificity) can not. By using a reverse plaque-forming cell assay, we counted the Ig-secreting cells in the blood of nonimmunized individuals. Isolated human lymphocytes were plated in gels together with erythrocytes coated with purified antibody to human Ig. After treatment with anti-Ig antibody and complement, the Ig-secreting cells formed hemolytic plaques. In 10 normal individuals, 1.2 +/- 0.4% of the plated mononuclear cells formed plaques; in an individual tested on 7 different days during 3 months, 1.1 +/- 0.2% of the cells formed plaques. From the number of mononuclear cells in the blood, we calculated 22 +/- 8 Ig-secreting cells per mm3 of blood. Enumerating Ig-secreting cells is a new direct assay for a B cell function and need not correlate with quantitating serum Ig. Thus, this assay should be useful for studying Ig-secretion in normal and altered states.
A new QC approach for 4D seismic surveys using towed streamer acquisition (2008)

Ever since marine 4D seismic surveys were first mooted as a tool for reservoir imaging and monitoring over time, the major challenge has been repeatability, making sure that all the factors determining one survey could be reproduced in subsequent surveys over the same location. The solution for the last six or seven years has been a form of repeatability QC which provides a measure of the positioning errors between the original baseline survey and the monitor surveys which follow.
Photonic crystal for gas sensing (2013)

Photonic crystal (PhCs) based sensing technology has gained more and more attention because of its obvious advantages in sensitivity, stability, security, miniaturisation, portability, on-line use and remote monitoring. Many PhC sensors have been proposed based on their novel structure and unique optical properties. In this review, we will describe the recent progress in the use of natural and artificial PhC materials for gas/vapor sensing, including Morpho butterfly wings and their mimicry of nanostructures, porous silicon, Bragg stacks, colloidal crystals and inverse opal. Here we will discuss the PhCs with different structures and their respective gas sensing properties, focusing on the description of the functional structure of the PhCs materials and their sensing mechanisms.
Microbial endocrinology (2014)

The ability of microorganisms, whether present as commensals within the microbiota or introduced as part of a therapeutic regimen, to influence behavior has been demonstrated by numerous laboratories over the last few years. Our understanding of the mechanisms that are responsible for microbiota-gut-brain interactions is, however, lacking. The complexity of the microbiota is, of course, a contributing factor. Nonetheless, while microbiologists approaching the issue of microbiota-gut-brain interactions in the behavior well recognize such complexity, what is often overlooked is the equal complexity of the host neurophysiological system, especially within the gut which is differentially innervated by the enteric nervous system. As such, in the search for common mechanisms by which the microbiota may influence behavior one may look for mechanisms which are shared by both host and microbiota. Such interkingdom signaling can be found in the shared production of neurochemical mediators that are found in both eukaryotes and prokaryotes. The study of the production and recognition of neurochemicals that are exactly the same in structure to those produced in the vertebrate organisms is known as microbial endocrinology. The examination of the microbiota from the vantage point of host-microbiota neuroendocrine interactions cannot only identify new microbial endocrinology-based mechanisms by which the microbiota can influence host behavior, but also lead to the design of interventions in which the composition of the microbiota may be modulated in order to achieve a specific microbial endocrinology-based profile beneficial to overall host behavior.
Reactivity of a functional carbonyl moiety in bovine aortic lysyl oxidase. Evidence against pyridoxal 5′-phosphate (1986)

Previous studies have pointed towards a cofactor role for pyridoxal 5'-phosphate (PLP) in lysyl oxidase, the enzyme that generates the peptidyl aldehyde precursor to the lysine-derived cross-linkages in elastin and collagen. The nature of a carbonyl moiety in purified bovine aortic lysyl oxidase was explored in the present study. A PLP dinitrophenylhydrazone could not be isolated from lysyl oxidase, although corresponding preparations of aspartate aminotransferase, a PLP-dependent enzyme, yielded this derivative, as revealed by h.p.l.c. Analysis of lysyl oxidase for PLP after reduction of the enzyme by NaBH4, a procedure that converts PLP-protein aldimines into stable 5'-phosphopyridoxyl functions, also proved negative in tests using monoclonal antibody specific for this epitope. Lysyl oxidase was competitively inhibited by phenylhydrazine, and inhibition became irreversible with time at 37 degrees C, displaying a first-order inactivation rate constant of 0.4 min-1 and KI of 1 microM. [14C]Phenylhydrazine was covalently incorporated into the enzyme in a manner that was prevented by prior modification of the enzyme with beta-aminopropionitrile, a specific active-site inhibitor, and which correlated with functional active-site content. The chemical stability of the enzyme-bound phenylhydrazine exceeded that expected of linkages between PLP and proteins. The absorption spectrum of the phenylhydrazine derivative of lysyl oxidase was clearly distinct from that of the phenylhydrazone of PLP. It is concluded that lysyl oxidase contains a carbonyl cofactor that is not identical with PLP and that is bound to the enzyme by a stable chemical bond.
A local curve-fitting method for the complex refractive index measurement of turbid media (2012)

An improved curve-fitting method for a simultaneous measurement of the real and imaginary parts of the complex refractive index of turbid media is demonstrated. Based on an introduction of angle-dependent light penetration into turbid media by Calhoun et al (2010 Opt. Lett. 35 1224), the fitting is performed on the rapid change part of the measured curve around the critical angle. Moreover, a technology to locate this part of the curve by differentiation is introduced. Experimental results on Intralipid solutions show that this method can significantly reduce the computation time as well as the fitting error between the measured curve and theoretical one.
Electro-reductive stripping of vanadium in solvent extraction process for separation of vanadium and molybdenum. (1991)

The separation of vanadium and molybdenum by solvent extraction followed by photoreductive stripping was investigated, using tri-n-octylmethylammonium chloride (TOMAC) as extractant. A low-pressure mercury lamp and a halogen lamp were used as light sources. Pentavalent vanadium was reduced photochemically to tetravalent or trivalent vanadium in organic solution as well as in aqueous solution, using isopropyl formate as a radical scavenger. The photoreduction of vanadium in TOMAC/benzene phase containing vanadyl and molybdate anions allowed the vanadium to be stripped into an aqueous phase selectively, leaving the molybdenum in the organic phase. The stripping yield of vanadium reached 100%. The separation factor of vanadium and molybdenum by single extraction followed by single selective stripping was 1000–2000 when using the mercury lamp and 170–430 when using the halogen lamp. The organic solution was not damaged by the photoreductive stripping and was reusable for repeated extraction and stripping.
Absent or low expression of the zeta chain in T cells at the tumor site correlates with poor survival in patients with oral carcinoma. (1998)

Immunohistology for expression of the CD3zeta and CD3epsilon chains in TIL was performed in 138 paraffin-embedded primary oral squamous cell carcinoma tissues and 10 nontumor, inflammatory lesions. Semiquantitative analysis of the staining intensity for zeta chain expression and number of zeta chain expression-positive cells distinguished tumors with absent or low zeta expression (42 of 132) from those with normal zeta expression (90 of 132). Zeta chain expression was inversely correlated with the tumor stage. Survival was significantly lower in patients whose TIL had absent or low zeta expression, controlling for stage (P = 0.003) and lymph node status (P = 0.0005). The prognostic value of zeta chain was restricted to patients with stage III or IV tumors (P = 0.003). The data indicate that absent or decreased zeta expression in TIL combined with tumor stage or nodal status defines a group of patients with oral squamous cell carcinoma who have an extremely poor prognosis.
LanczosNet: Multi-Scale Deep Graph Convolutional Networks (2019)

We propose the Lanczos network (LanczosNet), which uses the Lanczos algorithm to construct low rank approximations of the graph Laplacian for graph convolution. Relying on the tridiagonal decomposition of the Lanczos algorithm, we not only efficiently exploit multi-scale information via fast approximated computation of matrix power but also design learnable spectral filters. Being fully differentiable, LanczosNet facilitates both graph kernel learning as well as learning node embeddings. We show the connection between our LanczosNet and graph based manifold learning methods, especially the diffusion maps. We benchmark our model against several recent deep graph networks on citation networks and QM8 quantum chemistry dataset. Experimental results show that our model achieves the state-of-the-art performance in most tasks. Code is released at: \url{https://github.com/lrjconan/LanczosNetwork}.
A Review on Recent Patents in Corrosion Inhibitors (2010)

Selection of an appropriate corrosion inhibitor, inhibitor combination or package is an exceptionally cost effective and materials saving measure in various industries. Current trends and novel approaches in corrosion inhibitors are reviewed here. Recent developments in the inhibition technology are discussed in accordance with the areas of application of inhibitors.
Near Infrared Spectroscopy and Chemometrics Studies of Temperature-Dependent Spectral Variations of Water: Relationship between Spectral Changes and Hydrogen Bonds (1995)

The present study aims to provide new insights into the temperature-dependent spectral variations in the near infrared (NIR) region of the spectrum of water by comparing chemometrics with spectroscopic analysis. Fourier transform (FT)-NIR spectra of water in the 9000–5500 cm −1 region have been measured over a temperature range of 5–85°C. The observed spectral changes have been analysed by both chemometrics, such as multilinear regression (MLR), principal component regression (PCR) and partial least squares (PLS) regression, and spectroscopic data analyses, such as second derivative, difference spectra and curve fitting. The second derivative of the NIR spectra of water suggests that an intense feature around 6900 cm −1 , due to the combination of antisymmetric and symmetric stretching modes of water, consists of at least five component spectra. Each component spectrum may be ascribed to the water species with no, one, two, three and four hydrogen bonds. Curve fitting has been performed for the 6900 cm −1 band and it has been found that the species with no hydrogen bonds increase largely with temperature, while those with more than two hydrogen bonds decrease. The temperature of water has been predicted by use of MLR, PCR and PLS regression. PCR and PLS regression loadings plots for Factor 1 of the models for the prediction of the temperature of water are almost identical with the difference spectrum of water between 5 and 85°C; both the loadings plots and the difference spectrum reflect strongly the changes in the hydrogen bonds of water. Loadings plots of Factor 1 of the PCR and PLS regression models are very similar to each other. It is very likely that since the temperature-dependent spectral variations of water in the NIR region are very regular, and the spectra have only very small noise and baseline changes, PCR and PLS regression select nearly identical factors.
Safety and feasibility of a cloud-based architecture for multi-vehicle system (2017)

Thesis: S.M. in Engineering and Management, Massachusetts Institute of Technology, System Design and Management Program, 2017.
Local collection, reaction and analysis with theta pipette emitters (2017)

A mobile nanofluidic device based on theta pipettes was developed for "collect-react-analyze" measurements of small volumes of a sample collected locally from biological samples. Specifically, we demonstrate execution of local reactions inside single cells and on Pseudomonas aeruginosa biofilms for targeted analysis of metabolites. Nanoliter volumes of the sample, post-reaction, were delivered to a mass spectrometer via electrospray ionization (ESI) for chemical analysis. A new strategy was developed where the additional barrel of a theta pipette was utilized both to enable chemical manipulations after sample collection and to electrospray the nanoliter sample volumes collected directly from the pipette tip. This strategy proved a robust method for ESI from nanometer sized tips without clogging or degradation of the emitter and obviated the need to coat glass pipettes with a conductive metal coating. Chemical reactions investigated include acid catalyzed degradation of oligosaccharides inside the pipette tip to increase the detection sensitivity of minor metabolites found in Allium cepa cells. Additionally, phenylboronic acid complexation of carbohydrates from single cells and liposaccharides from biofilms was also performed inside the pipette tip for selective detection of carbohydrates and liposaccharides with cis-diols.
A Multifunctional Role for Adjuvant Anti-4-1BB Therapy in Augmenting Antitumor Response by Chimeric Antigen Receptor T Cells (2017)

Adoptive immunotherapy utilizing chimeric antigen receptor (CAR) T cells has demonstrated high success rates in hematologic cancers, but results against solid malignancies have been limited to date, due in part to the immunosuppressive tumor microenvironment. Activation of the 4-1BB (CD137) pathway using an agonistic α-4-1BB antibody is known to provide strong costimulatory signals for augmenting and diversifying T-cell responses. We therefore hypothesized that a combination of α-4-1BB and CAR T-cell therapy would result in improved antitumor responses. Using a human-Her2 self-antigen mouse model, we report here that α-4-1BB significantly enhanced CAR T-cell efficacy directed against the Her2 antigen in two different established solid tumor settings. Treatment also increased the expression of IFNγ and the proliferation marker Ki67 in tumor-infiltrating CAR T cells when combined with α-4-1BB. Strikingly, α-4-1BB significantly reduced host immunosuppressive cells at the tumor site, including regulatory T cells and myeloid-derived suppressor cells, correlating with an increased therapeutic response. We conclude that α-4-1BB has a multifunctional role for enhancing CAR T-cell responses and that this combination therapy has high translational potential, given current phase I/II clinical trials with α-4-1BB against various types of cancer. <i>Cancer Res; 77(6); 1296-309. ©2017 AACR</i>.
Altered Immune System Glycosylation Causes Colitis in α1,2-Fucosyltransferase Transgenic Mice (2004)

Altered glycosylation in hFUT1 mice has a profound influence on T-cell development and this defect, rather than a mucosal barrier defect, is crucial for the development of colitis.
Quantum computation with doped silicon cavities (2010)

We propose an architecture for quantum computing involving substitutional donors in photonic-crystal silicon cavities and the optical initialization, manipulation, and detection processes already demonstrated in ion traps and other atomic systems. Our scheme leads to easily achievable requirements on the positioning of the donors and considerably simplifies the implementation of the building blocks required for the operation of silicon-based quantum computing devices, including realization of one- and two-qubit gates, initialization, and readout of the qubits. Detailed consideration of the processes involved, using state-of-the-art values for the relevant parameters, indicates that this architecture leads to errors per gate compatible with fault-tolerant quantum computation and should be useful for quantum simulations and quantum optics applications.
Distress During the Induction of Anesthesia and Postoperative Behavioral Outcomes (1999)

We determined whether children who are extremely anxious during the induction of anesthesia are more at risk of developing postoperative negative behavioral changes compared with children who appear calm during the induction process.Children (n = 91) aged 1-7 yr scheduled for general anesthesia and elective outpatient surgery were recruited. Using validated measures of preoperative anxiety and postoperative behaviors, children were evaluated during the induction of general anesthesia and on Postoperative Days 1, 2, 3, 7, and 14. Using a multivariate logistic regression model, in which the dependent variable was the presence or absence of postoperative negative behavioral changes and the independent variables included several potential predictors, we demonstrated that anxiety of the child, time after surgery, and type of surgical procedure were predictors for postoperative maladaptive behavior. The frequency of negative postoperative behavioral changes decreased with time after surgery, and the frequency of negative postoperative behavioral changes increased when the child exhibited increased anxiety during the induction of anesthesia. Finally, we found a significant correlation (r) of 0.42 (P = 0.004) between the anxiety of the child during induction and the excitement score on arrival to the postanesthesia care unit. We conclude that children who are anxious during the induction of anesthesia have an increased likelihood of developing postoperative negative behavioral changes. We recommend that anesthesiologists advise parents of children who are anxious during the induction of anesthesia of the increased likelihood that their children will develop postoperative negative behavioral changes such as nightmares, separation anxiety, and aggression toward authority. Implications: Anesthesiologists who care for children who are anxious during the induction of anesthesia should inform parents that these children have an increased likelihood of developing postoperative negative behavioral changes. (Anesth Analg 1999;88:1042-7)
The Robotics Revolution Will Be Soft: Soft Robotics Proliferate-Along with Their Sources of Inspiration (2018)

When soft robotics first emerged, it was defined (as breakthroughs often are) by what it was that its traditional counterparts were not, i.e., soft. A decade in, the nomenclature remains apt. The pliant materials used in soft robotics are often both a defining trait and a source of advantage. Soft robots continue to make headlines with their ability to squeeze, octopus-like, through narrow crevices; change shape; and survive impacts that would crush a traditional rigid robot. They distinguish themselves from their hard counterparts with their damage resilience, complex movements, and suitability for use with the human body.
Methods for drift stabilization and photomultiplier linearization for photometric ellipsometers and polarimeters (1978)

We describe simple modifications to photometric polarimeter and ellipsometer systems that greatly reduce nonlinearity, component drift, and digital noise effects. A photomultiplier feedback circuit is described and analyzed that varies the effective system linearity by means of a single control. Linearity to 5 x 10(-4) over more than three orders of magnitude of incident light intensity is obtained. Effective double-beam stability to 5 x 10(-5) is achieved by blocking the source intensity over part of an extended measurement cycle. These refinements permit photometric instruments to approach accuracy capabilities compatible with their precision capabilities, and also allow measurements to be made in the presence of ambient scattered light, at high sample temperatures, or using solid-state detectors for which the zero reference is not well defined. As an example, we give the dielectric function of Ge measured from 1.5 to 5.8 eV at a sample temperature of 800 degrees C.