gebhart/patrepeval huggingface dataset:
Production of recombinant cytochrome b558 allows reconstitution of the phagocyte NADPH oxidase solely from recombinant proteins (1993)

Phagocytic white blood cells contain a multicomponent oxidase that generates microbicidal products by catalyzing electron transfer from NADPH to molecular oxygen. Activation of this oxidase requires interactions of a unique membrane flavocytochrome with the cytosolic proteins p47phox, p67phox, and p21Rac. This flavocytochrome, designated cytochrome b558, is a heteromer comprising a 22-kDa alpha-subunit (p22phox) and a glycosylated approximately 91-kDa beta-subunit (gp91phox). Cytochrome b558 was expressed in Sf9 insect cells coinfected with recombinant baculoviruses carrying cDNAs for p22phox and gp91phox. Membranes of these cells contained a b-type cytochrome with a dithionite-reduced minus oxidized difference spectrum similar to that of neutrophil cytochrome b558. The recombinant cytochrome b558 beta-subunit was heterogeneously N-glycosylated as demonstrated by its susceptibility to cleavage with endoglycosidases F and H. In contrast to the neutrophil cytochrome b558, a portion of the N-linked oligosaccharide was of the high mannose type. Recombinant cytochrome b558 supported superoxide production in a cell-free assay containing recombinant p47phox, p67phox, and p21Rac. The enzymatic turnover of the partially purified recombinant cytochrome b558 and neutrophil cytochrome b558 were similar (approximately 100-160 mol of superoxide generated/s/mol of cytochrome heme, range of two experiments) and the native and recombinant cytochromes showed similar requirements for NADPH and exogenous FAD. These studies represent the first reconstitution of the NADPH oxidase solely from recombinant proteins and define a model system to explore the structure and function of cytochrome b558.
Cellphone-Based Hand-Held Microplate Reader for Point-of-Care Testing of Enzyme-Linked Immunosorbent Assays (2015)

Standard microplate based enzyme-linked immunosorbent assays (ELISA) are widely utilized for various nanomedicine, molecular sensing, and disease screening applications, and this multiwell plate batched analysis dramatically reduces diagnosis costs per patient compared to nonbatched or nonstandard tests. However, their use in resource-limited and field-settings is inhibited by the necessity for relatively large and expensive readout instruments. To mitigate this problem, we created a hand-held and cost-effective cellphone-based colorimetric microplate reader, which uses a 3D-printed opto-mechanical attachment to hold and illuminate a 96-well plate using a light-emitting-diode (LED) array. This LED light is transmitted through each well, and is then collected via 96 individual optical fibers. Captured images of this fiber-bundle are transmitted to our servers through a custom-designed app for processing using a machine learning algorithm, yielding diagnostic results, which are delivered to the user within ∼1 min per 96-well plate, and are visualized using the same app. We successfully tested this mobile platform in a clinical microbiology laboratory using FDA-approved mumps IgG, measles IgG, and herpes simplex virus IgG (HSV-1 and HSV-2) ELISA tests using a total of 567 and 571 patient samples for training and blind testing, respectively, and achieved an accuracy of 99.6%, 98.6%, 99.4%, and 99.4% for mumps, measles, HSV-1, and HSV-2 tests, respectively. This cost-effective and hand-held platform could assist health-care professionals to perform high-throughput disease screening or tracking of vaccination campaigns at the point-of-care, even in resource-poor and field-settings. Also, its intrinsic wireless connectivity can serve epidemiological studies, generating spatiotemporal maps of disease prevalence and immunity.
Structural Characterization of a Spin-Assisted Colloid−Polyelectrolyte Assembly: Stratified Multilayer Thin Films (2010)

The assembly of polyelectrolytes and gold nanoparticles yields stratified multilayers with very low roughness and high structural perfection. The films are prepared by spin-assisted layer-by-layer self-assembly (LbL) and are characterized by X-ray reflectivity (XRR), UV-vis spectroscopy, atomic force microscopy (AFM), and transmission electron microscopy (TEM). Typical structures have four repeat units, each of which consists of eight double layers (DL) of poly(sodium 4-styrenesulfonate)/poly(allylamine hydrochloride), one monolayer of gold nanoparticles (10 nm diameter), and another layer of poly(allylamine hydrochloride). XRR scans show small-angle Bragg peaks up to seventh order, evidencing the highly stratified structure. Pronounced Kiessig fringes indicate a low global roughness, which is confirmed by local AFM measurements. TEM images corroborate the layered structure in the growth direction and nicely show the distinct separation of the individual particle layers. An AFM study reveals the lateral gold particle distribution within one individual particle layer. Interestingly, the spin-assisted deposition of polyelectrolytes reduces the roughness induced by the particle layers, leading to self-healing of roughness defects and a rather perfect stratification.
Chemically Modified DNA Substrates Implicate the Importance of Electrostatic Interactions for DNA Unwinding by Dda Helicase (2004)

Helicase-catalyzed disruption of double-stranded nucleic acid is vital to DNA replication, recombination, and repair in all forms of life. The relative influence of specific chemical interactions between helicase and the substrate over a series of multistep catalytic events is still being defined. To this end, three modified DNA oligonucleotides were designed to serve as substrates for the bacteriophage T4 helicase, Dda. A 5'-DNA-PNA-DNA-3' chimera was synthesized, thereby, conferring both a loss of charge and altering the conformational flexibility of the oligonucleotide. The second modified oligonucleotide possessed a single methylphosphonate replacement on the phosphate backbone, creating a gap in the charge distribution of the substrate. The third modification introduced an abasic site into the oligonucleotide sequence. This abasic site retains the charge distribution of the normal DNA substrate yet alters the conformational flexibility of the oligonucleotide. The loss of a base also serves to disrupt the hydrogen-bonding lattice, the intramolecular base-stacking interactions, as well as the intermolecular base-stacking interactions between aromatic amino acid side chains and the substrate. Our results indicate that a gap in the charge distribution along the backbone of the substrate has a more pronounced effect upon helicase-catalyzed unwinding than does the loss of a single base. While all three substrates exhibited some degree of inhibition, analysis of both pre-steady-state and excess enzyme experiments places a greater value upon the electrostatic interactions between helicase and the substrate.
Water vapor retrieval using the FLAASH atmospheric correction algorithm (2004)

FLAASH (Fast Line-of-sight Atmospheric Analysis of Spectral Hypercubes) is a first-principles atmospheric correction algorithm for visible to shortwave infrared (SWIR) hyperspectral data. The algorithm consists of two main steps. The first is retrieval of atmospheric parameters, visibility (which is related to the aerosol type and distribution) and column water vapor. The second step is solving the radiation transport equation for the given aerosol and column water and transformation to surface reflectance. The focus of this paper is on the FLAASH water vapor retrieval algorithm. Modeled radiance values in the spectral region of one water vapor absorption feature are calculated from MODTRAN 4 using several different water vapor amounts and are used to generate a Look-Up Table (LUT). The water band typically used is 1130 nm but either the 940 or 820 nm band may also be used. Measured radiance values are compared to the LUT to determine the column water vapor amount for each pixel in the scene. We compare the results of water retrievals for each of these bands and also the results of their corresponding reflectance retrievals.
Extrafollicular antibody responses (2003)

In adaptive antibody responses, B cells are induced to grow either in follicles where they form germinal centers or in extrafollicular foci as plasmablasts. Extrafollicular growth typically occurs in the medullary cords of lymph nodes and in foci in the red pulp of the spleen. It is not a feature of secondary lymphoid tissue associated with the internal epithelia of the body. All types of naïve and memory B cells can be recruited into extrafollicular responses. These responses are associated with immunoglobulin class switching but, at the most, only low-level hypermutation.
Priming of tumor-specific T cells in the draining lymph nodes after immunization with interleukin 2-secreting tumor cells: three consecutive stages may be required for successful tumor vaccination. (1995)

Although both CD4+ and CD8+ T cells are clearly required to generate long-lasting anti-tumor immunity induced by s.c. vaccination with interleukin 2 (IL-2)-transfected, irradiated M-3 clone murine melanoma cells, some controversy continues about the site and mode of T-cell activation in this system. Macrophages, granulocytes, and natural killer cells infiltrate the vaccination site early after injection into either syngeneic euthymic DBA/2 mice or athymic nude mice and eliminate the inoculum within 48 hr. We could not find T cells at the vaccination site, which argues against the concept that T-cell priming by the IL-2-secreting cancer cells occurs directly at that location. However, reverse transcription-PCR revealed transcripts indicative of T-cell activation and expansion in the draining lymph nodes of mice immunized with the IL-2-secreting vaccine but not in mice vaccinated with untransfected, irradiated M-3 cells. We therefore propose that the antigen-presenting cells, which invade the vaccination site, process tumor-derived antigens and, subsequently, initiate priming of tumor-specific T lymphocytes in lymphoid organs. These findings suggest a three-stage process for the generation of effector T cells after vaccination with IL-2-secreting tumor cells: (i) tumor-antigen uptake and processing at the site of injection by antigen-presenting cells, (ii) migration of antigen-presenting cells into the regional draining lymph nodes, where T-cell priming occurs, and (iii) circulation of activated T cells that either perform or initiate effector mechanisms leading to tumor cell destruction.
Life Cycle of A Block Buster Drug: Discovery and Development of Omeprazole (PrilosecTM) (2002)

Block buster drugs share a variety of common features, among which is the tendency to create entirely new markets. For example, an early "informed" estimate of the potential market size for the hypothetically "perfect" peptic ulcer drug was thirty-five million dollars. Based on current sales, however, we reckon this hypothesis to have underestimated the actual market demand for omeprazole (Prilosec) by about 400-fold. Similarly, prior to the introduction of the "retired" block busters chlordiazepoxide and diazepam (Librium and Valium), the market for "minor tranquilizers" in the treatment of anxiety and neurosis did not exist. Thus, once an emerging block buster seems to be therapeutically working, it is not unusual for diagnostic rates of the disease for which it is indicated and efficacious to actually increase. Top block buster drugs generally have or appear to have a high margin of safety.
Control of threshold voltage of organic field-effect transistors with double-gate structures (2005)

We fabricated pentacene field-effect transistors with planar-type double-gate structures, where the top- and bottom-gate electrodes can independently apply voltage biases to channel layers. The threshold voltage of organic transistors is changed systematically in a wide range from −16to−43V when the voltage bias of the top-gate electrode is changed from 0to+60V. The mobility in the linear regime is almost constant (0.2cm2∕Vs) at various voltage biases of the top-gate electrode and the on/off ratio is 106.
New routes to poly(4,4-dialkylcyclopentadithiophene-2,6-diyls)Electronic supplementary information (ESI) available: partial MALDI-TOF mass spectrum of polymer 5. See http://www.rsc.org/suppdata/jm/b2/b206477d/ (2002)

Two new polymerisation routes to poly(4,4-dioctylcyclopentadithiophene-2,6-diyl) are reported. The polymer prepared by Kumada type cross-coupling showed significantly reduced molecular weight over that prepared by direct oxidative polymerisation using iron(III) chloride. The higher molecular weight polymer was shown to have extended conjugation by UV-visible spectroscopy.
Coordinate Regulation of the Gel-forming Mucin Genes at Chromosome 11p15.5* (2013)

Four of the genes that encode gel-forming mucins, which are major components of the mucus layer protecting many epithelial surfaces, are clustered at chromosome 11p15.5 and show both cell- and tissue-specific expression patterns. We aimed to determine whether the individual genes were coordinately regulated by mechanisms involving higher order chromatin structure. CCCTC-binding factor (CTCF) sites were predicted in silico and CTCF occupancy then evaluated by chromatin immunoprecipitation. CTCF was found at many sites across the gene cluster, and its binding was correlated with mucin gene expression. Next, siRNA-mediated depletion of CTCF was shown to increase MUC2 expression in A549 lung carcinoma cells and both MUC6 and MUC5AC expression in LS180 colon carcinoma cells. These changes correlated with loss of CTCF binding at multiple sites, although others retained occupancy. In cells actively expressing the mucins, the gene cluster was shown by chromosome conformation capture to form looped three-dimensional structures with direct interactions between the MUC2 promoter region, regions 30 kb 5' to it, close to the MUC6 promoter and others near the 3' end of MUC5AC, >170 kb away. Finally, to demonstrate the importance of CTCF binding to mucin gene expression, Calu-3 lung carcinoma cells were exposed to lipopolysaccharide (LPS). LPS increased the expression of MUC2 and MUC5AC and reduced MUC5B. CTCF occupancy was concurrently depleted at specific binding sites close to these genes. These data suggest that CTCF binding and cell type-specific long-range interactions across the 11p15.5 gene cluster are critical mechanisms for coordinating gel-forming mucin gene expression.
Arginine restores cholinergic relaxation of hypercholesterolemic rabbit thoracic aorta. (1991)

We conclude that the endothelium-dependent relaxation is normalized in hypercholesterolemic rabbit thoracic aorta by in vivo exposure to L-arginine, the precursor for EDRF.
Effect of essential oils on Aspergillus spore germination, growth and mycotoxin production: a potential source of botanical food preservative (2014)

In conclusion, the essential oils from T. ammi can be a potential source of safe natural food preservative for food commodities contamination by storage fungi.
cDNA and amino acid sequences of two members of the human P450IIC gene subfamily (1987)

Journal Article cDNA and amino acid sequences of two members of the human P450IIC gene subfamily Get access Shioko Kimura, Shioko Kimura Laboratory of Molecular Carcinogenesis, National Cancer InstituteBethesda, MD 20892, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Jullia Pastewka, Jullia Pastewka Laboratory of Molecular Carcinogenesis, National Cancer InstituteBethesda, MD 20892, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Harry V. Gelboin, Harry V. Gelboin Laboratory of Molecular Carcinogenesis, National Cancer InstituteBethesda, MD 20892, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Frank J. Gonzalez Frank J. Gonzalez Laboratory of Molecular Carcinogenesis, National Cancer InstituteBethesda, MD 20892, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 15, Issue 23, 10 December 1987, Pages 10053–10054, https://doi.org/10.1093/nar/15.23.10053 Published: 10 December 1987 Article history Received: 21 October 1987 Published: 10 December 1987
Dynamics of a Pig Slurry Microbial Community during Anaerobic Storage and Management (2006)

The microbial community of a pig slurry on a farm was monitored for 6 months using both molecular and cultural approaches. Sampling was carried out at all the different stages of effluent handling, from the rearing build-up to slurry spreading. Total DNA of each sample was extracted and analyzed by PCR-single-strand conformation polymorphism (SSCP) analysis using primers targeting the 16S rRNA genes from the archaeal and bacterial domains and also the Eubacterium-Clostridium, Bacillus-Streptococcus-Lactobacillus, and Bacteroides-Prevotella groups. A comparison of the SSCP profiles showed that there were rapid changes in the dominant bacterial community during the first 2 weeks of anaerobic storage and that the community was relatively stable thereafter. Several bacterial populations, identified as populations closely related to uncultured Clostridium and Porphyromonas and to Lactobacillus and Streptococcus cultured species commonly isolated from pig feces, remained present and dominant from the rearing build-up to the time of spreading. Enumeration of fecal indicators (enterococci and Escherichia coli) performed in parallel using cultural methods revealed the same trends. On the other hand, the archaeal community adapted slowly during pig slurry storage, and its diversity increased. A shift between two hydrogenotrophic methanogenic Methanobrevibacter populations from the storage pit to the pond was observed. Microorganisms present in pig slurry at the time of spreading could not be detected in soil after spreading by either molecular or cultural techniques, probably because of the detection limit inherent in the two techniques.
Shadow removal for aerial imagery by information theoretic intrinsic image analysis (2012)

We present a novel technique for shadow removal based on an information theoretic approach to intrinsic image analysis. Our key observation is that any illumination change in the scene tends to increase the entropy of observed texture intensities. Similarly, the presence of texture in the scene increases the entropy of the illumination function. Consequently, we formulate the separation of an image into texture and illumination components as minimization of entropies of each component. We employ a non-parametric kernel-based quadratic entropy formulation, and present an efficient multi-scale iterative optimization algorithm for minimization of the resulting energy functional. Our technique may be employed either fully automatically, using a proposed learning based method for automatic initialization, or alternatively with small amount of user interaction. As we demonstrate, our method is particularly suitable for aerial images, which consist of either distinctive texture patterns, e.g. building facades, or soft shadows with large diffuse regions, e.g. cloud shadows.
The design of large real-time systems: the time-triggered approach (2002)

The time-triggered (TT) architecture approach supports the spatial partitioning of a large, distributed real-time system into a set of autonomous subsystems with small control-free data-sharing interfaces between them. This paper presents such a TT architecture and gives a detailed description of the interface between an autonomous time-triggered communication subsystem based on the TTP protocol and the host computer within a node of this architecture. This interface acts as a temporal firewall that eliminates the possibility of control error propagation from one subsystem to another subsystem. It thus facilitates the independent development and validation of the subsystems and supports the composability of the distributed architecture with respect to timeliness, validation, and certification.
Cross-Linked Block Copolymer/Ionic Liquid Self-Assembled Blends for Polymer Gel Electrolytes with High Ionic Conductivity and Mechanical Strength (2013)

Poly(propylene oxide)–poly(ethylene oxide)–poly(propylene oxide) (PPO–PEO–PPO) block copolymers (BCPs) with cross-linkable end groups were synthesized, blended with an ionic liquid (IL) diluent, and cross-linked to form polymer gel electrolytes. The IL prevented crystallization of PEO at high concentrations, enabling fast ion transport. In addition, the IL was selective for the PEO block, inducing strong microphase separation in what are otherwise disordered or weakly ordered BCP melts. Cross-linking the BCPs in the presence of the IL resulted in the formation of solid, elastic gels with high ionic conductivities—greater than 1.0 mS/cm at 25 °C for some compositions. However, it was found that neither the presence or absence of microphase separation nor the BCP composition of the microphase separated gels substantially influenced ionic conductivity. Increasing the cross-link density through the use of phase-selective PEO- and PPO-based cross-linking reagents was also evaluated. It was revealed that confinement of cross-links to the PPO rich domains through the use of PPO-based diacrylates enhanced the mechanical strength of the gels without detriment to the ionic conductivity. Conversely, cross-linking in the PEO-rich domains through the use of PEO-based acrylates significantly reduced conductivity. Isolation of cross-links within a minor nonconducting domain in a microphase separated gel is a viable strategy for mechanical property enhancement without a large sacrifice in conductivity, effectively decoupling ionic conductivity and mechanical strength. This approach yielded solid-like gel electrolytes fabricated from BCPs that can be produced inexpensively, with ionic conductivities of 0.64 mS/cm at 25 °C and a frequency independent storage modulus of approximately 400 kPa.
Vaccine strategies against Epstein‐Barr virus‐associated diseases: lessons from studies on cytotoxic T‐cell‐mediated immune regulation (1999)

Development of a vaccine against Epstein-Barr virus (EBV) is constrained by the latency phenotypes adopted by different EBV-associated diseases. Over the last few years an immense body of information on the pattern of viral gene expression in EBV-associated diseases and the role of cytotoxic T cells in the control of these diseases has accumulated. It would seem reasonable to suggest that emerging technologies are at a level where vaccine trials aimed at controlling infectious mononucleosis, post-transplant lymphoproliferative disease, nasopharyngeal carcinoma and Hodgkin's disease are justified. On the other hand, a more cautious approach may be required for the development of vaccines or immunotherapeutic strategies against Burkitt's lymphoma.