gebhart/patrepeval huggingface dataset:
Application of environmental sample processor (ESP) methodology for quantifying Pseudo‐nitzschia australis using ribosomal RNA‐targeted probes in sandwich and fluorescent in situ hybridization formats (2006)

In this contribution, we assess the application of methodology used in a novel in situ remote sampling platform, the environmental sample processor (ESP), for the identification and enumeration of a harmful algal species, the domoic acid‐producing diatom Pseudo‐nitzschia australis , using 2 molecular assays: a sandwich hybridization assay (SHA) and fluorescent in situ hybridization (FISH). Both the SHA and FISH assays were initially designed as laboratory‐based methods that are now emulated in the ESP. Response of the SHA to a range of concentrations of P. australis using the laboratory (96‐well plate) and ESP (DNA probe array) formats showed that the two were highly correlated. Enumeration of cells filtered and archived for FISH using a manifold designed for laboratory applications agreed well with counts of cells filtered and archived in the ESP at ≥2.5 × 10 4 cells L −1 . At lower concentrations, it becomes statistically unlikely to derive a reliable abundance estimate, suggesting that FISH is better suited for qualitative analyses unless the target organism is very abundant. We also assessed the suitability of an oligonucleotide as synthetic target sequence to act as a SHA reagent quality control and internal standard for the plate assay. This was successful, but the probe and/or associated reagents were stable for only ~60 days. Our results show that the ESP is capable of detecting P. australis in near real‐time and also supports whole‐cell archival samples, making it a potentially useful tool for future research and monitoring initiatives.
Techniques for Mammalian Cell Tissue Culture (2006)

This appendix opens with detailed discussions on the latest principles of sterile technique and preparation of culture media. Step-by-step protocols describe trypsinizing and subculturing monolayer cultures, passaging suspension cultures, freezing and thawing cells, counting cells using a hemacytometer, and preparing cells for transport.
Catalytic activities of synthetic octadeoxyribonucleotides as coenzymes of poly(ADP‐ribose) polymerase and the identification of a new enzyme inhibitory site (1987)

The catalytic activity of highly purified poly(ADP-ribose) polymerase was determined at constant NAD+ concentration and varying concentrations of sDNA or synthetic octadeoxyribonucleotides of differing composition. The coenzymic activities of deoxyribonucleotides were compared in two ways: graphic presentation of the activation of poly(ADP-ribose) polymerase in the presence of a large concentration range of deoxyribonucleotides and by calculating kD values for the deoxyribonucleotides. As determined by method i, auto-mono-ADP-ribosylation of the enzyme protein at 25 nM NAD+ was maximally activated at 1:1 octamer/enzyme molar ratios by the octadeoxyribonucleotide derived from the regulatory region of SV40 DNA (duplex C). At a 0.4:1 sDNA/enzyme ratio, sDNA was the most active coenzyme for mono-ADP-ribosylation. At 200 microM NAD+, resulting in polymer synthesis and with histones as secondary polymer acceptors, duplex C was the most active coenzyme, and the octamer containing the steroid hormone receptor binding consensus sequence of DNA was a close second, whereas sDNA exhibited an anomalous biphasic kinetics. sDNA was effective on mono-ADP-ribosylation at a concentration 150-200 -times lower than on polymer formation. When comparison of deoxyribonucleotides was based on method ii (kD values), by far the most efficiently binding coenzyme for both mono and polymer synthesis was sDNA, followed by duplex C, with (dA-dT)8 exhibiting the weakest binding. The synthetic molecule 6-amino-1,2-benzopyrone (6-aminocoumarin) competitively inhibited the coenzymic function of synthetic octadeoxyribonucleotides at constant concentration of NAD+, identifying a new inhibitory site of poly(ADP-ribose) polymerase.
Determination of the Carnosic Acid Content in Wild and Cultivated Rosmarinus officinalis (1998)

The concentration of carnosic acid in a representative selection of leaves from wild and cultivated populations of Rosmarinus officinalis was determined by reversed-phase HPLC following extraction with supercritical carbon dioxide. Different sources of variability including season, genetics, leaf age, and growing origin (wild or cultivated) were considered. Variability in the carnosic acid content among rosemary leaves appears to be largely due to seasonal and environmental factors, in addition to their individual origin (genetics). The results reveal excellent correlation (r = 0.93) between the carnosic acid concentration and photoperiod. The results presented can be used to improve the selection of raw materials for the extraction of carnosic acid from rosemary. Keywords: Rosmarinus officinalis; carnosic acid; antioxidant; supercritical fluid extraction
Synthesis and properties of modified oligonucleotides. (1991)

Phosphorothioate oligonucleotide analogs conjugated to cholesteryl by a neutral, 6 atom linker are more effective inhibitors of HIV-1 in cell culture than the corresponding analogs conjugated via a phosphorothioate group. The antiviral activity correlates with the hydrophobic character of the oligonucleotide. Some new synthetic methodology is also discussed.
Growth plate damage, a feature of juvenile idiopathic arthritis, can be induced by adenoviral gene transfer of oncostatin M: A comparative study in gene‐deficient mice (2003)

IL-1, but not IL-6, TNFalpha, or iNOS, plays an important role in joint disease induced by intraarticular gene transfer of OSM in mice. The effect of OSM on murine connective tissue and the presence of OSM in human synovial fluid make involvement of OSM in human arthropathies very likely.
Uptake of a nido-carboranylporphyrin by human glioma xenografts in athymic nude mice and by syngeneic ovarian carcinomas in immunocompetent mice. (1990)

A tetraphenylporphyrin bearing four dicarbollide ([B9C2H11]-) cages linked to the o-phenyl ring positions by anilide bonds, known as boronated tetraphenylporphyrin (BTPP), has been synthesized in excellent yield from tetra-(o-aminophenyl) porphyrin and carborane carbonyl chloride followed by base-assisted cage opening and ion exchange to give the highly water-soluble potassium salt. Preliminary studies showed that BTPP accumulates in liver and in a syngeneic ovarian carcinoma, but not in normal brain parenchyma, of mice infused with BTPP subcutaneously for 6 or 7 days via surgically implanted osmotic minipumps. In this study, the uptake of boron was measured in human gliomas xenografted subcutaneously to athymic nude mice in which BTPP was infused intraperitoneally or subcutaneously or both for 3 or 7 days by using similar minipumps. Immunocompetent mice bearing a syngeneic ovarian carcinoma were similarly infused to provide comparative data. Bulk concentrations of boron up to 18 micrograms/g of glioma and up to 45 micrograms/g of carcinoma were observed when up to 102 micrograms/g of tissue was present in the liver after 7 days of BTPP infusion. Glioma boron concentrations were increased by approximately 80% on the average (up to 33 micrograms/g) when correspondingly greater amounts of BTPP were infused in only 3 days. Cell counts and chemical tests on blood samples from individual mice indicate that BTPP causes moderate hepatotoxicity and thrombocytopenia. This hepatohematic toxicity syndrome should be taken into account if BTPP or a similar agent is used for boron neutron-capture therapy (BNCT) of human malignancies.
A novel high performance utility interactive photovoltaic inverter system (2002)

This paper presents a novel photovoltaic inverter system that can achieve not only a sinusoidal AC output current synchronized with the utility line voltage but also a generation power control on each of the photovoltaic modules connected in series. The proposed inverter system is composed of a half bridge inverter and novel generation control circuit that can compensate for the reduction in output power caused by the shadow covering the photovoltaic modules. The proposed generation control circuit can make the operation point on each of the photovoltaic modules correspond to the maximum power point individually, and the generation power control on each of the photovoltaic modules is executed only by detecting the total output power of the photovoltaic system. Furthermore, the low frequency ripple voltages on the series-connected DC bus capacitors caused by the utility interactive inverter operation are reduced owing to the effect of the generation control circuit. Hence, the average value of photovoltaic generation power is much increased. The effectiveness of the proposed system is confirmed experimentally and through simulation results.
Developments in delivery of medications for inner ear disease (2013)

The inner ear is accessible through the middle ear via the oval and round windows allowing diffusion of drugs into the perilymph. With a better understanding of the physiology of the inner ear and the underlying molecular causes of inner ear disease there is great potential for the development of novel therapeutics that can be locally administered. At present, there is a rapid development of drugs to target diverse inner ear diseases that cause sensorineural hearing loss and balance dysfunction.
Total skin electron beam therapy for cutaneous T-cell lymphoma: A nationwide cohort study from Denmark (2011)

In conclusion, the present study confirms that high-dose TSEBT is an effective, but generally not a curative therapy in the management of CTCL. High-dose treatment yielded significantly better results than low-dose treatment with 4 Gy. TSEBT offers significant palliation in most patients when other skin-directed or systemic treatments have failed.
Dynamic light scattering as a relative tool for assessing the molecular integrity and stability of monoclonal antibodies (2007)

(2007). Dynamic light scattering as a relative tool for assessing the molecular integrity and stability of monoclonal antibodies. Biotechnology and Genetic Engineering Reviews: Vol. 24, No. 1, pp. 117-128.
Selective Cleavage of the Heregulin Receptor ErbB-4 by Protein Kinase C Activation (1996)

The 180-kDa transmembrane tyrosine kinase ErbB-4 is a receptor for the growth factor heregulin. 125I-Heregulin binding to NIH 3T3 cells overexpressing the ErbB-4 receptor is rapidly decreased by 12-O-tetradecanoylphorbol-13-acetate (TPA) pretreatment. Immunologic analysis demonstrates that TPA treatment of cells induces the proteolytic cleavage of ErbB-4, producing an 80-kDa cytoplasmic domain fragment, which contains a low level of phosphotyrosine, and a 120-kDa ectodomain fragment, which is released into the extracellular medium. Cleavage of ErbB-4 was also enhanced by other protein kinase C activators, i.e. platelet-derived growth factor, ionomycin, and synthetic diacylglycerol, while protein kinase C inhibition or down-regulation suppressed the TPA stimulation of ErbB-4 degradation. TPA did not induce the degradation of related receptors (ErbB-1, ErbB-2, and ErbB-3) in the EGF receptor family. The phorbol ester-induced cleavage of ErbB-4 occurs within or close to the ectodomain, as the 80-kDa cytoplasmic domain fragment is recognized by antibody to the ErbB-4 carboxyl terminus and is membrane-associated. Coprecipitation experiments show that, while the 80-kDa ErbB-4 fragment is associated with the SH2-containing molecules PLC-gamma1 and Shc, TPA did not induce the phosphorylation of these substrates in intact cells. In addition, kinase assays in vitro indicate that the 80-kDa fragment is not an active tyrosine kinase. These results show that protein kinase C negatively regulates heregulin signaling through the ErbB-4 receptor by the activation of a selective proteolytic mechanism.
Five Percent Lidocaine Cream Applied Simultaneously to the Skin and Mucosa of the Lips Creates Excellent Anesthesia for Filler Injections (2005)

This "anesthetic cream block" is easier to perform and better tolerated than injectable anesthetics. Use of this technique is likely to expand the range of physicians who perform filler injections on the lips and will probably also expand the range of patients who wish to have filler injections done on their lips and who (because they had little or no discomfort) are willing to return for additional filler injections in the future.
Mannose-binding lectin deficiency alters the development of fungal asthma: effects on airway response, inflammation, and cytokine profile (2004)

Aspergillus fumigatus is a major fungal pathogen that may be fatal to immunocompromised individuals and causes airway hyperreactivity and remodeling in sensitized individuals. Herein, we examined the role of mannose-binding lectin (MBL), a complement-activating plasma protein, during pulmonary innate and allergic immune responses directed against A. fumigatus spores or conidia. Neither group of nonsensitized MBL-A-sufficient (MBL-A+/+) nor -deficient (MBL-A-/-) mice challenged with an intravenous or intratracheal (i.t.) bolus of A. fumigatus spores experienced fungus-induced mortality, but marked airway remodeling was observed in MBL-A-/- mice challenged i.t. with conidia. In a model of chronic fungal asthma, MBL-A+/+ and MBL-A-/- A. fumigatus-sensitized mice were examined at days 4 and 28 after an i.t. challenge with A. fumigatus conidia. Airway hyperresponsiveness in sensitized MBL-A-/- mice was significantly decreased at both times after conidia challenge compared with the sensitized MBL-A+/+ group. In the sensitized MBL-A-/- mice, whole lung T helper cell type 2 cytokine levels were significantly decreased at day 4 after conidia, and whole lung interferon-gamma levels were significantly increased at day 28 after conidia when compared with controls. However, histological evidence showed similar airway remodeling at day 28 after conidia (i.e., subepithelial fibrosis and goblet cell metaplasia) in the two groups of mice. Thus, these findings show that MBL-A is not required for mouse survival following exposure to A. fumigatus conidia, and this murine collectin isoform contributes to the development and maintenance of airway hyperresponsiveness but not chronic airway remodeling during chronic fungal asthma.
High frequency of allelic deletion on chromosome 17p in advanced colorectal cancer (1994)

Allelic loss on chromosome 17p may be a useful prognostic marker in cases of colorectal cancer.
Scalable etched-pillar, AlAs-oxide definedvertical cavity lasers (1996)

Etched-pillar, bottom-emitting vertical cavity lasers have been fabricated using lateral oxidation of AlAs. The devices have threshold currents as low as 315 µA for a 4 µm × 4 µm, three quantum well active region. Using the data and a numerical model the authors extract excess optical and carrier losses and an effective surface recombination velocity for the devices. The data show that size dependent optical scattering persists as the lasers are scaled to smaller sizes, but lateral carrier leakage is suppressed, allowing for scaling of lasers to small sizes to achieve lower threshold currents.
Garbage collector memory accounting in language-based systems (2004)

Language run-time systems are often called upon to safely execute mutually distrustful tasks within the same run-time, protecting them from other tasks' bugs or otherwise hostile behavior Well-studied access controls exist in systems such as Java to prevent unauthorized reading or writing of data, but techniques to measure and control resource usage are less prevalent. In particular, most language run-time systems include no facility to account for and regulate heap memory usage on a per-task basis. This oversight can be exploited by a misbehaving task, which might allocate and hold live enough memory to cause a denial-of-service attack, crashing or slowing down other tasks. In addition, tasks can legitimately share references to the same objects, and traditional approaches that charge memory to its allocator fail to properly account for this sharing. We present a method for modifying the garbage collector, already present in most modern language run-time systems, to measure the amount of live memory reachable from each task as it performs its regular duties. Our system naturally distinguishes memory shared across tasks from memory reachable from only a single task without requiring incompatible changes to the semantics of the programming language. Our prototype implementation imposes negligible performance overheads in a variety of benchmarks, yet provides enough information for the expression of rich policies to express the limits on a task's memory usage.
Directly fed millimetre-wave two-arm spiral antenna (2010)

An 18 to 110 GHz two-arm Archimedean spiral antenna directly fed with a Dyson balun is designed, fabricated, and measured. The feed line includes a monolithically integrated rectangular coaxial line impedance transformer designed to reduce the nominal antenna impedance from ∼180 to 80 Ω and to match that impedance to the nominal system&apos;s impedance of 50 Ω. Full-wave modelling and impedance measurements are used to assess antenna performance. A VSWR&lt;2.5:1 is obtained throughout the measured band.
Sequential recruitment of steroid receptor coactivator-1 (SRC-1) and p300 enhances progesterone receptor-dependent initiation and reinitiation of transcription from chromatin (2001)

Employing a cell-free chromatin transcription system that recapitulates progesterone receptor (PR)-mediated transcription in vivo, we have investigated further the coactivator functions of steroid receptor coactivator-1 (SRC-1) in terms of its functional domains as well as cooperation with other coactivators in PR transactivation. By analyzing wild-type and mutant SRC-1 with liganded PR in the chromatin transcription system in vitro, the basic helix-loop-helix/Per-Arnt-Sim domain, the p300-binding domain, and the carboxyl-terminal region (containing the PR-binding site) of SRC-1 were shown to be important for PR transactivation. Although in context of a synthetic promoter its histone acetyltransferase activity was nonessential for PR-mediated transcription, SRC-1 was observed to act synergistically with p300 to enhance PR transactivation from chromatin. Moreover, SRC-1 and p300 were found to function cooperatively to increase the efficiency of productive transcription initiation and reinitiation. Further analysis of synergism between SRC-1 and p300 revealed an obligatory "sequential" recruitment of SRC-1 and p300 to liganded PR. Efficient recruitment of p300 required the presence of SRC-1. In addition, functional analysis of SRC-2 and SRC-3 coactivators indicated that the SRC family modulated PR transactivation from chromatin by a similar mechanism.
A spectrum of monoclonal antibodies reactive with human mammary tumor cells. (1981)

Splenic lymphocytes of mice, immunized with membrane-enriched fractions of metastatic human mammary carcinoma tissues, were fused with the NS-1 non-immunoglobulin-secreting murine myeloma cell line. This resulted in the generation of hybridoma cultures secreting immunoglobulins reactive in solid-phase radioimmunoassays with extracts of metastatic mammary carcinoma cells from involved livers, but not with extracts of apparently normal human liver. As a result of further screening of immunoglobulin reactivities and double cloning of cultures, 11 monoclonal antibodies were chosen that demonstrated reactivities with human mammary tumor cells and not with apparently normal human tissues. These monoclonal antibodies could be placed into at least five major groups on the basis of their differential binding to the surface of various live human mammary tumor cells in culture, to extracts of mammary tumor tissues, or to tissue sections of mammary tumor cells studied by the immunoperoxidase technique. Whereas a spectrum of reactivities to mammary tumors was observed with the 11 monoclonal antibodies, no reactivity was observed to apparently normal cells of the following human tissues: breast, lymph node, lung, skin, testis, kidney, thymus, bone marrow, spleen, uterus, thyroid, intestine, liver, bladder, tonsils, stomach, prostate, and salivary gland. Several of the antibodies also demonstrated a "pancarcinoma" reactivity, showing binding to selected non-breast carcinomas. None of the monoclonal antibodies showed binding to purified ferritin or carcinoembryonic antigen. Monoclonal antibodies of all five major groups, however, demonstrated binding to human metastatic mammary carcinoma cells both in axillary lymph nodes and at distal sites.
Effect of 5-Alpha-Reductase Inhibition on Sex-Hormone-Binding Globulin in Elderly Men (1994)

In this study we examined the possibility that chronic reduction in serum dihydrotestosterone (DHT) attained by pharmacologic inhibition of 5 alpha-reductase modulates serum sex-hormone-binding globulin (SHBG) levels in elderly men. Twenty-one men, ages 58-79 years (mean 66) with benign prostatic hypertrophy were treated with the 5 alpha-reductase inhibitor finasteride (5 mg daily) for 12 months. Serum DHT declined by 80% (p < 0.001) and total testosterone rose by 14% (p < 0.05). Serum SHBG concentration remained unchanged (44.1 +/- 4.5 vs 45.2 +/- 5.7 nmol/l for pre- and post-therapy levels, respectively). Thus, the conversion of testosterone to DHT is not required to maintain the androgenic effect on serum SHBG concentration in elderly men.
A genome-wide association study for late-onset Alzheimer's disease using DNA pooling (2008)

We have validated the pooling method for GWA studies by both identifying the APOE locus and by observing a strong enrichment for significantly associated SNPs. We provide evidence for LRAT as a novel candidate gene for LOAD. LRAT plays a prominent role in the Vitamin A cascade, a system that has been previously implicated in LOAD.
Phosphorylation-dependent Monoclonal Tau Antibodies Do Not Reliably Report Phosphorylation by Extracellular Signal-regulated Kinase 2 at Specific Sites (1997)

Analysis of phosphorylation of tau, the microtubule-associated proteins hyperphosphorylated in Alzheimer's disease, is often performed using phosphorylation-sensitive monoclonal antibodies thought to report the presence or absence of one or two specific phosphorylations (cognate sites). Using several such antibodies we found a much more complicated relationship between phosphorylation at specific sites, as monitored by two-dimensional phosphopeptide mapping, and antibody recognition of these sites. Multiple phosphorylation of tau in several stages by the brain extracellular signal-regulated kinase 2 isoform PK40 suggested that phosphorylation at cognate sites is sometimes necessary (but not sufficient) to induce a change of antibody reactivity and in some cases is not even necessary in the background of multiple phosphorylation at other sites. No single phosphorylation site was found to be responsible for any level of gel mobility shift associated with phosphorylation. Tau acquired its maximal gel mobility retardation and final immunochemical profile at substoichiometric phosphorylation of most sites. This suggests that many alternate phosphorylation patterns can produce the same conformational and immunochemical presentation on sodium dodecyl sulfate-gel electrophoresis. Although PK40(erk2) prefers some phosphorylation sites, most notably Ser235, followed by Ser199 or Ser202 and Thr205, the phosphorylation of multiple Ser/Thr-Pro sites is not highly sequential. Ser396 is one of the least preferred sites and seems to require prior phosphorylation at Ser404.