gebhart/patrepeval huggingface dataset:
Long-term antidepressant administration alters corticotropin-releasing hormone, tyrosine hydroxylase, and mineralocorticoid receptor gene expression in rat brain. Therapeutic implications. (1991)

Imipramine is the prototypic tricyclic antidepressant utilized in the treatment of major depression and exerts its therapeutic efficacy only after prolonged administration. We report a study of the effects of short-term (2 wk) and long-term (8 wk) administration of imipramine on the expression of central nervous system genes among those thought to be dysregulated in imipramine-responsive major depression. As assessed by in situ hybridization, 8 wk of daily imipramine treatment (5 mg/kg, i.p.) in rats decreased corticotropin-releasing hormone (CRH) mRNA levels by 37% in the paraventricular nucleus (PVN) of the hypothalamus and decreased tyrosine hydroxylase (TH) mRNA levels by 40% in the locus coeruleus (LC). These changes were associated with a 70% increase in mRNA levels of the hippocampal mineralocorticoid receptor (MR, type I) that is thought to play an important role in mediating the negative feedback effects of low levels of steroids on the hypothalamic-pituitary-adrenal (HPA) axis. Imipramine also decreased proopiomelanocortin (POMC) mRNA levels by 38% and glucocorticoid receptor (GR, type II) mRNA levels by 51% in the anterior pituitary. With the exception of a 20% decrease in TH mRNA in the LC after 2 wk of imipramine administration, none of these changes in gene expression were evident as a consequence of short-term administration of the drug. In the light of data that major depression is associated with an activation of brain CRH and LC-NE systems, the time-dependent effect of long-term imipramine administration on decreasing the gene expression of CRH in the hypothalamus and TH in the LC may be relevant to the therapeutic efficacy of this agent in depression.
Dissecting the substrate recognition of 3- O -sulfotransferase for the biosynthesis of anticoagulant heparin (2012)

Heparin is a polysaccharide-based natural product that is used clinically as an anticoagulant drug. Heparan sulfate 3-O-sulfotransferase (3-OST) is an enzyme that transfers a sulfo group to the 3-OH position of a glucosamine unit. 3-OST is present in multiple isoforms, and the polysaccharides modified by these different isoforms perform distinct biological functions. 3-OST isoform 1 (3-OST-1) is the key enzyme for the biosynthesis of anticoagulant heparin. Here, we report the crystal structure of the ternary complex of 3-OST-1, 3'-phosphoadenosine 5'-phosphate, and a heptasaccharide substrate. Comparisons to previously determined structures of 3-OST-3 reveal unique binding modes used by the different isoforms of 3-OST for distinguishing the fine structures of saccharide substrates. Our data demonstrate that the saccharide substrates display distinct conformations when interacting with the different 3-OST isoforms. Site-directed mutagenesis data suggest that several key amino residues, including Lys259, Thr256, and Trp283 in 3-OST-3 and Arg268 in 3-OST-1, play important roles in substrate binding and specificity between isoforms. These results deepen our understanding of the biosynthetic mechanism of heparan sulfate and provide structural information for engineering enzymes for an enhanced biosynthetic approach to heparin production.
Progress on CD-AFM tip width calibration standards (2012)

The National Institute of Standards and Technology (NIST) is developing a new generation of standards for calibration of CD-AFM tip width. These standards, known as single crystal critical dimension reference materials (SCCDRM) have features with near-vertical sidewalls. This is accomplished using preferential etching on (110) silicon-on-insulator (SOI) substrates. As such, these structures are particularly useful for CD-AFM tip width calibration. As part of a previous generation of SCCDRMs that was released to the Member Companies of SEMATECH, we were able to deliver structures with linewidths ranging from as low as 50 nm up to 240 nm. These typically had expanded uncertainties (k = 2) of between 1.5 nm and 2 nm. Subsequently, these chips were used as a traceable source of tip width calibration for CD-AFM by SEMATECH and several Member Companies. We are now working on a new generation of SCCDRMs with the goal of reducing linewidth expanded uncertainties, and we are using our new CD-AFM to support this development. The features are patterned using electron beam lithography with equipment available in the new nanofabrication facility within the Center for Nanoscale Science and Technology (CNST) at NIST. Intact features as small as 10 nm have been observed with line width roughness (LWR) sufficiently low to support 1 nm expanded uncertainties. We believe it will be possible to fabricate features as small as 5 nm, and we are now working to refine the fabrication process and to assess the limits of our approach.
Effect of boundary scattering on the thermal conductivity of TiNiSn-based half-Heusler alloys (2008)

TiNiSn-based half-Heusler alloys have been of significant interest for their potential as thermoelectric materials. They exhibit promising electronic transport properties as revealed through high Seebeck coefficient and moderate electrical resistivity values. The chief disadvantage of these materials is a comparatively high lattice thermal conductivity. Attempts to ``tune'' the lattice thermal conductivity $({\ensuremath{\kappa}}_{L})$ in these materials have led to the comparison and analysis of the thermal conductivity of two series of Ti- and Zr-based half-Heusler alloys. In the first series, ${\mathrm{Ti}}_{1\ensuremath{-}y}{\mathrm{Zr}}_{y}\mathrm{Ni}{\mathrm{Sn}}_{0.95}{\mathrm{Sb}}_{0.05}$, a significant reduction in ${\ensuremath{\kappa}}_{L}$ is observed, with the substitution of large concentrations of Zr $(y\ensuremath{\geqslant}25%)$ at Ti site, which is most likely due to mass fluctuation scattering. In the second series, $\mathrm{Ti}\mathrm{Ni}{\mathrm{Sn}}_{1\ensuremath{-}x}{\mathrm{Sb}}_{x}$, a nonsystematic increase in ${\ensuremath{\kappa}}_{L}$ is observed, with minute amounts of Sb doping $(x\ensuremath{\leqslant}5%)$ at the Sn site. Extensive microstructural analysis in a $\mathrm{Ti}\mathrm{Ni}{\mathrm{Sn}}_{1\ensuremath{-}x}{\mathrm{Sb}}_{x}$ series reveals a correlation between ${\ensuremath{\kappa}}_{L}$ and the average grain diameter in these materials, which is in good agreement with theoretical predictions related to phonon boundary scattering. In addition, a comparison of the calculated phonon mean free path in each of the series of compounds shows some insight into the two different phonon scattering mechanisms.
A rational approach to tuning the pKa values of rhodamines for living cell fluorescence imaging (2011)

A novel strategy to systematically tune the pK(a) values of rhodamines is described. This strategy was applied to rationally develop compound 1e with a pK(a) of 6.5, the highest among rhodamine amide derivatives, and it could be employed to detect acidic pH variations in living cells with a turn-on signal.
Facile Reduction of Zeolite-Encapsulated Viologens with Solvated Electrons and Selective Dispersion of Inter- and Intramolecular Dimers of Propylene-Bridged Bisviologen Radical Cation (2000)

Zeolite-Y (Y), zeolite-L (L), mordenite (M), and ZSM-5 exchanged with methyl viologen C1VC12+ and N‘,N‘ ‘-trimethylenebis(1-methyl-4,4‘-bipyridinium) (henceforth bisviologen) C1V2+-C3-VC12+ were prepared. Treatment of the dried, viologen-doped zeolites with solvated electrons in diethyl ether readily yields the corresponding viologen radical cation, i.e., C1VC1•+ and C1V•+-C3-VC1•+ within the zeolite pores. Although C1V•+-C3-VC1•+ readily folds to its intramolecular dimer C3[C1V•+]2 in solution, it remains in the open form in the four zeolites. C1VC1•+ readily dimerizes to [C1VC1•+]2 at high concentrations in L but not in other zeolites. However, C1V•+-C3-VC1•+ does not dimerize by itself in any of the four zeolites even at high concentrations. C1VC1•+ readily dimerizes in Y, L, and M when the pores are filled with water. The hydration-induced dimerization also works well for C1V•+-C3-VC1•+ in L and M. This leads to selective formation of the unprecedented intermolecular dimer of bisviologen radical cation, i.e., [C1V•+-C3-VC1•+]2 in L and M. The intramolecular analogue C3[C1V•+]2 can also be dispersed into Y, L, and M by direct occlusion of its bisperchlorate salt from the acetonitrile solution. The broad ∼530 nm band of the viologen radical dimer splits into two when the viologen radical moieties are forced to juxtapose in the collinear conformation within the narrow and straight channels of L and M. The near-infrared band of the viologen radical dimer progressively blue shifts with decreasing the interannular distance. This paper thus demonstrates a novel use of zeolites to selectively disperse inter- and intramolecular dimers of diradical dication and to lock the viologen radical dimers into the collinear conformation which allows us to delineate the spectral variation of viologen radical dimers with changing the interannular conformation and distance.
The sensitivity of in vitro erythropoietic progenitor cells to different erythropoietin reagents during development and the role of cell death in culture. (1996)

With the availability of several recombinant erythropoietin (Epo) reagents, it has been possible to undertake a systematic study of the relative Epo sensitivity of late erythroid colony-forming units (CFU-E) in 8.5-day embryos, 13.5-day fetal liver, and adult bone marrow of the mouse. All Epo preparations tested, including one from impure sheep and a highly purified human native Epo preparation, produced parallel, but displaced, dose-response curves when Epo concentration was plotted against percent CFU-E response calculated from the optimal Epo concentration. It was found that the CFU-E derived from 8.5-day embryos demonstrated the greatest Epo sensitivity which decreased in fetal liver and adult bone marrow CFU-E populations. Modifications to the culture system allowed CFU-E to be stimulated with as little as 0.003 mU/mL, equivalent to approximately 0.03 fg Epo. Under these culture conditions, no evidence for apoptosis was found, although a normal programmed cell death function cannot be ruled out.
Practical Math for Health Fitness Professionals (1996)

Introduction to metabolic mathematics review of general math mathematical units and problem solving cardiovascular dynamics and calculations pulmonary function calculations resting energy expenditure energy cost of level walking energy cost of uphill walking oxygen consumption during running cycle and arm ergometer metabolic equations calculations for bench stepping submaximal exercise testing and related math nutrition math.
Use of medical emergency team responses to reduce hospital cardiopulmonary arrests (2004)

Increased use of MET may be associated with fewer cardiopulmonary arrests.
Optimizing Non-Antibiotic Treatments for Patients with Acne: A Review (2016)

Acne is a very common non-infectious skin condition that is frequently treated in dermatological practices. Because acne is often chronic and may persist for years, safe and effective long-term maintenance therapy is often required. Given the increasing frequency of antibiotic-resistant bacteria and the gravity of the consequences of this trend, it behooves dermatologists to maximize use of non-antimicrobial therapy when treating acne. In this review of the literature we present data regarding the efficacy and appropriate use of non-antimicrobial treatments for acne. A variety of topical and oral treatment options exist that can be used in a step-wise manner according to the patients' severity and therapeutic response. Non-antimicrobial treatments can be highly efficacious at controlling acne, especially when used as maintenance therapy. While antibiotics have a role in acne treatment, they should not be used as monotherapy, and lengthy courses of antibiotic use are discouraged.
Monitoring Circulating Î³Î´ T Cells in Cancer Patients to Optimize Î³Î´ T Cell-Based Immunotherapy (2014)

The success of γδ T cell-based immunotherapy, where the cytotoxic activity of circulating γδ T lymphocytes is activated by nitrogen-containing bisphosphonates (n-BP), or possibly by bispecific antibodies or the combination of both, requires a profound knowledge of patients' γδ T cells. A possible influence of radio- or chemotherapy on γδ T cells as well as their reported exhaustion after repetitive treatment with n-BP or their lack of response to various cancers can be easily determined by the monitoring assays described in this perspective article. Monitoring the absolute cell numbers of circulating γδ T cell subpopulations in small volumes of whole blood from cancer patients and determining γδ T cell cytotoxicity using the Real-Time Cell Analyzer can give a more comprehensive assessment of a personalized tumor treatment. Possible future directions such as the combined usage of n-BP or phosphorylated antigens together with bispecific antibodies that selectively target γδ T cells to tumor-associated antigens, will be discussed. Such strategies induce expansion and enhance γδ T cell cytotoxicity and might possibly avoid their exhaustion and overcome the immunosuppressive tumor microenvironment.
Tumor-Associated Macrophages and Survival in Classic Hodgkin's Lymphoma (2010)

An increased number of tumor-associated macrophages was strongly associated with shortened survival in patients with classic Hodgkin's lymphoma and provides a new biomarker for risk stratification.
Efficacy of Multifunnel Traps for Capturing Emerald Ash Borer (Coleoptera: Buprestidae): Effect of Color, Glue, and Other Trap Coatings (2011)

Tens of thousands of adhesive-coated purple prism traps are deployed annually in the United States to survey for the invasive emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae). A reusable, more user-friendly trap is desired by program managers, surveyors, and researchers. Field assays were conducted in southeastern Michigan to ascertain the feasibility of using nonsticky traps as survey and detection tools for emerald ash borer. Three nonsticky trap designs, including multifunnel (Lindgren), modified intercept panel, and drainpipe (all painted purple) were compared with the standard purple prism trap; no statistical differences in capture of emerald ash borer adults were detected between the multifunnel design and the prism. In subsequent color comparison assays, both green- and purple-painted multifunnel traps (and later, plastic versions of these colors) performed as well or better than the prism traps. Multifunnel traps coated with spray-on adhesive caught more beetles than untreated traps. The increased catch, however, occurred in the traps' collection cups and not on the trap surface. In a separate assay, there was no significant difference detected between glue-coated traps and Rain-X (normally a glass treatment)-coated traps, but both caught significantly more A. planipennis adults than untreated traps.
Oral delivery of gastro-resistant microencapsulated typhoid vaccine (2009)

Oral vaccination has long been regarded as the best alternative to conventional parenteral vaccination considering practical, economical, and immunological aspects. The purpose of this study was to develop albumin-chitosan mixed matrix microsphere-filled coated capsule formulations of Typhoid Vi antigen and to determine whether it can induce antigen-specific mucosal and systemic immune responses on oral administration. Formulations with Typhoid Vi antigen were prepared and filled into hard gelatin capsules (size # 9) and enteric coated. Formulations were characterized and administered to Sprague-Dawley rats to evaluate the induction of immune response to the antigen. The results indicated that the particle size, zeta potential, swelling, and disintegration rates were optimal for the oral delivery of microencapsulated vaccines. In vivo studies displayed multifold increase of antigen-specific IgG and IgA levels 8 weeks after oral immunization. No statistically significant difference in the antigen-specific IgG and IgA levels were found between oral and parenteral injection groups 8 weeks after vaccination. On the basis of the results of the study, it can be concluded that the oral administration of Typhoid Vi antigen microspheres was successful in inducing antigen-specific systemic and mucosal immune response.
Crystal Structure-Based Virtual Screening for Fragment-like Ligands of the Human Histamine H 1 Receptor (2011)

The recent crystal structure determinations of druggable class A G protein-coupled receptors (GPCRs) have opened up excellent opportunities in structure-based ligand discovery for this pharmaceutically important protein family. We have developed and validated a customized structure-based virtual fragment screening protocol against the recently determined human histamine H(1) receptor (H(1)R) crystal structure. The method combines molecular docking simulations with a protein-ligand interaction fingerprint (IFP) scoring method. The optimized in silico screening approach was successfully applied to identify a chemically diverse set of novel fragment-like (≤22 heavy atoms) H(1)R ligands with an exceptionally high hit rate of 73%. Of the 26 tested fragments, 19 compounds had affinities ranging from 10 μM to 6 nM. The current study shows the potential of in silico screening against GPCR crystal structures to explore novel, fragment-like GPCR ligand space.
G protein-coupled receptors in hypothalamic circuits involved in metabolic diseases. (2004)

G protein-coupled receptors (GPCRs) are cellular surface proteins that span seven transmembrane domains and constitute the largest family of receptors in the genome. They are highly expressed in the central nervous system, and particularly in the hypothalamus, a structure known to be involved in the regulation of energy balance. This review describes the cellular distribution of GPCRs within hypothalamic regions involved in the control of energy balance, and their signaling pathways. An approach which uses knowledge of these features might help to identify and prioritize targets for drug development and strengthen our understanding of the neurobiology of eating disorders.
Do the Survivin (BIRC5) Splice Variants Modulate or Add to the Prognostic Value of Total Survivin in Breast Cancer? (2006)

All variants of survivin exhibited particular associations with clinicopathologic characteristics (age, histology, grade, and steroid hormone receptor status) of breast cancer patients. Survival analyses suggest a modulating role of survivin 2alpha and survivin-3B on the biological function of total survivin.
Direct evidence of NO production in rat hippocampus and cortex using a new fluorescent indicator (1998)

The biological functions of nitric oxide in the neuronal system remain controversial. Using a novel fluorescence indicator, DAF-2 DA, for direct detection of NO, we examined both acute rat brain slices and organotypic culture of brain slices to ascertain NO production sites. The fluorescence intensity in the CA1 region of the hippocampus was augmented, especially after stimulation with NMDA, in acute brain slices. This NO production in the CA1 region was also confirmed in cultured hippocampus. This is the first direct evidence of NO production in the CA1 region. There were also fluorescent cells in the cerebral cortex after stimulation with NMDA. Imaging techniques using DAF-2 DA should be very useful for the clarification of neuronal NO functions.
Lipid Rafts in Higher Plant Cells (2004)

A large body of evidence from the past decade supports the existence of functional microdomains in membranes of animal and yeast cells, which play important roles in protein sorting, signal transduction, or infection by pathogens. They are based on the dynamic clustering of sphingolipids and cholesterol or ergosterol and are characterized by their insolubility, at low temperature, in nonionic detergents. Here we show that similar microdomains also exist in plant plasma membrane isolated from both tobacco leaves and BY2 cells. Tobacco lipid rafts were found to be greatly enriched in a sphingolipid, identified as glycosylceramide, as well as in a mixture of stigmasterol, sitosterol, 24-methylcholesterol, and cholesterol. Phospho- and glycoglycerolipids of the plasma membrane were largely excluded from lipid rafts. Membrane proteins were separated by one- and two-dimensional gel electrophoresis and identified by tandem mass spectrometry or use of specific antibody. The data clearly indicate that tobacco microdomains are able to recruit a specific set of the plasma membrane proteins and exclude others. We demonstrate the recruitment of the NADPH oxidase after elicitation by cryptogein and the presence of the small G protein NtRac5, a negative regulator of NADPH oxidase, in lipid rafts.
Flow Map Layout (2006)

Cartographers have long used flow maps to show the movement of objects from one location to another, such as the number of people in a migration, the amount of goods being traded, or the number of packets in a network. The advantage of flow maps is that they reduce visual clutter by merging edges. Most flow maps are drawn by hand and there are few computer algorithms available. We present a method for generating flow maps using hierarchical clustering given a set of nodes, positions, and flow data between the nodes. Our techniques are inspired by graph layout algorithms that minimize edge crossings and distort node positions while maintaining their relative position to one another. We demonstrate our technique by producing flow maps for network traffic, census data, and trade data.
Cementless revision of cemented stem failures associated with massive femoral bone loss. A technical note. (1992)

A revision technique of the failed cemented femoral stem was developed using a standard cementless porous-coated prosthesis. The advantages of this technique are that the prosthesis has apposition to autogenic bone rather than allograft; problems of long stem can be avoided; supplementary allograft provides enough strength to allow early weight bearing; it facilitates the extraction of the distal cement; and further revision is relatively easy in the healed, viable bone bed.
Sed—a non-interactive text editor (1990)

Sed is a non-interactive context editor that runs on the UNIX † operating system. Sed is designed to be especially useful in three cases: 1) To edit files too large for comfortable interactive editing; 2) To edit any size file when the sequence of editing commands is too complicated to be comfortably typed in interactive mode. 3) To perform multiple ‘global ’ editing functions efficiently in one pass through the input. This memorandum constitutes a manual for users of sed.
Studies on the control of antibody synthesis. VII. Change in affinity of direct and indirect plaque-forming cells with time after immunization in the mouse: loss of high affinity plaques late after immunization. (1975)

The change in avidity of anti-hapten antibody with time after immunization was studied in mice at the level of the antibody-forming cell. A progressive increase in avidity was seen in both direct and indirect plaque-forming cells. Late (38 days) after immunization with a large dose of antigen there was a preferential loss of high avidity plaque-forming cells and the average avidity decreased. High avidity memory cells were still present since boosting resulted in the prompt appearance of very high avidity plaque-forming cells. There was a strong positive correlation between the avidity of the direct and the indirect plaque-forming cells present in the same spleen. A pattern of change in avidity and heterogeneity of avidity similar to that observed with intact animals was seen in lethally irradiated mice reconstituted with normal spleen and thymus cells.