gebhart/patrepeval huggingface dataset:
A human neuroblastoma cell line expresses mu and delta opioid receptor sites. (1986)

A series of neuroblastoma cell lines were screened for the presence of opioid receptor sites with the tracers [3H]diprenorphine (mu, delta, kappa ligand) and [3H]naloxone (mu-selective ligand). One human neuroblastoma cell line, SK-N-SH, displayed avid binding for both tracers. Binding experiments with multiple tracers revealed the presence of both mu and delta sites. These sites were stereospecific, saturable, and proteinaceous in character. Saturation binding experiments provided an estimate of 50,000 mu and 10,000 delta sites/cell. NaCl (100 mM) and guanine nucleotide, guanylyl imidodiphosphate (50 microM), reduced opioid agonist but not antagonist binding to these sites. Etorphine at 1 nM inhibited prostaglandin E1-stimulated cyclic AMP production by approximately 20%, which was reversible by naloxone. The opioid-binding sites on SK-N-SH cells closely resemble the previously reported mu and delta sites in human and rodent brain. Therefore, the SK-N-SH neuroblastoma cell line represents a useful tool to study the molecular functions of opioid receptors.
Escherichia coli expressing a Neisseria gonorrhoeae opacity-associated outer membrane protein invade human cervical and endometrial epithelial cell lines. (1992)

Members of the opacity-associated (Opa) outer membrane protein family of Neisseria gonorrhoeae have been proposed to mediate adherence to and invasion of cultured human epithelial cells. We transformed Escherichia coli with a plasmid containing a gonococcal opa gene fused in-frame to the leader sequence of the beta-lactamase gene as described by Palmer et al. [Palmer, L., Brooks, G. F. & Falkow, S. (1989) Mol. Microbiol. 3, 663-671]. These transformed E. coli [E. coli (opa)] expressed the heat-modifiable opa gene product (the Opa protein) in their outer membrane and adhered to and invaded ME-180 human endocervical epithelial cells. In a 2-h adherence assay, an average of 26.7 E. coli (opa) adhered per ME-180 cell, whereas the control E. coli carrying only the expression vector (pKT279) did not adhere at all (less than 0.15 bacterium per cell). We investigated the ability of the adherent E. coli (opa) to invade ME-180 epithelial cells by using a gentamicin selection assay. We recovered up to 1 x 10(6) gentamicin-resistant bacteria per monolayer when ME-180 cells were infected with E. coli (opa) compared to less than 10 bacteria when the epithelial cells were infected with the same number of control E. coli (pKT279). The kinetics and level of invasion by E. coli (opa) were similar to invasion by Opa+ N. gonorrhoeae. Maximum invasion occurred 4 h after infection with 4 x 10(7) bacteria. Transmission electron microscopy studies confirmed that E. coli (opa) invaded ME-180 cells. In comparative studies, the number of E. coli (opa) that invaded HEC-1-B human endometrial epithelial cells was about an order of magnitude less than the number that invaded ME-180 cells, and E. coli (opa) did not invade Chang human conjunctival epithelial cells at all. The observations that early (less than 4 h) invasion by E. coli (opa) was dramatically inhibited, in a dose-responsive manner, by the actin-disrupting reagent cytochalasin D but later invasion (8-24 h) was not suggest that invasion mediated by Opa proteins may occur by two mechanisms, only one of which is dependent upon microfilament function. Transmission electron microscopy also revealed that infected epithelial cells had a dramatically increased amount of cytoplasmic fibrillar material surrounding the nucleus. The function and genesis of this material remain unclear. These studies indicate that at least one gonococcal Opa protein is an invasin.
Physicochemical properties of collagen, gelatin and collagen hydrolysate derived from bovine limed split wastes (2006)

Collagen, gelatin and collagen hydrolysate were prepared from bovine limed split wastes by different preparative processes. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis showed that the molecular weight distribution of collagen was very narrow (about 200 and 100kDa for β and a chains respectively) compared with those of gelatin (less than 300kDa and wide distribution) and collagen hydrolysate (less than 50kDa and wide distribution ). The isoelectric points of collagen, gelatin and collagen hydrolysate were 8.26, 4.88 and 4.54 respectively determined by Zeta potential titration. Circular dichroism (CD) spectra revealed that there were two peaks, a positive peak around 221nm and a negative peak around 192nm for collagen, which are the characteristics of collagen triple helix. However, gelatin and collagen hydrolysate lacked any positive peaks around 220nm, suggesting random coils. The denaturation temperature of collagen was about 37.5°C determined by the viscosity method, the helix-coil transitions for gelatin and collagen hydrolysate were not present in the heating process. Collagen reaggregated to fibrils at 35°C monitored at 313nm. In contrast, gelatin and collagen hydrolysate lost the ability of fibril formation. Collagen was more resistant to trypsin hydrolysis compared with gelatin and collagen hydrolysate. In addition, the collagen membrane exhibited superior features such as higher enthalpy, greater network structure and better physical/mechanical properties compared with those of the gelatin membrane. Therefore, collagen isolated from limed split wastes can be a high value product due to its special characteristics and has many potential future applications in biomaterials, functional additives, cosmetics and pharmaceutical industries.
30 GHz direct modulation bandwidth in detuned loadedInGaAsP DBR lasers at 1.55 µm wavelength (1997)

An increased resonance frequency and reduced damping of the resonance peak leading to a record high modulation bandwidth of 30 GHz were observed in 1.55 µm InGaAsP DBR lasers. These results are attributed to the mechanism of detuned loading.
Receptor-Mediated Activation of Heterotrimeric G-Proteins in Living Cells (2001)

Receptor-mediated activation of heterotrimeric GTP-binding proteins (G-proteins) was visualized in living Dictyostelium discoideum cells by monitoring fluorescence resonance energy transfer (FRET) between alpha- and beta- subunits fused to cyan and yellow fluorescent proteins. The G-protein heterotrimer rapidly dissociated and reassociated upon addition and removal of chemoattractant. During continuous stimulation, G-protein activation reached a dose-dependent steady-state level. Even though physiological responses subsided, the activation did not decline. Thus, adaptation occurs at another point in the signaling pathway, and occupied receptors, whether or not they are phosphorylated, catalyze the G-protein cycle. Construction of similar energy-transfer pairs of mammalian G-proteins should enable direct in situ mechanistic studies and applications such as drug screening and identifying ligands of newly found G-protein-coupled receptors.
The emerging role of class-3 semaphorins and their neuropilin receptors in oncology (2014)

The semaphorins, discovered over 20 years ago, are a large family of secreted or transmembrane and glycophosphatidylinositol -anchored proteins initially identified as axon guidance molecules crucial for the development of the nervous system. It has now been established that they also play important roles in organ development and function, especially involving the immune, respiratory, and cardiovascular systems, and in pathological disorders, including cancer. During tumor progression, semaphorins can have both pro- and anti-tumor functions, and this has created complexities in our understanding of these systems. Semaphorins may affect tumor growth and metastases by directly targeting tumor cells, as well as indirectly by interacting with and influencing cells from the micro-environment and vasculature. Mechanistically, semaphorins, through binding to their receptors, neuropilins and plexins, affect pathways involved in cell adhesion, migration, invasion, proliferation, and survival. Importantly, neuropilins also act as co-receptors for several growth factors and enhance their signaling activities, while class 3 semaphorins may interfere with this. In this review, we focus on the secreted class 3 semaphorins and their neuropilin co-receptors in cancer, including aspects of their signaling that may be clinically relevant.
On the Equivalence of Nonnegative Matrix Factorization and Spectral Clustering (2005)

Current nonnegative matrix factorization (NMF) deals with X = FGT type. We provide a systematic analysis and extensions of NMF to the symmetric W = HHT, and the weighted W = HSHT. We show that (1) W = HHT is equivalent to Kernel if-means clustering and the Laplacian-based spectral clustering. (2) X = FGT is equivalent to simultaneous clustering of rows and columns of a bipartite graph. Algorithms are given for computing these symmetric NMFs.
Long-term Visual Outcome of Arteriovenous Adventitial Sheathotomy on Branch Retinal Vein Occlusion Induced Macular Edema (2008)

Considering the favorable natural course of BVO and the unproven effect of reperfusion on macular edema, surgical efficacy of arteriovenous adventitial sheathotomy requires further evaluation.
A Review of the Pinned Photodiode for CCD and CMOS Image Sensors (2014)

The pinned photodiode is the primary photodetector structure used in most CCD and CMOS image sensors. This paper reviews the development, physics, and technology of the pinned photodiode.
Local- and distant-charge compensation ofEu3+ions in defect centers ofSrTiO3 (1992)

Site-selective spectroscopy of rare-earth-doped materials has proven to be a powerful method for investigating solid-state defect chemistry at the atomic level. In this paper, the spectral transitions of single-crystal and polycrystalline samples of ${\mathrm{SrTiO}}_{3}$:${\mathrm{Eu}}^{3+}$ are sorted by site-selective laser spectroscopy into the major and minor sites that are found in this perovskite-structure material. The major site is shown to have crystal-field multiplicities, relative fluorescence and absorption intensities, level lifetimes, and level degeneracies that are consistent with the tetragonal symmetry associated with a distantly-charge-compensated center. The electronic and vibronic levels for all the visible transitions are determined for this center. These levels exhibit temperature-dependent splittings and shifting that reflects the cubic-tetragonal phase transition that occurs at 106 K. In addition, there are eleven other centers that are assigned to centers with local compensation by vacancies or electronic defects. Electronic defects are also evident from the photobleaching and photoinduced darkening that is also observed in these samples. These effects are observed in both single-crystal and polycrystalline samples, although the linewidths and line shapes of the polycrystalline samples are shown to be dependent on the preparation conditions.
Mass Spectrometric Immunoassay (1995)

A new, general method of immunoassay is demonstrated. The approach is based on the microscale immunoaffinity capture of target antigens followed by mass-specific identification and quantitation using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Immunoaffinity capture of antigens effectively overcomes signal suppression effects typically encountered during traditional matrix-assisted laser desorption/ionization analysis of complex biological mixtures while simultaneously concentrating the analyte into a small volume. Mass spectrometric detection of antigens is unambiguous, as antigen signals are observed at characteristic mass-to-charge values in the mass spectrum, offering a high level of immunity to artifacts due to nonbiospecific retention of mixture components. However, the most important aspect of such mass-specific detection is the ability to use a single assay to screen biological systems for the presence of multiple, mass-resolved antigens. Analyte quantitation is possible by using a single antibody to capture both the antigen and an antigen variant which has been chemically modified to have a different mass. With proper calibration, the relative signal intensities of the two species in the mass spectrum can be used to determine the antigen concentration. Sample incubation and processing methods were such that a typical analysis could be performed in less than 1 h while subnanomolar sensitivities were maintained. The technique has been used for the rapid, selective, and quantitative screening of human blood for the presence of myotoxin a, and Mojave toxin form the venoms of the prairie rattlesnakes, Crotalus viridis viridis, and and the Mojave rattlesnake, Crotalus scutulatus scutulatus.
Enantioselective and Enantioconvergent Syntheses of Building Blocks for the Total Synthesis of Cyclopentanoid Natural Products (1984)

The cyclopentenoid lactone 1 and its enantiomer ent-1 were prepared enantiomerically pure on the mole scale from meso-tetrahydrophthalic acid anhydride. The key step is the partial saponification of dimethyl tetrahydrophthalate 2 with commercially available pig liver esterase.
Novel Methodology for Fabrication of Tissue-Engineered Tubular Constructs Using Magnetite Nanoparticles and Magnetic Force (2005)

Novel technologies for creating three-dimensional constructs with complex shapes would be highly useful in tissue engineering. In the present study, tubular structures were constructed using magnetic force. Magnetite nanoparticles in cationic liposomes were taken up by target cells. The magnetically labeled cells were seeded onto ultralow-attachment plates, and a magnet was placed under the wells. After 24 h of culture, the magnetically labeled cells formed a cell sheet. Subsequently, when a cylindrical magnet was rolled onto the cell sheet, the cell sheet was attracted to the magnet and formed a tube around it. The magnet was then removed, leaving behind a tubular structure. Two types of tissue were used to create tubular structures: urinary tissue, consisting of a monotypic urothelial cell layer; and vascular tissue, consisting of heterotypic layers of endothelial cells, smooth muscle cells, and fibroblasts. The present results suggest that this novel methodology using magnetite nanoparticles and magnetic force, which we have termed "magnetic force-based tissue engineering" (Mag-TE), is a promising approach to constructing tissue-engineered tubular structures.
Characterization, by Molecular Cloning, of Smaller Forms of Thyroid Peroxidase Messenger Ribonucleic Acid in Human Thyroid Cells as Alternatively Spliced Transcripts* (1990)

The mRNA for human thyroid peroxidase (hTPO) is 3.1 kilobases (kb) in size, coding for a protein of 933 amino acids. However, there is controversy as to whether other hTPO mRNA transcripts exist in thyroid cells. There is one report of the existence of 2.1- and 1.7-kb transcripts (hTPO mRNA species I and II), representing up to half of the hTPO mRNA in TSH-stimulated human thyroid cells. On the other hand, numerous other studies have only observed 3.1-kb hTPO mRNA transcripts. The nature of these putative 2.1- and 1.7-kb mRNA transcripts, if present, is unknown. We now report the isolation and characterization of two smaller hTPO cDNA species, designated hTPO cDNA I and II. cDNA I and II are 1753 and 1044 basepairs (bp) in size, with open reading frames of only 225 and 174 amino acids, respectively. Comparison of the nucleotide sequences of cDNA I and II with available hTPO genomic sequence reveals that cDNA I consists of exons 1-6 (654 bp) and the 5'-end of intron 6 (1099 bp); cDNA II contains exons 1-5 (486 bp) and an unidentified DNA tract of 558 bp further down-stream, presumably an intron. Confirmation that cDNA I and II correspond to mRNA transcripts I and II, respectively, was provided by Northern blot analysis with DNA probes specific for cDNA I and II. hTPO mRNA transcripts I and II are present in TSH-stimulated and TSH-deprived human thyroid cells in culture as well as in intact thyroid tissue. In summary, the present data 1) demonstrate directly that hTPO mRNA transcripts I and II exist in human thyroid cells, 2) explain the discrepant data in the literature regarding their existence, 3) elucidate their molecular structure, 4) indicate that they are generated by alternative splicing, and 5) demonstrate that hTPO mRNA I and II exist in the thyroid gland in vivo as well as in thyroid cells in culture.
Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA (2017)

Blood circulates throughout the human body and contains molecules drawn from virtually every tissue, including the microbes and viruses which colonize the body. Through massive shotgun sequencing of circulating cell-free DNA from the blood, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome. Analyzing cumulative sequence data from 1,351 blood samples collected from 188 patients enabled us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel with little or no sequence homology in any existing databases. The vast majority of these novel contigs possess coding sequences, and we have validated their existence both by finding their presence in independent experiments and by performing direct PCR amplification. When their nearest neighbors are located in the tree of life, many of the organisms represent entirely novel taxa, showing that microbial diversity within the human body is substantially broader than previously appreciated.
The Toxicology of Perfluorooctanoate (2004)

PFOA is a peroxisome proliferator (PPAR agonist) and exerts morphological and biochemical effects characteristic of PPAR agonists. These effects include increased β-oxidation of fatty acids, increases in several cytochrome P-450 (CYP450)-mediated reactions, and inhibition of the secretion of very low-density lipoproteins and cholesterol from the liver. These effects on lipid metabolism and transport result in a reduction of cholesterol and triglycerides in serum and an accumulation of lipids in the liver. The triad of tumors observed (liver, Leydig cell, and pancreatic acinar-cell) is typical of many PPAR agonists and is believed to involve nongenotoxic mechanisms. The hepatocellular tumors observed in rats are likely to have been the result of the activation of the peroxisome proliferator activated receptor α (PPARα). The tumors observed in the testis (Leydig-cell) have been hypothesized to be associated with an increased level of serum estradiol in concert with testicular growth factors. The mechanism responsible for the acinarcell tumors of the pancreas in rats remains the subject of active investigation. The mechanism resulting in the hepatocellular tumors in rats (PPARα activation) is not likely to be relevant to humans. Similarly, the proposed mechanism for Leydig-cell tumor formation is of questionable relevance to humans. Acinar tumors of the pancreas are rare in humans, and the relevance of the these tumors, as found in rats, to humans is uncertain. Epidemiological investigations and medical surveillance of occupationally exposed workers have not found consistent associations between PFOA exposure and adverse health effects.
Matrix-bound thrombospondin promotes angiogenesis in vitro (1994)

Thrombospondin (TSP) is a multidomain adhesive protein postulated to play an important role in the biological activity of the extracellular matrix. To test this hypothesis, TSP-containing fibrin and collagen matrices were evaluated for their capacity to support angiogenesis and cell growth from explants of rat aorta. This serum-free model allowed us to study the angiogenic effect of TSP without the interference of attachment and growth factors present in serum. TSP promoted dose-dependent growth of microvessels and fibroblast-like cells. The number of microvessels in TSP-containing collagen and fibrin gels increased by 136 and 94%, respectively. The TSP effect was due in part to cell proliferation since a 97% increase in [3H]thymidine incorporation by the aortic culture was observed. The effect was TSP-specific because TSP preparations adsorbed with anti-TSP antibody showed no activity. TSP did not promote angiogenesis directly since no TSP-dependent growth of isolated endothelial cells could be demonstrated. Rather TSP directly stimulated the growth of aortic culture-derived myofibroblasts which in turn promoted microvessel formation when cocultured with the aortic explants. Angiogenesis was also stimulated by myofibroblast-conditioned medium. Partial characterization of the conditioned medium suggests that the angiogenic activity is due to heparin-binding protein(s) with molecular weight > 30 kD. These results indicate that matrix-bound TSP can indirectly promote microvessel formation through growth-promoting effects on myofibroblasts and that TSP may be an important stimulator of angiogenesis and wound healing in vivo.
Phosphorothioate-Modified Oligodeoxynucleotides Inhibit Human Cytomegalovirus Replication by Blocking Virus Entry (2008)

Studies in animal models have provided evidence that Toll-like receptor 9 (TLR9) agonists, such as synthetic oligodeoxynucleotides (ODNs) that contain immunostimulatory deoxycytidyl-deoxyguanosine (CpG) motifs (CpG ODNs), protect against a wide range of viral pathogens. This antiviral activity has been suggested to be indirect and secondary to CpG-induced cytokines and inflammatory responses triggered through TLR9 activation. However, few studies have addressed the potential of CpG ODNs as direct antiviral agents. Here, we report on the ability of some CpG ODNs to directly suppress, almost completely, human cytomegalovirus (HCMV) replication in both primary fibroblasts and endothelial cells. Murine CMV replication was inhibited as well, whereas no inhibition was observed for herpes simplex virus type 1, adenovirus, or vesicular stomatitis virus. The antiviral activity of these ODNs was significantly reduced when they were added after virus adsorption, indicating that their action may be primarily targeted to the very early phases of the HCMV cycle. In fact, the B-class prototype CpG ODN 2006 effectively prevented the nuclear localization of pp65 and input viral DNA, which suggests that it inhibits HCMV entry. Moreover, a CpG 2006 control, ODN 2137 without CpG motifs, also showed a potent inhibitory activity on the HCMV entry phase, indicating that the anticytomegaloviral activity is independent of the CpG motif. In contrast, a phosphodiester version of CpG 2006 showed reduced antiviral activity, indicating that the inhibitory activity is dependent on the phosphorothioate backbone of the ODN. These results suggest that this yet-unrecognized activity of CpG ODNs may be of interest in the development of novel anticytomegaloviral molecules.
Arabinosyl Cytosine: A Useful Agent in the Treatment of Acute Leukemia in Adults (1968)

Abstract Arabinosyl cytosine (ara-C), a synthetic pyrimidine nucleoside related to the normal metabolites cytidine and deoxycytidine, has been found capable of producing marrow remission at tolerable doses in acute myelocytic and acute lymphocytic leukemia in adults. There were 16 per cent remissions complete in all aspects, 3 per cent complete except for hemoglobin level, and 6 per cent partial remissions among 180 adults with acute myelocytic leukemia treated with any one of 8 variants of infusion duration or daily dose of ara-C. Twenty-four per cent of 37 adults with acute lymphocytic or unclassified leukemia had complete or partial remissions. The comparison of 1, 4, 12 and 24 hours infusion of ara-C (to total dose tolerated) does not show significant superiority for any one group. The complete remission rate with 1 or 12 hour infusions, however, is 25 per cent (superior to that obtained with 6-mercaptopurine) and the recommended schedule of treatment for ara-C based on these data is, therefore, daily infusions of 100 or 50 mg./m.2 in one hour for approximately 3 to 6 weeks followed by maintenance therapy of once weekly subcutaneous injection of 30 mg./m.2 of ara-C. Platelet transfusions should be available when ara-C is used.