gebhart/patrepeval huggingface dataset:
Identification of 20 genes aberrantly methylated in human breast cancers (2005)

Aberrant methylation of CpG islands (CGI) not only plays a role in gene silencing, but is also a potential cancer biomarker. To identify more CGI aberrantly methylated in human breast cancers, we carried out a genome-wide search for aberrant methylation, using methylation-sensitive-representational difference analysis. CGI in 5' upstream regions of 20 genes, TSPAN-2, AK5, LOC284999, HOXD11, FLJ25161, XT3, PCDH10, PCDHGB6, SIM1, LOC346978, COE2, TDH (FLJ25033), LOC346419, FLJ33790, GJB2, AMN, LOC201164, DLX4, DCC and FOXA2, were found to be methylated in at least one of 8 breast cancer cell lines. Fifteen of the 20 genes were methylated in more than one of 21 primary breast cancers in Stages I or II, and especially, those of LOC346978, HOXD11, SIM1, PCDHGB6 and FLJ25161 were methylated in more than 10 cancers. All the breast cancers had some aberrant methylation. Among the 13 genes whose CGI were completely methylated in one or more cell lines, FOXA2 and XT3 were expressed in normal human mammary epithelial cells (HMEC) and were not expressed in cancer cell lines with complete methylation. The other 11 genes examined were barely expressed, or not expressed even in HMEC. Our results showed that breast cancer cells accumulate aberrant methylation of the CGI identified here. This may serve as markers for early-stage breast cancers and suggests that aberrant methylation targets transcriptionally inactive genes in vivo.
O-Glycosylation of the V2 vasopressin receptor (1999)

The human V2 vasopressin receptor contains one consensus site for N-linked glycosylation at asparagine 22 in the predicted extracellular amino terminal segment of the protein. This segment also contains clusters of serines and threonines that are potential sites for O-glycosylation. Mutagenesis of asparagine 22 to glutamine abolished N-linked glycosylation of the V2 receptor (N22Q-V2R), without altering its function or level of expression. The N22Q-V2R expressed in transfected cells migrated in denaturing acrylamide gels as two protein bands with a difference of 7000 Da. Protein labeling experiments demonstrated that the faster band could be chase to the slower one suggesting the presence of O-linked sugars. Sialidase treatment of membranes from cells expressing the N22Q-V2R or of immunoprecipitated metabolically labeled V2R accelerated the migration of the protein in acrylamide gels demonstrating the existence of O-glycosylation, the first time this type of glycosylation has been found in a G protein coupled receptor. Synthesis of metabolically labeled receptor in the presence of 1 mM phenyl-N-acetyl-alpha-D-galactosaminide, a competitive inhibitor of N-acetyl-alpha-D-galactose and N-acetylneuraminic acid transferases, also produced a receptor that migrated faster in denaturing gels. Serines and threonines present in the amino terminus were analyzed by alanine scanning mutagenesis to identify the acceptor sites. O-glycosylation was found at most serines and threonines present in the amino terminus. Because the disappearance of a site opened the availability of others to the transferases, the exact identification of the acceptor sites was not feasible. The wild type V2R expressed in HEK 293, COS, or MDCK cells underwent N- and O-linked glycosylation. The mutant V2R bearing all serine/threonine substitutions by alanine at the amino terminus yielded a receptor functionally indistinguishable from the wild type protein, whose mobility in polyacrylamide gels was no longer affected by sialidase treatment.
Riboflavin-ultraviolet a corneal cross-linking for keratoconus (2009)

Riboflavin-UVA corneal cross-linking is a safe and promising method for keratoconus. Larger studies with longer follow up are recommended.
A Burkholderia cepacia complex non-ribosomal peptide-synthesized toxin is hemolytic and required for full virulence (2012)

Members of the Burkholderia cepacia complex (Bcc) have recently gained notoriety as significant bacterial pathogens due to their extreme levels of antibiotic resistance, their transmissibility in clinics, their persistence in bacteriostatic solutions, and their intracellular survival capabilities. As pathogens, the Bcc are known to elaborate a number of virulence factors including proteases, lipases and other exoproducts, as well as a number of secretion system associated effectors. Through random and directed mutagenesis studies, we have identified a Bcc gene cluster capable of expressing a toxin that is both hemolytic and required for full Bcc virulence. The Bcc toxin is synthesized via a non-ribosomal peptide synthetase mechanism, and appears to be related to the previously identified antifungal compound burkholdine or occidiofungin. Further testing shows mutations to this gene cluster cause a significant reduction in both hemolysis and Galleria mellonella mortality. Mutation to a glycosyltransferase gene putatively responsible for a structural-functional toxin variant causes only partial reduction in hemolysis. Molecular screening identifies the Bcc species containing this gene cluster, of which several strains produce hemolytic activity.
Sensitive and rapid quantification of C-reactive protein using quantum dot-labeled microplate immunoassay (2012)

The developed assay meets the needs of the rapid, sensitive and high-throughput determination of hs-CRP levels within a short time using minimal resources. In addition, the developed assay can also be used to detect and quantify other diagnostic biomarkers by immobilizing specific monoclonal antibodies.
Silicon dioxide thin films prepared by chemical vapor deposition from tetrakis(diethylamino)silane and ozone (1994)

Silicon dioxide thin films were prepared by a low-temperature atmospheric-pressure chemical vapor deposition method. The raw materials were tetrakis(diethylamino)silane and ozone in oxygen gas. The amorphous films were obtained at a substrate temperature above 200 °C. The films were superior in chemical stability and hardness to the films which were prepared from tetraethoxysilane and ozone.
Ciliary neurotrophic factor (1994)

Ciliary neurotrophic factor (CNTF) was first identified and partially purified from embryonic chick eye tissues. Subsequently, it was shown that CNTF is also present in large amounts in sciatic nerves of adult rats and rabbits, which led to its final purification and cloning. CNTF is not secreted by the classical secretory pathway involving the endoplasmatic reticulum and Golgi complex, but can be detected in high quantities within the cytoplasm of myelinating Schwann cells and astrocytes using immunohistochemistry. CNTF supports survival and/or differentiation of a variety of neuronal cell types including sensory, sympathetic, and motoneurons. Also, nonneuronal cells, such as oligodendrocytes, microglial cells, liver cells, and skeletal muscle cells, respond to exogenously administered CNTF, both in vitro and in vivo. During development, expression of CNTF is very low, if indeed it is expressed at all, and the phenotype of mice lacking endogenous CNTF after inactivation of the CNTF gene by homologous recombination suggests that CNTF does not play a crucial role for responsive cells during embryonic development. However, motoneurons are lost postnatally in mice lacking endogenous CNTF, suggesting that CNTF acts physiologically on the maintenance of these cells. The ability of exogenous CNTF to protect against motoneuron loss following lesion or in other animal models indicates that CNTF might be useful in the treatment of human motoneuron disorders, provided appropriate means of administration can be found.
Colorectal Cancer Cell Lines Are Representative Models of the Main Molecular Subtypes of Primary Cancer (2014)

Human colorectal cancer cell lines are used widely to investigate tumor biology, experimental therapy, and biomarkers. However, to what extent these established cell lines represent and maintain the genetic diversity of primary cancers is uncertain. In this study, we profiled 70 colorectal cancer cell lines for mutations and DNA copy number by whole-exome sequencing and SNP microarray analyses, respectively. Gene expression was defined using RNA-Seq. Cell line data were compared with those published for primary colorectal cancers in The Cancer Genome Atlas. Notably, we found that exome mutation and DNA copy-number spectra in colorectal cancer cell lines closely resembled those seen in primary colorectal tumors. Similarities included the presence of two hypermutation phenotypes, as defined by signatures for defective DNA mismatch repair and DNA polymerase ε proofreading deficiency, along with concordant mutation profiles in the broadly altered WNT, MAPK, PI3K, TGFβ, and p53 pathways. Furthermore, we documented mutations enriched in genes involved in chromatin remodeling (ARID1A, CHD6, and SRCAP) and histone methylation or acetylation (ASH1L, EP300, EP400, MLL2, MLL3, PRDM2, and TRRAP). Chromosomal instability was prevalent in nonhypermutated cases, with similar patterns of chromosomal gains and losses. Although paired cell lines derived from the same tumor exhibited considerable mutation and DNA copy-number differences, in silico simulations suggest that these differences mainly reflected a preexisting heterogeneity in the tumor cells. In conclusion, our results establish that human colorectal cancer lines are representative of the main subtypes of primary tumors at the genomic level, further validating their utility as tools to investigate colorectal cancer biology and drug responses.
Angiogenesis in acute and chronic leukemias and myelodysplastic syndromes (2000)

Angiogenesis has been associated with the growth, dissemination, and metastasis of solid tumors. The aims of this study were to evaluate the vascularity and the levels of angiogenic factors in patients with acute and chronic leukemias and myelodysplastic syndromes (MDS). The numbers of blood vessels were measured in 145 bone marrow biopsies and the levels of vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF), tumor necrosis growth factor-alpha (TNF-alpha), tumor growth factor-alpha (TGF-alpha), and hepatocyte growth factor (HGF) were determined in 417 plasma samples. Except for chronic lymphocytic leukemia (CLL), vascularity was significantly higher in all leukemias and MDS compared with control bone marrows. The highest number of blood vessels and largest vascular area were found in chronic myeloid leukemia (CML). VEGF, bFGF, and HGF plasma levels were significantly increased in acute myeloid leukemia (AML), CML, CLL, chronic myelomonocytic leukemia (CMML), and MDS. HGF, TNF-alpha, and bFGF but not VEGF were significantly increased in acute lymphoblastic leukemia (ALL). TNF-alpha levels were significantly increased in all diseases except for AML and MDS. No significant increase was found in TGF-alpha in any leukemia or MDS. The highest plasma levels of VEGF were in CML, and the highest plasma levels of bFGF were in CLL. The levels of HGF were highest in CMML. These data suggest that vascularity and angiogenic factors are increased in leukemias and MDS and may play a role in the leukemogenic process.
Synthesis and Optical, Electrochemical, and Electron-Transporting Properties of Silicon-Bridged Bithiophenes (1999)

A series of bithiophene derivatives bearing an intramolecular monosilanylene or disilanylene bridge between the β,β‘-positions were synthesized, and their properties were investigated. UV spectral and cyclic voltammetric analyses of the silicon-bridged bithiophenes indicated that they have lower lying LUMOs, relative to those for bithiophene and methylene bridged bithiophenes, probably due to σ*−π* interaction between the silicon atom(s) and bithiophene π-orbitals, in good agreement with the results of theoretical calculations using simplified model compounds based on RHF/6-31G. The silicon-bridged bithiophenes exhibit high electron-transporting properties, and triple-layer-type electroluminescent (EL) devices, using the silicon-bridged bithiophenes, tris(8-quinolinolato)aluminum(III) complex (Alq), and N,N‘-diphenyl-N,N‘-di-m-tolylbiphenyl-4,4‘-diamine (TPD) as the electron-transporting, emitting, and hole-transporting layers, respectively, emitted strong EL.
Dilute nitride GaInNAs and GaInNAsSb solar cells by molecular beam epitaxy (2007)

Dilute nitride films with a roughly 1 eV band gap can be lattice-matched to gallium arsenide and germanium, and therefore could become a critical component in next-generation multijunction solar cells. To date most dilute nitride solar cells have been plagued with poor efficiency, due in large part to short diffusion lengths. This study focuses on two techniques aimed at improving the quality of dilute nitride films grown by molecular beam epitaxy: the utilization of biased deflection plates installed in front of the nitrogen plasma source, and the introduction of antimony during growth. Results from GaInNAs cells grown with and without deflection plates, and GaInNAsSb solar cells are reported. The use of biased deflection plates during GaInNAs growth improved every aspect of solar cell performance. For the GaInNAs devices grown with deflection plates, the dark current density, open-circuit voltage, and fill factor were the best of the devices studied. The GaInNAsSb cells had the highest quantum efficiency, almost 80% at maximum, mainly due to low background doping densities providing these devices with wide depletion widths. The GaInNAsSb materials also had quite narrow band gaps of 0.92 eV. Because of the high collection efficiency coupled with the narrow band gap, the sub-GaAs short-circuit current density produced by the GaInNAsSb cells is 14.8 mA∕cm2, which was the highest of the devices studied. This current is nearly 50% greater than the best dilute nitride solar cells in the literature, and is the first dilute nitride cell to produce enough current to current match the upper two subcells in a triple-junction device, composed of GaInP/InGaAs/GaInNAsSb.
Possible Role of Histamine in Rheumatoid Arthritis (1981)

Basophilocytes from patients with rheumatoid arthritis (RA) responded to leukocyte nuclei from normal persons with histamine release; a similar histamine release induced by the nuclear components RNA and DNA has been demonstrated previously. A role of histamine in RA is also supported by the findings of clinical improvement during treatment with H1 and H2 antihistamines in six of 12 patients with RA in active phase, whereas four showed definite deterioration.
Identification of Rat Rosa26 Locus Enables Generation of Knock-In Rat Lines Ubiquitously Expressing tdTomato (2012)

Recent discovery of a method for derivation and culture of germline-competent rat pluripotent stem cells (PSCs) enables generation of transgenic rats or knock-out rats via genetic modification of such PSCs. This opens the way to use rats, as is routine in mice, for analyses of gene functions or physiological features. In mouse or human, one widely used technique to express a gene of interest stably and ubiquitously is to insert that gene into the Rosa26 locus via gene targeting of PSCs. Rosa26 knock-in mice conditionally expressing a reporter or a toxin gene have contributed to tracing or ablation of specific cell lineages. We successfully identified a rat orthologue of the mouse Rosa26 locus. Insertion of tdTomato, a variant of red fluorescent protein, into the Rosa26 locus of PSCs of various rat strains allows ubiquitous expression of tdTomato. Through germline transmission of one Rosa26-tdTomato knock-in embryonic stem cell line, we also obtained tdTomato knock-in rats. These expressed tdTomato ubiquitously throughout their bodies, which indicates that the rat Rosa26 locus conserves functions of its orthologues in mouse and human. The new tools described here (targeting vectors, knock-in PSCs, and rats) should be useful for a variety of research using rats.
Tratado SEIMC de enfermedades infecciosas y microbiología clínica (2005)

Severe optic disk hemorrhage may occur after phacoemulsification in advanced glaucoma patients. Systemic vascular factors, such as chronic hypertension and old age, and surgical complications, such as posterior capsule rupture and postoperative IOP elevation, would further increase the risk. For phacoemulsification in advanced glaucoma cases, extra care should be taken to control intraoperative IOP fluctuations and monitor postoperative IOP.
The Continuing Evolution of Psychiatric Neurosurgery (2000)

Abstract In this article, the authors examine the growth of the discipline of psychiatric surgery from the earliest lesioning procedures to the neuroaugmentative strategies used today. Special attention is paid to the neural circuitry that underlies psychiatric disorders and how surgical manipulation of these circuits might result in the amelioration of the disease state. Also examined is the effect that the technology curve has had on psychiatric surgery with regard to functional imaging and neurosurgical equipment. Finally, the authors use the current state of psychiatric surgery to speculate on some of the future directions that psychiatric neurosurgical procedures might take.
Generation of human induced pluripotent stem cells by simple transient transfection of plasmid DNA encoding reprogramming factors (2010)

Simple transient transfection of plasmid DNA encoding reprogramming factors is sufficient to generate human iPS cells from primary fibroblasts that are free of exogenous DNA integrations. This approach is highly accessible and could expand the use of iPS cells in the study of human disease and development.
Iodine125 labeled anti-epidermal growth factor receptor-425 in the treatment of malignant astrocytomas. A pilot study. (1991)

In 1986, a pilot Phase I/II project was initiated using Iodine-125 labeled anti-epidermal growth factor receptor-425 in the treatment of patients with recurrent glioblastoma multiforme of the brain. The monoclonal antibody was administered intra-arterially by the internal carotid arterial system or the vertebral arterial system depending upon the blood supply to the tumor. The treatment program was repeated at intervals for two or three times. Demonstrated was the intense localization of the monoclonal antibody in the brain tumor prior to therapy using Indium-111 labeled anti-epidermal growth factor receptor-425. This localization was demonstrated prior to any therapy as well as after failure from primary radiation therapy with or without concomitant chemotherapy. To date, 15 patients have been treated following recurrence of their glioma (1/15 metastatic adenocarcinoma) with the monoclonal antibody labeled with Iodine-125. Of the 15 patients, there has been one surgically documented complete response, two partial responders, and five patients with stable disease. The results indicate the potential activity of this radiolabeled monoclonal antibody and have prompted continued accession of patients into a Phase II study as a part of the primary treatment regimen (surgery, radiation therapy with or without chemotherapy) followed by administration of the Iodine-125 labeled anti-epidermal growth factor receptor-425.
Perspective of Recent Progress in Immobilization of Enzymes (2011)

The commercial application of biocatalysts depends on the development of effective methods of immobilization. The immobilization of enzymes greatly increases the stability of enzymes and eases the burden of enzyme cost and thus, is widely pursued for efficient, selective, and environmentally friendly catalysis. This brief perspective focuses on recent development in the area of enzyme immobilization in porous materials. Recent work regarding the immobilization of enzymes in inorganic mesoporous materials as well as the modifications to those materials is summarized in this paper. The configuration of supported enzyme as membranes and fibers may facilitate their application in areas that require a biocatalytic process. Enzymes immobilized in or on fibrous membranes provide high surface area for high throughput biocatalysis. These membrane bioreactors also allow for biotransformations to be carried out within a continuous flow process while maintaining enzyme stability under operating conditions as a result from the enzyme immobilization. A summary of efforts to prepare immobilized enzymes in fibers and electrospun fibers will also be discussed.
Insulin Is a Mitogen for Isolated Epiphyseal Growth Plate Chondrocytes from the Fetal Lamb* (1990)

Insulin acts directly as a mitogen on isolated embryonic tissues but has been shown to be inactive at physiological concentrations on several fetal cell types. Since insulin availability is obligatory for optimal fetal growth, we have investigated its mitogenic actions on chondrocytes isolated from the epiphyseal growth plates of fetal lambs. Chondrocytes were isolated from the proximal tibial growth plate of lamb fetuses between 40 and 130 days gestation using collagenase and were cultured in monolayer before use between passages 2 and 6. The synthesis of DNA was assessed from the incorporation of [3H]thymidine after incubation in medium supplemented with glucose (0.7 mM-25 mM) with or without insulin (0.08 nM-167 nM). Increase in cell number was assessed after incubation with test medium for up to 8 days. Insulin substantially increased both DNA synthesis, and cell number, compared to control incubations with a biphasic dose response; an initial 3- to 5-fold increase in DNA synthesis occurring at approximately 1 nM insulin with a second response seen at approximately 50 nM. Within the physiological range of concentrations insulin was only 50% as active as insulin-like growth factor I (IGF I), but was 15 times more active than IGF II. Similar effects of insulin were observed throughout the fetal age range, although the DNA synthetic rate in basal medium declined with both fetal age and cell passage number. The mitogenic actions of insulin were glucose-dependent and were maximal in the presence of 2.7 mM glucose. Insulin did not cause any change in chondrocyte cell cycle duration. Chondrocytes released immunoreactive IGF II but no detectable IGF I. While exposure to insulin concentrations of approximately 50 nM or greater resulted in a statistically significant increase in IGF II release from chondrocytes, no change in IGF II release was seen in response to physiological insulin concentrations. However, exposure of cells to a blocking monoclonal antibody against human IGF I, McAb SM 1.2, which also negates the mitogenic actions of IGF II, consistently reduced insulin-stimulated DNA synthesis suggesting that IGF II presence may be necessary for optimal insulin action. Combination experiments using maximal concentrations of IGF I (13.3 nM) and increasing amounts of insulin (0.16 nM-1.67 nM) showed additive effects on DNA synthesis, suggesting that each hormone was acting through distinct receptor populations. We conclude that insulin, at physiological concentrations, may exert direct growth-promoting actions at the epiphyseal growth plates of the fetal lamb throughout gestation.
Lentiviral vector for hemophilia gene therapy (2004)

be relevant in patients with SLE.These include the known proapoptotic (antiendothelial cell antibodies, anti-dsDNA antibodies, lupus anticoagulant, inflammatory mediators, neutrophil proteases) and antiapoptotic (glucocorticoids, cyclosporine A) agents. 1,5 One approach could involve exposure of endothelial cells in vitro to serum from patients with SLE, neutralization of known proapoptotic factors to gain an impression of their relative importance in SLE, and testing of available antiapoptotic stimuli as agents that may be useful for subsequent clinical trials.This may permit a rational advance toward therapies that will improve the prognosis in patients with SLE.