gebhart/patrepeval huggingface dataset:
Transforming growth factors from neoplastic and nonneoplastic tissues. (1983)

Transforming growth factors (TGFs) are a heterogeneous family of polypeptides that induce anchorage-independent growth in nonneoplastic anchorage-dependent cells. They have been found in many tissues, both neoplastic and nonneoplastic. All TGFs isolated thus far are of low molecular weight (6000-25,000), are acid and heat stable, and are inactivated by reagents that reduce disulfide bonds. TGFs have been classified as type alpha or type beta based on their interactions with the receptor for epidermal growth factor (EGF) and their requirement for EGF (or an EGF-like polypeptide) for functional activity. TGF-alpha and TGF-beta act synergistically. TGF-alpha induces phosphorylation of tyrosine in the EGF receptor. TGF-beta, isolated from bovine sources, accelerates experimental wound healing in rats.
Using miRNA expression data for the study of human cancer (2008)

Aim Mature microRNAs (miRNAs) belong to a very large group of small non-coding RNAs that regulate gene expression. miRNAs are differentially expressed in human cancers, such as colorectal neoplasia, pediatric Burkitt lymphoma, lung cancer, large cell lymphoma, glioblastoma and B-cell lymphomas. We systematically employed a microarray platform containing probes for mature miRNA as well as precursor molecules, to investigate the miRNA profiles in hematological and solid cancers.Methods. We dealt with miRNAs profiling in a large number of human tissues and tumors to identify specific signature of miRNAs. The microarrays results were verified with the TaqMan Array Human MicroRNA Panel v1.0 (Early Access) in conjunction with Multiplex RT. To efficiently mine data from thousands of miRNA experiments we developed a specialized bioinformatic system.Results. We characterized novel miRNAs and determined the changes which underline tumorigenesis from normal precursors to cancer and from primary to metastatic tumors. We designed and built the AdmiR MySQL database and a JAVA interface for the management and analysis of miRNome in human tissues. The more than 8 000 miRNA chips stored and annotated in the system allow us to investigate the association of miRNA with prognosis and survival across different types of tumors and patients' groups.Conclusion. The expression data in AdmiR indicate that miRNAs are involved in cancer pathogenesis and support their function as either dominant or recessive cancer genes.
Preparation of novel CO2 "molecular basket" of polymer modified MCM-41 (2002)

Introduction Fossil fuels will remain the mainstay of energy production well into the 21st century. The availability of these fuels to provide clean, affordable energy is essential for prosperity and security in the world. However, an increase in the concentration of CO2 in the atmosphere due to carbon emissions is expected to occur unless energy systems incorporate carbon emission reduction concepts. Carbon sequestration, along with reduced carbon content of fuels and improved efficiency of energy production and use are considered to be viable ways to stabilize and ultimately reduce the concentration of this greenhouse gas. For carbon sequestration, the costs of separation and capture are generally estimated to make up about three quarters of the total costs of ocean or geologic sequestration. Novel technologies to decrease the cost of CO2 separation have great social and commercial value. Adsorption is one of the promising methods that could be applicable for separating CO2 from gas mixtures. Generally, molecular sieves and activated carbons yield relatively high adsorption capacity. However, these adsorption capacities rapidly decline with incremental increase in temperature and separation factors are low. For practical use, many of the separations require operation at relatively high temperature, e.g., ~150 C for flue gas. Developing an adsorbent with high CO2 selectivity and high CO2 adsorption capacity, which can also be operated at relatively high temperature, is critical for the success of this method. Recently, we developed a new kind of high-capacity, highly selective CO2 adsorbent, which is a CO2 “molecular basket”. By loading the sterically branched polymer polyethylenimine (PEI), which has branched chains with numerous CO2-capturing sites such as amino groups, into the large pore volume of MCM-41, its adsorption capacity was significantly increased. In this paper, the preparation approaches to further improve the CO2 adsorption performance of the novel “molecular basket” are reported. The synergetic effect of the MCM-41 on the adsorption of CO2 by the PEI is discussed.
Generation of chemiluminescence in experimental autoimmune uveitis (1991)

Using experimental model of uveitis, the inflammation-associated chemiluminescence was measured by luminol amplification method. The induction of uveitis in Lewis rats was carried out by immunizing bovine S-antigen in complete Freund's adjuvant on hind foot-pad. The chemiluminescence activity from six sets of retina and choroid measured at the peak of inflammation was found to be in the range of 300,000-400,000 counts, amounting to nearly 20-fold increase from non-immunizated control animals under the same conditions. The phagocyte-derived superoxide anion and hydroxyl radical appear to be the two major radicals in the chemiluminescent species. This was revealed by in vitro suppression of chemiluminescence by 5,400 units of superoxide dismutase and 10 mM of D-mannitol. The decreases in counts were 21% and 35% for superoxide dismutase and D-mannitol respectively. The presence of hydrogen peroxide was not established since catalase with dose up to 20,000 units did not cause any significant suppression in counts. In the time sequence studies covering the entire course of uveitis development, the level of chemiluminescent species at day 9 postimmunization increased to 1.5-fold that of day 0, continued to increase to a maximum of 18-fold on day 12 and decreased slowly to about 3-fold in day 19. The pattern of increase appears to coincide with our previous findings in the number of polymorphonuclear leukocytes, the extent of membrane lipid peroxidation and the degree of retinal degeneration. Thus, these radicals play an important role in initiation as well as perpetuation of the membrane oxidative processes that lead to retinal degeneration.
BiP/GRP78 Is an Intracellular Target for MDA-7/IL-24 Induction of Cancer-Specific Apoptosis (2006)

Melanoma differentiation-associated gene-7/interleukin-24 (mda-7/IL-24) is a unique member of the IL-10 gene family that induces cancer-selective growth suppression and apoptosis in a wide spectrum of human cancers in cell culture and animal models. Additionally, recent clinical trials confirm safety and document significant clinical activity of mda-7/IL-24 in patients with diverse solid cancers and melanomas. Despite intensive study the molecular basis of tumor-cell selectivity of mda-7/IL-24 is not well characterized. Using deletion analysis, a specific mutant of MDA-7/IL-24, M4, consisting of amino acids 104 to 206, is described that retains the cancer-specific growth-suppressive and apoptosis-inducing properties of the full-length protein. Employing rationally designed mutational analysis, we show that MDA-7/IL-24 and M4 physically interact with BiP/GRP78 through their C and F helices, localize in the endoplasmic reticulum, and activate p38 MAPK and GADD gene expression, culminating in cancer-selective apoptosis. These studies provide novel mechanistic insights into the discriminating antitumor activity of MDA-7/IL-24 by elucidating BiP/GRP78 as a defined intracellular target of action and present an unparalleled opportunity to develop improved therapeutic versions of this cancer-specific apoptosis-inducing cytokine.
Discovery of Novel Quinoline-Based Estrogen Receptor Ligands Using Peptide Interaction Profiling (2004)

Traditional approaches to discovery of selective estrogen receptor modulators (SERMs) have relied on ER binding and cell-based estrogen response element-driven assays to identify compounds that are osteoprotective but nonproliferative in breast and uterine tissues. To discover new classes of potential SERMs, we have employed a cell-free microsphere-based binding assay to rapidly characterize ERalpha interactions with conformation-sensing cofactor or phage display peptides. Peptide profiles of constrained triarenes were compared to known proliferative and nonproliferative ER ligands to discover potent quinoline-based ligands with minimal Ishikawa cell stimulation.
Stable nuclear transformation of Gonium pectorale (2009)

Flanking sequences that include promoters from C. reinhardtii and from V. carteri work in G. pectorale and allow the functional expression of heterologous genes, such as the selectable marker gene aphVIII of S. rimosus or the co-transformed, codon-optimized G. princeps luciferase gene, which turned out to be a suitable reporter gene in Gonium. The availability of a method for transformation of Gonium makes genetic engineering of this species possible and allows for detailed studies in molecular evolution using the unicellular Chlamydomonas, the 16-celled Gonium, and the multicellular Volvox.
Picrylamino‐substituted heterocycles. V. pyridines (1972)

Abstract The condensation of various aminopyridines with picryl chloride and picryl fluoride has been investigated as part of our continuing effort in the field of picrylamino‐substituted heterocycles. In addition to the expected picrylamino derivatives we obtained the 1‐picryl derivatives of the imino forms of some of the amines.
CLASS: constrained transcript assembly of RNA-seq reads (2013)

CLASS is available from http://sourceforge.net/projects/splicebox.
Measuring diachronic language distance using perplexity: Application to English, Portuguese, and Spanish (2019)

Abstract The objective of this work is to set a corpus-driven methodology to quantify automatically diachronic language distance between chronological periods of several languages. We apply a perplexity-based measure to written text representing different historical periods of three languages: European English, European Portuguese, and European Spanish. For this purpose, we have built historical corpora for each period, which have been compiled from different open corpus sources containing texts as close as possible to its original spelling. The results of our experiments show that a diachronic language distance based on perplexity detects the linguistic evolution that had already been explained by the historians of the three languages. It is remarkable to underline that it is an unsupervised multilingual method which only needs a raw corpora organized by periods.
Recombination and deletion of sequences in shuttle vector plasmids in mammalian cells. (1985)

Shuttle vector plasmids were constructed with directly repeated sequences flanking a marker gene. African green monkey kidney (AGMK) cells were infected with the constructions, and after a period of replication, the progeny plasmids were recovered and introduced into bacteria. Those colonies with plasmids that had lost the marker gene were identified, and the individual plasmids were purified and characterized by restriction enzyme digestion. Recombination between the repeated elements generated a plasmid with a precise deletion and a characteristic restriction pattern, which distinguished the recombined molecules from those with other defects in the marker gene. Recombination among the following different sequences was measured in this assay: (i) the simian virus 40 origin and enhancer region, (ii) the AGMK Alu sequence, and (iii) a sequence from plasmid pBR322. Similar frequencies of recombination among these sequences were found. Recombination occurred more frequently in Cos1 cells than in CV1 cells. In these experiments, the plasmid population with defective marker genes consisted of the recombined molecules and of the spontaneous deletion-insertion mutants described earlier. The frequency of the latter class was unaffected by the presence of the option for recombination represented by the direct repeats. Both recombination and deletion-insertion mutagenesis were stimulated by double-strand cleavage between the repeated sequences and adjacent to the marker, and the frequency of the deletion-insertion mutants in this experiment was again independent of the presence of the direct repeats. We concluded that although recombination and deletion-insertion mutagenesis were both stimulated by double-strand cleavage, the molecules which underwent the two types of change were drawn from separate pools.
GaN-Based High Power Blue-Violet Laser Diodes (2001)

The epitaxial lateral overgrowth (ELO) technique is an important technology for improving the characteristics of GaN-based laser diodes (LDs). The photoluminescence intensities from GaN and GaInN multiple quantum well active layers in the ELO-GaN wing region were found to be higher than those in the seed region. This indicates that the density of dislocations in the wing region could be reduced significantly. This is evidenced by dislocation densities of less than 10 6 cm -2 as determined from transmission emission microscopy and etching-pit-density measurements. The cleaved facets of LDs on ELO-GaN and sapphire were observed by atomic forced microscopy. Although the roughness of GaN cleaved facets on sapphire were high ( Ra &gt;10 nm), the roughness in the ELO-GaN wing region was found to be as smooth as that of GaAs cleaved facet ( Ra &lt;1 nm). The characteristics of LDs on ELO-GaN were found to be superior to those on sapphire as a result of smoother facets and lower dislocation densities.
Bulk density logging with high-energy gammas produced by fast neutron reactions with formation oxygen atoms (2002)

Borehole logging for formation density has been an important geophysical measurement for many years in the minerals, geotechnical, oil, and natural gas industries. The conventional gamma-gamma backscatter method has performed well in open, smooth boreholes. However, the method has limited depth of investigation and has not been quantitative in cased holes. A new method of logging earth formations for bulk density uses 14-MeV neutrons to produce high threshold energy reactions with formation nuclei, resulting in emission of high-energy gamma rays. The attenuation of the high-energy gammas as they transport back to the logging tool provides a measure of formation density. Computer modeling indicates the new density logging method penetrates deeply into the formation and can compensate for many interfering borehole and formation effects.
Synthesis and binding properties of conjugates between oligodeoxynucleotides and daunorubicin derivatives (1997)

Conjugation of an anthracycline to a triplex-forming oligonucleotide (TFO) allows delivery of this drug to a specific DNA site, preserving the intercalation geometry of this class of anticancer agents. Conjugate 11, in which the TFO is linked via a hexamethylene bridge to the O-4 on the D ring of the anthraquinone moiety, affords the most stable triple helix, through intercalation of the planar chromophore between DNA bases and binding of both the TFO and the amino sugar to the major and the minor groove respectively.
Mutant p53 tumor suppressor alleles release ras-induced cell cycle growth arrest. (1991)

Overexpression of an activated ras gene in the rat embryo fibroblast line REF52 results in growth arrest at either the G1/S or G2/M boundary of the cell cycle. Both the DNA tumor virus proteins simian virus 40 large T antigen and adenovirus 5 E1a are able to rescue ras induced lethality and cooperate with ras to fully transform REF52 cells. In this report, we present evidence that the wild-type activity of the tumor suppressor gene p53 is involved in the negative growth regulation of this model system. p53 genes encoding either a p53Val-135 or p53Pro-193 mutation express a highly stable p53 protein with a conformation-dependent loss of wild-type activity and the ability to eliminate any endogenous wild-type p53 activity in a dominant negative manner. In cotransfection assays, these mutant p53 genes are able to rescue REF52 cells from ras-induced growth arrest, resulting in established cell lines which express elevated levels of the ras oncoprotein and show morphological transformation. Full transformation, as assayed by tumor formation in nude mice, is found only in the p53Pro-193-plus-ras transfectants. These cells express higher levels of the ras protein than do the p53Val-135-plus-ras-transfected cells. Transfection of REF52 cells with ras alone or a full-length genomic wild-type p53 plus ras results in growth arrest and lethality. Therefore, the selective event for p53 inactivation or loss during tumor progression may be to overcome a cell cycle restriction induced by oncogene overexpression (ras). These results suggest that a normal function of p53 may be to mediate negative growth regulation in response to ras or other proliferative inducing signals.
Biocompatible coatings for luminal and outer surfaces of small‐caliber artificial grafts (1996)

Luminal and outer surfaces and small-caliber vascular grafts at an early implantation period may require completely opposite cellular responses: minimal cellular adhesion and fibrin formation for a luminal surface versus potent cellular adhesion and migration and matrix generation for an outer surface. Differentiated biocompatible design of luminal and outer surfaces into small-caliber artificial grafts may lead to successful healing. We molecularly designed photocurable extracellular matrices (ECMs): photocurable chondroitin sulfate (CS) and hyaluronic acid (HA) for the luminal surface coating and photocurable gelatin for the outer surface coating. All of them were partially derivatized with photodimerizable groups such as thymine, cinnamate, and coumarin groups and converted to produce water-insoluble gels upon ultraviolet irradiation. In vitro study showed that platelet adhesion on photogelled CS and HA was significantly reduced, whereas endothelial cells adhered well on photogelled gelatin. These materials were individually coated and photogelled onto respective surfaces of artificial grafts (inner diameter [ID], 5 mm). During acute-phase implantation into dogs for up to 1 week, minimal cell adhesion was observed on the luminal surface, which was uniformly covered by photogelled CS or HA. Heparin impregnation of photocured ECM reduced fibrin formation. On the other hand, enhanced tissue ingrowth was noted at the outer surface. Although these ECM-coated grafts need further improvement in molecular design and coating techniques, photocurable ECMs may contribute to successful healing and a high patency rate of small-caliber artificial grafts. © 1996 John Wiley & Sons, Inc.
Mesenchymal Stem Cells Can Be Differentiated Into Endothelial Cells In Vitro (2004)

Human bone marrow-derived mesenchymal stem cells (MSCs) have the potential to differentiate into mesenchymal tissues like osteocytes, chondrocytes, and adipocytes in vivo and in vitro. The aim of this study was to investigate the in vitro differentiation of MSCs into cells of the endothelial lineage. MSCs were generated out of mononuclear bone marrow cells from healthy donors separated by density gradient centrifugation. Cells were characterized by flow cytometry using a panel of monoclonal antibodies and were tested for their potential to differentiate along different mesenchymal lineages. Isolated MSCs were positive for the markers CD105, CD73, CD166, CD90, and CD44 and negative for typical hematopoietic and endothelial markers. They were able to differentiate into adipocytes and osteocytes after cultivation in respective media. Differentiation into endothelial-like cells was induced by cultivation of confluent cells in the presence of 2% fetal calf serum and 50 ng/ml vascular endothelial growth factor. Laser scanning cytometry analysis of the confluent cells in situ showed a strong increase of expression of endothelial-specific markers like KDR and FLT-1, and immunofluorescence analysis showed typical expression of the von Willebrand factor. The functional behavior of the differentiated cells was tested with an in vitro angiogenesis test kit where cells formed characteristic capillary-like structures. We could show the differentiation of expanded adult human MSCs into cells with phenotypic and functional features of endothelial cells. These predifferentiated cells provide new options for engineering of artificial tissues based on autologous MSCs and vascularized engineered tissues.
Interstitial pO2 in Ischemic Penumbra and Core are Differentially Affected following Transient Focal Cerebral Ischemia in Rats (2004)

Stroke causes heterogeneous changes in tissue oxygenation, with a region of decreased blood flow, the penumbra, surrounding a severely damaged ischemic core. Treatment of acute ischemic stroke aims to save this penumbra before its irreversible damage by continued ischemia. However, effective treatment remains elusive due to incomplete understanding of processes leading to penumbral death. While oxygenation is central in ischemic neuronal death, it is unclear exactly what actual changes occur in interstitial oxygen tension (pO2) in ischemic regions during stroke, particularly the penumbra. Using the unique capability of in vivo electron paramagnetic resonance (EPR) oximetry to measure localized interstitial pO2, we measured both absolute values, and temporal changes of pO2 in ischemic penumbra and core during ischemia and reperfusion in a rat model. Ischemia rapidly decreased interstitial pO2 to 32% +/- 7.6% and 4% +/- 0.6% of pre-ischemic values in penumbra and core, respectively 1 hour after ischemia. Importantly, whilst reperfusion restored core pO2 close to its pre-ischemic value, penumbral pO2 only partially recovered. Hyperoxic treatment significantly increased penumbral pO2 during ischemia, but not in the core, and also increased penumbral pO2 during reperfusion. These divergent, important changes in pO2 in penumbra and core were explained by combined differences in cellular oxygen consumption rates and microcirculation conditions. We therefore demonstrate that interstitial pO2 in penumbra and core is differentially affected during ischemia and reperfusion, providing new insights to the pathophysiology of stroke. The results support normobaric hyperoxia as a potential early intervention to save penumbral tissue in acute ischemic stroke.
Human Embryonic Stem Cell Protocols (2006)

A comprehensive collection of diverse techniques for the molecular and cellular manipulation of human embryonic stem (hES) cells. These readily reproducible methods have been optimized for the derivat
Misfolding of the Cystic Fibrosis Transmembrane Conductance Regulator and Disease (2008)

Understanding the structural basis for defects in protein function that underlie protein-based genetic diseases is the fundamental requirement for development of therapies. This situation is epitomized by the cystic fibrosis transmembrane conductance regulator (CFTR)-the gene product known to be defective in CF patients-that appears particularly susceptible to misfolding when its biogenesis is hampered by mutations at critical loci. While the primary CF-related defect in CFTR has been localized to deletion of nucleotide binding fold (NBD1) residue Phe508, an increasing number of mutations (now ca. 1,500) are being associated with CF disease of varying severity. Hundreds of these mutations occur in the CFTR transmembrane domain, the site of the protein's chloride channel. This report summarizes our current knowledge on how mutation-dependent misfolding of the CFTR protein is recognized on the cellular level; how specific types of mutations can contribute to the misfolding process; and describes experimental approaches to detecting and elucidating the structural consequences of CF-phenotypic mutations.