gebhart/patrepeval huggingface dataset:
Thyroid hormone regulates the oxytocin gene. (1992)

Endocrine factors involved in the transcriptional regulation of the oxytocin (OT) gene were investigated in heterologous expression systems. Plasmids having a 5'-flanking region of the rat OT gene (-363/+16) or the human OT gene (-382/+41) cloned in front of the firefly luciferase gene were co-transfected with an expression vector for the rat thyroid hormone receptor alpha in P19 embryonal carcinoma (EC) cells. Thyroid hormone (T3) stimulated the activity of the rat and human OT promoters about 10-fold. In MCF-7 breast tumor cells transfected with the human OT promoter-luciferase fusion gene, T3 stimulation through endogenous thyroid hormone receptors was about 5-fold. Co-transfection experiments in P19EC cells using 5' deletion mutants of the rat OT gene showed that thyroid hormone responsiveness was located in two regions, one located between nucleotides -195 and -172, the other between nucleotides -172 and -148. Each region accounted for about 3-fold T3 stimulation. Gel retardation analysis using extracts from HeLa cells over-producing the c-erbA/TR alpha protein showed specific binding to the -172/-148 element, while no binding occurred on the -195/-172 element. The -172/-148 element which contains the imperfect estrogen response element, GGTGACCTTGACC, has inverted as well as direct repeats of the TGACC motif. Mutagenesis of TGACC motifs separately reduced thyroid hormone responsiveness by about 50%. However, simultaneous mutation of two TGACC motifs abolished the responsiveness to T3 completely. There was no cooperativity between the activated thyroid hormone and estrogen receptors in transfected MCF-7 cells nor in thyroid hormone receptor and estrogen receptor co-transfected P19EC cells. Negative interactions between these two receptors were observed and gel retardation assays showed interaction between the two receptors proteins. It was shown in an in vivo experiment that treatment of rats with thyroid hormone increased hypothalamic OT mRNA levels, the pituitary OT content, as well as OT levels in blood. The results reveal thyroid hormone as a physiological regulator of OT gene expression, which stimulates OT promoter activity directly through interaction with a thyroid hormone-response element in the OT gene.
Patulin and Penicillic Acid (1976)

The mycotoxins patulin (4-hydroxy-4H-furo[3,2-c]pyran-2(6H)-one) and penicillic acid (3-methoxy-5-methyl-4-oxo-2,5-hexadienoic acid) are metabolites of several fungi, primarily species of Aspergillus and Penicillium. Their chemical and physical properties and biosynthesis are discussed. Recent work on analytical methods, reports of natural occurrence, and stability in foods and feeds are emphasized. Both patulin and penicillic acid inhibit DNA, RNA, protein synthesis, and some enzymes containing SH groups. The precise mode of toxic action remains uncertain. Since both patulin and penicillic acid are toxic and have been implicated in carcinogenesis and since patulin causes mutations in yeasts, they are potentially dangerous. The biological effects of orally ingested patulin and penicillic acid need further study to assess their potential health hazard.
Immune responses to dsRNA: Implications for gene silencing technologies (2005)

Nucleic acid-induced gene silencing, such as RNA interference (RNAi), induces a multitude of responses in addition to the knockdown of a gene. This is best understood in the context of the antiviral immune response, from which the processes of RNAi are thought to be derived. Viral challenge of a vertebrate host leads to an intricate series of responses that orchestrate antiviral immunity. The success of this multifaceted system in overcoming viral encounters hinges on complex pathogen-host interactions. One aspect of these interactions, the nucleic acid-based immune response, is key to the successful resolution of a viral challenge. In particular, dsRNA, a nucleic acid associated with viral replication, is involved in numerous interactions contributing to induction, activation and regulation of antiviral mechanisms. Specifically, dsRNA is responsible for stimulating important protective responses, such as the activation of dicer-related antiviral pathways, induction of type 1 IFN, and stimulation of dsRNA-activated protein kinase and oligoadenylate synthetase. Furthermore, the modulation and shaping of this overall immune response is facilitated through nucleic acid interactions with pattern recognition receptors such as toll-like receptor 3. These diverse dsRNA-induced antiviral responses have implications for biotechnologies that use dsRNA to harness one arm of the host antiviral machinery for silencing a specific target gene. The interlinked nature of these response elements means that it may be difficult to completely isolate one element from the other arms of the antiviral response program of an organism. Thus, it is beneficial to understand all aspects of the immune response to dsRNA in order to manipulate these systems and minimize unwanted non-specific effects.
Microassay for Glucose-Induced Preproinsulin mRNA Expression to Assess Islet Functional Potency for Islet Transplantation (2010)

The measurement of glucose-induced premature INS mRNA normalized by mature INS mRNA can be used to assess the functional quality of human islets and may predict islet function after transplantation in type 1 diabetic patients.
Pegylated peptides IV (1995)

Conditions have been developed for the site-specific pegylation (NH2-terminus, side-chain and carboxy-terminus) of a potent analog of growth hormone-releasing factor, [Ala15]-hGRF(1-29)-NH2. These pegylated peptides were prepared by solid-phase peptide synthesis using the Fmoc/tBu strategy, and were fully characterized by analytical HPLC, amino-acid analysis, 1H-NMR spectroscopy and laser desorption mass spectrometry. Biological activities of hGRF analogs were determined in vitro utilizing stimulation of growth hormone release by cultured rat pituitary cells as an index. GH-releasing potencies of the pegylated hGRF analogs were compared to a series of model analogs of [Ala15]-hGRF(1-29)-NH2 that were acetylated or protected as the ethylamides at the pegylation sites. It was found that acetylation at the NH2-terminus resulted in reduced potency, which was not further affected when the NH2-terminus was pegylated, regardless of the size of poly(ethyleneglycol) (PEG) employed (e.g. PEG2000 or PEG5000). Pegylation at Asp8 or Lys12 decreased biological potency, a situation which was exacerbated by increasing the molecular weight of PEG. Pegylation at Lys21 or Asp25 did not significantly affect biological activity. The C-terminal model peptide, [Ala15,Orn(Ac)30]-hGRF(1-29)-NH2, was the most potent analog identified in this series (ca. 4-5-fold that of hGRF(1-44)-NH2. The COOH-terminal pegylated analogs retained this increased level of biological activity independent of PEG molecular weight. These studies demonstrate that a biologically active peptide can be pegylated and retain the full in vitro potency of the peptide. However, the biological activity is highly dependent on the site of pegylation and, in some cases, the molecular weight of PEG (degree of pegylation) moiety used.
Neoplastic transformation and tumorigenesis associated with overexpression of phospholipase D isozymes in cultured murine fibroblasts (2001)

Phospholipase D (PLD) has been suggested to play an important role in a variety of cellular functions. PLD activity has been shown to be significantly elevated in many tumours and transformed cells, suggesting the possibility that PLD might be involved in tumorigenesis. In this study, we have established stable cell lines overexpressing PLD1 and PLD2 from fibroblast cells. These cells, but not control cells, showed altered growth properties and anchorage-independent growth in soft agar. Both PLD1 and PLD2 also induced an up-regulation of the activity of matrix metalloprotease-9 as detected by zymograms. Furthermore, both PLD1 and PLD2 transformants, but not vector-transfectants, induced undifferentiated sarcoma when transplanted into nude mice. Both PLD1- and PLD2-mediated cell cycle distributions in stable cell lines revealed an increased fraction of cells in the S phase compared with control cells. Interestingly, the level of cyclin D3 protein, known as an activator of G(1) to S phase transition in the cell cycle, was aberrantly high in cells overexpressing PLD1 and PLD2 compared with control cells. These results suggest that overexpression of PLD isozymes may play an important role in neoplastic transformation.
Anti-angiogenic action of hyperthermia by suppressing gene expression and production of tumour-derived vascular endothelial growth factor in vivo and in vitro (2002)

Vascular endothelial growth factor is an important angiogenic factor for tumour progression because it increases endothelial-cell proliferation and remodels extracellular matrix in blood vessels. We demonstrated that hyperthermia at 42 degrees C, termed heat shock, suppressed the gene expression and production of vascular endothelial growth factor in human fibrosarcoma HT-1080 cells and inhibited its in vitro angiogenic action on human umbilical vein endothelial cells. The gene expression of alternative splicing variants for vascular endothelial growth factor, VEGF121, VEGF165 and VEGF189, was constitutively detected in HT-1080 cells, but the VEGF189 transcript was less abundant than VEGF121 and VEGF165. When HT-1080 cells were treated with heat shock at 42 degrees C for 4 h and then maintained at 37 degrees C for another 24 h, the gene expression of all vascular endothelial growth factor variants was suppressed. In addition, HT-1080 cells were found to produce abundant VEGF165, but much less VEGF121, both of which were inhibited by heat shock. Furthermore, the level of vascular endothelial growth factor in sera from six cancer patients was significantly diminished 2-3 weeks after completion of whole-body hyperthermia at 42 degrees C (49.9+/-36.5 pg x ml(-1), P<0.01) as compared with that prior to the treatment (177.0+/-77.5 pg x ml(-1)). On the other hand, HT-1080 cell-conditioned medium showed vascular endothelial growth factor-dependent cell proliferative activity and the augmentation of pro-matrix metalloproteinase-1 production in human umbilical vein endothelial cells. The augmentation of endothelial-cell proliferation and pro-matrix metalloproteinase-1 production was poor when human umbilical vein endothelial cells were treated with conditioned medium from heat-shocked HT-1080 cells. These results suggest that hyperthermia acts as an anti-angiogenic strategy by suppressing the expression of tumour-derived vascular endothelial growth factor production and thereby inhibiting endothelial-cell proliferation and extracellular matrix remodelling in blood vessels.
Structural Characterization, Optical Properties, and Improved Solubility of Carbon Nanotubes Functionalized with Wilkinson's Catalyst (2002)

Oxidized carbon nanotubes have been reacted with Wilkinson's complex. It has been found that the Rh metal coordinates to these nanotubes through the increased number of oxygen atoms, forming a hexacoordinate structure around the Rh atom. The reaction process increases oxidized nanotube solubility in DMSO (>150 mg/L) as well as to a certain extent in DMF and THF. The functionalization process results in exfoliation of larger bundles of SWNTs and may select for the presence of distributions of smaller-diameter tubes. Optical data on the derivatized adducts suggest the possibility of interesting charge-transfer behavior across the metal-nanotube interface. An application has been made of this system as supports for homogeneous catalysis.
Promoting Critical Thinking, and Information Instruction in a Biochemistry Course. (2007)

The explosive growth of the amount of information requires students to achieve competency in retrieving, managing, analyzing, and using information effectively. To help students function successfully in the information era, librarians need to focus on developing students' critical thinking and transferable learning abilities. This article describes a one-shot instruction session that teaches biochemistry students how to access, search, and evaluate information sources.
Recognizing on-line handwritten Chinese character via FARG matching (2002)

The paper presents a novel method for online handwritten Chinese character recognition. In our method, each category of character is described by a fuzzy attributed relational graph (FARG). A relaxation algorithm is developed to match the input pattern with every FARG. For decision making, a similarity measure is established via statistical technique to calculate the matching degree between the input pattern and referenced FARG, according to which the recognition result is determined. The principle of our method makes it very robust against stroke connection and stroke order variation as well as stroke shape deformation. A database of 22530 samples collected from 6 subjects is used to test our recognition system which can recognize 3755 categories of Chinese characters. The result shows that our method is very effective: a top 1 recognition rate of 98.8% and a top 10 of 99.7% are reached.
Biochemical characterization of Wnt-Frizzled interactions using a soluble, biologically active vertebrate Wnt protein (1999)

Biochemical studies of Wnt signaling have been hampered by difficulties in obtaining large quantities of soluble, biologically active Wnt proteins. In this paper, we report the production in Drosophila S2 cells of biologically active Xenopus Wnt8 (XWnt8). Epitope- or alkaline phosphatase-tagged XWnt8 proteins are secreted by concentrated S2 cells in a form that is suitable for quantitative biochemical experiments with yields of 5 and 0.5 mg per liter, respectively. Conditions also are described for the production in 293 cells of an IgG fusion of the cysteine-rich domain (CRD) of mouse Frizzled 8 with a yield of 20 mg/liter. We demonstrate the use of these proteins for studying the interactions between soluble XWnt8 and various Frizzled proteins, membrane anchored or secreted CRDs, and a set of insertion mutants in the CRD of Drosophila Frizzled 2. In a solid phase binding assay, the affinity of the XWnt8-alkaline phosphatase fusion for the purified mouse Frizzled 8-CRD-IgG fusion is approximately 9 nM.
Myofibrillogenesis visualized in living embryonic cardiomyocytes (1997)

Myofibril formation was visualized in cultured live cardiomyocytes that were transfected with plasmids expressing green fluorescent protein (GFP) linked to the Z-band protein, alpha-actinin. The expression of this fluorescent protein provided an in vivo label for structures containing alpha-actinin. The GFP-alpha-actinin fusion protein was incorporated into Z-bands, intercalated discs, and attachment plaques, as well as into the punctate aggregates, or Z-bodies, that are thought to be the precursors of Z-bands. Observations of live cells over several days in culture permitted us to test aspects of several theories of myofibril assembly that had been proposed previously based on the study of fixed cells. Fine fibrils, called premyofibrils, that formed de novo at the spreading edges of cardiomyocytes, contained punctate concentrations of alpha-actinin, termed Z-bodies. The punctate Z-bodies grew and aligned with Z-bodies in adjacent fibrils. With increasing time, adjacent fibrils and Z-bodies appeared to fuse and form mature myofibrils and Z-bands in cytoplasmic regions where the linear arrays of Z-bodies had been. These new myofibrils became aligned with existing myofibrils at their Z-bands to form myofibrils that spanned the length of the spread cell. These results are consistent with a model that postulates that the fibrils that form de novo near the cell membrane are premyofibrils-i.e., the precursors of mature myofibrils.
Palladium-Catalyzed Oxygenation of Unactivated sp3 C−H Bonds (2004)

This communication describes a new palladium-catalyzed method for the oxygenation of unactivated sp3 C-H bonds. A wide variety of alkane substrates containing readily available oxime and/or pyridine directing groups are oxidized with extremely high levels of chemo-, regio-, and in some cases diastereoselectivity. The substrate scope of these reactions is discussed, and the high selectivities are rationalized on the basis of the requirements of putative palladium alkyl intermediates.
X-ray powder diffraction characterization of the large-volume unit cell of the M8 murataite polytype (2016)

We have used conventional X-ray powder diffraction to study one of the largest volume inorganic mixed oxide unit-supercell structures done so far. This necessitated some small-angle X-ray scattering-like observations at low angles from &lt;2° 2 θ to concord with electron diffraction, which had indicated an 8 × 8 × 8 huge volume supercell of a fluorite-type basic sub-cell. Emphasis is on the detection of, possibly very weak, fingerprint, low-angle/long lines/peaks which will indicate the (often unsuspected) presence of complex polytypic arrangements of simple very strong basic sub-cells and so facilitate future synthetic studies.
Resist-Free Patterning of Surface Architectures in Polymer-Based Microanalytical Devices (2004)

The ability to form patterns of chemically reactive surface functionalities in microanalytical devices using a simple photopatterning approach without the need for photoresist-based methods is described. Direct UV exposure of the surfaces of poly(methyl methacrylate), PMMA, and poly(carbonate), PC, microfluidic devices through optical masks leads to the production of patterns of near monolayer quantities of surface carboxylic acid groups as determined by surface coverage, X-ray photoelectron spectroscopy, and fluorescence microscopy experiments. Formation of the reactive carboxylic acid groups without significant physical (topographical) damage to the polymer device substrates is achieved by use of low UV fluence and exposure times. Modification of the patterned, surface carboxylic acid groups with metals, thermally responsive polymers, and antibodies results in microfluidic devices possessing metallic interconnects and detection electrodes and the ability to capture intact biological cells and proteins from solution.
Research Progress on Health Functions of Red Adzuki Bean (2009)

This paper mainly reviews the research progress on health functions of red adzuki bean in recent years.Red adzuki bean is a kind of popular food in Asian countries and regions,such as China,Japan and Korea.Red adzuki beans contain a variety of bioactive substances including polyphenols,tannins,phytic acid,and saponin etc.Modern research indicates that red adzuki bean has various health functions,including anti-oxidation,anti-diabetic effect,hepatoprotective activity,helping nephropathy recovery,anticancer,antibacterial and antivirus,and so on.
RFLP and physical mapping with an rDNA‐specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4 (1996)

Ribosomal RNA genes are organized in tandem arrays called nucleolus organizer regions (NORs). In a prior study, RFLP mapping on pulsed-field gels placed NOR2 at the northern tip of Arabidopsis thaliana chromosome 2. New polymorphisms have allowed the other NOR, NOR4, to be mapped to the northern tip of chromosome 4. To map NOR-associated loci, rDNA-specific cleavage by I-Ppol, an endonuclease with a 15 nucleotide recognition sequence involved in rDNA-homing of a mobile, self-splicing Group I intron in Physarum was exploited. I-Ppol digestion of A. thaliana genomic DNA liberated two telomere-containing fragments no larger than 13 kbp, and telomere polymorphisms identified using I-Ppol cosegregated with NOR2 and NOR4. Restriction mapping suggested that telomere-proximal rRNA genes are oriented with their 5' ends nearest the chromosome ends and their 3' ends nearest the centromere. This orientation was confirmed using the polymerase chain reaction to clone one of the telomere-rDNA junctions, most likely the junction on chromosome 4. The telomeric repeats join the terminal rRNA gene downstream of its promoter, suggesting that this first gene is inactive. Subtelomeric repetitive DNAs are absent at the telomere-rDNA junction. Localization of NOR2, NOR4 and their associated telomeres, TEL2N and TEL4N, respectively, provides end points for the genetic and physical maps of chromosomes 2 and 4.
Ohmic contact technology in III nitrides using polarization effects of cap layers (2002)

A technology for low-resistance ohmic contacts to III nitrides is presented. The contacts employ polarization-induced electric fields in strained cap layers grown on lattice-mismatched III-nitride buffer layers. With appropriate choice of the cap layer, the electric field in the cap layer reduces the thickness of the tunnel barrier at the metal contact/semiconductor interface. Design rules for polarization-enhanced contacts are presented giving guidance for composition and thickness of the cap layer for different III-nitride buffer layers. Experimental results for ohmic contacts with p-type InGaN and GaN cap layers are markedly different from samples without a polarized cap layer thus confirming the effectiveness of polarization-enhanced ohmic contacts.
RNA aptamers that bind flavin and nicotinamide redox cofactors (1995)

RNA molecules that specifically bind riboflavin (Rb) and beta-nicotinamide mononucleotide (NMN) have been isolated by in vitro selection. A simple structural motif containing intramolecular G-quartets was found to bind tightly to oxidized riboflavin (Kd = 1-5 micromolar). DNA versions of the consensus sequence also bind, but with weaker affinity. DMS protection experiments show that the quartet structure of these aptamers is stabilized by interaction with the flavin. As a measure of their redox specificity, the aptamers do not show significant differential binding between oxidized and reduced forms of a 5-deazariboflavin derivative that is a close structural analog of riboflavin. In contrast to the lack of redox specificity of the riboflavin aptamers, RNAs selected for binding to the nicotinamide portion of NAD discriminate between NAD and NADH in solution by over an order of magnitude. A mutagenized pool based on one of the NMN aptamer sequences was used to reselect for NMN binding. Comparison of the reselected sequences led to the identification of the binding region of the aptamer. A complex secondary structure containing two interacting stem-loops is proposed for the minimal NMN-binding RNA. The same mutagenized pool was used to select for increased discrimination between NMN and NMNH. From these reselected sequences, a mutation within the binding region was identified that increases specificity for NMN. These experiments show that RNA can bind these cofactors with low micromolar affinity and, in the case of nicotinamide cofactors, can discriminate between the two redox states. These cofactor binding motifs may provide a framework for generating new ribozymes that catalyze redox reactions similar to those found in basic metabolic pathways.
Activation of a CrkL-Stat5 Signaling Complex by Type I Interferons (1999)

Type I interferons (IFNalpha and IFNbeta) transduce signals by inducing tyrosine phosphorylation of Jaks and Stats, as well as the CrkL adapter, an SH2/SH3-containing protein which provides a link to downstream pathways that mediate growth inhibition. We report that Stat5 interacts constitutively with the IFN receptor-associated Tyk-2 kinase, and during IFNalpha stimulation its tyrosine-phosphorylated form acts as a docking site for the SH2 domain of CrkL. CrkL and Stat5 then form a complex that translocates to the nucleus. This IFN-inducible CrkL-Stat5 complex binds in vitro to the TTCTAGGAA palindromic element found in the promoters of a subset of IFN-stimulated genes. Thus, during activation of the Type I IFN receptor, CrkL functions as a nuclear adapter protein and, in association with Stat5, regulates gene transcription through DNA binding.