gebhart/patrepeval huggingface dataset:
The CArG boxes in the promoter of the Arabidopsis floral organ identity gene APETALA3 mediate diverse regulatory effects (1998)

APETALA3 is a MADS box gene required for normal development of the petals and stamens in the Arabidopsis flower. Studies in yeast, mammals and plants demonstrate that MADS domain transcription factors bind with high affinity to a consensus sequence called the CArG box. The APETALA3 promoter contains three close matches to the consensus CArG box sequence. To gain insights into the APETALA3 regulatory circuitry, we have analyzed the APETALA3 promoter using AP3::uidA(GUS) fusions. 496 base pairs of APETALA3 promoter sequence 5' to the transcriptional start directs GUS activity in the same temporal and spatial expression pattern as the APETALA3 RNA and protein in wild-type flowers. A synthetic promoter consisting of three tandem repeats of a 143 base pair sequence directs reporter gene activity exclusively to petals and stamens in the flower. We have analyzed the role of the CArG boxes by site-specific mutagenesis and find that the three CArG boxes mediate discrete regulatory effects. Mutations in CArG1 result in a decrease in reporter expression suggesting that CArG1 is the binding site for a positively acting factor or factors. Mutations in CArG2 result in a decrease in reporter expression in petals, but the expression pattern in stamens is unchanged. By contrast, mutations in CArG3 result in an increase in the level of reporter gene activity during early floral stages suggesting that CArG3 is the binding site for a negatively acting factor.
Overcoming the “Oxidant Problem”: Strategies to Use O2 as the Oxidant in Organometallic C–H Oxidation Reactions Catalyzed by Pd (and Cu) (2012)

Oxidation reactions are key transformations in organic chemistry because they can increase chemical complexity and incorporate heteroatom substituents into carbon-based molecules. This principle is manifested in the conversion of petrochemical feedstocks into commodity chemicals and in the synthesis of fine chemicals, pharmaceuticals, and other complex organic molecules. The utility and function of these molecules correlate directly with the presence and specific placement of oxygen and nitrogen heteroatoms and other functional groups within the molecules. Methods for selective oxidation of C-H bonds have expanded significantly over the past decade, and their role in the synthesis of organic chemicals will continue to increase. Our group's contributions to this field are linked to our broader interest in the development and mechanistic understanding of aerobic oxidation reactions. Molecular oxygen (O(2)) is the ideal oxidant. Its low cost and lack of toxic byproducts make it a highly appealing reagent that can address key "green chemistry" priorities in industry. With strong economic and environmental incentives to use O(2), the commmodity chemicals industry often uses aerobic oxidation reactions. In contrast, O(2) is seldom used to prepare more-complex smaller-volume chemicals, a limitation that reflects, in part, the limited synthetic scope and utility of existing aerobic reactions. Pd-catalyzed reactions represent some of the most versatile methods for selective C-H oxidation, but they often require stoichiometric transition-metal or organic oxidants, such as Cu(II), Ag(I), or benzoquinone. This Account describes recent strategies that we have identified to use O(2) as the oxidant in these reactions. In Pd-catalyzed C-H oxidation reactions that form carbon-heteroatom bonds, the stoichiometric oxidant is often needed to promote difficult reductive elimination steps in the catalytic mechanism. To address this challenge, we have identified new ancillary ligands for Pd that promote reductive elimination, or replaced Pd with a Cu catalyst that undergoes facile reductive elimination from a Cu(III) intermediate. Both strategies have enabled O(2) to be used as the sole stoichiometric oxidant in the catalytic reactions. C-H oxidation reactions that form the product via β-hydride or C-C reductive elimination steps tend to be more amenable to the use of O(2). The use of new ancillary ligands has also overcome some of the limitations in these methods. Mechanistic studies are providing insights into some (but not yet all) of these advances in catalytic reactivity.
Formation of large coronary arteries by cardiac progenitor cells (2008)

Coronary artery disease is the most common cause of cardiac failure in the Western world, and to date there is no alternative to bypass surgery for severe coronary atherosclerosis. We report that c-kit-positive cardiac progenitor cells (CPCs) activated with insulin-like growth factor 1 and hepatocyte growth factor before their injection in proximity of the site of occlusion of the left coronary artery in rats, engrafted within the host myocardium forming temporary niches. Subsequently, CPCs divided and differentiated into endothelial cells and smooth muscle cells and, to a lesser extent, into cardiomyocytes. The acquisition of vascular lineages appeared to be mediated by the up-regulation of hypoxia-inducible factor 1alpha, which promoted the synthesis and secretion of stromal-derived factor 1 from hypoxic coronary vessels. Stromal-derived factor 1 was critical in the conversion of CPCs to the vascular fate. CPCs formed conductive and intermediate-sized coronary arteries together with resistance arterioles and capillaries. The new vessels were connected with the primary coronary circulation, and this increase in vascularization more than doubled myocardial blood flow in the infarcted myocardium. This beneficial effect, together with myocardial regeneration attenuated postinfarction dilated myopathy, reduced infarct size and improved function. In conclusion, locally delivered activated CPCs generate de novo coronary vasculature and may be implemented clinically for restoration of blood supply to the ischemic myocardium.
FIELD EVALUATION OF FENITROTHION FOR POST-ATTACK CONTROL OF THE SOUTHERN PINE BEETLE1 (1986)

One and 2% fenitrothion caused high mortality of southern pine beetles, Dendroctonus frontalis Zimmermann within billets removed from infested trees which had been sprayed. Mortality of beetles through 72 hours post-emergence was significantly higher than mortality of those which emerged from billets from lindane-treated trees. Although lindane is superior to fenitrothion for prevention of SPB attack, fenitrothion was more effective for remedial control.
Pattern matching and associative artificial neural networks for water distribution system time series data analysis (2013)

Water distribution systems, and other infrastructures, are increasingly being pervaded by sensing technologies, collecting a growing volume of data aimed at supporting operational and investment decisions. These sensors monitor system characteristics, i.e. flows, pressures and water quality, such as in pipes. This paper presents the application of pattern matching techniques and binary associative neural networks for novelty detection in such data. A protocol for applying pattern matching to automatically recognise specific waveforms in time series based on their shapes is described together with a system called Advanced Uncertain Reasoning Architecture (AURA) Alert for autonomous determination of novelty. AURA is a class of binary neural network that has a number of advantages over standard artificial neural network techniques for condition monitoring including a sound theoretical basis to determine the bounds of the system operation. Results from application to several case studies are provided including both hydraulic and water quality data. In the case of pattern matching, the results demonstrated some transferability of burst patterns across District Metered Areas; however limitations in performance and difficulties with assembling pattern libraries were found. Results for the AURA system demonstrate the potential for robust event detection across multiple parameters providing valuable information for diagnosis; one example also demonstrates the potential for detection of precursor information, vital for proactive management.
A new superfamily of putative NTP‐binding domains encoded by genomes of small DNA and RNA viruses (1990)

Statistically significant similarity was revealed between amino acid sequences of NTP-binding pattern-containing domains which are among the most conserved protein segments in dissimilar groups of ss and dsDNA viruses (papova-, parvo-, geminiviruses and P4 bacteriophage), and RNA viruses (picorna-, como- and nepoviruses) with small genomes. Within the aligned domains of 100-120 amino acid residues, three highly conserved sequence segments have been identified, i.e. 'A' and 'B' motifs of the NTP-binding pattern, and a third, C-terminal motif 'C', not described previously. The sequence of the 'B' motif in the proteins of the new superfamily is unusually variable, with substitutions, in some of the members, of the Asp residue conserved in other NTP-binding proteins. The 'C' motif is characterized by an invariant Asn residue preceded by a stretch of hydrophobic residues. As the new superfamily included a well studied DNA and RNA helicase, T antigen of SV40, helicase function could be tentatively assigned also to the other related viral putative NTP-binding proteins. On the other hand, the possibility of different and/or multiple functions for some of these proteins is discussed.
Binding and regulation of cellular functions by monoclonal antibodies against human tumor necrosis factor receptors. (1990)

The present study was undertaken to further characterize the interaction of monoclonal antibodies (mAbs) against tumor necrosis factor (TNF) receptors with different targets, and to assess their ability to influence TNF effects on U937 and human endothelial cell (HEC) functions. Actions of recombinant TNF-alpha on U937 and HEC were effectively inhibited by Htr-5 and Utr-1, and to a greater extent by a combination of both mAbs. These observations indicate that TNF interaction with antigenically different components of membrane receptors (p55 and p75) represents a crucial step in transduction of signals for TNF toxicity against U937 and TNF activation of HEC functions.
Three-Dimensional BioAssembly Tool for Generating Viable Tissue-Engineered Constructs (2004)

The primary emphasis of tissue engineering is the design and fabrication of constructs for the replacement of nonfunctional tissue. Because tissue represents a highly organized interplay of cells and extracellular matrix, the fabrication of replacement tissue should mimic this spatial organization. This report details studies evaluating the use of a three-dimensional, direct-write cell deposition system to construct spatially organized viable structures. A direct-write bioassembly system was designed and fabricated to permit layer-by-layer placement of cells and extracellular matrix on a variety of material substrates. Human fibroblasts suspended in polyoxyethylene/polyoxypropylene were coextruded through a positive displacement pen delivery onto a polystyrene slide. After deposition, approximately 60% of the fibroblasts remained viable. Bovine aortic endothelial cells (BAECs) suspended in soluble collagen type I were coextruded via microdispense pen delivery onto the hydrophilic side of flat sheets of polyethylene terephthalate. After deposition with a 25-gauge tip, approximately 86% of the BAECs were viable. When maintained in culture for up to 35 days, the constructs remained viable and maintained their original spatial organization. These results indicate the potential for utilizing a direct-write, three-dimensional bioassembly tool to create viable, patterned tissue-engineered constructs.
Utilizing the C-terminal cleavage activity of a protein splicing element to purify recombinant proteins in a single chromatographic step (1998)

A conventional affinity protein purification system often requires a separate protease to separate the target protein from the affinity tag. This paper describes a unique protein purification system in which the target protein is fused to the C-terminus of a modified protein splicing element (intein). A small affinity tag is inserted in a loop region of the endonuclease domain of the intein to allow affinity purification. Specific mutations at the C-terminal splice junction of the intein allow controllable C-terminal peptide bond cleavage. The cleavage is triggered by addition of thiols such as dithiothreitol or free cysteine, resulting in elution of the target protein while the affinity-tagged intein remains immobilized on the affinity column. This system eliminates the need for a separate protease and allows purification of a target protein without the N-terminal methionine. We have constructed general cloning vectors and demonstrated single-column purification of several proteins. In addition, we discuss several factors that may affect the C-terminal peptide bond cleavage activity.
Repression of a malignant cell-substratum adhesion phenotype by inhibiting the production of the anti-adhesive proteoglycan, PG-M/versican (1994)

Malignantly transformed cells usually display a rosette-like morphology of substratum adhesions (called podosomes) and disorganized microfilaments, and are often associated with elevated production of chondroitin sulphate. We previously showed that many tissues and cells express alternatively spliced multiforms of the large chondroitin sulphate proteoglycan termed PG-M (versican is one of the short transcripts). Since PG-M/versican inhibits many types of cell-substratum adhesion and is found to be excluded from focal contacts of cultured fibroblasts, it is likely that this proteoglycan is generally involved in regulating cell-substratum adhesion. We report here that PG-M/versican is selectively excluded from podosomes of human osteosarcoma cells and that specific inhibition of its biosynthesis by an antisense method suppresses such a malignant cell-adhesive phenotype. The results support the idea that PG-M/versican acts as an anti-adhesive molecule and raise the possibility that PG-M/versican controls one type of cancer cell behaviour.
Calcitonin Gene-Related Peptide-Mediated Depressor Effect and Inhibiting Vascular Hypertrophy of Rutaecarpine in Renovascular Hypertensive Rats (2007)

Calcitonin gene-related peptide (CGRP), the predominant neurotransmitter in capsaicin-sensitive sensory nerves, is a potent vasodilator and inhibits proliferation of vascular smooth muscle cells. Previous investigations have demonstrated that the hypotensive effect of rutaecarpine (Rut) is associated to stimulation of CGRP synthesis and release via activation of the vanilloid receptor subtype 1 (VR1) in the phenol-induced hypertensive rat. This study tested whether the depressor effect and inhibiting vascular hypertrophy of Rut is mediated by endogenous CGRP in 2-kidney, 1-clip (2K1C) hypertensive rats. Systolic blood pressure (SBP) was measured by tail-cuff method in conscious. Mesenteric arteries were isolated for examination of morphological changes. The concentration of CGRP in the plasma and the expression of CGRP mRNA in dorsal root ganglia (DRG) were measured. Chronic administration of Rut (10, 20, or 40 mg/kg/day, respectively) for 4 weeks caused a depressor effect and significantly regressed the lumen diameter and decreased the medium thickness of mesenteric arteries in hypertensive rats concomitantly with an increase in the plasma concentration of CGRP and the expression of CGRP mRNA in DRG. In conclusion, chronic administration of Rut can reduce blood pressure and relieve mesenteric artery hypertrophy in the 2K1C hypertensive rats, and the effects of Rut may be related to stimulation of CGRP synthesis and release.
The Photoassimilation of Organic Compounds by Autotrophic Blue-green Algae (1967)

SUMMARY Four obligately photoautotrophic blue-green algae were shown to assimilate acetate. This reaction was light dependent and was greatly decreased in the absence of carbon dioxide. Acetate was incorporated mainly into the ethanol extractable (lipid) fraction of the organisms and into the protein fraction. Only four amino acids (glutamate, proline, arginine, leucine) were significantly radioactive as a result of the incorporation of (1-) or (2-)14C-acetate. Partial degradations of amino acids derived from specifically labelled acetate and enzyme assays on crude cell-free extracts of Anacystis nidulans support the operation of established pathways for the biosynthesis of these amino acids. Growth of blue-green algae was not significantly affected by the presence of moderate concentrations of the sodium salts of the lower fatty acids, with the exception of propionate, low concentrations of which inhibited growth.
Structures of APRIL-Receptor Complexes (2004)

TACI is a member of the tumor necrosis factor receptor superfamily and serves as a key regulator of B cell function. TACI binds two ligands, APRIL and BAFF, with high affinity and contains two cysteine-rich domains (CRDs) in its extracellular region; in contrast, BCMA and BR3, the other known high affinity receptors for APRIL and BAFF, respectively, contain only a single or partial CRD. However, another form of TACI exists wherein the N-terminal CRD is removed by alternative splicing. We find that this shorter form is capable of ligand-induced cell signaling and that the second CRD alone (TACI_d2) contains full affinity for both ligands. Furthermore, we report the solution structure and alanine-scanning mutagenesis of TACI_d2 along with co-crystal structures of APRIL.TACI_d2 and APRIL.BCMA complexes that together reveal the mechanism by which TACI engages high affinity ligand binding through a single CRD, and we highlight sources of ligand-receptor specificity within the APRIL/BAFF system.
Protein Kinase C δ Inhibits the Proliferation of Vascular Smooth Muscle Cells by Suppressing G1 Cyclin Expression (1997)

To elucidate the physiological role of protein kinase C (PKC) delta, a ubiquitously expressed isoform in vascular smooth muscle cells (VSMC), PKC delta was stably overexpressed in A7r5 cells, rat clonal VSMC. The [3H]thymidine incorporation in A7r5 overexpressed with PKC delta (DVs) was suppressed to 37.1 +/- 16.3% (mean +/- S.D.) of the level in control or A7r5 transfected with vector alone (EVs). The reduction of [3H]thymidine incorporation was strongly correlated with overexpressed PKC levels. Moreover, transient transfection of a dominant negative mutant of PKC delta restored the reduced proliferation in DVs. Flow cytometry analysis demonstrated that DVs were arrested in the G0/G1 phase of the cell cycle. Expression of cyclins D1 and E and retinoblastoma protein phosphorylation were reduced, while the protein levels of p27 were elevated in DVs as compared with EVs. There were no significant differences in the expression of c-fos, c-jun, c-myc, cyclin D2, D3, cyclin-dependent kinase 2, cyclin-dependent kinase 4, and p21 among the clones. We conclude that PKC delta inhibits the proliferation of VSMC by arresting cells in G1 via mainly inhibiting the expression of cyclin D1 and cyclin E.
Spin-Transfer Torque Memories: Devices, Circuits, and Systems (2016)

Spin-transfer torque magnetic memory (STT-MRAM) has gained significant research interest due to its nonvolatility and zero standby leakage, near unlimited endurance, excellent integration density, acceptable read and write performance, and compatibility with CMOS process technology. However, several obstacles need to be overcome for STT-MRAM to become the universal memory technology. This paper first reviews the fundamentals of STT-MRAM and discusses key experimental breakthroughs. The state of the art in STT-MRAM is then discussed, beginning with the device design concepts and challenges. The corresponding bit-cell design solutions are also presented, followed by the STT-MRAM cache architectures suitable for on-chip applications.
Anatomic Study of Innervation of the Anterior Hip Capsule (2017)

Branches of the FNs and ONs consistently provided innervation to the anterior hip capsule. The AON also contributed innervation in many specimens. The relationship of the articular branches from these 3 nerves to the inferomedial acetabulum and the space between the anterior inferior iliac spine and iliopubic eminence may suggest potential sites for radiofrequency ablation.
Enzymatic Profiling System in a Small-Molecule Microarray (2003)

[reaction: see text] We have developed a microarray-based strategy for detection of three major classes of hydrolytic enzymes on the basis of their catalytic activities. This enables the sensitive detection of proteins not merely by their bindings but rather by their enzymatic activities. This may provide a valuable tool for screening, identification, and characterization of new enzymes in a high-throughput fashion.
A myelin proteolipid protein-LacZ fusion protein is developmentally regulated and targeted to the myelin membrane in transgenic mice. (1993)

Transgenic mice were generated with a fusion gene carrying a portion of the murine myelin proteolipid protein (PLP) gene, including the first intron, fused to the E. coli LacZ gene. Three transgenic lines were derived and all lines expressed the transgene in central nervous system white matter as measured by a histochemical assay for the detection of beta-galactosidase activity. PLP-LacZ transgene expression was regulated in both a spatial and temporal manner, consistent with endogenous PLP expression. Moreover, the transgene was expressed specifically in oligodendrocytes from primary mixed glial cultures prepared from transgenic mouse brains and appeared to be developmentally regulated in vitro as well. Transgene expression occurred in embryos, presumably in pre- or nonmyelinating cells, rather extensively throughout the peripheral nervous system and within very discrete regions of the central nervous system. Surprisingly, beta-galactosidase activity was localized predominantly in the myelin in these transgenic animals, suggesting that the NH2-terminal 13 amino acids of PLP, which were present in the PLP-LacZ gene product, were sufficient to target the protein to the myelin membrane. Thus, the first half of the PLP gene contains sequences sufficient to direct both spatial and temporal gene regulation and to encode amino acids important in targeting the protein to the myelin membrane.
An endotoxin-induced serum factor that causes necrosis of tumors. (1975)

In studying "hemorrhagic necrosis" of tumors produced by endotoxin, it was found that the serum of bacillus Calmette--Guerin (BCG)-infected mice treated with endotoxin contains a substance (tumor necrosis factor; TNF) which mimics the tumor necrotic action of endotoxin itself. TNF-positive serum is as effective as endotoxin itself in causing necrosis of the sarcoma Meth A and other transplanted tumors. A variety of tests indicate that TNF is not residual endotoxin, but a factor released from host cells, probably macrophages, by endotoxin. Corynebacteria and Zymosan, which like BCG induce hyperplasia of the reticulo-endothelial system, can substitute for BCG in priming mice for release of TNF by endotoxin. TNF is toxic in vitro for two neoplastic cell lines; it is not toxic for mouse embryo cultures. We propose that TNF mediates endotoxin-induced tumor necrosis, and that it may be responsible for the suppression of transformed cells by activated macrophages.
Hormone receptor status, tumor characteristics, and prognosis: a prospective cohort of breast cancer patients (2007)

Compared to women with ER+/PR+ tumors, women with ER+/PR-, ER-/PR+, or ER-/PR- tumors experienced higher risks of mortality, which were largely independent of the various demographic and clinical tumor characteristics assessed in this study. The higher relative mortality risks identified among ER-/PR- patients with small or low-grade tumors raise the question of whether there may be a beneficial role for adjuvant chemotherapy in this population.