gebhart/patrepeval huggingface dataset:
Overview of Research onBombyx morimicroRNA (2014)

MicroRNAs (miRNAs) constitute some of the most significant regulatory factors involved at the post-transcriptional level after gene expression, contributing to the modulation of a large number of physiological processes such as development, metabolism, and disease occurrence. This review comprehensively and retrospectively explores the literature investigating silkworm, Bombyx mori L. (Lepidoptera: Bombicidae), miRNAs published to date, including discovery, identification, expression profiling analysis, target gene prediction, and the functional analysis of both miRNAs and their targets. It may provide experimental considerations and approaches for future study of miRNAs and benefit elucidation of the mechanisms of miRNAs involved in silkworm developmental processes and intracellular activities of other unknown non-coding RNAs.
Cloning of a cDNA Encoded by a Member of the Arabidopsis thaliana ATP Sulfurylase Multigene Family (1996)

An Arabidopsis thaliana ATP sulfurylase cDNA (ASA1), encoding a putative chloroplastic isoform, has been cloned by functional complementation of a Saccharomyces cerevisiae (met3) ATP sulfurylase mutant which also has a poor sulfate transport capacity. Homologous complementation of the yeast mutant with the ATP sulfurylase gene restores both ATP sulfurylase function and sulfate transport. Heterologous complementation restores only ATP sulfurylase function as demonstrated by low [35S]sulfate influx measurements and selenate resistance. A structural relationship between ATP sulfurylase and sulfate membrane transporters in yeast is proposed. The sequence of ASA1 is homologous to deduced plant and animal ATP sulfurylase sequences. Analyses indicate a potential tyrosine phosphorylation site which is unique to higher eukaryote sequences. ASA1 is specified by a single copy gene that is part of a multigene family in A. thaliana. At least two ASA1 copies are found in Brassica napus plants. ASA1 transcripts were found in all organs examined, with the highest transcript abundance and ATP sulfurylase activity in leaves or cotyledons. Absence of sulfate from culture media transiently increased B. napus transcript abundance, indicating that initially, the response to sulfate deprivation is transcriptionally regulated.
Role of c-MET in Upper Aerodigestive Malignancies From Biology to Novel Therapies (2005)

Overactivation and defective downregulation of receptor tyrosine kinase (RTK) pathways have been implicated in human carcinogenesis. RTKs represent an important class of anticancer novel therapeutic target. Some RTKs are known to be protooncogenes that can mediate signal transduction, alteration of reactive oxygen species (ROS), cellular proliferation, cell motility and migration, apoptosis, and survival. c-MET is a unique RTK that regulates a wide variety of cellular functions. c-MET has been shown to be overexpressed or mutated in a variety of human malignancies. Stimulation of c-MET via its natural ligand hepatocyte growth factor/ scatter factor (HGF/SF) leads to a plethora of biological and biochemical effects in the cell. Activation of c-MET signaling can lead to cell motility and scattering, angiogenesis, proliferation, branching morphogenesis, invasion, and eventual metastasis. This review summarizes the structure and functions of c-MET, with particular emphasis on its role in upper aerodigestive malignancies. The unique biological functions altered by c-MET and its mutations are discussed as well. Finally, c-MET, when mutated or overexpressed in malignant cells, serves as an important therapeutic target, and the most recent data with respect to its inhibition are also summarized in this review.
Differential Complementation of Bcr-Abl Point Mutants with c-Myc (1994)

A complementation strategy was developed to define the signaling pathways activated by the Bcr-Abl tyrosine kinase. Transformation inactive point mutants of Bcr-Abl were tested for complementation with c-Myc. Single point mutations in the Src-homology 2 (SH2) domain, the major tyrosine autophosphorylation site of the kinase domain, and the Grb-2 binding site in the Bcr region impaired the transformation of fibroblasts by Bcr-Abl. Hyperexpression of c-Myc efficiently restored transformation activity only to the Bcr-Abl SH2 mutant. These data support a model in which Bcr-Abl activates at least two independent pathways for transformation. This strategy may be useful for discerning signaling pathways activated by other oncogenes.
Nanostructured Materials for Hydrogen Storage (2010)

This chapter contains sections titled: Introduction Hydrogen Storage by Physisorption Hydrogen Storage by Chemisorption Summary References
The Group I Strain of Streptococcus mutans , UA140, Produces Both the Lantibiotic Mutacin I and a Nonlantibiotic Bacteriocin, Mutacin IV (2001)

Strains of Streptococcus mutans produce at least three mutacins, I, II, and III. Mutacin II is a member of subgroup AII in the lantibiotic family of bacteriocins, and mutacins I and III belong to subgroup AI in the lantibiotic family. In this report, we characterize two mutacins produced by UA140, a group I strain of S. mutans. One is identical to the lantibiotic mutacin I produced by strain CH43 (F. Qi et al., Appl. Environ. Microbiol. 66:3221-3229, 2000); the other is a nonlantibiotic bacteriocin, which we named mutacin IV. Mutacin IV belongs to the two-peptide, nonlantibiotic family of bacteriocins produced by gram-positive bacteria. Peptide A, encoded by gene nlmA, is 44 amino acids (aa) in size and has a molecular mass of 4,169 Da; peptide B, encoded by nlmB, is 49 aa in size and has a molecular mass of 4,826 Da. Both peptides derive from prepeptides with glycines at positions -2 and -1 relative to the processing site. Production of mutacins I and IV by UA140 appears to be regulated by different mechanisms under different physiological conditions. The significance of producing two mutacins by one strain under different conditions and the implication of this property in terms of the ecology of S. mutans in the oral cavity are discussed.
Scaffold-attached regions from the human interferon .beta. domain can be used to enhance the stable expression of genes under the control of various promoters (1991)

We have transfected DNA corresponding to the complete chromatin domain of human interferon beta (huIFN-beta) gene into mouse L cells. In this construct, which is flanked by scaffold-attached regions (SARs), the gene's transcription was enhanced 20-30-fold with respect to DNAs containing only the immediate regulatory elements. To elucidate the role of SAR elements in the transcriptional enhancement, their position was varied relative to several artificial promoter-gene combinations. It was found that SARs enhance general promoter functions in an orientation- and partially distance-independent manner; their effect is restricted to the integrated state of transfected templates. During the phase of transient expression, SAR elements were generally found to have an antagonizing effect.
Characterization of the fracture toughness of micro-sized tungsten single crystal notched specimens (2012)

Fracture experiments using micrometer-sized notched cantilevers were conducted to investigate the possibility of determining fracture mechanical parameters for the semi-brittle material tungsten. The experiments were also used to improve the understanding of semi-brittle fracture processes for which single crystalline tungsten serves as a model material. Due to the large plastic zone in relation to the micrometer sample size, linear elastic fracture mechanics is inapplicable and elastic-plastic fracture mechanics has to be applied. Conditional fracture toughness values J Q were calculated from corrected force vs. displacement diagrams. Crack growth was accessible by direct observation of in-situ experiments as well as with the help of unloading compliances. As a further tool, fracture toughness can be determined via crack tip opening displacement. The micro samples behave more ductile and exhibit higher fracture toughness values compared to macro-sized single crystals and fail by stable crack propagation.
The Use of Pre-Hospital Mild Hypothermia after Resuscitation from Out-of-Hospital Cardiac Arrest (2008)

Hypothermia has emerged as a potent neuroprotective modality following resuscitation from cardiac arrest. Although delayed hospital cooling has been demonstrated to improve outcome after cardiac arrest, in-field cooling begun immediately following the return of spontaneous circulation may be more beneficial. Cooling in the field following resuscitation, however, presents new challenges, in that the cooling method has to be portable, safe, and effective. Rapid infusion of intravenous fluid at 4 degrees C, the use of a cooling helmet, and cooling plates have all been proposed as methods for field cooling, and are all in various stages of clinical and animal testing. Whether field cooling will improve survival and neurologic outcome remains an important unanswered clinical question.
Early Dramatic Recovery During Intravenous Tissue Plasminogen Activator Infusion (2002)

Early dramatic recovery in acute MCA stroke patients treated with intravenous tPA is relatively frequent. The benefit of dramatic recovery is maintained at 24 hours and over the long term. TCD monitoring suggests that dramatic recovery is a result of early restoration of MCA flow during the tPA infusion. The consistent pattern of early clinical recovery may help explain the mechanisms by which thrombolysis improves outcome and could suggest targets for enhancing the therapeutic effect of intravenous tPA.
Quinazoline Ligands Induce Cancer Cell Death through Selective STAT3 Inhibition and G-Quadruplex Stabilization (2020)

The signal transducer and activator of transcription 3 (STAT3) protein is a master regulator of most key hallmarks and enablers of cancer, including cell proliferation and the response to DNA damage. G-Quadruplex (G4) structures are four-stranded noncanonical DNA structures enriched at telomeres and oncogenes' promoters. In cancer cells, stabilization of G4 DNAs leads to replication stress and DNA damage accumulation and is therefore considered a promising target for oncotherapy. Here, we designed and synthesized novel quinazoline-based compounds that simultaneously and selectively affect these two well-recognized cancer targets, G4 DNA structures and the STAT3 protein. Using a combination of in vitro assays, NMR, and molecular dynamics simulations, we show that these small, uncharged compounds not only bind to the STAT3 protein but also stabilize G4 structures. In human cultured cells, the compounds inhibit phosphorylation-dependent activation of STAT3 without affecting the antiapoptotic factor STAT1 and cause increased formation of G4 structures, as revealed by the use of a G4 DNA-specific antibody. As a result, treated cells show slower DNA replication, DNA damage checkpoint activation, and an increased apoptotic rate. Importantly, cancer cells are more sensitive to these molecules compared to noncancerous cell lines. This is the first report of a promising class of compounds that not only targets the DNA damage cancer response machinery but also simultaneously inhibits the STAT3-induced cancer cell proliferation, demonstrating a novel approach in cancer therapy.
Treatment of metastatic cancer with tetrathiomolybdate, an anticopper, antiangiogenic agent: Phase I study. (2000)

Preclinical and in vitro studies have determined that copper is an important cofactor for angiogenesis. Tetrathiomolybdate (TM) was developed as an effective anticopper therapy for the initial treatment of Wilson's disease, an autosomal recessive disorder that leads to abnormal copper accumulation. Given the potency and uniqueness of the anticopper action of TM and its lack of toxicity, we hypothesized that TM would be a suitable agent to achieve and maintain mild copper deficiency to impair neovascularization in metastatic solid tumors. Following preclinical work that showed efficacy for this anticopper approach in mouse tumor models, we carried out a Phase I clinical trial in 18 patients with metastatic cancer who were enrolled at three dose levels of oral TM (90, 105, and 120 mg/day) administered in six divided doses with and in-between meals. Serum ceruloplasmin (Cp) was used as a surrogate marker for total body copper. Because anemia is the first clinical sign of copper deficiency, the goal of the study was to reduce Cp to 20% of baseline value without reducing hematocrit below 80% of baseline. Cp is a reliable and sensitive measure of copper status, and TM was nontoxic when Cp was reduced to 15-20% of baseline. The level III dose of TM (120 mg/ day) was effective in reaching the target Cp without added toxicity. TM-induced mild copper deficiency achieved stable disease in five of six patients who were copper deficient at the target range for at least 90 days.
Regional and Cellular Mapping of cAMP Response Element-Mediated Transcription during Naltrexone-Precipitated Morphine Withdrawal (2002)

Chronic opiate exposure is associated with upregulation of the cAMP signaling pathway and the transcription factor cAMP response element-binding protein in the locus ceruleus (LC) and certain other brain areas. To determine whether these adaptations ultimately affect transcription mediated by the cAMP response element (CRE), we induced morphine dependence in CRE-LacZ transgenic mice and performed a regional and cellular mapping of beta-galactosidase (beta-gal) expression during naltrexone-precipitated withdrawal. Consistent with our model of opiate dependence, beta-gal expression increased in the LC, but decreased in the lateral ventral tegmental area (VTA) and dorsal raphe nucleus (DRN). In addition, withdrawal increased beta-gal expression in the continuum of the extended amygdala and nucleus accumbens, macrostructures associated with the coupling of emotional stimuli to motor and autonomic responses. At the cellular level, in the central nucleus of the amygdala, beta-gal was found in cells both with and without mu opioid receptors as well as in corticotropin-releasing factor-expressing cells. In nucleus accumbens, beta-gal was expressed in several major subpopulations of neurons. In LC, beta-gal expression was induced predominantly in tyrosine hydroxylase-expressing cells, whereas in the VTA and DRN the majority of cells expressing beta-gal were nonmonoaminergic. These results show that molecular adaptations to chronic morphine alter CRE-mediated transcription during opiate withdrawal in physiologically salient regions involved in arousal, reward, mood, and affective responses. We propose that CRE-mediated transcription serves as a functional marker for neuronal plasticity during withdrawal. CRE-mediated transcription may itself contribute to re-establishing homeostasis in the organism through target gene regulation in these regions.
Combination of compressed sensing and parallel imaging for highly accelerated first‐pass cardiac perfusion MRI (2010)

First-pass cardiac perfusion MRI is a natural candidate for compressed sensing acceleration since its representation in the combined temporal Fourier and spatial domain is sparse and the required incoherence can be effectively accomplished by k-t random undersampling. However, the required number of samples in practice (three to five times the number of sparse coefficients) limits the acceleration for compressed sensing alone. Parallel imaging may also be used to accelerate cardiac perfusion MRI, with acceleration factors ultimately limited by noise amplification. In this work, compressed sensing and parallel imaging are combined by merging the k-t SPARSE technique with sensitivity encoding (SENSE) reconstruction to substantially increase the acceleration rate for perfusion imaging. We also present a new theoretical framework for understanding the combination of k-t SPARSE with SENSE based on distributed compressed sensing theory. This framework, which identifies parallel imaging as a distributed multisensor implementation of compressed sensing, enables an estimate of feasible acceleration for the combined approach. We demonstrate feasibility of 8-fold acceleration in vivo with whole-heart coverage and high spatial and temporal resolution using standard coil arrays. The method is relatively insensitive to respiratory motion artifacts and presents similar temporal fidelity and image quality when compared to Generalized autocalibrating partially parallel acquisitions (GRAPPA) with 2-fold acceleration.
Composition of Grignard compounds. VI. Nature of association in tetrahydrofuran and diethyl ether solutions (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComposition of Grignard compounds. VI. Nature of association in tetrahydrofuran and diethyl ether solutionsFrank W. Walker and E. C. AshbyCite this: J. Am. Chem. Soc. 1969, 91, 14, 3845–3850Publication Date (Print):July 1, 1969Publication History Published online1 May 2002Published inissue 1 July 1969https://pubs.acs.org/doi/10.1021/ja01042a027https://doi.org/10.1021/ja01042a027research-articleACS PublicationsRequest reuse permissionsArticle Views920Altmetric-Citations117LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Nuclear transfer of putative rabbit embryonic stem cells leads to normal blastocyst development (1995)

Rabbit embryonic stem-like cells, characterized by embryoid body formation and differentiation into cell types representative of all three germ layers, were studied for their ability to promote early embryonic development after nuclear transfer. After culture of the reconstructed embryos, 23% (n = 35) developed successfully into morulae or blastocysts, compared with 34% (n = 62) for cloned embryos derived from nuclear transfer with embryonic blastomeres. The cloned embryos from the embryonic stem-like cells appeared normal, with an average of 26% inner cell mass cells, similar to that of control non-manipulated embryos (25%) or cloned embryos from blastomeres (25%). Thus, nuclear transfer of rabbit embryonic stem-like cells leads to early embryonic development that is indistinguishable from blastomere fusion. These results have implications for the development of gene targeting in a species (rabbit) that may be a more suitable model for studying certain human diseases. In addition, this technique may be applicable to other species from which putative embryonic stem cells have been derived, particularly agriculturally important animals.
Erythropoietin administration protects retinal neurons from acute ischemia-reperfusion injury (2002)

Erythropoietin (EPO) plays an important role in the brain's response to neuronal injury. Systemic administration of recombinant human EPO (rhEPO) protects neurons from injury after middle cerebral artery occlusion, traumatic brain injury, neuroinflammation, and excitotoxicity. Protection is in part mediated by antiapoptotic mechanisms. We conducted parallel studies of rhEPO in a model of transient global retinal ischemia induced by raising intraocular pressure, which is a clinically relevant model for retinal diseases. We observed abundant expression of EPO receptor (EPO-R) throughout the ischemic retina. Neutralization of endogenous EPO with soluble EPO-R exacerbated ischemic injury, which supports a crucial role for an endogenous EPO/EPO-R system in the survival and recovery of neurons after an ischemic insult. Systemic administration of rhEPO before or immediately after retinal ischemia not only reduced histopathological damage but also promoted functional recovery as assessed by electroretinography. Exogenous EPO also significantly diminished terminal deoxynucleotidyltransferase-mediated dUTP end labeling labeling of neurons in the ischemic retina, implying an antiapoptotic mechanism of action. These results further establish EPO as a neuroprotective agent in acute neuronal ischemic injury.
A magnetic trap for living cells suspended in a paramagnetic buffer (2004)

This manuscript describes the fabrication and use of a three-dimensional magnetic trap for diamagnetic objects in an aqueous solution of paramagnetic ions; this trap uses permanent magnets. It demonstrates trapping of polystyrene spheres, and of various types of living cells: mouse fibroblast (NIH-3T3), yeast (Saccharomyces cerevisiae), and algae (Chlamydomonas reinhardtii). For a 40mM solution of gadolinium (III) diethylenetriaminepentaacetic acid (Gd·DTPA) in aqueous buffer, the smallest cell (particle) that could be trapped had a radius of ∼2.5μm. The trapped particle and location of the magnetic trap can be translated in three dimensions by independent manipulation of the permanent magnets. This letter a1so characterizes the biocompatibility of the trapping solution.
Direct observation of sulfur dimers in alkanethiol self-assembled monolayers on Au(111) (1999)

High-resolution electron-energy-loss spectra of octadecanethiol self-assembled monolayers (SAM's) on Au thin films have been obtained after annealing the sample to various temperatures. Annealing to 375 K results in the appearance of the S-S stretch at 530 ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$, a direct observation of sulfur dimers for alkanethiol SAM's adsorbed on Au. The appearance of dimers following annealing is explained by the presence of an activation barrier to the formation of gauche defects at the S-C bond.
Protoplast Formation in Escherichia coli (1976)

A procedure for protoplast formation in Escherichia coli is described. Removal of the cell wall was confirmed by examination of cells in thin-section preparations.
Cytochrome c and dATP-mediated Oligomerization of Apaf-1 Is a Prerequisite for Procaspase-9 Activation (1999)

To elucidate the mechanism of activation of procaspase-9 by Apaf-1, we produced recombinant full-length Apaf-1 and purified it to complete homogeneity. Here we show using gel filtration that full-length Apaf-1 exists as a monomer that can be transformed to an oligomeric complex made of at least eight subunits after binding to cytochrome c and dATP. Apaf-1 binds to cytochrome c in the absence of dATP but does not form the oligomeric complex. However, when dATP is added to the cytochrome c-bound Apaf-1 complex, complete oligomerization occurs, suggesting that oligomerization is driven by hydrolysis of dATP. This was supported by the observation that ATP, but not the nonhydrolyzable adenosine 5'-O-(thiotriphosphate), can induce oligomerization of the Apaf-1-cytochrome c complex. Like the spontaneously oligomerizing Apaf-530, which lacks its WD-40 domain, the oligomeric full-length Apaf-1-cytochrome c complex can bind and process procaspase-9 in the absence of additional dATP or cytochrome c. However, unlike the truncated Apaf-530 complex, the full-length Apaf-1 complex can release the mature caspase-9 after processing. Once released, mature caspase-9 can process procaspase-3, setting into motion the caspase cascade. These observations indicate that cytochrome c and dATP are required for oligomerization of Apaf-1 and suggest that the WD-40 domain plays an important role in oligomerization of full-length Apaf-1 and the release of mature caspase-9 from the Apaf-1 oligomeric complex.