gebhart/patrepeval huggingface dataset:
Protein phosphatase 2A1 is the major enzyme in vertebrate cell extracts that dephosphorylates several physiological substrates for cyclin-dependent protein kinases. (1993)

Okadaic acid (2 nM) inhibited by 80-90% the protein phosphatase activities in diluted extracts of rat liver, human fibroblasts, and Xenopus eggs acting on three substrates (high mobility group protein-I(Y), caldesmon and histone H1) phosphorylated by a cyclin-dependent protein kinase (CDK) suggesting that a type-2A phosphatase was responsible for dephosphorylating each protein. This result was confirmed by anion exchange chromatography of rat liver and Xenopus extracts, which demonstrated that the phosphatases acting on these substrates coeluted with the two major species of protein phosphatase 2A, termed PP2A1 and PP2A2. When matched for activity toward glycogen phosphorylase, PP2A1 was five- to sevenfold more active than PP2A2 and 35-fold to 70-fold more active than the free catalytic subunit (PP2Ac) toward the three CDK-labeled substrates. Protein phosphatases 1, 2B, and 2C accounted for a negligible proportion of the activity toward each substrate under the assay conditions examined. The results suggest that PP2A1 is the phosphatase that dephosphorylates a number of CDK substrates in vivo and indicate that the A and B subunits that are associated with PP2Ac in PP2A1 accelerate the dephosphorylation of CDK substrates, while suppressing the dephosphorylation of most other proteins. The possibility that PP2A1 activity is regulated during the cell cycle is discussed.
<title>Large-area flat-panel amorphous silicon imagers</title> (1995)

Flat-panel x-ray imaging arrays based upon thin-film electronics are increasingly under development and investigation for a variety of applications. Our research has progressed to the point where three large area designs have now been fabricated, including a new 26 X 26 cm<SUP>2</SUP> array. These arrays are the largest self-scanning, solid-state imaging arrays thus far reported. In all probability, they represent only the first examples of an entirely new class of real-time imaging devices whose properties offer significant advantages over current radiographic and fluoroscopic x-ray technologies. A general overview of the current state of this emerging imaging technology is presented. Our large area array designs are described and x-ray images from a high resolution array are presented. Future challenges as well as anticipated trends and developments are discussed.
Suppression of Cyclin D1 by Hypoxia-Inducible Factor-1 via Direct Mechanism Inhibits the Proliferation and 5-Fluorouracil–Induced Apoptosis of A549 Cells (2010)

Hypoxia-inducible factor (HIF) and cyclin D1 are both key mediators of cell growth and proliferation in normal and cancer cells. However, the interrelation between HIF and cyclin D1 remains unclear. In the present study, we observed the inverse correlation between cyclin D1 and HIF-1 in hypoxia condition. Overexpression of the dominant negative mutant of HIF-1alpha (DN-HIF) significantly enhanced cyclin D1 expression upon hypoxia or arsenite exposure, suggesting the negative regulation of cyclin D1 by HIF-1. Furthermore, we found that the impairment of HIF-1 increased cyclin D1 expression in A549 pulmonary cancer cells, which in turn promoted G1-S cell cycle transition and cell proliferation. Cyclin D1 expression was increased in s.c. xenograft of DN-HIF stably transfected A549 cells in nude mice compared with that of control cells. Chromatin immunoprecipitation assay revealed that HIF-1 was able to directly bind to the promoter region of cyclin D1, which indicates that the negative regulation of cyclin D1 by HIF-1 is through a direct mechanism. Inhibition of histone deacetylase (HDAC) by pretreatment of cells with trichostatin A or specific knockdown of HDAC7 by its shRNA antagonized the suppression of cyclin D1 by HIF-1, suggesting that HDAC7 is required for HIF-1-mediated cyclin D1 downregulation. Moreover, we found that 5-fluorouracil-triggered apoptosis of DN-HIF-transfected A549 cells was reduced by sicyclin D1 (cyclin D1-specific interference RNA) introduction, suggesting that clinical observation of HIF-1 overexpression-associated chemoresistance might be, at least partially, due to the negative regulation of cyclin D1.
Molecular mechanisms of retroviral integration site selection (2014)

Retroviral replication proceeds through an obligate integrated DNA provirus, making retroviral vectors attractive vehicles for human gene-therapy. Though most of the host cell genome is available for integration, the process of integration site selection is not random. Retroviruses differ in their choice of chromatin-associated features and also prefer particular nucleotide sequences at the point of insertion. Lentiviruses including HIV-1 preferentially integrate within the bodies of active genes, whereas the prototypical gammaretrovirus Moloney murine leukemia virus (MoMLV) favors strong enhancers and active gene promoter regions. Integration is catalyzed by the viral integrase protein, and recent research has demonstrated that HIV-1 and MoMLV targeting preferences are in large part guided by integrase-interacting host factors (LEDGF/p75 for HIV-1 and BET proteins for MoMLV) that tether viral intasomes to chromatin. In each case, the selectivity of epigenetic marks on histones recognized by the protein tether helps to determine the integration distribution. In contrast, nucleotide preferences at integration sites seem to be governed by the ability for the integrase protein to locally bend the DNA duplex for pairwise insertion of the viral DNA ends. We discuss approaches to alter integration site selection that could potentially improve the safety of retroviral vectors in the clinic.
Failure to Relax Negative Supercoiling of DNA Is a Primary Cause of Mitotic Hyper-recombination in Topoisomerase-deficient Yeast Cells (2002)

In the yeast Saccharomyces cerevisiae, DNA topoisomerases I and II can functionally substitute for each other in removing positive and negative DNA supercoils. Yeast Delta top1 top2(ts) mutants grow slowly and present structural instability in the genome; over half of the rDNA repeats are excised in the form of extrachromosomal rings, and small circular minichromosomes strongly multimerize. Because these traits can be reverted by the extrachromosomal expression of either eukaryotic topoisomerase I or II, their origin is attributed to the persistence of unconstrained DNA supercoiling. Here, we examine whether the expression of the Escherichia coli topA gene, which encodes the bacterial topoisomerase I that removes only negative supercoils, compensates the phenotype of Delta top1 top2(ts) yeast cells. We found that Delta top1 top2(ts) mutants expressing E. coli topoisomerase I grow faster and do not manifest rDNA excision and minichromosome multimerization. Furthermore, the recombination frequency in repeated DNA sequences, which is increased by nearly two orders of magnitude in Delta top1 top2(ts) mutants relative to the parental TOP+ cells, is restored to normal levels when the bacterial topoisomerase is expressed. These results indicate that the suppression of mitotic hyper-recombination caused by eukaryotic topoisomerases I and II is effected mainly by the relaxation of negative rather than positive supercoils; they also highlight the potential of unconstrained negative supercoiling to promote homologous recombination.
Specific release of granulocyte-macrophage colony-stimulating factor, tumor necrosis factor-alpha, and IFN-gamma by human tumor-infiltrating lymphocytes after autologous tumor stimulation (1991)

Tumor-infiltrating lymphocytes (TIL) have been cultured from a variety of human tumors, and some melanoma TIL have demonstrated specific, MHC-restricted recognition of autologous tumor in short term lysis assays. The current study investigates cytokine release by TIL as an indicator of specific tumor recognition. We have identified two of four melanoma and one of seven breast carcinoma TIL cultures that specifically release granulocyte-macrophage-CSF, TNF-alpha, and IFN-gamma after autologous tumor stimulation. The other cultures either do not secrete cytokine or secrete cytokine in a nonspecific fashion. The amount of specific cytokine released is directly related to the number of TIL and stimulating tumor cells. Studies of TIL, from two melanoma patients, separated into CD4+ and CD8+ populations revealed that CD8+ cells were responsible for virtually all of the specific cytokine secretion, although both populations released cytokines when activated by immobilized anti-CD3 antibody. Specific cytokine release by CD8+ TIL was inhibited by anti-MHC class I mAb. Specific cytokine release was also detected from a CD4+ breast cancer TIL culture, and this was inhibited by anti-MHC class II mAb. The clinical significance of this specific mode of immune antitumor reactivity is currently under investigation.
Clinical relevance of animal models for cerebral ischaemia (1998)

Euro-Neuro '98: First International Update on Neuro-Anaesthesia and Neuro-Intensive Care; Genk, Belgium, 5-7 February 1998
Oxidized phosphatidylserine–CD36 interactions play an essential role in macrophage-dependent phagocytosis of apoptotic cells (2006)

The phagocytosis of apoptotic cells within an organism is a critical terminal physiological process in programmed cell death. Evidence suggests that apoptotic cell engulfment and removal by macrophages is facilitated by phosphatidylserine (PS) displayed at the exofacial surface of the plasma membrane; however, neither the macrophage receptors responsible for PS recognition, nor characterization of the PS molecular species potentially involved, have been clearly defined. We show that the class B scavenger receptor CD36 plays an essential role in macrophage clearance of apoptotic cells in vivo. Further, macrophage recognition of apoptotic cells via CD36 is shown to occur via interactions with membrane-associated oxidized PS (oxPS) and, to a lesser extent, oxidized phosphatidylcholine, but not nonoxidized PS molecular species. Mass spectrometry analyses of oxPS species identify structures of candidate ligands for CD36 in apoptotic membranes that may facilitate macrophage recognition. Collectively, these results identify oxPS-CD36 interactions on macrophages as potential participants in a broad range of physiologic processes where macrophage-mediated engulfment of apoptotic cells is involved.
Conformational characteristics of luliberin. Circular dichroism and fluorescence studies (1976)

By circular dichroism and fluorescence spectroscopy, the conformation of luliberin (luteinizing hormone-releasing hormone) has been investigated under various conditions of pH and solvents. Several structural parameters have been defined which seem predominant for the maintenance of the hormone in some privileged conformation(s). Formation of an intramolecular hydrogen bond between CO (His) and NH (Ser) seems likely when dissolving the hormone in organic solvent such as dioxane. Energy transfer has been demonstrated between Tyr and Trp residues. Calculation of the energy-transfer efficiency at different pH's allowed us to estimate in the range of 10 A the distance which separates these residues. Evidence is also provided for a charge-transfer interaction between protonated histidine and tryptophan. These data suggest that, when luliberin has organized structure (under appropriate surrounding conditions), its conformational pattern would resemble that of beta-turn structure in which a beta bend would exist at the level of the aromatic residues.
ChemInform Abstract: Palladium‐Catalyzed Preparation of exo‐Aryl Derivatives of the Norbornane Skeleton. (1989)

Abstract Coupling of the norbornene and norbornadiene derivatives (I) with the aryl iodides (II) or with the bromostyrene (IV) in the presence of a palladium(II) catalyst leads to the formation of the exo‐hydroarylated or exo‐hydrovinylated derivatives (III) and (V) respectively.
The diagnostic accuracy of different natriuretic peptides in the investigation of canine cardiac disease (2007)

Canine NT-proBNP appears to be a useful marker of the presence of cardiac disease, although concentrations must be interpreted in the light of the patient's renal function.
Using Active NVRAM for Cloud I/O (2011)

A well-known problem for large scale cloud applications is how to scale their I/O performance. While next generation storage class memories like phase change memory and Memristors offer potential for high I/O bandwidths, if left unchecked, the raw volumes and rates of I/O already present in current cloud applications can quickly overwhelm future I/O infrastructures. This fact is motivating research on 'data staging' in which I/O and data movement actions are enhanced with computations that process data before or while moving it across I/O channels -- in situ -- to filter or reduce it, to better organize it for subsequent access (e.g., by other applications as in coupled codes), or to analyze it to quickly derive important insights about the application producing those large data volumes. This paper proposes a technique that uses and exploits 'Active NVRAM' (non volatile memory) for staging I/O. Active NVRAMs are node-local NVRAMs that are embedded with a low power system-on-chip compute element. These active compute elements can be used to operate on output data asynchronously with the tasks performed by computational node elements, to reduce data or to perform some of the data processing required for data analytics before data is moved to longer term storage. The paper describes the Active NVRAM design, sample ways in which it is used for I/O acceleration, and initial performance results evaluating the opportunities for and limitations of the Active NVRAM approach.
B-Cell-Specific DNA Binding by an E47 Homodimer (1995)

B cells express a unique E-box-binding activity that contains basic helix-loop-helix (bHLH) proteins encoded by the E2A gene. E2A proteins play a central role in immunoglobulin gene transcription and are also required for the generation of the B-lymphocyte lineage. In muscle, E2A proteins bind DNA as heterodimers with muscle-specific bHLH partners, such as MyoD and myogenin, and these heterodimers are thought to be both necessary and sufficient for muscle determination in cultured cells. Our results indicate that in B cells, the bHLH partners for E2A proteins are not B-cell-restricted proteins, but are the E2A proteins themselves. UV cross-linking, gel purification, and the analysis of "forced heterodimers" indicate that BCF1 is primarily a homodimer of the E2A protein E47. Since E47 is widely expressed, our results argue for a difference in the inherent DNA-binding properties of the E47 protein in B cells and may help explain the restricted B-lineage defect observed in E2A-deficient mice.
2,4-D and Mycoleptodiscus terrestris for control of Eurasian watermilfoil. (2005)

Growth chamber studies were conducted to evaluate theimpact of an indigenous fungal pathogen,Mycoleptodiscus terrestris(Gerd.) Ostazeski, and the herbicide 2,4-D appliedalone and in combination with one another, on the growth ofa nuisance submersed plant, Eurasian watermilfoil (MyriophyllumspicatumL.)(PDF has 6 pages.)
Study on the Correlation Between Temperament and Development of Infant and Toddler. (2002)

To find the correlation of temperament and infant and toddle development. The temperament traits and levels of development were assessed in 233 infants and toddlers. Carey's Revised Infant Temperament Questionnaire (RITQ) and Toddler Temperament Scale (TTS) were adopted to assess temperament in this study. And Bayley Scales of Infant Development was used to test the intelligence development of infants and toddlers. There was no gender difference among the distributions of temperament types. Although there was no significant difference of development quotient (DQ) among different temperament groups, there was a tendency that the higher percentage of low and high DQ in negative temperament groups than positive groups. There was significant difference correlation between mental development index and rhythmicity. It suggested that the higher development level,the higher physiological rhythmicity. [Conclusions] It seems that there be correlation between temperament and intelligence. But the correlation is limited in early childhood by biological differentiation and development, as well as low socialization. Anyway, more appropriate ways in education for negative temperament children should benefit the potential in their intelligence development.
Advances in Sympathetic Nerve Recording in Humans (2012)

In humans, sympathetic activity is commonly assessed by measuring the efferent traffic in the peroneal nerve. The firing activity is the sum of several active neurons, which have the tendency to fire together in a bursting manner. While the estimation of overall sympathetic nervous activity using this multiunit recording approach has advanced our understanding of sympathetic regulation in health and disease no information is gained regarding the underling mechanisms generating the bursts of sympathetic activity. The introduction of single-unit recording has been a major step forward, enabling the examination of specific sympathetic firing patterns in diverse clinical conditions. Disturbances in sympathetic nerve firing, including high firing probabilities, high firing rates or high incidence of multiple firing, or a combination of both may impact on noradrenaline release and effector response, and therefore have clinical implications with regards to the development and progression of target organ damage. Understanding the mechanisms and consequences of specific firing patterns would permit the development of therapeutic strategies targeting these nuances of sympathetic overdrive.
Raman Spectroscopy of Blood and Blood Components (2017)

Blood is a bodily fluid that is vital for a number of life functions in animals. To a first approximation, blood is a mildly alkaline aqueous fluid (plasma) in which a large number of free-floating red cells (erythrocytes), white cells (leucocytes), and platelets are suspended. The primary function of blood is to transport oxygen from the lungs to all the cells of the body and move carbon dioxide in the return direction after it is produced by the cells' metabolism. Blood also carries nutrients to the cells and brings waste products to the liver and kidneys. Measured levels of oxygen, nutrients, waste, and electrolytes in blood are often used for clinical assessment of human health. Raman spectroscopy is a non-destructive analytical technique that uses the inelastic scattering of light to provide information on chemical composition, and hence has a potential role in this clinical assessment process. Raman spectroscopic probing of blood components and of whole blood has been on-going for more than four decades and has proven useful in applications ranging from the understanding of hemoglobin oxygenation, to the discrimination of cancerous cells from healthy lymphocytes, and the forensic investigation of crime scenes. In this paper, we review the literature in the field, collate the published Raman spectroscopy studies of erythrocytes, leucocytes, platelets, plasma, and whole blood, and attempt to draw general conclusions on the state of the field.
Signatures of Depression in Non‐Stationary Biometric Time Series (2009)

This paper is based on a discussion that was held during a special session on models of mental disorders, at the NeuroMath meeting in Stockholm, Sweden, in September 2008. At this occasion, scientists from different countries and different fields of research presented their research and discussed open questions with regard to analyses and models of mental disorders, in particular depression. The content of this paper emerged from these discussions and in the presentation we briefly link biomarkers (hormones), bio-signals (EEG) and biomaps (brain-maps via EEG) to depression and its treatments, via linear statistical models as well as nonlinear dynamic models. Some examples involving EEG-data are presented.
Evidence for FHL1 as a novel disease gene for isolated hypertrophic cardiomyopathy (2012)

Hypertrophic cardiomyopathy (HCM) is characterized by asymmetric left ventricular hypertrophy, diastolic dysfunction and myocardial disarray. HCM is caused by mutations in sarcomeric genes, but in >40% of patients, the mutation is not yet identified. We hypothesized that FHL1, encoding four-and-a-half-LIM domains 1, could be another disease gene since it has been shown to cause distinct myopathies, sometimes associated with cardiomyopathy. We evaluated 121 HCM patients, devoid of a mutation in known disease genes. We identified three novel variants in FHL1 (c.134delA/K45Sfs, c.459C>A/C153X and c.827G>C/C276S). Whereas the c.459C>A variant was associated with muscle weakness in some patients, the c.134delA and c.827G>C variants were associated with isolated HCM. Gene transfer of the latter variants in C2C12 myoblasts and cardiac myocytes revealed reduced levels of FHL1 mutant proteins, which could be rescued by proteasome inhibition. Contractility measurements after adeno-associated virus transduction in rat-engineered heart tissue (EHT) showed: (i) higher and lower forces of contraction with K45Sfs and C276S, respectively, and (ii) prolonged contraction and relaxation with both mutants. All mutants except one activated the fetal hypertrophic gene program in EHT. In conclusion, this study provides evidence for FHL1 to be a novel gene for isolated HCM. These data, together with previous findings of proteasome impairment in HCM, suggest that FHL1 mutant proteins may act as poison peptides, leading to hypertrophy, diastolic dysfunction and/or altered contractility, all features of HCM.
Fabrication and characterization of freestanding GaAs∕AlGaAs core-shell nanowires and AlGaAs nanotubes by using selective-area metalorganic vapor phase epitaxy (2005)

We fabricated GaAs∕AlGaAs core-shell nanowires by using selective-area metalorganic vapor phase epitaxy. First, GaAs nanowires were selectively grown on partially masked GaAs (111)B substrates; then AlGaAs was grown to form freestanding heterostructured nanowires. Investigation of nanowire diameter as a function of AlGaAs growth time suggested that the AlGaAs was grown on the sidewalls of the GaAs nanowires, forming GaAs∕AlGaAs core-shell structures. Microphotoluminescence measurements of GaAs and GaAs∕AlGaAs core-shell nanowires reveal an enhancement of photoluminescence intensity in GaAs∕AlGaAs core-shell structures. Based on these core-shell nanowires, AlGaAs nanotubes were formed by using anisotropic dry etching and wet chemical preferential etching to confirm the formation of a core-shell structure and to explore a new class of materials.