gebhart/patrepeval huggingface dataset:
Gene expression in Citrus sinensis fruit tissues harvested from huanglongbing-infected trees: comparison with girdled fruit (2012)

Distribution of viable Candidatus Liberibacter asiaticus (CaLas) in sweet orange fruit and leaves ('Hamlin' and 'Valencia') and transcriptomic changes associated with huanglongbing (HLB) infection in fruit tissues are reported. Viable CaLas was present in most fruit tissues tested in HLB trees, with the highest titre detected in vascular tissue near the calyx abscission zone. Transcriptomic changes associated with HLB infection were analysed in flavedo (FF), vascular tissue (VT), and juice vesicles (JV) from symptomatic (SY), asymptomatic (AS), and healthy (H) fruit. In SY 'Hamlin', HLB altered the expression of more genes in FF and VT than in JV, whereas in SY 'Valencia', the number of genes whose expression was changed by HLB was similar in these tissues. The expression of more genes was altered in SY 'Valencia' JV than in SY 'Hamlin' JV. More genes were also affected in AS 'Valencia' FF and VT than in AS 'Valencia' JV. Most genes whose expression was changed by HLB were classified as transporters or involved in carbohydrate metabolism. Physiological characteristics of HLB-infected and girdled fruit were compared to differentiate between HLB-specific and carbohydrate metabolism-related symptoms. SY and girdled fruit were smaller than H and ungirdled fruit, respectively, with poor juice quality. However, girdling did not cause misshapen fruit or differential peel coloration. Quantitative PCR analysis indicated that many selected genes changed their expression significantly in SY flavedo but not in girdled flavedo. Mechanisms regulating development of HLB symptoms may lie in the host disease response rather than being a direct consequence of carbohydrate starvation.
Protective V127 prion variant prevents prion disease by interrupting the formation of dimer and fibril from molecular dynamics simulations (2016)

Recent studies uncovered a novel protective prion protein variant: V127 variant, which was reported intrinsically resistant to prion conversion and propagation. However, the structural basis of its protective effect is still unknown. To uncover the origin of the protective role of V127 variant, molecular dynamics simulations were performed to explore the influence of G127V mutation on two key processes of prion propagation: dimerization and fibril formation. The simulation results indicate V127 variant is unfavorable to form dimer by reducing the main-chain H-bond interactions. The simulations of formed fibrils consisting of β1 strand prove V127 variant will make the formed fibril become unstable and disorder. The weaker interaction energies between layers and reduced H-bonds number for V127 variant reveal this mutation is unfavorable to the formation of stable fibril. Consequently, we find V127 variant is not only unfavorable to the formation of dimer but also unfavorable to the formation of stable core and fibril, which can explain the mechanism on the protective role of V127 variant from the molecular level. Our findings can deepen the understanding of prion disease and may guide the design of peptide mimetics or small molecule to mimic the protective effect of V127 variant.
Resolving the distinct stages in erythroid differentiation based on dynamic changes in membrane protein expression during erythropoiesis (2009)

Erythropoiesis is the process by which nucleated erythroid progenitors proliferate and differentiate to generate, every second, millions of nonnucleated red cells with their unique discoid shape and membrane material properties. Here we examined the time course of appearance of individual membrane protein components during murine erythropoiesis to throw new light on our understanding of the evolution of the unique features of the red cell membrane. We found that the accumulation of all of the major transmembrane and all skeletal proteins of the mature red blood cell, except actin, accrued progressively during terminal erythroid differentiation. At the same time, and in marked contrast, accumulation of various adhesion molecules decreased. In particular, the adhesion molecule, CD44 exhibited a progressive and dramatic decrease from proerythroblast to reticulocyte; this enabled us to devise a new strategy for distinguishing unambiguously between erythroblasts at successive developmental stages. These findings provide unique insights into the genesis of red cell membrane function during erythroblast differentiation and also offer a means of defining stage-specific defects in erythroid maturation in inherited and acquired red cell disorders and in bone marrow failure syndromes.
Identification of a 190-kDa Vascular Endothelial Growth Factor 165 Cell Surface Binding Protein on a Human Glioma Cell Line (1997)

Vascular endothelial growth factor (VEGF) is an angiogenesis factor for which two signaling protein tyrosine kinase receptors, Flt1 and KDR, have been identified. We describe here a 190-kDa component present on a human glioma cell line that binds VEGF165 with high affinity. In contrast, VEGF121 is bound only with low affinity, suggesting that the C-terminal part of VEGF165 is important for interaction with the 190-kDa component. No internalization or stimulation of tyrosine phosphorylation was recorded after ligand binding to the 190-kDa component, suggesting that it may not be directly involved in signaling; its function may be to present ligand or stabilize ligand binding to signaling receptors.
Two-mode division multiplexing in a silicon-on-insulator ring resonator (2014)

Mode-division multiplexing (MDM) is an emerging multiple-input multiple-output method, utilizing multimode waveguides to increase channel numbers. In the past, silicon-on-insulator (SOI) devices have been primarily focused on single-mode waveguides. We present the design and fabrication of a two-mode SOI ring resonator for MDM systems. By optimizing the device parameters, we have ensured that each mode is treated equally within the ring. Using adiabatic Bezier curves in the ring bends, our ring demonstrated a signal-to-crosstalk ratio above 18 dB for both modes at the through and drop ports. We conclude that the ring resonator has the potential for filtering and switching for MDM systems on SOI.
Varicella-zoster virus as a live vector for the expression of foreign genes. (1987)

The previous demonstration of the efficacy and tolerability of the Oka strain of varicella-zoster virus (VZV) in clinical trials involving vaccination of both normal and immunocompromised individuals has laid the foundation for its use in preventing chickenpox. In this context, VZV could be useful as a vector for vaccinating against other infectious agents as well. As an initial application, a live recombinant VZV expressing Epstein-Barr virus (EBV) membrane glycoproteins (gp350/220) was generated by inserting a gene fusion of the VZV gpI promoter and hydrophobic leader-encoding sequence with the gp350/220 coding sequence into the thymidine kinase (TK) gene of VZV (Oka). Insertion of the foreign DNA into the thymidine kinase gene was demonstrated by Southern blot analysis and the ability of the recombinant virus to replicate in the presence of bromodeoxyuridine. RNA splicing, glycosylation, and plasma membrane presentation of gp350/220 in cells infected with the recombinant virus were similar to those seen in EBV-infected cells. In addition, the expression of VZV-specific glycoproteins was unaltered by the concomitant expression of this large foreign glycoprotein. Thus, VZV can be used as a live viral vector for active immunization against EBV and other pathogens.
Mechanical Strain Enhances Extracellular Matrix-Induced Gene Focusing and Promotes Osteogenic Differentiation of Human Mesenchymal Stem Cells Through an Extracellular-Related Kinase-Dependent Pathway (2007)

Human mesenchymal stem cells (hMSCs) are a population of multipotent bone marrow cells capable of differentiating along multiple lineages, including bone. Our recently published proteomics studies suggest that focusing of gene expression is the basis of hMSC osteogenic transdifferentiation, and that extracellular matrix proteins play an important role in controlling this focusing. Here, we show that application of a 3-5% tensile strain to a collagen I substrate stimulates osteogenesis in the attached hMSCs through gene focusing via a MAP kinase signaling pathway. Mechanical strain increases expression levels of well-established osteogenic marker genes while simultaneously reducing expression levels of marker genes from three alternate lineages (chondrogenic, adipogenic, and neurogenic). Mechanical strain also increases matrix mineralization (a hallmark of osteogenic differentiation) and activation of extracellular signal-related kinase 1/2 (ERK). Addition of the MEK inhibitor PD98059 to reduce ERK activation decreases osteogenic gene expression and matrix mineralization while also blocking strain-induced down-regulation of nonosteogenic lineage marker genes. These results demonstrate that mechanical strain enhances collagen I-induced gene focusing and osteogenic differentiation in hMSCs through the ERK MAP kinase signal transduction pathway.
Proteins of the inter-alpha-trypsin inhibitor family stabilize the cumulus extracellular matrix through their direct binding with hyaluronic acid. (1994)

We have previously identified a glycoprotein of the inter-alpha-trypsin inhibitor family of proteins as a serum factor responsible for the stabilization of the expanding cumulus mass. In this study, the mechanism of interaction of this cumulus extracellular matrix stabilizing factor (cESF) with hyaluronic acid (HA) has been explored. It was found that the pH optimum for binding of cESF and HA is 7 and that binding is sensitive to ionic strength. The dissociation constant is about 1.9 x 10(-8) M in 10 mM sodium phosphate buffer (pH 7.2). Circular dichroism studies show that cESF contains about 24% alpha-helical and 42% beta-sheet structure. Gross conformational changes in cESF, however, are not detected in the presence of HA. We also found that modification of lysine residues of cESF with citraconic anhydride greatly reduced its binding with HA and completely abolished its cumulus stabilizing activity, and deblocking lysine residues restored its capacity to bind with HA and its cumulus matrix stabilizing activity. This evidence supports the hypotheses that cESF stabilizes the expanding cumulus extracellular matrix by directly binding with HA and that cESF may serve as a structural protein to organize the formation of the cumulus extracellular matrix. Our evidence also supports the view that binding of cESF and HA is through a stereo-specific charge interaction. Putative binding sites of cESF that interact with HA are postulated.
The Role of Insulin, Insulin Growth Factor, and Insulin‐Degrading Enzyme in Brain Aging and Alzheimer′s Disease (2005)

Most brain insulin comes from the pancreas and is taken up by the brain by what appears to be a receptor-based carrier. Type 2 diabetes animal models associated with insulin resistance show reduced insulin brain uptake and content. Recent data point to changes in the insulin receptor cascade in obesity-related insulin resistance, suggesting that brain insulin receptors also become less sensitive to insulin, which could reduce synaptic plasticity. Insulin transport to the brain is reduced in aging and in some animal models of type 2 diabetes; brain insulin resistance may be present as well. Studies examining the effect of the hyperinsulinic clamp or intranasal insulin on cognitive function have found a small but consistent improvement in memory and changes in brain neuroelectric parameters in evoked brain potentials consistent with improved attention or memory processing. These effects appear to be due to raised brain insulin levels. Peripheral levels of Insulin Growth Factor-1 (IGF-I) are associated with glucose regulation and influence glucose disposal. There is some indication that reduced sensitivity to insulin or IGF-I in the brain, as observed in aging, obesity, and diabetes, decreases the clearance of Abeta amyloid. Such a decrease involves the insulin receptor cascade and can also increase amyloid toxicity. Insulin and IGF-I may modulate brain levels of insulin degrading enzyme, which would also lead to an accumulation of Abeta amyloid.
Mast cells synthesize, store, and release nerve growth factor. (1994)

Mast cells and nerve growth factor (NGF) have both been reported to be involved in neuroimmune interactions and tissue inflammation. In many peripheral tissues, mast cells interact with the innervating fibers. Changes in the behaviors of both of these elements occur after tissue injury/inflammation. As such conditions are typically associated with rapid mast cell activation and NGF accumulation in inflammatory exudates, we hypothesized that mast cells may be capable of producing NGF. Here we report that (i) NGF mRNA is expressed in adult rat peritoneal mast cells; (ii) anti-NGF antibodies clearly stain vesicular compartments of purified mast cells and mast cells in histological sections of adult rodent mesenchymal tissues; and (iii) medium conditioned by peritoneal mast cells contains biologically active NGF. Mast cells thus represent a newly recognized source of NGF. The known actions of NGF on peripheral nerve fibers and immune cells suggest that mast cell-derived NGF may control adaptive/reactive responses of the nervous and immune systems toward noxious tissue perturbations. Conversely, alterations in normal mast cell behaviors may provoke maladaptive neuroimmune tissue responses whose consequences could have profound implications in inflammatory disease states, including those of an autoimmune nature.
Enhanced Boiling Heat Transfer in Parallel Microchannels With Diffusion Brazed Wire Mesh (2010)

Flow boiling is an important process in energy conversion applications such as power generation and heating, ventilating, and air conditioning systems. Recently, it has drawn interest in the high heat flux electronics cooling community. Flow boiling enhancement, in addition, has the benefit of early onset of nucleate boiling, potentially lowering wall superheat, and increasing the heat transfer coefficient and critical heat flux (CHF). The objective of this paper was to investigate the use of fine metal wire mesh screens to enhance nucleate boiling in microchannels. Contact resistance between the wire mesh and channel heating surface was essentially eliminated by employing a diffusion brazing process to attach the screen to the wall. The parallel microchannels were 1000 μm in width and 510 μm in depth. A dielectric working fluid, HFE 7000, was investigated during this paper. Flow boiling results were compared for channels with and without wire mesh. According to the flow boiling curves obtained in this investigation for the bare and mesh channels, the amount of wall superheat was substantially reduced for the mesh channels at all four stream-wise locations. This indicated that nucleate boiling in the mesh channel was enhanced due to the increase of nucleation sites the mesh introduced. The mesh channels also displayed a higher flow boiling heat transfer coefficient. Both the nucleate boiling dominated regime and convective evaporation dominated regime were identified, with the overall trend of increasing the flow boiling heat transfer coefficient with respect to vapor quality until this quantity reached approximately 0.4. The CHF for the mesh channel was also significantly higher than that for the bare channel. The flow boiling enhancement was achieved with no apparent pressure drop penalty. The results presented here provide a practical means to implement this surface enhancement technique.
Association of the DF3/MUC1 breast cancer antigen with Grb2 and the Sos/Ras exchange protein. (1995)

The DF3/MUC1 mucin-like glycoprotein is aberrantly overexpressed in human breast carcinomas. Although the precise functional role of this protein remains unclear, the cytoplasmic tail contains potential tyrosine phosphorylation sites for binding to Src homology 2 (SH2) domains. In the present studies using human MCF-7 breast cancer cells, we show that tyrosine phosphorylated DF3 directly interacts with the SH2 domain of the adaptor protein Grb2. The findings indicate that a pYTNP site in DF3 is responsible for this interaction. The results also demonstrate that the DF3/Grb2 complex associates with the guanine nucleotide exchange protein Sos. Because Sos binds to the SH3 domains of Grb2 and, thereby, associates with Ras at the cell membrane, formation of a DF3/Grb2/Sos complex supports a role for DF3 in intracellular signaling.
Abnormally high expression of proteasomes in human leukemic cells. (1990)

Proteasomes are eukaryotic ring-shaped or cylindrical particles with multicatalytic protease activities. To clarify the involvement of proteasomes in tumorigenesis of human blood cells, we compared their expression in human hematopoietic malignant tumor cells with that in normal peripheral blood mononuclear cells. Immunohistochemical staining showed considerably increased concentrations of proteasomes in leukemic cells from the bone marrow of patients with various types of leukemia and the predominant localization of these proteasomes in the nuclei. Moreover, enzyme immunoassay and Northern blot analysis indicated that the concentrations of proteasomes and their mRNA levels were consistently much higher in a variety of malignant human hematopoietic cell lines than in resting peripheral lymphocytes and monocytes from healthy adults. Proteasome expression was also greatly increased in normal blood mononuclear cells during blastogenic transformation induced by phytohemagglutinin; their expression increased in parallel with induction of DNA synthesis and returned to the basal level with progress of the cell cycle. Thus, abnormally high expression of proteasomes may play an important role in transformation and proliferation of blood cells and in specific functions of hematopoietic tumor cells.
Ultraviolet light-emitting diodes operating in the 340nm wavelength range and application to time-resolved fluorescence spectroscopy (2004)

We report on the development of UV light-emitting diodes in the 340nm wavelength range, based on quaternary AlGaInN quantum-well active media. Output powers up to 1mW from small area devices (&amp;lt;100μm diameter) directly off a planar chip have been achieved. The devices have been operated as subnanosecond pulsed sources to demonstrate their applicability to compact time-resolved fluorescence spectroscopy.
Heparin-Induced Spinal Fractures (1979)

A 27-year-old woman received heparin sodium for 152 days because of antepartum iliofemoral thrombophlebitis. At the end of this time, spinal osteoporosis and multiple vertebral fractures became clinically evident and were attributed to the prolonged administration of heparin. Previously reported cases of "heparin osteoporosis" were reviewed. The significance of the daily dose of heparin and the duration of therapy are reemphasized. This therapeutic complication and the management of antepartum iliofemoral thrombophlebitis are discussed. Prolonged administration of heparin in daily doses exceeding 10,000 units is potentially hazardous.
Controlled switching of the wetting behavior of biomimetic surfaces with hydrogel-supported nanostructures (2008)

An important feature of biological systems is their response to external stimuli with subsequent changes in properties and function. The ability to “engineer” adaptiveness into next-generation materials is becoming a key requirement and challenge in chemistry, materials science and engineering. Recently we have described new hybrid nano/microstructures capable of dynamic actuation by a hydrogel “muscle”. Here we demonstrate the application of a variation of such biomimetic surfaces in controlled reversible switching of the surface wetting behavior. Arrays of rigid nanostructures were integrated with responsive hydrogel films by performing in situ polymerization in microscopic confinement of two surfaces. The attachment of hydrogel was achieved through a multifunctional polymeric anchoring layer. Using two different attachment strategies, several designs involving an array of either attached or free-standing nanocolumns embedded in the hydrogel film are described. We demonstrate a superhydrophobic–hydrophilic transition (so-called “direct response”) or a hydrophilic–superhydrophobic transition (“reverse response”), respectively, upon the exposure of these two structures to water. We show that all the changes in the wetting behavior are reversible and the structures return to their original superhydrophobic or hydrophilic state upon drying. The ability to design surfaces with reversible changes in their wetting behavior may have exciting applications as “smart,” responsive materials with tunable water-repelling or water-attracting properties.
Toward an on demand service-oriented architecture (2005)

The success of an on demand e-business requires that business process, application, and information technology (IT) infrastructure integration merge into a comprehensive and cohesive architecture, where business process transformation drives service-oriented development and on demand enterprise computing. This enabling architecture is often described as a service-oriented architecture (SOA) and is a prerequisite accelerator for on demand solutions. The primary focus of SOA has been on dynamic reconfiguration of services from defined business processes, and on developing business services based on Web services and, more recently, grid services. Current descriptions of SOA are less focused on overall IT infrastructure enablement, both from a business policy perspective and within the context of service-oriented development. In this paper, we extend the current thinking on SOA to include a more comprehensive integration of business process transformation and the enabling technologies of service-oriented development and policy-based IT management. We call this extension on demand SOA. We develop these concepts by using an existing scenario: a financial services sector “Life Change” business process scenario, which involves distributed and disjoint transactions as well as stateless high-performance computing (HPC) applications.