gebhart/patrepeval huggingface dataset:
Supplementary Discussion from Coexpression Network Analysis Identifies Transcriptional Modules Related to Proastrocytic Differentiation and Sprouty Signaling in Glioma (2023)

Supplementary Discussion from Coexpression Network Analysis Identifies Transcriptional Modules Related to Proastrocytic Differentiation and Sprouty Signaling in Glioma
E11/gp38 Selective Expression in Osteocytes: Regulation by Mechanical Strain and Role in Dendrite Elongation (2006)

Within mineralized bone, osteocytes form dendritic processes that travel through canaliculi to make contact with other osteocytes and cells on the bone surface. This three-dimensional syncytium is thought to be necessary to maintain viability, cell-to-cell communication, and mechanosensation. E11/gp38 is the earliest osteocyte-selective protein to be expressed as the osteoblast differentiates into an osteoid cell or osteocyte, first appearing on the forming dendritic processes of these cells. Bone extracts contain large amounts of E11, but immunostaining only shows its presence in early osteocytes compared to more deeply embedded cells, suggesting epitope masking by mineral. Freshly isolated primary osteoblasts are negative for E11 expression but begin to express this protein in culture, and expression increases with time, suggesting differentiation into the osteocyte phenotype. Osteoblast-like cell lines 2T3 and Oct-1 also show increased expression of E11 with differentiation and mineralization. E11 is highly expressed in MLO-Y4 osteocyte-like cells compared to osteoblast cell lines and primary osteoblasts. Differentiated, mineralized 2T3 cells and MLO-Y4 cells subjected to fluid flow shear stress show an increase in mRNA for E11. MLO-Y4 cells show an increase in dendricity and elongation of dendrites in response to shear stress that is blocked by small interfering RNA specific to E11. In vivo, E11 expression is also increased by a mechanical load, not only in osteocytes near the bone surface but also in osteocytes more deeply embedded in bone. Maximal expression is observed not in regions of maximal strain but in a region of potential bone remodeling, suggesting that dendrite elongation may be occurring during this process. These data suggest that osteocytes may be able to extend their cellular processes after embedment in mineralized matrix and have implications for osteocytic modification of their microenvironment.
Conserved Molecular Players for Axon Guidance and Angiogenesis (2005)

Neuronal guidance cues attract or repel axons and/or neurons and play important roles in the pathfinding of neuronal networks and the functioning of nervous system. Prominent among them are the families of ephrins, semaphorins, Slits and netrins and their cognate cell-surface receptors. Due to their biological significance, extensive research has been carried out in the last ten years or so. Angiogenesis is a cellular process of capillary sprouting and configuring of neovasculatures, which shares many developmental, anatomical, physiological and pathophysiological features with the neural counterparts. This review will summarize the emerging evidence indicating the common molecular mechanisms underlying both axon guidance (including neuronal migration) and angiogenesis for exquisite regulation of proper wiring of both systems.
Structural properties of multilayer heterostructure for quantum-cascade lasers grown by MBE growth (2018)

GaAs/AlGaAs heterostructure with 226 quantum cascades was synthesized by molecular-beam epitaxy. Structural and optical properties studies have shown high level of homogeneity and quality of epitaxial structure.
Synthesis and Characterization of N-Methyl-Substituted Germocanes. Crystal Structure of MeN(CH2CH2O)2GeBr2 (2003)

The reaction of GeHal 4 with MeN(CH 2 CH 2 OSiMe 3 ) 2 affords dihalogermocanes MeN(CH 2 CH 2 O) 2 GeHal 2 (1, Hal = Br; 2, Hal = Cl). Treatment of Me 2 Ge(NMe 2 ) 2 with MeN(CH 2 CH 2 OH) 2 leads to dimethylgermocane MeN(CH 2 CH 2 O) 2 GeMe 2 (3). The composition and structure of 1-3 were established by elemental analyses, 1 H, 13 C NMR spectroscopy, and mass spectrometry. The crystal structure of 1 is reported; structural data obtained from geometry DFT optimization on 1 are in good agreement with experimental results. Values of the electron density in the N→Ge bond critical point and the Laplacian of charge density for 1-3 indicate a closed-shell interaction between the Ge and N atoms.
Embryonic Stem Cells Transplanted In Utero Survive and Produce Teratocarcinomas in a Murine Model. (2007)

Abstract Introduction: Embryonic stem (ES) cells have the capacity to differentiate into any cell type. We have previously established an in vivo murine model for the study of the in vivo differentiation of ES cells. The aim of this study was to monitor tumor formation in this model. Materials and Methods: Murine ESC genetically engineered to express yellow fluorescent protein (YFP-ES cells) were cultured on mitomycin-treated feeder layers for four days prior to in utero transplantation in medium containing leukemia inhibitory factor. A cell dose of 5x104 YFP-ES cells (H-2b) was injected in utero intraperitoneally in the fetuses of Balb/c (H-2d) and C57BL/6 (H-2b) pregnant mice at E12- E14. The presence of YFP-ES cell-derived cells was analyzed in various tissues of the liveborn offsprings of different ages by fluorescence microscopy and quantified by digitalized fluorescence microscopy of frozen section from various tissues and organs and analysis of tissue supernatants for the presence of the YFP signal. Tumor formation was monitored in liveborn offsprings for up to one year and tissue sections were examined by routine and fluorescent microscopy. Results: The YFP-fluorescent cells derived from YFP-ES cells were detected in liver and thymus without any evidence of migration in other organs. Extensive peritoneal teratocarcinomas with supradiaphragmatic involvement were generated in two out of five allogeneic in utero transplantation of YFP-ES cells. Tumor formation was not observed in the groups transplanted in utero with fetal liver or adult bone marrow hematopoietic cells, or in the control group. Clinical and histopathological pictures suggestive of graft-versus -host disease were also observed in two out of five mice transplanted in utero. Conclusion: The promise and the potential risks of the ESC transplantation have to be carefully considered due to the high risk of teratoma/teratocarcinoma occurrence. Protocols using pre-differentiated cells from ES or adult stem cells may constitute a better approach for cellular therapies.
Notch Suppresses Angiogenesis and Progression of Hepatic Metastases (2015)

The Notch pathway plays multiple key roles in tumorigenesis, and its signaling components have therefore aroused great interest as targets for emerging therapies. Here, we show that inhibition of Notch, using a soluble receptor Notch1 decoy, unexpectedly caused a remarkable increase in liver metastases from neuroblastoma and breast cancer cells. Increased liver metastases were also seen after treatment with the γ-secretase inhibitor PF-03084014. Transgenic mice with heterozygous loss of Notch1 demonstrated a marked increase in hepatic metastases, indicating that Notch1 signaling acts as metastatic suppressor in the liver microenvironment. Inhibition of DLL1/4 with ligand-specific Notch1 decoys increased sprouting of sinusoidal endothelial cells into micrometastases, thereby supporting early metastatic angiogenic growth. Inhibition of tumor-derived JAG1 signaling activated hepatic stellate cells, increasing their recruitment to vasculature of micrometastases, thereby supporting progression to macrometastases. These results demonstrate that inhibition of Notch causes pathologic activation of liver stromal cells, promoting angiogenesis and growth of hepatic metastases. Our findings have potentially serious implications for Notch inhibition therapy.
Hypolipidemic effects of protein hydrolysates from Trachinotus ovatus and identification of peptides implied in bile acid-binding activity using LC-ESI-Q-TOF-MS/MS (2020)

In the present work, analysis of the hypolipidemic properties of <i>Trachinotus ovatus</i> protein hydrolysates (TOPHs) and identification of peptides with bile acid-binding activity were performed. Hydrolysates prepared by trypsin digestion exhibited the highest <i>in vitro</i> bile acid-binding capacities compared with hydrolysates prepared with the other four proteases and were mainly composed of small peptides and amino acids with molecular weights <3 kDa, accounting for 77.30%. Among the five ultra-filtration fractions of TOPHs, TOPHs-5 (<3 kDa) exhibited the highest <i>in vitro</i> bile acid-binding capacity, which was equivalent to 77.97% of cholestyramine at the same concentration. A total of 68 peptides were identified from TOPHs-5 by LC-ESI-Q-TOF-MS/MS and 9 of them had hydrophobicity of more than 60%. These highly hydrophobic peptides might be associated with the bile acid-binding activity of TOPHs-5. <i>In vivo</i> experiments indicated that the TOPHs could effectively reduce total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and the atherogenic index (AI), while they could evidently increase the high-density lipoprotein cholesterol (HDL-C) content. Furthermore, TOPHs exerted a marked protective effect on hepatorenal function, as evidenced by decreased levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT) and creatinine (CREA). Histopathological studies confirmed that TOPHs evidently protected the liver from histological alterations. In summary, for the first time, hypolipidemic effects and subsequential identification were obtained from TOPHs, which are promising natural ingredients that could potentially be employed in the management of hyperlipidemia.
TEXAS BOILING TEST FOR EVALUATING MOISTURE SUSCEPTIBILITY OF ASPHALT MIXTURES (1984)

This report contains a description of the development and use of the Texas Boiling Test to evaluate stripping of materials susceptible to moisture damage. Included is a review of comparison of boiling tests currently in use by several agencies and a recommended tentative test procedure. Preliminary testing indicated that three factors related to testing were important. These factors were the number of times the aggregate and asphalt was heated and mixed before testing, the initial temperature to which the aggregate was heated prior to mixing, and the type of water used for boiling. These three factors were investigated to determine the effect off their variation on test results. Tests were performed on eight mixtures of which five had stripped in the field and three had not. Each mixture and its individual aggegate components were tested to determine whether the results could be used to differentiate between stripping and nonstripping mixtures. Based on these tests and other field testing it was tentatively concluded that mixtures that retained less than 70 percent of the asphalt on the aggregate are moisture susceptible and require treatment. Test results indicate that valuable information is provided by the Texas Boiling Test. The test is simple and easy to perform; it can be performed either in the laboratory during mixture design or on the field-mixed materials. In general, the Texas Boiling Test offers good potential for use in detecting moisture susceptible mixtures before they are placed in the field. (Author)
Comparison Of BRDF Data From Two Scatterometers (1987)

The first serious attempts to measure optical scatter and use it to infer surface finish quality came about through the use of total integrated scatter (TIS) measurements. [1,2] In the early 1970&apos;s, one of the ASTM study groups ran a series of round robin measurements to determine the validity of comparing (TIS) measurements from one lab to another. Initial results were very discouraging. TIS values varied over orders of magnitude between labs and measurements were difficult to repeat from one round to the next at the same lab. Slowly, experience was gained in reducing operator error, limiting contamination problems and recognizing basic differences between the instruments under use. The importance of surface spatial frequency bandwidths was recognized and comparison results showed some improvement. In the mid-seventies, measurement of scatter, as a function of angle from specular, was used to obtain more information about surface finish. [2,3,4,5,6] The scatter research of the 1970&apos;s is now being combined with the computers of the 1980&apos;s to produce fast, accurate scatter inspection systems to help meet the increased demands for low scatter optics. [2,7] Although most of these systems produce the bidirectional scatter (reflectance, transmission) distribution function (BSDF, BRDF, BTDF), some are capable of producing surface statistics as well. The BRDF can be used to calculate a surface power spectral density (PSD) function, which in turn provides values of root mean square roughness and a transverse length parameter. The question of how these instruments relate to the surface statistic nproduced by surface profiling instruments is now being studied. [8] More basic, however, is the old question of whether BRDF (or PSD) measurements can be repeated from lab to lab. The authors decided to do a comparison between a Lawrence Livermore National Laboratory instrument, the Angle Resolved Scatterometer (ARS) [2], and a Complete Angle Scatter Instrument (CASI) developed at Toomay, Mathis &amp; Associates. [7]
Synthesis of Anthradithiophene Containing Conjugated Polymers via a Cross-coupling Strategy (2020)

New conjugated polymers that incorporate dihexylanthradithiophene (DHADT) in the main chain were prepared by Stille and Sonogashira cross-coupling polymerization reactions. The polymerization chemistry is enabled by a soluble 5,11-dibromodihexylanthradithiophene monomer that is capable of cross-coupling reactions. Four readily soluble DHADT containing co-polymers were prepared and characterized experimentally and computationally. These polymers possess HOMO energies of -5.18 eV to -5.43 eV and LUMO energies of -3.0 eV to -2.82 eV. The notable optical features include broad absorption and band gaps ranging from 1.62 eV to 2.15 eV.
Incidence and Natural History of Mycobacterium avium -Complex Infections in Patients with Advanced Human Immunodeficiency Virus Disease Treated with Zidovudine (1992)

To determine the incidence and natural history of Mycobacterium avium-complex infections in persons with advanced human immunodeficiency virus (HIV) infection, we studied a multicenter cohort of 1,020 persons with acquired immunodeficiency syndrome (AIDS) or the AIDS-related complex (ARC) and CD4 cell count < 0.250 x 10(9)/L initially treated with zidovudine between April 1987 and April 1988. M. avium-complex infections developed in 123 (12%) patients during follow-up, with a 2-yr actuarial risk of 19%. Patients with an initial diagnosis of Pneumocystis carinii pneumonia were more likely to develop M. avium-complex infections than patients with an initial diagnosis of another opportunistic disease or of ARC (p = 0.002). Individuals developing M. avium-complex infections had lower baseline CD4 cell counts, hematocrits, lymphocyte counts, and total white blood cell counts than those who did not develop M. avium-complex infection. During follow-up, individuals who developed M. avium-complex infections were more likely to have severe anemia, to experience zidovudine dose reductions, and to die than were patients without M. avium-complex (p < 0.001). By proportional hazards analysis, a baseline CD4 cell count < 0.100 x 10(9)/L, development of severe anemia, P. carinii pneumonia during follow-up, and zidovudine dose interruption were significantly associated with subsequently developing M. avium-complex infection. A proportional hazards analysis of survival showed that M. avium-complex infection, severe anemia, zidovudine dose interruption, occurrence of an opportunistic infection, CD4 cell count < 0.100 x 10(9)/L, baseline AIDS diagnosis, and transfusion independently predicted an increased risk of death.(ABSTRACT TRUNCATED AT 250 WORDS)
Clavicipitalean Fungi (2003)

Historical Perspectives:Human Interactions with Clavicipitalean Fungi. TAXONOMY AND DIVERSITY. A Taxonomic Review of the Clavicipitaceous Anamorphs Parasitizing Nematodes and Other Microinvertebrates. Clavicipitaceous Anamorphs. The Plant-Infecting Clavicipitaleans. Distinguishing Features of the Tribe Balansieae. Taxonomy and Diversity of EpichloA Endophytes. Diversity and Speciation in Claviceps. Nigrocornus scleroticus,A Common Old World Balansioid Fungus. ECOLOGY AND EVOLUTION. Processes of Species Evolution in EpichloA/Neotyphodium Endophytes of Grasses. Interkingdom Host Shift in the Cordyceps Fungi. The Evolutionary Strategy of Claviceps. MOLECULAR GENETICS AND PHYSIOLOGY. Secondary Metabolites of Clavicipitalean Fungi. Molecular Genetics of Ergot Alkaloid Biosynthesis. Genetic Manipulation of Clavicipitalean Endophytes. Molecular Aspects of Host -Pathogen Interactions and Ergot Alkaloid Biosynthesis in Claviceps. IMPACTS AND APPLICATIONS. Ergot Alkaloid Toxicity. Commercial Applications of Endophytic Fungi. Use of Clavicipitalean Fungi for the Biological Control of Arthropod Pests. Evidence for Nematode Defense in Symbiotic Grasses. Index.
Development of a Constitutive Material Model with Progressive Failure and Damage for Woven Thermoplastic Composites (2016)

This paper describes the behavior of the DuPontâ„¢ Vizilonâ„¢ thermoplastic composite sheet materials and matches this to composite models as implemented in Abaqus [1] and LS-DYNA [2]. The performance of the models with the corresponding material parameters are evaluated by simulating material specimen tests and structural beam component. The results show limitations of current composite material models in Abaqus [1] when applied to thermoplastics. To obtain a more accurate description of the actual material behavior, DuPont has developed a User material model by combining both plastic deformation of the thermoplastic matrix material with a more classical composite damage model for the description of the nonlinear permanent deformation of the woven continuous fiber reinforcement. The results obtained with this model are presented, demonstrating accurate prediction results and the potential of this model for thermoplastic composites.
Location normalization for information extraction (2002)

Ambiguity is very high for location names. For example, there are 23 cities named 'Buffalo' in the U.S. Country names such as 'Canada', 'Brazil' and 'China' are also city names in the USA. Almost every city has a Main Street or Broadway. Such ambiguity needs to be handled before we can refer to location names for visualization of related extracted events. This paper presents a hybrid approach for location normalization which combines (i) lexical grammar driven by local context constraints, (ii) graph search for maximum spanning tree and (iii) integration of semi-automatically derived default senses. The focus is on resolving ambiguities for the following types of location names: island, town, city, province, and country. The results are promising with 93.8% accuracy on our test collections.
Screening for osteoporosis after trauma (2014)

Diagnostic study, level II.
Lipoprotein Particle Size and Concentration by Nuclear Magnetic Resonance and Incident Type 2 Diabetes in Women (2010)

In this prospective study of women, NMR lipoprotein size and concentrations were associated with incident type 2 diabetes and remained significant after adjustment for established risk factors, including HDL cholesterol and triglycerides.
The Electrochemical Properties and Mechanism of Formation of Anodic Oxide Films on Mg-Al Alloys (2003)

The electrochemical properties and the mechanism of formation of anodic oxide films on Mg alloys containing 0-15 mass% Al, when anodized in NaOH solution, were investigated by focusing on the effects of anodizing potential, Al content, and anodizing time. The intensity ratio of Mg(OH)₂ in the XRD analysis decreased with increasing applied potential, while that of MgO increased. Mg(OH)₂ was barely detected at 80 V, while MgO was readily detected. The anti-corrosion properties of anodized specimens at each constant potential were better than those of non-anodized specimens. The specimen anodized at an applied potential of 3 V had the best anti-corrosion property. The intensity ratio of the β phase increased with aluminum content in Mg-Al alloys. During anodizing, the active dissolution reaction occurred preferentially in β phase until about 4 min, and then the current density increased gradually until 7 min. The dissolution reaction progressed in α phase, which had a lower Al content. In the anodic polarization test in 0.017 mol·<TEX>$dm^{-3}$</TEX> NaCl and 0.1 mol·<TEX>$dm^{-3}$</TEX> Na₂SO₄ at 298 K, the current density of Mg-15 mass% Al alloy anodized for 10 min increased, since the anodic film that forms on the α phase is a non-compacted film. The anodic film on the α phase at 30 min was a compact film as compared with that at 10 min.
Effect of Hydrostatic Pressure on Martensitic Transformations in Fe&ndash;Ni and Fe&ndash;Ni&ndash;C Alloys (1988)

Effects of hydrostatic pressure on martensitic transformations in Fe-29.9Ni and Fe-24.6Ni-1.8C (at%) alloys have been investigated by means of electrical resistivity and magnetization measurements and optical microscopy under a pressure of up to 1.5 GPa. As a result, the followings were found: Transformation temperatures under hydrostatic pressure, Ms′, shift from that under no pressure, Ms, and the amount of the shift, ΔMs=Ms−Ms′, increases curvilinearly with increasing hydrostatic pressure. In the increasing manner of ΔMs, however, a considerable difference is recognized between the Invar Fe–Ni alloy and the non-Invar Fe–Ni–C alloy. The amount of the martensites induced at Ms′ decreases with increasing hydrostatic pressure. Morphology of the hydrostatic pressure-induced martensites is the same as that of the thermally-induced ones irrespective of the formation temperature. A thermodynamical analysis for the hydrostatic pressure dependence of the transformation temperature shows that other effects should be taken into consideration besides the effect that the volume expansion associated with the martensitic transformation is opposed to hydrostatic pressure as has previously been proposed.
ChemInform Abstract: GEM‐CHLORO(TRIMETHYLSILYL)ALLYLLITHIUM‐ A NOVEL AMBIDENT NUCLEOPHILE (1979)

Abstract Da die direkte Metallierung von (I) nur in geringer Ausbeute oder nur als Zwischenprodukt zu (V) fuhrt, ist der Umweg über die Umlagerungsprodukte (II) und (III) nötig.
Note on edge waves in a stratified fluid (1966)

The solution given by Gerstner for water waves of finite amplitude, which is valid for a semi-infinite liquid of arbitrary stratification, is reconsidered. By a transformation of co-ordinates, it is shown to represent edge waves propagating along a sloping shore.
Molecular engineering of Surfaces Using Self-Assembled Monolayers (2005)

The self-assembly of molecules into structurally organized monolayers (SAMs) uses the flexibility of organic chemistry and coordination chemistry to generate well-defined, synthetic surfaces with known molecular and macroscopic properties. The process of designing monolayers with a specified structure gives a high level of control over the molecular-level composition in the direction perpendicular to a surface; soft lithographic technique gives useful (if lower) resolution in the plane of the surface. Alkanethiolates adsorbed on gold, silver, mercury, palladium and platinum are currently the best-defined systems of SAMs. They provide substrates for a number of applications-from studies of wetting and electron transport to patterns for growing mammalian cells. SAMs have made organic surfaces a central part of surface science. Understanding the principles by which they form, and connecting molecular-level structure with macroscopic properties, opens a wide range of areas to study and exploitation.