gebhart/patrepeval huggingface dataset:
Promotion of Feeder-Independent Self-Renewal of Embryonic Stem Cells by Retinol (Vitamin A) (2008)

Retinol, the alcohol form of vitamin A, maintains pluripotency of mouse embryonic stem cells (ESCs) by the overexpression of Nanog, which is a key transcription factor for their self-renewal. ESCs represent the most promising source of all types of cells for regenerative medicine and drug discovery. These cells maintain pluripotency through a complex interplay of different signaling pathways and transcription factors including leukemia inhibitory factor (LIF), homeodomain protein Nanog, and Oct3/4. Nanog, however, plays a key role in maintaining the pluripotency of mouse and human ESCs. Overexpression of nanog by heterologous promoters can maintain pluripotency of ESCs in the absence of LIF. Also, Nanog alone is sufficient for the self-renewal of ESCs while maintaining the Oct4 levels. Normally, mouse and human ESCs are cultured over mouse embryonic fibroblasts as feeders to maintain pluripotency. Although feeder cells provide important growth(-)promoting factors, their use involves several cumbersome and time-consuming steps. Here we demonstrate that retinol can support feeder-independent self-renewal of ESCs in long-term cultures without affecting their pluripotency. The effect of retinol is independent of the strain background, and the cells maintain complete potential to differentiate into all the primary germ layers in embryoid bodies and in chimeric animals. Self-renewal of ESCs by retinol is not mediated by retinoic acid. The studies demonstrate for the first time that a physiologically relevant small molecule has growth-promoting effect on the self-renewal of ESCs by activating the endogenous machinery to overexpress a critical gene for pluripotency.
Creutzfeldt‐Jakob disease in a recipient of human pituitary‐derived gonadotrophin (1990)

A forty-year-old female presented with an unsteady gait 13 years after receiving an eight-month course of human pituitary-derived gonadotrophin injections as treatment for infertility. Over the next ten months the patient subsequently developed generalised myoclonic jerks and dementia and finally died. Neuropathological examination revealed changes in the brain consistent with Creutzfeldt-Jakob disease. This is the first reported case of Creutzfeldt-Jakob disease in a recipient of human derived gonadotrophin.
Direct Guanidinylation of Aryl and Heteroaryl Halides via Copper-Catalyzed Cross-Coupling Reaction (2011)

A modified Ullmann reaction using p-methoxybenzyl (PMB) guanidine as guanidinylation agent yielded various aryl and heteroaryl guanidines in good yields.
Identification of Mrj, a DnaJ/Hsp40 Family Protein, as a Keratin 8/18 Filament Regulatory Protein (2000)

To elucidate the function of keratins 8 and 18 (K8/18), major components of the intermediate filaments of simple epithelia, we searched for K8/18-binding proteins by screening a yeast two-hybrid library. We report here that human Mrj, a DnaJ/Hsp40 family protein, directly binds to K18. Among the interactions between DnaJ/Hsp40 family proteins and various intermediate filament proteins that we tested using two-hybrid methods, Mrj specifically interacted with K18. Immunostaining with anti-Mrj antibody showed that Mrj colocalized with K8/18 filaments in HeLa cells. Mrj was immunoprecipitated not only with K18, but also with the stress-induced and constitutively expressed heat shock protein Hsp/c70. Mrj bound to K18 through its C terminus and interacted with Hsp/c70 via its N terminus, which contains the J domain. Microinjection of anti-Mrj antibody resulted in the disorganization of K8/18 filaments, without effects on the organization of actin filaments and microtubules. Taken together, these results suggest that Mrj may play an important role in the regulation of K8/18 filament organization as a K18-specific co-chaperone working together with Hsp/c70.
Comparative Mapping of Recombinant Proteins and Glycoproteins by Plasma Desorption and Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (1994)

The mass spectrometric (MS) techniques of 252Cf-plasma desorption (PD) and matrix-assisted laser desorption/ionization (MALDI) are compared in the molecular weight determination and the mapping analysis of several recombinant proteins and glycoproteins. MALDI MS analysis exhibited better sensitivity and mass measurement accuracy and a remarkably short analysis time compared with PD MS analysis. The latter was not successful in the analysis of rhIFN-gamma and the higher mass mammalian cell-derived IL-5 glycoproteins. Mapping of the Escherichia coli-derived rhIFN alpha-2b and rhIL-4 proteins, by direct PD or MALDI MS analysis of the trypsin-generated peptide mixtures provided signals for ca. 95% and 88% of the expected tryptic peptides, respectively. Peptide signals below m/z 1500 were generally more intense in the PD mass spectra, while higher mass signals were more intense in the MALDI mass spectra. Both PD and MALDI MS analyses provided a rapid confirmation of the existing two and three disulfide bonds in the rhIFN alpha-2b and rhIL-4 proteins, respectively. In the mapping of the CHO IL-4 glycoprotein, detection of the trypsin-generated glycopeptides was only possible by MALDI, where their detection was greatly improved by using the super-DHB (sDHB) matrix, a 9:1 mixture of 2,5-dihydroxybenzoic acid (DHB) with 2-hydroxy-5-methoxybenzoic acid. This sDHB matrix also generated significantly enhanced and better resolved MALDI peptide signals, which in turn resulted in a much improved mass measurement accuracy.
p53-Independent Roles of MDM2 in NF-κB Signaling: Implications for Cancer Therapy, Wound Healing, and Autoimmune Diseases (2012)

Murine double minute-2 (MDM2) is an intracellular molecule with multiple biologic functions. It serves as a negative regulator of p53 and thereby limits cell cycle arrest and apoptosis. Because MDM2 blockade suppresses tumor cell growth in vitro and in vivo, respective MDM2 inhibition is currently evaluated as anti-cancer therapy in clinical trials. However, the anti-proliferative effects of MDM2 inhibition also impair regenerative cell growth upon tissue injury. This was so far documented for tubular repair upon postischemic acute kidney injury and might apply to wound healing responses in general. Furthermore, MDM2 has numerous p53-independent effects. As a new entry, MDM2 was identified to act as a co-transcription factor for nuclear factor-kappa-light-enhancer of activated B cells (NF-κB) at cytokine promoters. This explains the potent anti-inflammatory effects of MDM2 inhibitors in vitro and in vivo. For example, the NF-κB-antagonistic and p53-agonistic activities of MDM2 inhibitors elicit potent therapeutic effects on experimental lymphoproliferative autoimmune disorders such as systemic lupus erythematosus. In this review, we discuss the classic p53-dependent, the recently discovered p53-independent, and the NF-κB-agonistic biologic functions of MDM2. We describe its complex regulatory role on p53 and NF-κB signaling and name areas of research that may help to foresee previously unexpected effects or potential alternative indications of therapeutic MDM2 blockade.
Electron-hole diffusion lengths > 175 μm in solution-grown CH 3 NH 3 PbI 3 single crystals (2015)

Long, balanced electron and hole diffusion lengths greater than 100 nanometers in the polycrystalline organolead trihalide compound CH3NH3PbI3 are critical for highly efficient perovskite solar cells. We found that the diffusion lengths in CH3NH3PbI3 single crystals grown by a solution-growth method can exceed 175 micrometers under 1 sun (100 mW cm(-2)) illumination and exceed 3 millimeters under weak light for both electrons and holes. The internal quantum efficiencies approach 100% in 3-millimeter-thick single-crystal perovskite solar cells under weak light. These long diffusion lengths result from greater carrier mobility, longer lifetime, and much smaller trap densities in the single crystals than in polycrystalline thin films. The long carrier diffusion lengths enabled the use of CH3NH3PbI3 in radiation sensing and energy harvesting through the gammavoltaic effect, with an efficiency of 3.9% measured with an intense cesium-137 source.
Measuring blood volume with fluorescent-labeled hydroxyethyl starch (2000)

These data support the view that hydroxyethyl starch provides a valid alternative to red cell labels as a means of calculating blood volume in patients. Labeling the starch with a fluorescent marker makes the assay procedure more sensitive and infinitely easier. The dose required is not high enough to affect the hemodynamic status of the patient.
Omega-3 Long Chain Polyunsaturated Fatty Acids for Treatment of Parenteral Nutrition–Associated Liver Disease: A Review of the Literature (2011)

Parenteral nutrition-associated liver disease (PNALD) is a complex disease that is diagnosed by clinical presentation, biochemical markers of liver injury, concurrent use of parenteral nutrition (PN), and negative workup for other causes of liver disease. For the past 30 years, clinicians have had few effective treatments for PNALD and when disease progressed to liver cirrhosis it was historically associated with poor outcomes. Within the past 5 years there has been some encouraging evidence for the potential benefits of fish oils, rich in omega-3 long-chain polyunsaturated fatty acids (ω3PUFA), in reversing liver injury associated with PN. This article reviews the current literature relating to ω3PUFA and PNALD.
Gas-phase cyclisation reactions of 1-(2-arylthiophenyl)alkaniminyl and 2-(aryliminomethyl)thiophenoxyl radicals (2001)

Flash vacuum pyrolysis (FVP) of the oxime ethers 12–14 and of the sulfides 18–20 at 650 °C (10−2–10−3 Torr) gave products derived from the corresponding iminyl and thiophenoxyl radicals. In all cases, benz[d]isothiazoles (e.g., 26) are formed as major products viaSHi mechanisms though the yields are greatest with the iminyl precursors. Alternative pathways observed from the thiophenoxyls in specific cases include the formation of the anilinobenzothiophene 36 and of dibenzothiophene 23, via an SHi process and a spirodienyl rearrangement, respectively. There is no evidence for significant interconversion of the iminyl and thiophenoxyl species.
Role of Cellulose Fibrils and Exopolysaccharides of Rhizobium leguminosarum in Attachment to and Infection of Vicia sativa Root Hairs (2005)

Infection and subsequent nodulation of legume host plants by the root nodule symbiote Rhizobium leguminosarum usually require attachment of the bacteria to root-hair tips. Bacterial cellulose fibrils have been shown to be involved in this attachment process but appeared not to be essential for successful nodulation. Detailed analysis of Vicia sativa root-hair infection by wild-type Rhizobium leguminosarum RBL5523 and its cellulose fibril-deficient celE mutant showed that wild-type bacteria infected elongated growing root hairs, whereas cellulose-deficient bacteria infected young emerging root hairs. Exopolysaccharide-deficient strains that retained the ability to produce cellulose fibrils could also infect elongated root hairs but infection thread colonization was defective. Cellulose-mediated agglutination of these bacteria in the root-hair curl appeared to prevent entry into the induced infection thread. Infection experiments with V sativa roots and an extracellular polysaccharide (EPS)- and cellulose-deficient double mutant showed that cellulose-mediated agglutination of the EPS-deficient bacteria in the infection thread was now abolished and that infection thread colonization was partially restored. Interestingly, in this case, infection threads were initiated in root hairs that originated from the cortical cell layers of the root and not in epidermal root hairs. Apparently, surface polysaccharides of R. leguminosarum, such as cellulose fibrils, are determining factors for infection of different developmental stages of root hairs.
A new approach to detecting memory access errors in C programs (2007)

Memory access errors such as out-of-bounds, pointer abuses, and illegal freeing are one of the principal reasons for failures of C programs. As a result, a number of research works have focused on the problem of dynamic detection of memory access errors in C programs. However, existing approaches have one or more of the following problems: inability to detect all memory errors, changing the memory allocation mechanism, incompatibility with libraries, and excessive performance overheads. In this paper, we suggest a new approach to cope with these problems. The primary goal of our approach is to present an effective technique with high precision, better performance, and the relatively low space overheads. Our approach combines source code transformation to improve accuracy and the efficient data structures (i.e., bitmap scheme) to obtain better performance.
663. 1 : 4-Diaryl-1 : 4-dihydro-1 : 2 : 4 : 5-tetrazines and derived substances (1950)

W. Baker, W. D. Ollis and V. D. Poole, J. Chem. Soc., 1950, 3389 DOI: 10.1039/JR9500003389
Conceptual Frameworks and Educational Policies (2006)

This research synthesis is framed by conceptual considerations, discussed in this chapter, as well as by methodological approaches (see Appendix). Three conceptual and policy issues that guide the work reviewed here are: (a) perspectives on the epistemology of science, that is, what counts as science and school science; (b) theoretical perspectives guiding the research literature; and (c) the policy context of high-stakes assessment and accountability.
Microwave tomography for functional imaging of extremity soft tissues: feasibility assessment (2007)

It is important to assess the viability of extremity soft tissues, as this component is often the determinant of the final outcome of fracture treatment. Microwave tomography (MWT) and sensing might be able to provide a fast and mobile assessment of such properties. MWT imaging of extremities possesses a complicated, nonlinear, high dielectric contrast inverse problem of diffraction tomography. There is a high dielectric contrast between bone and soft tissue in the extremities. A contrast between soft tissue abnormalities is less pronounced when compared with the high bone-soft tissue contrast. The goal of this study was to assess the feasibility of MWT for functional imaging of extremity soft tissues, i.e. to detect a relatively small contrast within soft tissues in closer proximity to high contrast boney areas. Both experimental studies and computer simulation were performed. Experiments were conducted using live pigs with compromised blood flow and compartment syndrome within an extremity. A whole 2D tomographic imaging cycle at 1 GHz was computer simulated and images were reconstructed using the Newton, MR-CSI and modified Born methods. Results of experimental studies demonstrate that microwave technology is sensitive to changes in the soft tissue blood content and elevated compartment pressure. It was demonstrated that MWT is feasible for functional imaging of extremity soft tissues, circulatory-related changes, blood flow and elevated compartment pressure.
A 2D-DIGE Approach To Identify Proteins Involved in Inside-Out Control of Integrins (2009)

Leukocyte integrins are functionally regulated by "inside-out" signaling, meaning that stimulus-induced signaling pathways act on the intracellular integrin tail and induce activation of the receptor at the outside. Both a change in conformation (affinity) and in clustering (avidity/valency) of the receptors has been described to occur. This inside-out signaling is essential for adequate migration of leukocytes to inflammatory sites; however, the exact underlying mechanism is not known. We used two variants of a mouse acute lymphocytic leukemia cell line (L1210), a suspension (L1210-S) and an adherent (L1210-A) variant that were characterized by nonactivated and activated integrins (beta(1), beta(2) and beta(3)), respectively. L1210-S and L1210-A cells were compared on protein expression profiles by two-dimensional fluorescence difference in-gel electrophoresis (2D-DIGE). We found 86 protein spots that were more than 1.25-fold different between L1210-A and L1210-S. Only 4 protein spots were more than 2.5-fold different. We identified 29 proteins by mass spectrometry among which were gelsolin, L-plastin, and Rho GTPase dissociation inhibitor 2. These proteins were upregulated in the L1210-A cells versus L1210-S, which was verified by Western blot analysis. Overexpression of gelsolin in U937 resulted in increased high affinity integrin expression and cell adhesion. Comparison of functionally different cell lines from similar origin by 2D-DIGE might be a successful approach to identify regulatory proteins involved in integrin inside-out control.
flk-1, an flt-related receptor tyrosine kinase is an early marker for endothelial cell precursors (1993)

ABSTRACT We have used RT-PCR to screen pluripotent murine embryonic stem cells to identify receptor tyrosine kinases (RTKs) potentially involved in the determination or differentiation of cell lineages during early mouse development. Fourteen different tyrosine kinase sequences were identified. The expression patterns of four RTKs have been examined and all are expressed in the mouse embryo during, or shortly after, gastrulation. We report here the detailed expression pattern of one such RTK, the flt-related gene flk-1. In situ hybridization analysis of the late primitive streak stage embryo revealed that flk-1 was expressed in the proximallateral embryonic mesoderm; tissue fated to become heart. By headfold stages, staining was confined to the endocardial cells of the heart primordia as well as to the blood islands of the visceral yolk sac and the developing allantois. Patchy, speckled staining was detected in the endothelium of all the major embryonic and extraembryonic blood vessels as they formed. During early organogenesis, expression was detected in the blood vessels of highly vascularized tissues such as the brain, liver, lungs and placenta. Since flk-1 was expressed in early mesodermal cells prior to any morphological evidence for endothelial cell differentiation (vasculogenesis), as well as in cells that form blood vessels from preexisting ones (angiogenesis), it appears to be a very early marker of endothelial cell precursors. We have previously reported that another novel RTK, designated tek, was expressed in differentiating endothelial cells. We show here that flk-1 transcripts are expressed one full embryonic day earlier than the first tek transcripts. The expression of these two RTKs appear to correlate with the specification and early differentiation of the endothelial cell lineage respectively, and therefore may play important roles in the establishment of this lineage.
Teaching Artificial Neural Systems To Drive: Manual Training Techniques For Autonomous Systems (1988)

We have developed a methodology for manually training autonomous control systems based on artificial neural systems (ANS). In applications where the rule set governing an expert&apos;s decisions is difficult to formulate, ANS can be used to extract rules by associating the information an expert receives with the actions he takes. Properly constructed networks imitate rules of behavior that permits them to function autonomously when they are trained on the spanning set of possible situations. This training can be provided manually, either under the direct supervision of a system trainer, or indirectly using a background mode where the network assimilates training data as the expert performs his day-to-day tasks. To demonstrate these methods we have trained an ANS network to drive a vehicle through simulated freeway traffic.
Determination of Surface Charge and Interface Trap Densities in Naturally Oxidized n-Type Si wafers Using ae Surface Photovoltages (1987)

An ac surface photovoltage method was applied in order to estimate the fixed oxide charge density in naturally oxidized n-type Si wafers. Three n-type Si wafers (100-mm diameter, 540-µm thick and a resistivity of 1.1 mΩ·m) were used after forming 2.4-nm oxide layers on their surfaces as the result of an alkaline rinse treatment. The ac surface photovoltages in the frequency range of 1 Hz to 10 kHz were analyzed using the half-sided junction model previously reported. The photon energy of the probing beam was 2.23 eV. The surface potential, fixed oxide charge and interface trap densities were determined to be –0.38 V, –0.93 mC·m -2 and 5×10 15 m -2 ·eV -1 , respectively.
Distribution of oxidation specific lipid-protein adducts and apolipoprotein B in atherosclerotic lesions of varying severity from WHHL rabbits. (1990)

Antisera and monoclonal antibodies generated against autologous malondialdehyde-conjugated low density lipoprotein (MDA-LDL), 4-hydroxynonenal conjugated LDL (4-HNE-LDL), and the protein fragments of apoprotein B resulting from the copper oxidation of LDL, as well as antibodies against apoprotein B, were used to immunostain atherosclerotic lesions of varying severity from Watanabe heritable hyperlipemic rabbits. In macrophage-rich fatty streaks and transitional lesions, all of the antibodies recognizing oxidation specific epitopes exhibited predominantly cell-associated staining in particulate and annular patterns. This is in contrast to the limited, extracellular, diffuse staining obtained with the antibodies recognizing apoprotein B. In more advanced lesions containing areas with reduced numbers of cells, there was increased extracellular, diffuse staining with the antibodies against oxidation specific epitopes and co-localization with apoprotein B. In addition, there were annular staining patterns associated with the necrotic core and increased staining of intimal and medial smooth muscle cells. We interpret these data as suggesting that in areas of lesions rich in macrophages, LDL is oxidized and taken up by the cells. In more advanced lesions that are relatively devoid of macrophages, both native and oxidized LDL, as well as oxidation products released from dead and decaying cells, are trapped in the matrix, out of reach of those cells capable of accumulating oxidized LDL.
Proteolytic inactivation of alpha 1-proteinase inhibitor and alpha 1-antichymotrypsin by oxidatively activated human neutrophil metalloproteinases. (1992)

Human neutrophils use the H2O2-myeloperoxidase-chloride system to generate chlorinated oxidants capable of activating metalloproteinase zymogens that hydrolyze not only native and denatured collagens, but also the serine proteinase inhibitor (serpin) alpha 1-proteinase inhibitor (alpha 1 PI). To identify the metalloenzyme that hydrolyzes and inactivates alpha 1 PI, neutrophil releasates were chromatographed over gelatin-Sepharose and divided into fractions containing either progelatinase or procollagenase. The gelatinase-containing fraction cleaved alpha 1 PI in a manner inhibitable by native type V, but not type I, collagen. Conversely, while the collagenase-containing fraction also cleaved alpha 1 PI, this activity was inhibited by type I, but not type V, collagen. Because type I and V collagens are competitive substrates for collagenase and gelatinase, respectively, each of the metalloproteinase zymogens were purified to apparent homogeneity and examined for alpha 1 PI-hydrolytic activities. Both purified gelatinase and collagenase inactivated alpha 1PI by hydrolyzing the serpin within its active-site loop at the Phe352-Leu353 and Pro357-Met358 bonds, albeit with distinct kinetic properties. Furthermore, purified collagenase, but not gelatinase, cleaved a second serpin, alpha 1-antichymotrypsin, by hydrolyzing the Ala362-Leu363 bond within its active-site loop. These data demonstrate that human neutrophils use chlorinated oxidants to activate collagenolytic metalloproteinases whose substrate specificities can be extended to members of the serpin superfamily.