gebhart/patrepeval huggingface dataset:
Sonic hedgehog signaling promotes motility and invasiveness of gastric cancer cells through TGF- -mediated activation of the ALK5-Smad 3 pathway (2007)

It is known that the activation of hedgehog (Hh) signaling is involved in the progression and invasion of various tumors, including gastric carcinoma. In this study, we investigated the impact of transforming growth factor (TGF)-beta signaling on the sonic hedgehog (Shh)-mediated invasion of gastric cancer cells. We found that higher concentrations of N-Shh enhanced cell motility and invasiveness in gastric cancer cells, whereas no increase was observed in cells that were treated with KAAD-cyclopamine (a Shh signaling inhibitor) or anti-Shh blocking antibodies. In addition, the N-Shh-induced migration and invasiveness of gastric cancer cells were reduced by treatment with anti-TGF-beta blocking antibody or TGF-beta1 small interfering RNA (siRNA) in presence of N-Shh when compared with control groups. Furthermore, TGF-beta1 secretion, TGF-beta-mediated transcriptional response, expression of activin receptor-like kinase (ALK) 5 protein and phosphorylation of Smad 3 were also enhanced by treatment with N-Shh, but not KAAD-cyclopamine, anti-Shh or TGF-beta1 blocking antibodies. Blockade of the ALK5 kinase in the presence of N-Shh significantly inhibited phosphorylation of Smad 3, activity of matrix metalloproteinases and Shh-induced cell motility/invasiveness. Importantly, transient expression of ALK5 siRNA or Smad 3 siRNA reduced the ability of N-Shh to stimulate migration and invasion of those cells compared with the cells treated with non-specific control siRNA. In summary, these results indicate that Shh promotes motility and invasiveness of gastric cancer cells through TGF-beta-mediated activation of the ALK5-Smad 3 pathway. Additionally, our findings are the first to suggest a role and mechanism for Shh signaling as it relates to the metastatic potential of gastric cancer, thereby indicating potential therapeutic molecular targets to decrease metastasis.
Synthesis, Characterization, and Surface Immobilization of Metal Nanoparticles Encapsulated within Bifunctionalized Dendrimers (2003)

Bifunctionalized poly(amidoamine) dendrimers having both quaternary ammonium groups and primary amines on their periphery were prepared. Pd and Pt nanoparticles were encapsulated within these dendrimers by extraction of the metal ions into their interior, followed by chemical reduction. The high positive charge on the surface of these dendrimers reduces the likelihood of agglomeration, and the unquaternized amine groups provide a reactive handle for immobilizing the dendrimer-encapsulated nanoparticles (DENs) onto surfaces. High-resolution transmission electron microscopy images reveal that both encapsulated Pd and Pt nanoparticles are nearly monodisperse with an average diameter of 1.7 ± 0.3 nm. Pd and Pt DENs were immobilized onto Au surfaces using an intermediary self-assembled monolayer as an adhesion layer. Only a small fraction of the resulting nanoparticle monolayer is lost when sonicated in an acidic aqueous solution or subjected to electrochemical cycling.
Identification of a New Class of Lipid Droplet-Associated Proteins in Plants 1(C)(W)(OPEN) (2013)

Lipid droplets in plants (also known as oil bodies, lipid bodies, or oleosomes) are well characterized in seeds, and oleosins, the major proteins associated with their surface, were shown to be important for stabilizing lipid droplets during seed desiccation and rehydration. However, lipid droplets occur in essentially all plant cell types, many of which may not require oleosinmediated stabilization. The proteins associated with the surface of nonseed lipid droplets, which are likely to influence the formation, stability, and turnover of this compartment, remain to be elucidated. Here, we have combined lipidomic, proteomic, and transcriptomic studies of avocado (Persea americana) mesocarp to identify two new lipid droplet-associated proteins, which we named LDAP1 and LDAP2. These proteins are highly similar to each other and also to the small rubber particle proteins that accumulate in rubber-producing plants. An Arabidopsis (Arabidopsis thaliana) homolog to LDAP1 and LDAP2, At3g05500, was localized to the surface of lipid droplets after transient expression in tobacco (Nicotiana tabacum) cells that were induced to accumulate triacylglycerols. We propose that small rubber particle protein-like proteins are involved in the general process of binding and perhaps the stabilization of lipid-rich particles in the cytosol of plant cells and that the avocado and Arabidopsis protein members reveal a new aspect of the cellular machinery that is involved in the packaging of triacylglycerols in plant tissues.
Peak-to-average power ratio reduction in OFDM based on transformation of partial transmit sequences (2006)

A novel scheme (transformation of partial transmit sequences, T-PTS) is proposed for the partial transmit sequence (PTS) method to reduce peak-to-average power ratio of OFDM signals. In T-PTS certain transformations are applied on partial transmit sequences to generate more candidates for increasing performance. Simulations show that T-PTS outperforms conventional PTS for the same number of subblocks; and both schemes have similar performance for the same candidate number, but T-PTS is less complex.
A New Powerful Reducing Agent—Sodium Borohydride in the Presence of Aluminum Chloride and Other Polyvalent Metal Halides1,2 (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA New Powerful Reducing Agent—Sodium Borohydride in the Presence of Aluminum Chloride and Other Polyvalent Metal Halides1,2Herbert C. Brown and B. C. Subba RaoCite this: J. Am. Chem. Soc. 1956, 78, 11, 2582–2588Publication Date (Print):June 1, 1956Publication History Published online1 May 2002Published inissue 1 June 1956https://pubs.acs.org/doi/10.1021/ja01592a070https://doi.org/10.1021/ja01592a070research-articleACS PublicationsRequest reuse permissionsArticle Views12928Altmetric-Citations201LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Local effects of silica on tumor growth inhibition. A histological study. (1975)

The subcutaneous implant of a fibrosarcoma covered with silica, in rats, resulted in a temporary retardation of tumor growth. The histological study demonstrated that the silica provoked, within and at the periphery of the tumor, inflammatory foci which altered the composition of the fundamental substance and which promoted the accumulation of principally macrophages in the interior as well as on the surface of the tumoral mass. Besides the macrophages of the host, a number of tumor cells do also phagocyte silica crystals, leading to destruction of all those cells. The authors are of the opinion that the local modifications provoked by silica, could have interfered in the adaptation of the tumor with its nutrient stroma. Of these modifications, the stroma sclerosis seems to be the most effective in the inhibition of tumor growth. Some correlations were suggested between the here described results and those obtained by other workers who have used other inflammatory agents of different nature.
A New Diagnostic Test for Arrhythmogenic Right Ventricular Cardiomyopathy (2009)

Routine immunohistochemical analysis of a conventional endomyocardial-biopsy sample appears to be a highly sensitive and specific diagnostic test for ARVC.
Antibody Engineering: Humanization, Affinity Maturation, and Selection Techniques (2009)

This chapter contains sections titled: Introduction Humanization Methods Affinity Maturation Selection Techniques Future Directions References
Reactive Molecules: The Neutral Reactive Intermediates in Organic Chemistry (1984)

Designed for advanced undergraduate and graduate organic chemistry students, here's an up-to-date, in-depth textbook on the chemistry of neutral reactive intermediates--free radicals, diradicals, carbenes, nitrenes, strained rings, and antiaromatics. Includes numerous tables of physical data and extensive references to present day research in the field.
Luminescence and Energy Transfer in Solutions of Rare-Earth Complexes. I. Enhancement of Fluorescence by Deuterium Substitution (1965)

Fluorescence yields and lifetimes of solutions of europium and terbium salts in solution are greatly enhanced by using deuterated solvents. The magnitude of increase varies from an 18-fold enhancement in yield and lifetime for an aqueous solution of europium nitrate to a twofold enhancement for europium ethylenediaminetetra-acetate dissolved in methanol. The enhancement is proportional to the fraction of deuterated solvent present. Results lead to conclusions that the dominant mode of radiationless deactivation of a rare-earth ion in solution is via loss of energy to hydrogen vibrations. Further, such loss is proportional to the number of hydrogen vibrations in the local rare-earth environment. Values for the rate constant for radiationless loss of energy to hydrogen vibrations are determined for the salts studied. The influence upon radiationless processes of complexing between the rare earth and anion is discussed. Likewise the dependence of the enhancement factor upon the rare-earth ion is considered. There is no evidence that the lifetime from the 5D1 level of europium nitrate is enhanced by deuterium substitution. This lifetime is ≤5 μsec in both D2O and H2O solutions.
Zebra striped network file system (1992)

The Zebra Striped Network File System by John Henry Hartman Doctor of Philosophy in Computer Science University of California at Berkeley Professor John Ousterhout, Chair This dissertation presents a new network file system, called Zebra, that provides high performance file access and is highly available. Zebra stripes file data across its servers, so that multiple servers may participate in a file access and the file access bandwidth therefore scales with the number of servers. Zebra is also highly available because it stores parity information in the style of a RAID [Patterson88] disk array; this increases storage costs slightly but allows the system to continue operation even while a single storage server is unavailable. Zebra is different from other striped network file systems in the way in which it stripes data. Instead of striping individual files (file-based striping), Zebra forms the data written by each client into an append-only log, which is then striped across the servers....
Least-square inversion with inexact adjoints. Method of conjugate directions: A tutorial (2000)

This tutorial describes the classic method of conjugate directions: the generalization of the conjugate-gradient method in iterative least-square inversion. I derive the algebraic equations of the conjugate-direction method from general optimization principles. The derivation explains the “magic” properties of conjugate gradients. It also justifies the use of conjugate directions in cases when these properties are distorted either by computational errors or by inexact adjoint operators. The extra cost comes from storing a larger number of previous search directions in the computer memory. A simple ratfor program and three examples illustrate the method.
Theory of NMR signal behavior in magnetically inhomogeneous tissues: The static dephasing regime (1994)

This paper is devoted to a theory of the NMR signal behavior in biological tissues in the presence of static magnetic field inhomogeneities. We have developed an approach that analytically describes the NMR signal in the static dephasing regime where diffusion phenomena may be ignored. This approach has been applied to evaluate the NMR signal in the presence of a blood vessel network (with an application to functional imaging), bone marrow (for two specific trabecular structures, asymmetrical and columnar) and a ferrite contrast agent. All investigated systems have some common behavior. If the echo time TE is less than a known characteristic time tc for a given system, then the signal decays exponentially with an argument which depends quadratically on TE. This is equivalent to an R2* relaxation rate which is a linear function of TE. In the opposite case, when TE is greater than tc, the NMR signal follows a simple exponential decay and the relaxation rate does not depend on the echo time. For this time interval, R2* is a linear function of a) volume fraction sigma occupied by the field-creating objects, b) magnetic field Bo or just the objects' magnetic moment for ferrite particles, and c) susceptibility difference delta chi between the objects and the medium.
Brain-Derived Neurotrophic Factor Contributes to Recovery of Skilled Reaching After Focal Ischemia in Rats (2009)

This study is the first to identify a critical role for BDNF in rehabilitation-induced recovery after stroke, and our results suggest that new treatments to enhance BDNF would constitute a promising therapy for promoting recovery of function after stroke.
Expression of the vascular endothelial growth factor (VEGF) receptor gene, KDR, in hematopoietic cells and inhibitory effect of VEGF on apoptotic cell death caused by ionizing radiation. (1995)

Vascular endothelial growth factor (VEGF) has been identified as a peptide growth factor specific for vascular endothelial cells. In this study, we demonstrated the expression of the KDR gene transcript, which encodes a cell surface receptor for VEGF, in normal human hematopoietic stem cells, megakaryocytes, and platelets as well as in human leukemia cell lines, HEL and CMK86. Moreover, we showed the expression of VEGF gene transcript in these normal fresh cells and cell lines. To elucidate biological functions of VEGF on hematopoiesis, we determined whether this growth factor has mitogenic activity to hematopoietic cells or the ability to suppress apoptotic cell death. The liquid culture and colony-formation assay revealed that VEGF suppressed apoptotic cell death of both CMK86 cells and normal hematopoietic stem cells caused by gamma-ray irradiation, although mitogenic activity of VEGF was not detected. The ability of VEGF to suppress apoptotic cell death was independent of the change of cell cycle distribution. These data suggest that VEGF may play an important role in survival or maintenance of hematopoietic stem cells due to the prevention of apoptotic cell death caused by some stresses such as ionizing radiation and that VEGF may give leukemia cells some abilities of resistance against radiotherapy in an autocrine or paracrine manner.
Substrate specificity of human prolyl-4-hydroxylase (1998)

Proline analogs (3-F, 3-Cl, 3-Br, 3,3-cyclopropyl, 3,3-methylene, 3-Me, and 4-Me) were synthesized, incorporated into CbzGlyPheXGlyOEt, and tested as substrate analogues/mechanistic probes for the human prolyl-4-hydroxylase catalyzed hydroxylation reaction. With the exception of the 3-fluoroproline containing peptide, none of these peptides were substrates for the enzyme.
A General Approach to One-Pot Fabrication of Crumpled Graphene-Based Nanohybrids for Energy Applications (2012)

Crumpled graphene oxide (GO)/graphene is a new type of carbon nanostructure that has drawn growing attention due to its three-dimensional open structure and excellent stability in an aqueous solution. Here we report a general and one-step approach to produce crumpled graphene (CG)-nanocrystal hybrids, which are produced by direct aerosolization of a GO suspension mixed with precursor ions. Nanocrystals spontaneously grow from precursor ions and assemble on both external and internal surfaces of CG balls during the solvent evaporation and GO crumpling process. More importantly, CG-nanocrystal hybrids can be directly deposited onto various current-collecting substrates, enabling their tremendous potential for energy applications. As a proof of concept, we demonstrate the use of hybrid electrodes of CG-Mn(3)O(4) and CG-SnO(2) in an electrochemical supercapacitor and a lithium-ion battery, respectively. The performance of the resulting capacitor/battery is attractive and outperforms conventional flat graphene-based hybrid devices. This study provides a new and facile route to fabricating high-performance hybrid CG-nanocrystal electrodes for various energy systems.
NCBI GEO: mining tens of millions of expression profiles--database and tools update (2006)

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment (MIAME)-compliant infrastructure that captures fully annotated raw and processed data. Several data deposit options and formats are supported, including web forms, spreadsheets, XML and Simple Omnibus Format in Text (SOFT). In addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in GEO. This paper provides a summary of the GEO database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. GEO is accessible at http://www.ncbi.nlm.nih.gov/geo/
Plant antitumor agents. VI. Isolation and structure of taxol, a novel antileukemic and antitumor agent from Taxus brevifolia (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPlant antitumor agents. VI. Isolation and structure of taxol, a novel antileukemic and antitumor agent from Taxus brevifoliaMansukhlal C. Wani, Harold Lawrence Taylor, Monroe E. Wall, Philip Coggon, and Andrew T. McPhailCite this: J. Am. Chem. Soc. 1971, 93, 9, 2325–2327Publication Date (Print):May 1, 1971Publication History Published online1 May 2002Published inissue 1 May 1971https://pubs.acs.org/doi/10.1021/ja00738a045https://doi.org/10.1021/ja00738a045research-articleACS PublicationsRequest reuse permissionsArticle Views11293Altmetric-Citations3049LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Expression of intercellular adhesion molecule-1 in atherosclerotic plaques. (1992)

Immunohistochemistry of human atherosclerotic arteries demonstrates expression of the intercellular adhesion molecule-1 (ICAM-1) on endothelial cells, macrophages, and smooth muscle cells of the plaques. Normal arterial endothelial cells and intimal smooth muscle outside plaques give weaker or negative reactions; these differ from the strong endothelial expression in small vessels. Quantitative color-image analysis of the endothelial layer shows increased expression of ICAM-1 in all subtypes of atherosclerotic lesions, except fibrous plaques. Endothelial expression of ICAM-1 may be involved in the recruitment of monocytes to the lesion, as suggested by its role in the entry of leukocytes, including monocytes, into foci of inflammation. Collaboration with other mechanisms, particularly chemoattractant factors, may be important for this effect. ICAM-1 enhanced monocyte recruitment is a potential mechanism for the growth of an atherosclerotic plaque.
Association of polymorphisms in the programmed cell death 1 (PD-1) and PD-1 ligand genes with ankylosing spondylitis in a Chinese population. (2011)

The results support a major role for PD-1/PD-L1 polymorphisms in disease susceptibility of AS.
Synthesis of Phase-shift Nanoemulsions with Narrow Size Distributions for Acoustic Droplet Vaporization and Bubble-enhanced Ultrasound-mediated Ablation (2012)

High-intensity focused ultrasound (HIFU) is used clinically to thermally ablate tumors. To enhance localized heating and improve thermal ablation in tumors, lipid-coated perfluorocarbon droplets have been developed which can be vaporized by HIFU. The vasculature in many tumors is abnormally leaky due to their rapid growth, and nanoparticles are able to penetrate the fenestrations and passively accumulate within tumors. Thus, controlling the size of the droplets can result in better accumulation within tumors. In this report, the preparation of stable droplets in a phase-shift nanoemulsion (PSNE) with a narrow size distribution is described. PSNE were synthesized by sonicating a lipid solution in the presence of liquid perfluorocarbon. A narrow size distribution was obtained by extruding the PSNE multiple times using filters with pore sizes of 100 or 200 nm. The size distribution was measured over a 7-day period using dynamic light scattering. Polyacrylamide hydrogels containing PSNE were prepared for in vitro experiments. PSNE droplets in the hydrogels were vaporized with ultrasound and the resulting bubbles enhanced localized heating. Vaporized PSNE enables more rapid heating and also reduces the ultrasound intensity needed for thermal ablation. Thus, PSNE is expected to enhance thermal ablation in tumors, potentially improving therapeutic outcomes of HIFU-mediated thermal ablation treatments.
Identical-Twin Bone Marrow Transplants for Leukemia (1994)

Identical-twin transplants in AML and CML are associated with increased relapse risk compared with HLA-identical sibling transplants. A similar trend was observed in ALL but was not statistically significant. Increased relapse in twin transplants is not explained by lack of graft-versus-host disease. Leukemia-free survival after twin and HLA-identical sibling transplants is similar because increased relapse in twins is offset by decreased treatment-related mortality.