gebhart/patrepeval huggingface dataset:
Cowden syndrome-associated germline succinate dehydrogenase complex subunit D (SDHD) variants cause PTEN-mediated down-regulation of autophagy in thyroid cancer cells (2017)

Thyroid cancer is a major component cancer of Cowden syndrome (CS), a disorder typically associated with germline mutations in PTEN. Germline variants in succinate dehydrogenase genes (SDHx) co-occurring with PTEN germline mutations confer a 2-fold increased prevalence (OR 2.7) of thyroid cancer compared to PTEN-associated CS but 50% decreased prevalence (OR 0.54) of thyroid cancer compared to SDHx-associated CS. We have previously shown that CS-associated SDHD variants G12S and H50R induce PTEN oxidation and nuclear accumulation in thyroid cancer. Our current study shows that SDHD-G12S and -H50R variants cause down-regulation of autophagy, demonstrating a role for SDHD in autophagy-associated pathogenesis of differentiated thyroid cancer. These findings could explain the increased prevalence of thyroid cancer in CS patients with SDHx germline mutations compared to those with PTEN mutations alone. Importantly, we demonstrate the dependence of this process on functional wild-type PTEN with reversal of decreased autophagy after PTEN knockdown. The latter could explain the clinically observed decrease in thyroid cancer prevalence in patients with co-existent PTEN mutations and SDHx variants. We also show that SDHD-G12S/H50R promotes mono-ubiquitination of PTEN, causing its translocation into the nucleus, upregulation of AKT and consequent phosphorylation of FOXO3a. Furthermore, SDHD-G12S/H50R-mediated increase in acetylation of FOXO3a further enhances AKT-associated phosphorylation of FOXO3a. This combination of phosphorylation and acetylation of FOXO3a results in its nuclear export for degradation and consequent down-regulation of FOXO3a-target autophagy-related gene (ATG) expression. Overall, our study reveals a novel mechanism of crosstalk amongst SDHD, PTEN and autophagy pathways and their potential roles in thyroid carcinogenesis.
Retino-cortical stimulus frequency-dependent gamma coupling: evidence and functional implications of oscillatory potentials (2016)

Long-range gamma band EEG oscillations mediate information transmission between distant brain regions. Gamma band-based coupling may not be restricted to cortex-to-cortex communication but may include extracortical parts of the visual system. The retinogram and visual event-related evoked potentials exhibit time-locked, forward propagating oscillations that are candidates of gamma oscillatory coupling between the retina and the visual cortex. In this study, we tested if this gamma coupling is present as indicated by the coherence of gamma-range (70-200 Hz) oscillatory potentials (OPs) recorded simultaneously from the retina and the primary visual cortex in freely moving, adult rats. We found significant retino-cortical OP coherence in a wide range of stimulus duration (0.01-1000 msec), stimulus intensity (800-5000 mcd/mm<sup>2</sup>), interstimulus interval (10-400 msec), and stimulus frequency (0.25-25 Hz). However, at low stimulus frequencies, the OPs were time-locked, flickering light at 25 Hz entrained continuous OP coherence (steady-state response, SSR). Our results suggest that the retina and the visual cortex exhibit oscillatory coupling at high-gamma frequency with precise time locking and synchronization of information transfer from the retina to the visual cortex, similar to cortico-cortical gamma coupling. The temporal fusion of retino-cortical gamma coherence at stimulus rates of theater movies may explain the mechanism of the visual illusion of continuity. How visual perception depends on early transformations of ascending sensory information is incompletely understood. By simultaneous measurement of flash-evoked potentials in the retina and the visual cortex in awake, freely moving rats, we demonstrate for the first time that time-locked gamma oscillatory potentials exhibit stable retino-cortical synchrony across a wide range of stimulus parameters and that the temporal continuity of coherence changes with stimulus frequency according to the expected change in the visual illusion of continuity.
Ab initio Molecular Orbital Study on Hydrogen Radical Addition Reactions to Graphite Surface and Subsequent Initial Surface Process in Silane Plasma Chemical Vapor Deposition (2003)

Hydrogen plasma treatment of a highly oriented pyrolytic graphite (HOPG) surface induces a marked change in the growth of a-Si:H film by glow-discharged decomposition of SiH4. Scanning tunneling microscope (STM) observation verified that the inhomogeneous islandlike growth on as-cleaved HOPG became homogenous after the surface was treated with hydrogen plasma. This drastic change in the surface chemical process could be reasonably interpreted by the ab initio molecular orbital calculations performed on the following reaction models: (1) C24H12 + H → HC24H12 and (2) HC24H12 + SiH3 → HC24H12SiH3. A stable energy minimum was obtained for H addition. H addition to the HOPG surface causes radical formation on the neighboring sp2 carbons, which were in turn spontaneously attacked by SiH3 radicals in the plasma to initiate homogeneous a-Si:H film growth. Without hydrogen plasma treatment, SiH3 radicals would attack the highly conjugated sp2 carbon surface. Therefore, a-Si:H film growth is presumed to be initiated at sparsely distributed defect sites that induce island growth.
The Proangiogenic Phenotype of Natural Killer Cells in Patients with Non-Small Cell Lung Cancer (2013)

The tumor microenvironment can polarize innate immune cells to a proangiogenic phenotype. Decidual natural killer (dNK) cells show an angiogenic phenotype, yet the role for NK innate lymphoid cells in tumor angiogenesis remains to be defined. We investigated NK cells from patients with surgically resected non-small cell lung cancer (NSCLC) and controls using flow cytometric and functional analyses. The CD56(+)CD16(-) NK subset in NSCLC patients, which represents the predominant NK subset in tumors and a minor subset in adjacent lung and peripheral blood, was associated with vascular endothelial growth factor (VEGF), placental growth factor (PIGF), and interleukin-8 (IL-8)/CXCL8 production. Peripheral blood CD56(+)CD16(-) NK cells from patients with the squamous cell carcinoma (SCC) subtype showed higher VEGF and PlGF production compared to those from patients with adenocarcinoma (AdC) and controls. Higher IL-8 production was found for both SCC and AdC compared to controls. Supernatants derived from NSCLC CD56(+)CD16(-) NK cells induced endothelial cell chemotaxis and formation of capillary-like structures in vitro, particularly evident in SCC patients and absent from controls. Finally, exposure to transforming growth factor-β(1) (TGFβ(1)), a cytokine associated with dNK polarization, upregulated VEGF and PlGF in peripheral blood CD56(+)CD16(-) NK cells from healthy subjects. Our data suggest that NK cells in NSCLC act as proangiogenic cells, particularly evident for SCC and in part mediated by TGFβ(1).
Rorγt+ innate lymphocytes and γδ T cells initiate psoriasiform plaque formation in mice (2012)

Psoriasis is a common, relapsing inflammatory skin disease characterized by erythematous scaly plaques. Histological manifestations of psoriasis include keratinocyte dysregulation and hyperproliferation, elongated rete ridges, and inflammatory infiltrates consisting of T cells, macrophages, dendritic cells, and neutrophils. Despite the availability of new effective drugs to treat psoriasis, the underlying mechanisms of pathogenesis are still poorly understood. Recent studies have shown that Aldara cream, used to treat benign skin abnormalities, triggers psoriasis-like disease in humans and mice and have implicated Th17 cells in disease initiation. Using this as a model, we found a predominant role for the Th17 signature cytokines IL-17A, IL-17F, and IL-22 in psoriasiform plaque formation in mice. Using gene-targeted mice, we observed that loss of Il17a, Il17f, or Il22 strongly reduced disease the severity of psoriasis. However, we found that Th17 cells were not the primary source of these pathogenic cytokines. Rather, IL-17A, IL-17F, and IL-22 were produced by a skin-invading population of γδ T cells and RORγt(+) innate lymphocytes. Furthermore, our findings establish that RORγt(+) innate lymphocytes and γδ T cells are necessary and sufficient for psoriatic plaque formation in an experimental disease model that closely resembles human psoriatic plaque formation.
Erratum: Compression, spectral broadening, and collimation in multiple, femtosecond pulse filamentation in atmosphere [Phys. Rev. A86, 033834 (2012)] (2014)

Received 15 November 2014DOI:https://doi.org/10.1103/PhysRevA.90.069902©2014 American Physical Society
Molecular Analysis of Fecal Microbiota in Elderly Individuals Using 16S rDNA Library and T‐RFLP (2003)

Fecal microbiota in six elderly individuals were characterized by the 16S rDNA libraries and terminal restriction fragment length polymorphism (T-RFLP) analysis. Random clones of 16S rRNA gene sequences were isolated after PCR amplification with universal primer sets from total genomic DNA extracted from feces of three elderly individuals. These clones were partially sequenced (about 500 bp). T-RFLP analysis was performed using 16S rDNA amplified from six subjects. The lengths of the terminal restriction fragment (T-RF) were analyzed after digestion by HhaI and MspI. Among 240 clones obtained, approximately 46% belonged to 27 known species. About 54% of the other clones were 56 novel "phylotypes" (at least 98% homology of clone sequence). These libraries included 83 species or phylotypes. In addition, about 13% (30 phylotypes) of these phylotypes were newly discovered in these libraries. A large number of species that are not yet known exist in the feces of elderly individuals. 16S rDNA libraries and T-RFLP analysis revealed that the majority of bacteria were Bacteroides and relatives, Clostridium rRNA cluster IV, IX, Clostridium rRNA subcluster XIVa, and "Gammaproteobacteria". The proportion of Clostridium rRNA subcluster XIVa was lower than in healthy adults. In addition, although Ruminococcus obeum and its closely related phylotypes were detected in high frequency in healthy young subjects, hardly any were detected in our elderly individuals. "Gammaproteobacteria" were detected at high frequency.
Nanotubules of bare boron clusters: Ab initio and density functional study (1997)

Using ab initio quantum-chemical and density functional methods we have determined novel structures of bare boron clusters. In addition to previously reported quasi-planar, convex and spherical cluster forms, boron nanotubules seem to be highly stable as well. These novel nanotubular structures are composed of hexagonal pyramids only and can be considered as segments of extended pipes. Applying a previously reported "Aufbau Principle", one can easily construct stable boron structures besides the new nanotubular clusters described below. Thus the Aufbau principle should help in illuminating the chemical and physical nature of new boron materials based on boron nanotubules.
Number‐average molecular weight of degraded iota‐carrageenan (1970)

Abstract The number‐average molecular weight (M̄ n ) of clinical degraded iota‐carrageenan has been determined by two chemical end‐group methods. The radiochemical method involves oxidation of the terminal reducing group to 3.6‐anhydrogalactonic acid, followed by methanolysis to convert this acid group into its methyl ester. Reduction with radioactive borotritiide followed by acid hydrolysis gives 3.6‐anhydrogalactitol from the methyl ester as the only labelled compound, which is separated by paper chromatography and the activity measured. Carrageenan with an inherent viscosity of 0.41 dl/g (in 0.1 M sodium chloride solution) gave an M̄ n value of 19,400. In the chemical method, the inactive 3.6‐anhydrogalactitol is separated by chromatography, oxidised with periodate, and the released formaldehyde determined colorimetrically with chromotropic acid. A mean M̄ n value of 15,600 was obtained. The two results compare well when minor deficiences in each method are taken into consideration.
Scanning tunneling microscopy of Langmuir–Blodgett films on graphite (1988)

We report the repeated observation at molecular resolution of lipid and fatty acid mono- and bimolecular layers on graphite in air. The films of di-myristoyl-phosphatidic acid and cadmium–arachidate were deposited by the Langmuir–Blodgett technique. This confirms the possibility of gaining scanning-tunneling microscopy (STM) images by electron transfer through layers more than 50 Å thick. Sample preparation, STM technique, and results are discussed.
Enkephalin-Fentanyl Multifunctional Opioids as Potential Neuroprotectants for Ischemic Stroke Treatment (2016)

In summary, the results of this study suggest that the multifunctional fluorinated enkephalin analog, LYS739 can be considered as a potential lead for ischemic stroke research and may provide advantages given the multimeric peptide-opiate structure.
The IL-1 family and inflammatory diseases. (2004)

IL-1 and its related family member IL-18 are primarily proinflammatory cytokines by their ability to stimulate the expression of genes associated with inflammation and autoimmune diseases. For IL-1 (IL-1alpha and IL-1beta), the most salient and relevant properties are the initiation of cyclooxygenase type 2 (COX-2), type 2 phospholipase A and inducible nitric oxide synthase (iNOS). This accounts for the large amount of prostaglandin-E2 (PGE2), platelet activating factor and nitric oxide (NO) produced by cells exposed to IL-1 or in animals or humans injected with IL-1. Another important member of the proinflammatory IL-1 family is IL-18. IL-18 is also an important player in autoimmune disease because of its ability to induce IFNgamma, particularly in combination with IL-12 or IL-15. Both IL-1 and IL-18 increase the expression of adhesion molecules such as intercellular adhesion molecule-1 (ICAM-1) on mesenchymal cells and vascular-cell adhesion molecule-1 (VCAM-1) on endothelial cells. This latter property promotes the infiltration of inflammatory and immunocompetent cells into the extravascular space. IL-1 and IL-18 are also an angiogenic factors by increasing the expression of vascular endothelial growth factor; IL-1 and IL-18 thus play a role in pannus formation and blood vessel supply. The strongest case for the importance of IL-1 in disease processes come from the administration of the IL-1 receptor antagonist, also a member of the IL-1 family and IL-18 binding protein (IL-18BP), a constitutively expressed and secreted protein that binds and neutralizes IL-18. Data from the human genome project have revealed other members of the IL-1 family. However, these appear to be antagonists rather than agonists. IL-1 also acts as an adjuvant during antibody production and stimulates bone marrow stem cells for differentiation in the myeloid series. IL-1 is distinct from tumor necrosis factor (TNF); IL-1 and TNFalpha share several biological properties but the salient difference is that TNF receptor signaling induces programmed cell death whereas IL-1 receptor signaling does not. In fact, IL-1 is a hematopoietic growth factor and IL-1 was administered to humans to reduce the nadir of white blood cells and platelets in patients during bone-marrow transplantation. This property, of IL-1 is not observed in the responses to TNFalpha. Furthermore, in animal models of destructive rheumatoid arthritis, IL-1 is necessary but TNFalpha is not.
mRNA sequencing of Eucalyptus urograndistrees supplemented with flavonoids shows changes on metabolic process and decrease of lignification (2011)

Background The flavonoids, naringenin-chalcone and narigenin, are intermediates in phenylpropanoid metabolism in plants, occupying the central position as primary intermediates in flavonoid biosynthesis and are synthesized by chalcone synthase (CHS) and chalcone isomerase (CHI) respectively.[1] It has been reported that supplementation of narigenin-chalcone and narigenin can inhibit the activity of 4CL in vitro, and suppress the growth and reduce lignin content in gramineous plants, while 4CL suppression affected plant phenotype and resulted on dwarfed trees on Pinus[2], and its down-regulation promoted enhanced growth phenotypes on transgenic aspens trees [3], also CHS expression controls flavonoid synthesis and reduced size phenotype on arabidopsis. [4] Eucalyptus is the main source of biomass for pulp and paper industries therefore it’s imperative to study the influence of flavonoid supplementation on Eucalyptus and what kind of overall impact it can have on plant development, especially wood formation and gene expression.
Behavioral and Environmental Interventions for Reducing Motor Vehicle Trauma (1986)

In recent decades, there has been remarkable growth in scientific research examining the multiple ways in which racism can adversely affect health. This interest has been driven in part by the striking persistence of racial/ethnic inequities in health and ...Read More
Spectroscopic characterization of triple-decker lanthanide porphyrin sandwich complexes. Effects of strong .pi..pi. interactions in extended assemblies (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSpectroscopic characterization of triple-decker lanthanide porphyrin sandwich complexes. Effects of strong .pi..pi. interactions in extended assembliesJohn K. Duchowski and David F. BocianCite this: J. Am. Chem. Soc. 1990, 112, 24, 8807–8811Publication Date (Print):November 1, 1990Publication History Published online1 May 2002Published inissue 1 November 1990https://pubs.acs.org/doi/10.1021/ja00180a023https://doi.org/10.1021/ja00180a023research-articleACS PublicationsRequest reuse permissionsArticle Views472Altmetric-Citations42LEARN 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
Recurrent upper airway infections and bacterial biofilms (2006)

Over 80 per cent (26/32; 81.3 per cent) of the tissue specimens were culture-positive. Bacterial biofilms (associated in most cases with coccoid bacteria) were observed in 65.6 per cent of the tissue samples.
RATIONALE AND AIMS OF THE ENABLING REDUCTION OF LOW-GRADE INFLAMMATION IN SENIORS: THE ENRGISE PILOT STUDY (2018)

Low-grade inflammation increases with aging and is associated with reduced walking speed, poor mobility, and disability. The ENRGISE (ENabling Reduction of low-Grade Inflammation in SEniors) Pilot study was designed to gather preliminary data on whether anti-inflammatory interventions improve or preserve walking ability in older adults with mobility limitations and elevated inflammation, a population at high risk of major mobility disability. The ENRGISE Pilot study compared the effects of Losartan (LO) (up to 100 mg/day), omega-3 fatty acids (ω-3) (up to 2.8 g/day), and LO+ω-3 vs. placebo on serum IL-6 and walking speed at 12-month follow-up in 289 older adults (70+ years of age) recruited at 5 clinical centers. This Pilot trial was designed to inform the feasibility of the full ENRGISE trial to assess whether targeting inflammation reduces mobility disability. The rationale for this trial and key decisions surrounding the selection of the anti-inflammatory compounds utilized will be discussed.
Targeting of epigenetic regulators in neuroblastoma (2018)

Approximately 15,000 new cases of pediatric cancer are diagnosed yearly in Europe, with 8-10% corresponding to neuroblastoma, a rare disease with an incidence of 8-9 cases per million children <15 years of age. Although the survival rate for low-risk and intermediate-risk patients is excellent, half of children with high-risk, refractory, or relapsed tumors will be cured, and two-thirds of the other half will suffer major side effects and life-long disabilities. Epigenetic therapies aimed at reversing the oncogenic alterations in chromatin structure and function are an emerging alternative against aggressive tumors that are or will become resistant to conventional treatments. This approach proposes targeting epigenetic regulators, which are proteins that are involved in the creation, detection, and interpretation of epigenetic signals, such as methylation or histone post-translational modifications. In this review, we focused on the most promising epigenetic regulators for targeting and current drugs that have already reached clinical trials.
Design and Processing of Advanced Lithium-Ion Electrode Materials (2016)

Significant interest in lithium- and manganese-rich (LMR) cathodes exists within the lithium-ion battery community. LMR electrodes, which incorporate a Li 2 MnO 3 motif into the structure [1], exhibit high capacities and have relatively low raw materials costs [2]. Despite these attributes, significant challenges to commercialization remain, including industrial considerations related to materials processing. Synthesis of commercialized materials and electrodes such as those based on LiCoO 2 (LCO) and LiNi­ 0.8 Co 0.15 Al 0.05 O 2 (NCA) has been highly optimized. However, less work has been done on the optimization and processing of promising new LMR compositions. Specifically, structurally-integrated “layered-layered-spinel” cathodes have been shown to provide improved rate capability, first-cycle efficiency, and possibly structural stability with cycling than their “layered-layered” counterparts [3]. However, these new chemistries have to date received little attention in the way of optimizing electrochemical performance through improved particle synthesis. This poster will detail important considerations for LMR particle synthesis through reactive crystallization, and highlight ongoing work at Argonne National Laboratory on the design and synthesis of advanced lithium-metal-oxide electrode materials. References M. M. Thackeray, C. S. Johnson, J. T. Vaughey, N. Li and S. A. Hackney, J. Mater. Chem. 15, 2257 (2005). K. G. Gallagher, S. Goebel, T. Greszler, M. Mathias, W. Oelerich, D. Eroglu, V. Srinivasan, Energy &amp; Environ. Sci. 7, 1555 (2014). B.R. Long, J. R. Croy, J.S. Park, J. Wen, D.J. Miller and M.M. Thackeray, J. Electrochem. Soc. 161, A2167 (2014). Acknowledgments Funding for this work from the Office of Vehicle Technologies of the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, is gratefully acknowledged. The submitted abstract has been created by UChicago Argonne, LLC, Operator of Argonne National Laboratory (“Argonne”). Argonne, a U.S. Department of Energy Office of Science laboratory, is operated under Contract No. DE-AC02-06CH11357. The U.S. Government retains for itself, and others acting on its behalf, a paid-up nonexclusive, irrevocable worldwide license in said article to reproduce, prepare derivative works, distribute copies to the public, and perform publicly and display publicly, by or on behalf of the Government.