gebhart/patrepeval huggingface dataset:
Structural Diversity of Eukaryotic Small Subunit Ribosomal RNAsa (1987)

The phylogenetic diversity of the eukaryotic kingdom was assessed by comparing the structural and evolutionary diversity of 18-20S ribosomal RNA genes. The coding regions for cytoplasmic small subunit ribosomal RNA genes vary in length from 1753 to 2305 nucleotides, and they appear to be evolutionary mosaics in which highly and partially conserved sequences are interspersed among regions that display very high rates of genetic drift. Structural similarities between these gene sequences were used to establish a phylogenetic framework for the eukaryotes. The extent of sequence variation within the eukaryotes exceeds that displayed within the eubacterial or archaebacterial lines of descent. The kinetoplastids and euglenoids represent the earliest branchings among the eukaryotes. These branchings preceded the divergence of lineages leading to the slime molds and apicomplexans and far antedate a radiative period that gave rise to the plants, animals, fungi, and other protists.
THE CONSTITUTION AND FUNDAMENTAL PROPERTIES OF SOLIDS AND LIQUIDS. PART I. SOLIDS. (1916)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE CONSTITUTION AND FUNDAMENTAL PROPERTIES OF SOLIDS AND LIQUIDS. PART I. SOLIDS.Irving LangmuirCite this: J. Am. Chem. Soc. 1916, 38, 11, 2221–2295Publication Date (Print):November 1, 1916Publication History Published online1 May 2002Published inissue 1 November 1916https://pubs.acs.org/doi/10.1021/ja02268a002https://doi.org/10.1021/ja02268a002research-articleACS PublicationsRequest reuse permissionsArticle Views12962Altmetric-Citations7584LEARN 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
Oxidative DNA damage is epigenetic by regulating gene transcription via base excision repair (2017)

Reactive oxygen species (ROS) have emerged as important cellular-signaling agents for cellular survival. Herein, we demonstrate that ROS-mediated oxidation of DNA to yield 8-oxo-7,8-dihydroguanine (OG) in gene promoters is a signaling agent for gene activation. Enhanced gene expression occurs when OG is formed in guanine-rich, potential G-quadruplex-forming sequences (PQS) in promoter-coding strands, initiating base excision repair (BER) by 8-oxoguanine DNA glycosylase (OGG1), yielding an abasic site (AP). The AP enables melting of the duplex to unmask the PQS, adopting a G-quadruplex fold in which apurinic/apyrimidinic endonuclease 1 (APE1) binds, but inefficiently cleaves, the AP for activation of vascular endothelial growth factor (<i>VEGF</i>) or endonuclease III-like protein 1 (<i>NTHL1</i>) genes. These details were mapped via synthesis of OG and AP analogs at single-nucleotide precision within the promoter of a luciferase reporter system. The reporters were analyzed in human and mouse cells while selectively knocking out or down critical BER proteins to identify the impact on luciferase expression. Identification of the oxidatively modified DNA base OG to guide BER activity in a gene promoter and impact cellular phenotype ascribes an epigenetic role to OG.
Clinical predictors of progression to Alzheimer disease in amnestic mild cognitive impairment (2007)

Progression from amnestic mild cognitive impairment to Alzheimer disease in this cohort was best determined by combining four common, easily administered, cognitive measures.
Uptake and distribution of specific and control monoclonal antibodies in subcutaneous xenografts following intratumor injection. (1991)

Nude mice bearing s.c. xenografts of the human colon adenocarcinoma HT29 were given intratumor injections of a mixture of 125I-labeled specific antibody (AUA1) and 131I-labeled control antibody (HMFG1), or with the labels reversed. After dissection at 1 and 4 h postadministration, both specific and control antibodies had 47-63% of the injected dose (% ID) in the tumor. By 24 h, the tumor contained 43 +/- 11% ID of AUA1 which persisted at around this level for 5 days and remained at nearly 20% ID at 18 days. In contrast, the HMFG1 activity was 23 +/- 9% ID at 24 h, which continued to fall and was less than 5% ID by 7 days. Normal organ levels were less than 2% ID/g for both antibodies, with HMFG1 being higher than AUA1 at all times, resulting in specificity indices greater than 20 by 5 days. Autoradiography of tumors removed 2 h postinjection of 125I-labeled AUA1 or HMFG1 showed high levels of antibody at the injection site. At 48 h and 7 days postinjection, the specific antibody was bound to the surface of tumor cells in islands remote from the injection site, whereas the control antibody was found only in the stroma and blood vessels, or as diffuse nonspecific uptake. These data indicate that intratumor injection of radiolabeled monoclonal antibodies may achieve high radiation doses in accessible tumors without systemic irradiation.
Alkaloid Composition of the Nicotiana Species (1990)

Abstract Plants from 64 Nicotiana species were sampled in the greenhouse in 1983 and 1984 and from the field in 1985 and 1986 for the purpose of developing a chemical profile of each species. Mature green leaves were harvested at flowering, freeze-dried and ground to pass a 1 mm screen prior to chemical analysis. In this study we report the type and amounts of nicotinoid alkaloids. Alkaloid values were determined by glass-capillary gas chromatography and were averaged over the two years for each environment. Both total alkaloids (mg g -1 dry weight) and the distribution (percentage composition) of nicotine, nornicotine, anabasine, and anatabine were highly correlated between years for greenhouse and field samples. Greenhouse and field data were highly correlated, although total-alkaloid levels were significantly higher from field-grown plants. All of the Nicotiana species tested contained a measurable alkaloid fraction (at least 10 µg g -1 ). There was a wide range in total-alkaloid levels with nearly a 200-fold difference among greenhouse-grown samples and a 400-fold difference among field-grown species. In general, total-alkaloid levels among the species were found to be relatively low. Eleven species were found to have a different alkaloid composition when green leaf and air-dried samples were compared. Evidence is presented for the association between alkaloid characteristics and the phylogenetic classification of the species in the genus.
Ventromedial hypothalamic regulation of hormonal and metabolic responses to exercise (1989)

Recent studies have indicated a neural regulation of hormonal and metabolic responses to exercise. Studies on the ventromedial hypothalamus (VMH) suggest that the VMH might be involved in neural control of exercise metabolism. We therefore studied 25 rats with or without Marcain-anesthetized VMH (Marcain and control rats, respectively) at rest or during treadmill running (26 m/min). The rats had cannulas aimed bilaterally at the VMH and chronic catheters in the left jugular vein and right carotid artery. At rest, glucose turnover and plasma concentrations of glucose, lactate, glycerol, epinephrine, norepinephrine, insulin, and corticosterone remained stable in control rats, whereas in Marcain rats these parameters, except for unchanged insulin and glucose utilization, increased after Marcain administration along with increases in hepatic and muscular glycogenolysis. During exercise, glucose turnover, hepatic and muscular glycogenolysis, and plasma concentrations of glucose, lactate, glycerol, catecholamines, and corticosterone increased, and insulin decreased in both Marcain and control rats. However, during exercise, initial hepatic glucose production, plasma catecholamines, and subsequent plasma glucose concentrations and overall hepatic glycogenolysis were lower in Marcain compared with control rats. In conclusion, glucose mobilization is enhanced by the VMH during exercise. The results suggest that decreased and increased activity in sympathetic inhibitory and facilitating VMH areas, respectively, are involved in the VMH's response to exercise.
Inhibition of histone deacetylases: a new strategy to target epigenetic modifications for anticancer treatment. (2000)

The role of epigenetic modifications due to deregulated acetylation of nucleosomes with respect to its role in progression and etiology of human cancer is discussed. Among the mediators of these phenomena are the histone deacetylases, a class of enzymes consisting of at least two subfamilies with a total of at least 7 members in mammals. Depending on the cell-type, inhibition of HDACs in cancer cells can lead to transcriptional activation and silencing of about 2% of human genes, cell-cycle arrest and induction of apoptosis and differentiation in vitro and in vivo. This paper discusses several inhibitors of HDACs primarily derived from natural sources, their physiological consequences in different in vitro and in vivo cancer-related systems, their stage of preclinical and clinical development as well as their potential as antineoplastic agents. It is of paramount importance to elucidate the molecular mechanisms resulting in cell-cycle arrest, apoptosis or differentiation after inhibition of HDACs and to investigate the physiological function of the different HDAC isoenzymes and their deregulation in human cancers in order to devise optimized therapeutic intervention in cancer patients.
Engineering Complex Tissues (2012)

Tissue engineering has emerged at the intersection of numerous disciplines to meet a global clinical need for technologies to promote the regeneration of functional living tissues and organs. The complexity of many tissues and organs, coupled with confounding factors that may be associated with the injury or disease underlying the need for repair, is a challenge to traditional engineering approaches. Biomaterials, cells, and other factors are needed to design these constructs, but not all tissues are created equal. Flat tissues (skin); tubular structures (urethra); hollow, nontubular, viscus organs (vagina); and complex solid organs (liver) all present unique challenges in tissue engineering. This review highlights advances in tissue engineering technologies to enable regeneration of complex tissues and organs and to discuss how such innovative, engineered tissues can affect the clinic.
Toward a framework for sulfoproteomics: Synthesis and characterization of sulfotyrosine‐containing peptides (2007)

Tyrosine sulfation is one of the most common post-translational modifications in secreted and transmembrane proteins and a key modulator of extracellular protein-protein interactions. Several proteins known to be tyrosine sulfated play important roles in physiological processes, and in some cases a direct link between protein function and tyrosine sulfation has been established. In blood coagulation, tyrosine sulfation of factor VIII is required for efficient binding of von Willebrand factor; in leukocyte adhesion, tyrosine sulfation of the P-selectin glycoprotein ligand-1 mediates high-affinity binding to P-selectin; and in leukocyte chemotaxis, tyrosine sulfation of chemokine receptors is required for optimal interaction with chemokine ligands. Furthermore, tyrosine sulfation has been implicated in several infectious diseases. In particular, tyrosine sulfation of the HIV-1 co-receptor CCR5 is required for viral entry into host cells and tyrosine sulfation of the Duffy antigen/receptor for chemokines is crucial for erythrocyte invasion by the malaria parasite plasmodium vivax. Despite increasing interest in tyrosine sulfation in recent years, the sulfoproteome still remains largely unexplored. To date, only a relatively small number of sulfotyrosine-containing peptides and proteins have been identified, and a specific role for tyrosine sulfation has not been established for most of these. Here, we provide an overview of the biology and enzymology of tyrosine sulfation and discuss recent developments in preparative and analytical methods that are central to sulfoproteome research.
P-selectin and platelet-activating factor mediate initial endotoxin-induced neutropenia. (1994)

Polymorphonuclear neutrophil (PMN) accumulation within damaged tissues, a hallmark of acute inflammation, is dependent upon initial adhesion to endothelial cells. In vitro studies suggest that P-selectin and platelet activating factor (PAF) are key molecules in this process by promoting the initial adhesion of PMN to endothelial cells. We report in vivo studies in which intravenous administration of lipopolysaccharide (LPS) to anesthetized rats caused a very rapid onset (< 5 min) of neutropenia, in association with induction of surface expression of P-selectin on microvascular endothelial cells in kidney, liver and lung; analogous induction of P-selectin expression by cultured endothelial cells was observed in response to LPS stimulation in vitro. In addition, treatment with an antibody (Ab) to P-selectin (or use of a PAF antagonist) blocked development of neutropenia in vivo for at least 15 min post-LPS injection, and Ab treatment was shown to block PMN accumulation in tissues. These studies document roles for P-selectin and PAF in the early adhesion of PMN to endothelial cells in vivo.
Modest truncation of the major capsid protein abrogates B19 parvovirus capsid formation (1995)

In vitro studies have suggested an important role for the minor capsid protein (VP1) unique region and the junction between VP1 and the major capsid protein (VP2) in the neutralizing immune response to B19 parvovirus. We investigated the role of the NH2-terminal region of the major structural protein in capsid structure by expressing progressively more truncated versions of the VP2 gene followed by analysis using immunoblotting and electron microscopy of density gradient-purified particles. Deletion of the first 25 amino acids (aa) of VP2 did not affect capsid assembly. Altered VP2 with truncations to aa 26 to 30, including a single amino acid deletion at position 25, failed to self-assemble but did participate with normal VP2 in the capsid structure. The altered region corresponds to the beginning of the beta A antiparallel strand. Truncations beyond aa 30 were incompatible with either self-assembly or coassembly, probably because of deletion of the beta B strand, which helps to form the core structure of the virus.
Rhino conservation in Garamba National Park (1990)

Between the 1,300 in 1963 and the 490 in 1976 there was no steady decline but a rapid drop until a rough estimate of 100 remained in 1966. The poaching in 1963 and 1964 resulted from civil war and was carried out by both rebels and the mercenaries employed to subdue them. After the Wildlife Department regained control of the Park the rhino population increased. If the figure of 100 was correct, the rate of increase must have been of the order of 14% per annum. Since the current rate is 11%, even if the 100 was somewhat an under-estimate it was probably not far out.
Multi-view 3D reconstruction for scenes under the refractive plane with known vertical direction (2011)

Images taken from scenes under water suffer distortion due to refraction. While refraction causes magnification with mild distortion on the observed images, severe distortions in geometry reconstruction would be resulted if the refractive distortion is not properly handled. Different from the radial distortion model, the refractive distortion depends on the scene depth seen from each light ray as well as the camera pose relative to the refractive surface. Therefore, it's crucial to obtain a good estimate of scene depth, camera pose and optical center to alleviate the impact of refractive distortion. In this work, we formulate the forward and back projections of light rays involving a refractive plane for the perspective camera model by explicitly modeling refractive distortion as a function of depth. Furthermore, for cameras with an inertial measurement unit (IMU), we show that a linear solution to the relative pose and a closed-form solution to the absolute pose can be derived with known camera vertical directions. We incorporate our formulations with the general structure from motion framework followed by the patch-based multiview stereo algorithm to obtain a 3D reconstruction of the scene. We show through experiments that the explicit modeling of depth-dependent refractive distortion physically leads to more accurate scene reconstructions.
Substrate specificity of a multifunctional calmodulin-dependent protein kinase. (1985)

The substrate specificity of the multifunctional calmodulin-dependent protein kinase from skeletal muscle has been studied using a series of synthetic peptide analogs. The enzyme phosphorylated a synthetic peptide corresponding to the NH2-terminal 10 residues of glycogen synthase, Pro-Leu-Ser-Arg-Thr-Leu-Ser-Val-Ser-Ser-NH2, stoichiometrically at Ser-7, the same residue phosphorylated in the parent protein. The synthetic peptide was phosphorylated with a Vmax of 12.5 mumol X min-1 X mg-1 and an apparent Km of 7.5 microM compared to values of 1.2 mumol X min-1 X mg-1 and 3.1 microM, respectively, for glycogen synthase. Similarly, a synthetic peptide corresponding to the NH2-terminal 23 residues of smooth muscle myosin light chain was readily phosphorylated on Ser-19 with a Km of 4 microM and a Vmax of 5.4 mumol X min-1 X mg-1. The importance of the arginine 3 residues NH2-terminal to the phosphorylated serine in each of these peptides was evident from experiments in which this arginine was substituted by either leucine or alanine, as well as from experiments in which its position in the myosin light chain sequence was varied. Positioning arginine 16 at residues 14 or 17 abolished phosphorylation, while location at residue 15 not only decreased Vmax 14-fold but switched the major site of phosphorylation from Ser-19 to Thr-18. It is concluded that the sequence Arg-X-Y-Ser(Thr) represents the minimum specificity determinant for the multifunctional calmodulin-dependent protein kinases. Studies with various synthetic peptide substrates and their analogs revealed that the specificity determinants of the multifunctional calmodulin-dependent protein kinase were distinct from several other "arginine-requiring" protein kinases.
Generating virtual camera compositions (2001)

This paper describes work in progress to automatically generate camera shots featuring the composition techniques of expert photographers. This effort builds upon an automated camera planner that computes a shot satisfying a given set of constraints. In this prior work, users manually specify the set of constraints and the numeric parameters for each. A typical two subject shot can be described by eleven constraints involving sixty numeric parameters. This work aims to develop a high-level interface to automatically generate such constraint sets. Photographic composition techniques such as composition in depth can be realized by automatically constructing appropriate sets of camera constraints then submitting them to a constraint solver.
Herpes Simplex Virus Type 1 Vector-Mediated Expression of Nerve Growth Factor Protects Dorsal Root Ganglion Neurons from Peroxide Toxicity (1999)

Nerve growth factor beta subunit (beta-NGF) transgene delivery and expression by herpes simplex virus type 1 (HSV-1) vectors was examined in a cell culture model of neuroprotection from hydrogen peroxide toxicity. Replication-competent (tk- K mutant background) and replication-defective (ICP4(-);tk- S mutant background) vectors were engineered to contain the murine beta-NGF cDNA under transcriptional control of either the human cytomegalovirus immediate-early gene promoter (HCMV IEp) (e.g., KHN and SHN) or the latency-active promoter 2 (LAP2) (e.g., KLN and SLN) within the viral thymidine kinase (tk) locus. Infection of rat B103 and mouse N2A neuronal cell lines, 9L rat glioma cells, and Vero cells with the KHN or SHN vectors resulted in the production of beta-NGF-specific transcripts and beta-NGF protein reaching a maximum at 3 days postinfection (p.i.). NGF protein was released into the culture media in amounts ranging from 10.83 to 352.86 ng/ml, with the highest levels being achieved in B103 cells, and was capable of inducing neurite sprouting of PC-12 cells. The same vectors produced high levels of NGF in primary dorsal root ganglion (DRG) cultures at 3 days. In contrast to HCMV IEp-mediated expression, the LAP2-NGF vectors showed robust expression in primary DRG neurons at 14 days. The neuroprotective effect of vector produced NGF was assessed by its ability to inhibit hydrogen peroxide-induced neuron toxicity in primary DRG cultures. Consistent with the kinetics of vector-mediated NGF expression, HCMV-NGF vectors were effective in abrogating the toxic effects of peroxide at 3 but not 14 days p.i. whereas LAP2-NGF vector transduction inhibited apoptosis in DRG neurons at 14 days p.i. but was ineffective at 3 days p.i. Similar kinetics of NGF expression were observed with the KHN and KLN vectors in latently infected mouse trigeminal ganglia, where high levels of beta-NGF protein expression were detected at 4 wks p.i. only from the LAP2; HCMV-NGF-driven expression peaked at 3 days but could not be detected during HSV latency at 4 weeks. Together, these results indicate that (i) NGF vector-infected cells produce and secrete mature, biologically active beta-NGF; (ii) vector-synthesized NGF was capable of blocking peroxide-induced apoptosis in primary DRG cultures; and (iii) the HCMV-IEp functioned to produce high levels of NGF for several days; but (iv) only the native LAP2 was capable of long-term expression of a therapeutic gene product in latently infected neurons in vivo.
MECHANISMS OF PHAGOCYTOSIS IN MACROPHAGES (1999)

Phagocytosis of pathogens by macrophages initiates the innate immune response, which in turn orchestrates the adaptive response. In order to discriminate between infectious agents and self, macrophages have evolved a restricted number of phagocytic receptors, like the mannose receptor, that recognize conserved motifs on pathogens. Pathogens are also phagocytosed by complement receptors after relatively nonspecific opsonization with complement and by Fc receptors after specific opsonization with antibodies. All these receptors induce rearrangements in the actin cytoskeleton that lead to the internalization of the particle. However, important differences in the molecular mechanisms underlying phagocytosis by different receptors are now being appreciated. These include differences in the cytoskeletal elements that mediate ingestion, differences in vacuole maturation, and differences in inflammatory responses. Infectious agents, such as M. tuberculosis, Legionella pneumophila, and Salmonella typhimurium, enter macrophages via heterogeneous pathways and modify vacuolar maturation in a manner that favors their survival. Macrophages also play an important role in the recognition and clearance of apoptotic cells; a notable feature of this process is the absence of an inflammatory response.