gebhart/patrepeval huggingface dataset:
Tissue-Specific Expression of a Gene Encoding a Cell Wall-Localized Lipid Transfer Protein from Arabidopsis (1994)

Nonspecific lipid transfer proteins (LTPs) from plants are characterized by their ability to stimulate phospholipid transfer between membranes in vitro. However, because these proteins are generally located outside of the plasma membrane, it is unlikely that they have a similar role in vivo. As a step toward identifying the function of these proteins, one of several LTP genes from Arabidoposis has been cloned and the expression pattern of the gene has been examined by analysis of the tissue specificity of beta-glucuronidase (GUS) activity in transgenic plants containing LTP promoter-GUS fusions and by in situ mRNA localization. The LTP1 promoter was active early in development in protoderm cells of embryos, vascular tissues, lignified tips of cotyledons, shoot meristem, and stipules. In adult plants, the gene was expressed in epidermal cells of young leaves and the stem. In flowers, expression was observed in the epidermis of all developing influorescence and flower organ primordia, the epidermis of the siliques and the outer ovule wall, the stigma, petal tips, and floral nectaries of mature flowers, and the petal/sepal abscission zone of mature siliques. The presence of GUS activity in guard cells, lateral roots, pollen grains, leaf vascular tissue, and internal cells of stipules and nectaries was not confirmed by in situ hybridizations, supporting previous observations that suggest that the reporter gene is subject to artifactual expression. These results are consistent with a role for the LTP1 gene product in some aspect of secretion or deposition of lipophilic substances in the cell walls of expanding epidermal cells and certain secretory tissues. The LTP1 promoter region contained sequences homologous to putative regulatory elements of genes in the phenylpropanoid biosynthetic pathway, suggesting that the expression of the LTP1 gene may be regulated by the same or similar mechanisms as genes in the phenylpropanoid pathway.
Characterization of the nucleational core complex responsible for mineral induction by growth plate cartilage matrix vesicles. (1993)

The factors that drive mineralization of matrix vesicles (MV) have proven difficult to elucidate; in the present studies, various detergent, chemical, and enzyme treatments were used to reveal the nature of the nucleational core. Incubation with detergents that permeabilized the membrane enhanced calcification of treated MV incubated in synthetic cartilage lymph. While detergents removed most of the membrane lipid, they left significant amounts of the MV annexins and nearly all of the Ca2+, Pi, and Zn2+. Extraction with 1 M NaCl removed much of the Ca2+ and Pi present in MV, markedly reducing Ca2+ accumulation; these effects could be prevented by low levels of Ca2+ and Pi in the NaCl extractant. Treatment with chymotrypsin appeared to damage proteins required for MV mineralization; further treatment with detergents to bypass the membrane reactivated MV mineralization. Treatment of MV with pH 6 citrate removed Ca2+ and Pi, destroying their ability to mineralize; subsequent treatment with detergents did not reactivate these MV. Incubation of the detergent-resistant core with o-phenanthroline complexed Zn2+ and stimulated mineralization; addition of Zn2+ to synthetic cartilage lymph blocked the ability of the core to mineralize. These studies show that once the nucleational core complex is formed, the membrane-enclosed domain is no longer essential for MV calcification. Our findings indicate that the MV core contains two main components as follows: a smaller membrane-associated complex of Ca2+, Pi, phosphatidylserine, and the annexins that nucleates crystalline mineral formation, and a larger pool of Ca2+ and Pi bound to lumenal proteins. These proteins appear to bind large amounts of mineral ions, stabilize the nucleational complex, and aid its transformation to the first crystalline phase. Once nucleated, the crystalline phase appears to feed on protein-bound mineral ions until external ions enter through the MV ion channels. Zn2+ appears to regulate gating of the ion channels and conversion of the nucleational complex to the crystalline state.
Ancient Origin and Molecular Features of the Novel Human T-Lymphotropic Virus Type 3 Revealed by Complete Genome Analysis (2006)

Human T-lymphotropic virus type 3 (HTLV-3) is a new virus recently identified in two primate hunters in Central Africa. Limited sequence analysis shows that HTLV-3 is distinct from HTLV-1 and HTLV-2 but is genetically similar to simian T-lymphotropic virus type 3 (STLV-3). We report here the first complete HTLV-3 sequence obtained by PCR-based genome walking using uncultured peripheral blood lymphocytes from an HTLV-3-infected person. The HTLV-3(2026ND) genome is 8,917 bp long and is genetically equidistant from HTLV-1 and HTLV-2, sharing about 62% identity. Phylogenetic analysis of all gene regions confirms this relationship and shows that HTLV-3 falls within the diversity of STLV-3, suggesting a primate origin. However, HTLV-3(2026ND) is unique, sharing only 87% to 92% sequence identity with STLV-3. SimPlot and phylogenetic analysis did not reveal any evidence of genetic recombination with either HTLV-1, HTLV-2, or STLV-3. Molecular dating estimates that the ancestor of HTLV-3 is as old as HTLV-1 and HTLV-2, with an inferred divergence time of 36,087 to 54,067 years ago. HTLV-3 has a prototypic genomic structure, with all enzymatic, regulatory, and structural proteins preserved. Like STLV-3, HTLV-3 is missing a third 21-bp transcription element found in the long terminal repeats of HTLV-1 and HTLV-2 but instead contains a unique activator protein-1 transcription factor upstream of the 21-bp repeat elements. A PDZ motif, like that in HTLV-1, which is important for cellular signal transduction and transformation, is present in the C terminus of the HTLV-3 Tax protein. A basic leucine zipper region located in the antisense strand of HTLV-1, believed to play a role in viral replication and oncogenesis, was also found in the complementary strand of HTLV-3. The ancient origin of HTLV-3, the broad distribution of STLV-3 in Africa, and the propensity of STLVs to cross species into humans all suggest that HTLV-3 may be prevalent and support the need for expanded surveillance for this virus.
A Role for Shc, Grb2, and Raf-1 in FcγRI Signal Relay (1996)

The activation of the serine/threonine kinase, Raf-1, serves to connect upstream protein tyrosine kinases to downstream signaling events. We previously reported that FcgammaRI stimulation of interferon gamma-differentiated U937 cells (termed U937IF cells) induces a mobility shift in Erk2. Herein, we report that cross-linking of FcgammaRI receptor in U937IF cells induces a marked tyrosine phosphorylation of Raf-1 (10-fold increase). Tyrosine phosphorylation of Raf-1 is induced by FcgammaRI activation and not by PMA (1 microg/ml), N-formyl-Met-Leu-Phe (1 microM), calcium ionophore (1 microM), thrombin (0.05 unit/ml), FcgammaRII, or FcgammaRIII stimulation. The kinetics of Raf-1 tyrosine phosphorylation is rapid, reaching peak levels 1-2 min after FcgammaRI activation, and the tyrosine phosphorylation of Raf-1 precedes the activation of the respiratory burst. FcgammaRI cross-linking induces the tyrosine phosphorylation of Shc; tyrosine-phosphorylated Shc binds to Grb2 forming a Shc-Grb2 complex. The data provide evidence that the FcgammaRI receptor signals via the upstream activation of nonreceptor protein tyrosine kinases, which leads to the subsequent activation of Ras family GTPases and serine/threonine kinases, Raf-1 and mitogen-activated protein kinase.
Specific Inhibition of PCR by Non-Extendable Oligonucleotides Using a 5′ to 3′ Exonuclease-Deficient DNA Polymerase (1997)

The Stoffel fragment of Taq DNA polymerase lacks the 5' to 3' exonuclease activity that hydrolyzes potentially blocking DNA strands during primer extension. We there-fore asked whether by using this fragment in the PCR, non-extendable, base-paired oligonucleotides could inhibit amplification in a sequence-dependent manner. Model targets were chosen from the partially conserved ribosomal 16S rDNA of three bacterial species: E. coli, Bacillus subtilis and Neisseria gonorrhoea. A single pair of primers was capable of amplifying a homologous 240-bp region from all three. Two non-extendable "blocking" oligonucleotides were synthesized with sequences complementary to the inter-primer regions of E. coli and B. subtilis, respectively. Both blockers were shown specifically to prevent amplification of their complementary targets, but not of the reciprocal control targets or of the reciprocal control targets or of the non-complementary N. gonorrhea. Specificity was further confirmed by an internal positive control. Similar inhibition was seen with mixtures of targets in a single reaction. With intact Taq DNA polymerase, no blocking was observed. Primers and blockers targeting specific regions of N. gonorrhoea rDNA were used to confirm the requirement that blockers be directed to the inter-primer region. Sequence-dependent amplification inhibition, such as that demonstrated here, would be applicable to PCR-related strategies using primers capable of using multiple targets, where such selective inhibition could be useful.
Effect of Dietary Essential Amino Acid Limitations upon Native Levels of Murine Serum Immunoglobulins, Transferrin, and Complement (1980)

Effects of dietary essential amino acid (leucine, isoleucine, valine, or lysine) limitations upon the native levels of serum immunoglobulin G (IgG), IgM, and IgA, as well as transferrin, the third component of complement (C3), and albumin were determined in CF1 mice by the radial immunodiffusion technique. Male mice fed the control diet and the isoleucine- or valine-limited diets exhibited lower levels of serum IgG than the female mice fed the same diets. Levels of IgG in female experimental mice were not significantly different than those in female control mice. Serum IgM levels in male or female mice fed the experimental diets were higher than those in the control mice. Except for the mice fed the isoleucine-limited diet, serum IgA levels were higher in male and female mice fed the experimental diets than in mice fed the control diet. Serum transferrin levels were not significantly different in mice fed the experimental diets when compared with mice fed the control diet. However, the levels of transferrin found in the peritoneal exudates were lower in mice fed the isoleucine- or lysine-limited diets than in mice fed the control diet. In mice fed the isoleucine- and lysine-limited diets, the levels of serum C3 were significantly lower than those in control mice. These results indicate that the native levels of serum immunoglobulins are increased in some instances and that the levels of serum C3 and the transferrin in the peritoneal fluid are significantly decreased in certain dietary groups of mice.
Transgenic expression of cholesterol 7α‐hydroxylase in the liver prevents high‐fat diet–induced obesity and insulin resistance in mice† (2010)

This study shows that Cyp7a1 plays a critical role in maintaining whole body lipid, glucose, and energy homeostasis. The induction of CYP7A1 expression with the expansion of the hydrophobic bile acid pool may be a potential therapeutic strategy for treating metabolic disorders such as fatty liver diseases, obesity, and diabetes in humans.
PCR Mutation Detection Protocols (2010)

Since the publication of the popular first edition, the explosion of DNA sequence information, the access to bioinformatics and mutation databases coupled with the ability to readily detect and confir
Role of Eukaryotic Initiation Factors during Cellular Stress and Cancer Progression (2016)

Protein synthesis can be segmented into distinct phases comprising mRNA translation initiation, elongation, and termination. Translation initiation is a highly regulated and rate-limiting step of protein synthesis that requires more than 12 eukaryotic initiation factors (eIFs). Extensive evidence shows that the transcriptome and corresponding proteome do not invariably correlate with each other in a variety of contexts. In particular, translation of mRNAs specific to angiogenesis, tumor development, and apoptosis is altered during physiological and pathophysiological stress conditions. In cancer cells, the expression and functions of eIFs are hampered, resulting in the inhibition of global translation and enhancement of translation of subsets of mRNAs by alternative mechanisms. A precise understanding of mechanisms involving eukaryotic initiation factors leading to differential protein expression can help us to design better strategies to diagnose and treat cancer. The high spatial and temporal resolution of translation control can have an immediate effect on the microenvironment of the cell in comparison with changes in transcription. The dysregulation of mRNA translation mechanisms is increasingly being exploited as a target to treat cancer. In this review, we will focus on this context by describing both canonical and noncanonical roles of eIFs, which alter mRNA translation.
Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution (2005)

Sites of transcription of polyadenylated and nonpolyadenylated RNAs for 10 human chromosomes were mapped at 5-base pair resolution in eight cell lines. Unannotated, nonpolyadenylated transcripts comprise the major proportion of the transcriptional output of the human genome. Of all transcribed sequences, 19.4, 43.7, and 36.9% were observed to be polyadenylated, nonpolyadenylated, and bimorphic, respectively. Half of all transcribed sequences are found only in the nucleus and for the most part are unannotated. Overall, the transcribed portions of the human genome are predominantly composed of interlaced networks of both poly A+ and poly A- annotated transcripts and unannotated transcripts of unknown function. This organization has important implications for interpreting genotype-phenotype associations, regulation of gene expression, and the definition of a gene.
In vivo birefringence and thickness measurements of the human retinal nerve fiber layer using polarization-sensitive optical coherence tomography (2004)

Glaucoma causes damage of the nerve fiber layer, which may cause loss of retinal birefringence. Therefore, PS-OCT is a potentially useful technique for the early detection of glaucoma. We built a fiber-based PS-OCT setup that produces real-time images of the human retina in vivo, coregistered with retinal video images of the location of PS-OCT scans. Preliminary measurements of a healthy volunteer show that the double-pass phase retardation per unit of depth of the RNFL is not constant and varies with location, with values between 0.18 and 0.37 deg/microm. A trend in the preliminary measurements shows that the nerve fiber layer located inferior and superior to the optic nerve head is more birefringent than the thinner layer of nerve fiber tissue in the temporal and nasal regions.
Synthesis of 3‐formyltetronic acid and enamine derivatives (1981)

Abstract The first reported synthesis of 3‐formyltetronic acid and its conversion to enamine derivatives is described. 3‐Dimethylaminomethylene‐2,4‐dioxotetrahydrofuran derivatives were also prepared by treatment of tetronic acids with dimethylformamide diethyl acetal. Nmr spectral studies are included.
The United States Reception of Durkheim's The Rules of Sociological Method (1995)

Durkheim has not always been treated by U.S. sociology as obviously important, as the career of The Rules shows. Initially, its social realism was strongly criticized. Gradually, however, more specialized study of Durkheim was done, which led to more contextualized understandings of his work. As U.S. sociology became more empirical the character of interest in The Rules shifted; by the 1960s, it was read in the light of Suicide, then newly translated, and interpreted as an ancestor of functionalism. The meanings imputed to key ideas such as the treatment of social facts as things also shifted. It is argued that his, then newly won, status as a founding father promoted more favorable interpretation of his meanings and that various factors in the social structure of the discipline also contributed to this change.
Nonvalvular Cardiovascular Device–Related Infections (2003)

M ore than a century ago, Osler took numerous syndrome descriptions of cardiac valvular infection that were incomplete and confusing and categorized them into the cardiovascular infections known as infective endocarditis. Because he was both a clinician and a pathologist, he was able to provide a meaningful outline of this complex disease. Technical advances have allowed us to better subcategorize infective endocarditis on the basis of microbiological etiology. More recently, the syndromes of infective endocarditis and endarteritis have been expanded to include infections involving a variety of cardiovascular prostheses and devices that are used to replace or assist damaged or dysfunctional tissues (Table Taken together, infections of these novel intracardiac, arterial, and venous devices are frequently seen in medical centers throughout the developed world. In response, the American Heart Association's Committee on Rheumatic Fever, Endocarditis, and Kawasaki Disease wrote this review to assist and educate clinicians who care for an increasing number of patients with nonvalvular cardiovascular device-related infections. Because timely guidelines 1,2 exist that address the prevention and management of intravascular catheter-related infections, these device-related infections are not discussed in the present Statement.
Accumulation of a Polyisoprene-linked Amino Sugar in Polymyxin-resistant Salmonella typhimurium andEscherichia coli (2001)

Polymyxin-resistant mutants of Escherichia coli and Salmonella typhimurium accumulate a novel minor lipid that can donate 4-amino-4-deoxy-l-arabinose units (l-Ara4N) to lipid A. We now report the purification of this lipid from a pss(-) pmrA(C) mutant of E. coli and assign its structure as undecaprenyl phosphate-alpha-l-Ara4N. Approximately 0.2 mg of homogeneous material was isolated from an 8-liter culture by solvent extraction, followed by chromatography on DEAE-cellulose, C18 reverse phase resin, and silicic acid. Matrix-assisted laser desorption ionization/time of flight mass spectrometry in the negative mode yielded a single species [M - H](-) at m/z 977.5, consistent with undecaprenyl phosphate-alpha-l-Ara4N (M(r) = 978.41). (31)P NMR spectroscopy showed a single phosphorus atom at -0.44 ppm characteristic of a phosphodiester linkage. Selective inverse decoupling difference spectroscopy demonstrated that the undecaprenyl phosphate group is attached to the anomeric carbon of the l-Ara4N unit. One- and two-dimensional (1)H NMR studies confirmed the presence of a polyisoprene chain and a sugar moiety with chemical shifts and coupling constants expected for an equatorially substituted arabinopyranoside. Heteronuclear multiple-quantum coherence spectroscopy analysis demonstrated that a nitrogen atom is attached to C-4 of the sugar residue. The purified donor supports in vitro conversion of lipid IV(A) to lipid II(A), which is substituted with a single l-Ara4N moiety. The identification of undecaprenyl phosphate-alpha-l-Ara4N implies that l-Ara4N transfer to lipid A occurs in the periplasm of polymyxin-resistant strains, and establishes a new enzymatic pathway by which Gram-negative bacteria acquire antibiotic resistance.
Effect of Empagliflozin on Liver Fat in Patients With Type 2 Diabetes and Nonalcoholic Fatty Liver Disease: A Randomized Controlled Trial (E-LIFT Trial) (2018)

When included in the standard treatment for type 2 diabetes, empagliflozin reduces liver fat and improves ALT levels in patients with type 2 diabetes and NAFLD.
Frequent expression loss of Inter-alpha-trypsin inhibitor heavy chain (ITIH) genes in multiple human solid tumors: A systematic expression analysis (2008)

Altogether, this is the first systematic analysis on the differential expression of ITIH genes in human cancer, showing frequent downregulation that may be associated with initiation and/or progression of these malignancies.
Irreversible Immobilization of Diisopropylfluorophosphatase in Polyurethane Polymers (2000)

The synthesis of polyurethane polymers in the presence of diisopropylfluorophosphatase (DFPase) has enabled the irreversible attachment of the enzyme to the polymeric matrix. The resulting bioplastic hydrolyzes diisopropylfluorophosphate (DFP) in buffered media up to 67% of the rate for the same amount of soluble enzyme. Above a DFPase concentration of approximately 0.1 mg/gfoam, the rate of the reaction catalyzed by the enzyme-containing polymer was controlled by internal mass transfer. Increasing foam hydrophilicity, via the use of nonionic surfactants during polymerization, significantly affected the structural properties of matrix, thereby enhancing the intrinsic and apparent efficiency of modified DFPase. The resulting reduction in internal mass transfer limitations was explained morphologically with electron microscopy.
A possible role for π‐stacking in the self‐assembly of amyloid fibrils (2002)

Amyloid fibril formation is assumed to be the molecular basis for a variety of diseases of unrelated origin. Despite its fundamental clinical importance, the mechanism of amyloid formation is not fully understood. When we analyzed a variety of short functional fragments from unrelated amyloid-forming proteins, a remarkable occurrence of aromatic residues was observed. The finding of aromatic residues in diverse fragments raises the possibility that pi-pi interactions may play a significant role in the molecular recognition and self-assembly processes that lead to amyloid formation. This is in line with the well-known central role of pi-stacking interactions in self-assembly processes in the fields of chemistry and biochemistry. We speculate that the stacking interactions may provide energetic contribution as well as order and directionality in the self-assembly of amyloid structures. Experimental data regarding amyloid formation and inhibition by short peptide analogs also support our hypothesis. The pi-stacking hypothesis suggests a new approach to understanding the self-assembly mechanism that governs amyloid formation and indicates possible ways to control this process.
Control of Organic Interfaces with a Thin Film of Silicon Monoxide between 8-Hydroxyquinoline Aluminum and Diamine Layers in an Organic EL Diode (1997)

The insertion of a thin film of silicon monoxide (SiO) at the interface of the 8-hydroxyquinoline aluminum (Alq 3 ) and the diamine derivative (TPD) layers in the electroluminescent (EL) diode enhances the emission from the Alq 3 layer. The mechanism of emission enhancement from the hetero interfaces has been discussed with respect to the emission spectra of the diodes containing a thin film of a marker layer which was inserted into the emissive layer near the interface. The SiO layer thickness dependence on EL intensity in the diode with the SiO layer has been discussed.
The effect of context switches on cache performance (1991)

article Free Access Share on The effect of context switches on cache performance Authors: Jeffrey C. Mogul View Profile , Anita Borg View Profile Authors Info & Claims ACM SIGARCH Computer Architecture NewsVolume 19Issue 2Apr. 1991 pp 75–84https://doi.org/10.1145/106975.106982Published:01 April 1991Publication History 122citation2,043DownloadsMetricsTotal Citations122Total Downloads2,043Last 12 Months181Last 6 weeks45 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF