gebhart/patrepeval huggingface dataset:
The hepatitis A virus polyprotein expressed by a recombinant vaccinia virus undergoes proteolytic processing and assembly into viruslike particles (1991)

Hepatitis A virus (HAV) contains a single-stranded, plus-sense RNA genome with a single long open reading frame encoding a polyprotein of approximately 250 kDa. Viral structural proteins are generated by posttranslational proteolytic processing of this polyprotein. We constructed recombinant vaccinia viruses which expressed the HAV polyprotein (rV-ORF) and the P1 structural region (rV-P1). rV-ORF-infected cell lysates demonstrated that the polyprotein was cleaved into immunoreactive 29- and 33-kDa proteins which comigrated with HAV capsid proteins VP0 and VP1. The rV-P1 construct produced a 90-kDa protein which showed no evidence of posttranslational processing. Solid-phase radioimmunoassays with human polyclonal anti-HAV sera and with murine or human neutralizing monoclonal anti-HAV antibodies recognized the rV-ORF-infected cell lysates. Sucrose density gradients of rV-ORF-infected cell lysates contained peaks of HAV antigen with sedimentation coefficients of approximately 70S and 15S, similar to those of HAV empty capsids and pentamers. Immune electron microscopy also demonstrated the presence of viruslike particles in rV-ORF-infected cell lysates. Thus, the HAV polyprotein expressed by a recombinant vaccinia virus demonstrated posttranslational processing into mature capsid proteins which assembled into antigenic viruslike particles.
An Immunodominant Conserved Region Within the Variable Domain of VlsE, the Variable Surface Antigen of Borrelia burgdorferi (1999)

Antigenic variation is an effective strategy evolved by pathogenic microbes to avoid immune destruction. Variable Ags such as the variable major protein of Borrelia hermsii, the variant surface glycoprotein of African trypanosomes, and the pilin of Neisseria gonorrhoeae include an immunodominant variable domain and one or more invariable domains that are not antigenic. Short, nonantigenic, invariable regions also may be present within the variable domain. VlsE (variable major protein-like sequence, expressed), the variable surface Ag of Borrelia burgdorferi, the Lyme disease spirochete, also contains both variable and invariable domains. In addition, interspersed within the VlsE variable domain there are six invariable regions (IR1-6) that together amount to half of this portion's primary structure. We show here that these IRs are conserved among strains and genospecies of the B. burgdorferi sensu lato complex. Surprisingly, unlike the invariable regions of variable major protein, variant surface glycoprotein, and pilin, which are not antigenic in natural infections, the most conserved of the IRs, IR6, is immunodominant in Lyme disease patients and in monkeys infected with B. burgdorferi. IR6 is exposed on the surface of VlsE, as assessed by immunoprecipitation experiments, but is inaccessible to Ab on the spirochete's outer membrane, as demonstrated by immunofluorescence and in vitro killing assays. VlsE thus significantly departs from the antigenic variation paradigm, whereby immunodominance is only manifest in variable portions. We submit that IR6 may act as a decoy epitope(s) and contribute to divert the Ab response from other, perhaps protective regions of VlsE.
neurogenin3 is required for the development of the four endocrine cell lineages of the pancreas (2000)

In the mammalian pancreas, the endocrine cell types of the islets of Langerhans, including the alpha-, beta-, delta-, and pancreatic polypeptide cells as well as the exocrine cells, derive from foregut endodermal progenitors. Recent genetic studies have identified a network of transcription factors, including Pdx1, Isl1, Pax4, Pax6, NeuroD, Nkx2.2, and Hlxb9, regulating the development of islet cells at different stages, but the molecular mechanisms controlling the specification of pancreatic endocrine precursors remain unknown. neurogenin3 (ngn3) is a member of a family of basic helix-loop-helix transcription factors that is involved in the determination of neural precursor cells in the neuroectoderm. ngn3 is expressed in discrete regions of the nervous system and in scattered cells in the embryonic pancreas. We show herein that ngn3-positive cells coexpress neither insulin nor glucagon, suggesting that ngn3 marks early precursors of pancreatic endocrine cells. Mice lacking ngn3 function fail to generate any pancreatic endocrine cells and die postnatally from diabetes. Expression of Isl1, Pax4, Pax6, and NeuroD is lost, and endocrine precursors are lacking in the mutant pancreatic epithelium. Thus, ngn3 is required for the specification of a common precursor for the four pancreatic endocrine cell types.
A Retrospective View of Corn Genetic Resources (1990)

Journal Article A Retrospective View of Corn Genetic Resources Get access A. F. Troyer A. F. Troyer From the Research and Development Department, De Kalb-Pfizer GeneticsDeKalb, Illinois Address reprint requests to Dr. Troyer, DeKalb-Pfizer Genetics, 3100 Sycamore Road, DeKalb, IL 60115 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 81, Issue 1, January 1990, Pages 17–24, https://doi.org/10.1093/oxfordjournals.jhered.a110920 Published: 01 January 1990
Gradient Pursuits (2008)

Sparse signal approximations have become a fundamental tool in signal processing with wide-ranging applications from source separation to signal acquisition. The ever-growing number of possible applications and, in particular, the ever-increasing problem sizes now addressed lead to new challenges in terms of computational strategies and the development of fast and efficient algorithms has become paramount. Recently, very fast algorithms have been developed to solve convex optimization problems that are often used to approximate the sparse approximation problem; however, it has also been shown, that in certain circumstances, greedy strategies, such as orthogonal matching pursuit, can have better performance than the convex methods. In this paper, improvements to greedy strategies are proposed and algorithms are developed that approximate orthogonal matching pursuit with computational requirements more akin to matching pursuit. Three different directional optimization schemes based on the gradient, the conjugate gradient, and an approximation to the conjugate gradient are discussed, respectively. It is shown that the conjugate gradient update leads to a novel implementation of orthogonal matching pursuit, while the gradient-based approach as well as the approximate conjugate gradient methods both lead to fast approximations to orthogonal matching pursuit, with the approximate conjugate gradient method being superior to the gradient method.
Highly Ordered Nanoporous Thin Films from Cleavable Polystyrene‐block‐poly(ethylene oxide) (2007)

A cleavable trityl ether juncture is introduced between polystyrene (PS) and poly(ethylene oxide) (PEO), and thus highly ordered nanoporous thin films have been prepared from self-assembled PS-b-PEO diblock copolymers, via the removal of PEO from solvent-annealed PS-b-PEO thin films in a simple two or one-step process. When patterned substrates are used, addressable nanopore arrays with a high degree of lateral order and a well-defined lattice orientation can be readily produced (see figure).
Improved outcome in adult B-cell acute lymphoblastic leukemia (1996)

A total of 68 adult patients with B-cell acute lymphoblastic leukemia (B-ALL) were treated in three consecutive adult multicenter ALL studies. The diagnosis of B-ALL was confirmed by L3 morphology and/or by surface immunoglobulin (Slg) expression with > 25% blast cell infiltration in the bone marrow (BM). They were characterized by male predominance (78%) and a median age of 34 years (15 to 65 y) with only 9% adolescents (15 to 20 y), but 28% elderly patients (50 to 65 y). The patients received either a conventional (N = 9) ALL treatment regimen (ALL study 01/81) or protocols adapted from childhood B-ALL with six short, intensive 5-day cycles, alternately A and B. In study B-NHL83 (N = 24) cycle A consisted of fractionated doses of cyclophosphamide 200 mg/m2 for 5 days, intermediate-dose methotrexate (IdM) 500 mg/m2 (24 hours), in addition to cytarabine (AraC), teniposide (VM26) and prednisone. Cycle B was similar except that AraC and VM26 were replaced by doxorubicin. Major changes in study B-NHL86 (N = 35) were replacement of cyclophosphamide by ifosphamide 800 mg/m2 for 5 days, an increase of IdM to high-dose, 1,500 mg/m2 (HdM) and the addition of vincristine. A cytoreductive pretreatment with cyclophosphamide 200 mg/m2, and prednisone 60 mg/m2, each for 5 days was recommended in study B-NHL83 for patients with high white blood cell (WBC) count (> 2,500/m2) or large tumor burden and was obligatory for all patients in study B-NHL86. Central nervous system (CNS) prophylaxis/treatment consisted of intrathecal methotrexate (MTX) therapy, later extended to the triple combination of MTX, AraC, and dexamethasone, and a CNS irradiation (24 Gy) after the second cycle. Compared with the ALL 01/81 study where all the patients died, results obtained with the pediatric protocols B-NHL83 and B-NHL86 were greatly improved. The complete remission (CR) rates increased from 44% to 63% and 74%, the probability of leukemia free survival (LFS) from 0% to 50% and 71% (P = .04), and the overall survival rates from 0% to 49% and 51% (P = .001). Toxicity, mostly hematotoxicity and mucositis, was severe but manageable. In both studies B-NHL83 and B-NHL86, almost all relapses occurred within 1 year. The time to relapse was different for BM, 92 days, and for isolated CNS and combined BM and CNS relapses, 190 days (P = .08). The overall CNS relapses changed from 50% to 57% and 17%, most probably attributable to the high-dose MTX and the triple intrathecal therapy. LFS in studies B-NHL83 and B-NHL86 was significantly influenced by the initial WBC count < or > 50,000/microL, LFS 71% versus 29% (P = .003) and hemoglobin value > or < 8 g/dL, LFS 67% versus 27% (P = .02). Initial CNS involvement had no adverse impact on the outcome. Elderly B-ALL patients (> 50 years) also benefited from this treatment with a CR rate of 56% and a LFS of 56%. It is concluded that this short intensive therapy with six cycles is effective in adult B-ALL. HdM and fractionated higher doses of cyclophosphamide or ifosphamide seem the two major components of treatment.
Platelet dose for prophylactic platelet transfusions (2010)

Although guidelines exist to deal with some aspects of platelet transfusion practice, many important clinical issues have not been addressed in large randomized controlled trials (RCTs). Slichter et al. conducted a RCT of prophylactic platelet transfusions to determine the effects of the dose of platelets on clinical signs of bleeding, the use of platelet and red cell transfusions, changes in the recipient's post-transfusion platelet count, days to next transfusion and adverse events (Effects of Prophylactic Platelet Dose on Transfusion Outcomes [PLADO] trial). The primary end point of the study (i.e., the percentage of patients in each group with at least one episode of bleeding of grade 2 or higher according to the WHO criteria) was not significantly different (71, 69 and 70% of patients in the low-, medium- and high-dose group, respectively). According to these data, one can conclude that the dose of platelets transfused has no significant effect on the incidence of bleeding in patients with hypoproliferative thrombocytopenia and platelet counts no greater than 10 × 10⁹/l.
Inhibition of α2-macroglobulin/proteinase-mediated degradation of amyloid β peptide by apolipoprotein E and α1-antichymotrypsin; Evidence that the α2-macroglobulin/proteinase complex mediates degradation of the Aβ peptide (1996)

The soluble amyloid β–peptide (Aβ), is produced from the amyloid β-protein precursor (AβPP) during normal cellular metabolism. The accumulation and deposition of extracellular Aβ in senile plaques, a characteristic neumpathological feature of Alzheimer's disease (AD), may occur as a result of increased Aβ synthesis or decreased degradation/clearance, or both. We now report that trypsinactivated α2-macroglobulin (α2M-T), efficiently degrades Aβ in vitro. Moreover; incubation of Aβ with α2M-T prevents the in vitro formation of Thioflavine-S positive Aβ fibrils as well as Aβ-induced toxicity of cultured human cortical neuronal (HCN-IA) cells. Two senile plaque-associated proteins, apolipoprotein E (apoE) and α1-antichymotrypsin (ACT), markedly inhibit α2M-T-mediated Aβ degradation by a process that does not involve inhibition of the α2M-T catalytic site. Thus, the degradation and clearance of Aβ by α2M-T may be impaired by the amyloidpromoting factors, apoE and ACT, both of which have been shown to be elevated in AD brain and to be possible genetic risk factors for AD.
Two-dimensional films of discotic molecules at an air-water interface (1982)

The possibility of forming Langmuir monolayers with disc-like molecules of benzene-hexa-alkanoates has been investigated for the first time. Surface pressure measurements show that these monolayers behave in many respects as the well-known films of fatty acids. The benzene ring plays the role of the polar head group while the alkanoates chains are the long aliphatic tails. Molecular dimensions can be derived from the surface pressure-concentration isotherms. The results indicate that the benzene rings lie flat at the interface. The projection of the molecular diameter onto the interface is practically identical to the lattice spacing measured in the liquid-crystalline columnar mesophases formed by benzene-hexa-alkanoates in bulk. These experiments allow to refute the interpretation of the liquid expanded-liquid condensed transition in terms of a second order isotropic → nematic phase transition, as recently proposed by several theoretical groups.
S-Layer Proteins (2000)

Cell walls are an important structural component of prokaryotic organisms and essential for many aspects of their life. Particularly, the diverse structures of the outermost boundary layers strongly reflect adaptations of organisms to specific ecological and environmental conditions ([6][1]).

Over
Transgenic Potato Plants, Control of Colorado Potato Beetle, 1991 (1992)

Abstract The experiment was a randomized complete block design with six replicates, planted 21 May at Presque Isle, ME on land that was in clover in 1990. Each replicate consisted of a single row of ten plants 30 cm apart and separated by two blank rows plus two rows of 'Russet Burbank' potatoes. A 3.0 m space of bare soil separated blocks and surrounded the experiment. Fertilization and hilling practices were normal for the area. Early and late blight were controlled with three foliar applications of Dithane Mi 45 (80 WP) (1.12 kg/ha on 18, 26 Jul, and 2 Aug) and Bravo 720 (840 g/ha on 9 and 23 Aug). Foliar insecticide applications were made with a Century boom sprayer, three nozzles per row at 6.3 kg/cm2 pressure and 0.94 kl/ha. Numbers of larvae and adults were counted weekly on 6 whole plants in each plot. When dates of counts and application were the same, beetle counts were made prior to application of insecticides. Analyses of variance were calculated following transformations of data using log10(x + 1). Transformed means of the sum of larvae and adult beetles were compared using DMR.T. The Asana treatment was applied on 17 Jul and 2 Aug at the label rate. The soil was classified as Caribou Loam, pH 5.2. Total monthly rainfall for Jun, Jul, and Aug was 3.7, 1.9, and 21.7 cm, respectively. The average temperature for these three months was 17.1, 19.0, and 19.3 deg. C.
Involvement of dileucine motifs in the internalization and degradation of the insulin receptor. (1995)

Vol 269, p. 26286 Page 26287: It is stated in Footnote 2 that we used the numbering system of Ebina et al. (1985). In fact, the dileucine sequence at positions 986 and 987 was numbered according to Ullrich et al. (1985). (In the numbering system of Ebina et al., the dileucine sequence should be denoted at positions 998 and 999.) Furthermore, the Δ1000 mutant receptor (used in the experiments contained in Figs. 4 and 5) was constructed by substituting a chain termination codon in place of the Arg codon at position 981 in the numbering system of Ullrich et al. (1985).
ALKALOIDBIOSYNTHESIS INPLANTS: Biochemistry, Cell Biology, Molecular Regulation, and Metabolic Engineering Applications (2001)

Recent advances in the cell, developmental, and molecular biology of alkaloid biosynthesis have heightened our appreciation for the complexity and importance of plant secondary pathways. Several biosynthetic genes involved in the formation of tropane, benzylisoquinoline, and terpenoid indole alkaloids have now been isolated. The early events of signal perception, the pathways of signal transduction, and the function of gene promoters have been studied in relation to the regulation of alkaloid metabolism. Enzymes involved in alkaloid biosynthesis are associated with diverse subcellular compartments including the cytosol, vacuole, tonoplast membrane, endoplasmic reticulum, chloroplast stroma, thylakoid membranes, and perhaps unique "biosynthetic" or transport vesicles. Localization studies have shown that sequential alkaloid biosynthetic enzymes can also occur in distinct cell types, suggesting the intercellular transport of pathway intermediates. Isolated genes have also been used to genetically alter the accumulation of specific alkaloids and other plant secondary metabolites. Metabolic modifications include increased indole alkaloid levels, altered tropane alkaloid accumulation, elevated serotonin synthesis, reduced indole glucosinolate production, redirected shikimate metabolism, and increased cell wall-bound tyramine formation. This review discusses the biochemistry, cell biology, molecular regulation, and metabolic engineering of alkaloid biosynthesis in plants.
Role of Peroxisome Proliferator-Activated Receptor-γ in Maintenance of the Characteristics of Mature 3T3-L1 Adipocytes (2002)

Peroxisome proliferator-activated receptor (PPAR)-gamma plays an important role in adipogenesis. However, the functions of PPAR-gamma in differentiated adipocytes have remained unclear. The role of PPAR-gamma in mature 3T3-L1 adipocytes was therefore investigated by overexpression of a dominant negative mutant of this protein (PPAR-gamma-DeltaC) that lacks the 16 COOH-terminal amino acids and that has been shown to prevent the thiazolidinedione-induced differentiation of 3T3-L1 cells into adipocytes. Overexpression of PPAR-gamma-DeltaC in mature 3T3-L1 adipocytes by adenovirus gene transfer resulted in a decrease in both cell size and intracellular triglyceride content, an increase in the extent of lipolysis, and a reduction in the rate of free fatty acid uptake. Furthermore, overexpression of this mutant reduced the abundance of mRNAs for several key enzymes that contribute to triglyceride and free fatty acid metabolism as well as the amounts of GLUT4, insulin receptor, insulin receptor substrate (IRS), and C/EBPalpha mRNAs. It also reduced both the concentration of IRS2 and the insulin-stimulated glucose uptake. These results suggest that PPAR-gamma plays an important role in mature 3T3-L1 adipocytes at least in part by maintaining the expression of genes that confer the characteristics of mature adipocytes.
METHODS in microbiology (1969)

Contributors. Preface. Determination of DNA Base Composition, J.L. Johnson. DNA Reassociation and RNA Hybridisation of Bacterial Nucleic Acids, J.L. Johnson. 16 S Ribosomal RNA Oligonucleotide Cataloguing, E. Stackebrandt, W. Ludwig, and G.E. Fox. Analysis of Ribosomal Proteins By Two-Dimensional Gel Electrophoresis, A. Bock. Analysis of the Chemical Composition and Primary Structure of Murein, K.H. Schleifer. Analysis of Lipopolysaccharides of Gram-Negative bacteria, H. Mayer, R.N. Tharanathan, and J. Weckesser. Lipid Analysis and the Relationship to Chemotaxonomy, T.G. Tornabene. Analysis of Carotenoids and Related Polyene Pigments, S. Liaaen-Jensen and A.G. Andrews. Analysis of Bacteriochlorophylls, J. Oelze. The Analysis of Cytochromes, C.W. Jones and R.K. Poole. Analysis of Isoprenoid Quinones, M.D. Collins. Index. Contents of Previous Volumes.
Contactless Determination of the Photoconductivity Action Spectrum, Exciton Diffusion Length, and Charge Separation Efficiency in Polythiophene-Sensitized TiO2 Bilayers (2003)

The flash-photolysis time-resolved microwave conductivity technique (FP-TRMC) has been used to study photoinduced charge separation in bilayers consisting of a smooth, transparent, 80 nm thick layer of anatase TiO2 onto which poly(3-hexylthiophene) (P3HT) sensitizer layers have been spin-coated. Interfacial charge separation, resulting from excitation of the polymer in the visible, is found to persist well into the millisecond time domain. Photoconductivity action spectra have been measured between 420 and 700 nm for P3HT layer thicknesses, L, from ∼2 to 200 nm. Using this electrodeless technique, the bilayers could be irradiated from either the polymer (“front”) or semiconductor (“back”) side. On front-side irradiation at 540 nm (close to the absorption maximum of the polymer), the efficiency of charge separation per incident photon (IPCSE) initially increased to a maximum value of 0.8% for L ≈ 10 nm. For thicker layers the IPCSE gradually decreased, eventually to 0.1% for L ≈ 170 nm. On back-side irradiation the IPCSE increased over the first 10 nm to a value close to the maximum found for front-side irradiation, and decreased only slightly for further increase in layer thickness. Analytical expressions for the thickness dependence based on exciton diffusion with a Lambert−Beer excitation profile have been used to fit the experimental data. Best fits were obtained for an exciton diffusion length, Λ (=√(Dτ) with D the diffusion coefficient and τ the natural lifetime), of 5.3 or 2.6 nm depending on whether excitons were taken to be reflected or quenched at the polymer/gas interface, respectively. The IPCSE decreased at high light intensities; an effect that is attributed to the occurrence of exciton−exciton annihilation within the polymer layer.
Nucleotide Analogues as Antiviral Agents (1989)

Virus-specific enzymes essential for viral nucleic acid replication or related functions are targets for inhibition by substrate or product nucleotide analogues in which one or more P-O bonds are replaced by a P-C bond. The simplest examples of these are PFA (phosphonoformic acid) and PAA (phosphonoacetic acid), representing analogues of 'pyrophosphate' moieties in nucleotides. The synthesis of a series of α-halogenated and α-oxo PAA and MDP (methanediphosphonate) derivatives is described and structure/activity relationships in their inhibition of several human (α,β,γ) and viral (HSV, EBV, HIV) DNA polymerases are presented. Inhibition of HIV RNA-directed DNA polymerase (reverse transcriptase) by PFA, α-oxophosphonoacetate and α-oxomethanediphosphonate is shown to be pH-and template-dependent. Combination of phosphonoacetate derivatives and anti-viral nucleosides into 'hybrid' nucleotide analogues is briefly discussed.
Advances and Challenges in Basic and Translational Research on Clusterin (2009)

Clusterin (CLU), known by several other names, has recently drawn much attention because of its association with cancer promotion and metastasis ( [1][1]– [3][2]). First discovered as serum apolipoprotein J with chaperoning properties for protein stabilization, CLU also can exist within the cell