gebhart/patrepeval huggingface dataset:
Inheritance of Podosphaera xanthii resistance in melon line '90625'. (2008)

Several races of Podosphaera xanthii have been described on melon. The\nIndian melon line ‘90625’ (PI 313970) which had already been described as resistant\nin the USA is a potential source of resistance for strains recently characterized in\nFrance. We have studied the inheritance of resistance in a Recombinant Inbred Line\npopulation between ‘Védrantais’ (susceptible) and ‘90625’ using a leaf disk technique\nwith 10 strains of P. xanthii. Potentially five genes could be present in ‘90625’. Two\nindependent semi-dominant genes (A and B) are involved in resistance to strains\n06Sm10 and S87-7 respectively. Resistance to the other strains seems to be under a\ndigenic control, including A and B or not, with three other recessive genes. Some of\nthese RILs could be used as additional differential lines for the characterization of the\nraces.
Interleukin-11 Signals through the Formation of a Hexameric Receptor Complex (2000)

Interleukin-11 (IL-11) is a member of the gp130 family of cytokines. These cytokines drive the assembly of multisubunit receptor complexes, all of which contain at least one molecule of the transmembrane signaling receptor gp130. IL-11 has been shown to induce gp130-dependent signaling through the formation of a high affinity complex with the IL-11 receptor (IL-11R) and gp130. Site-directed mutagenesis studies have identified three distinct receptor binding sites of IL-11, which enable it to form this high affinity receptor complex. Here we present data from immunoprecipitation experiments, using differentially tagged forms of ligand and soluble receptor components, which show that multiple copies of IL-11, IL-11R, and gp130 are present in the receptor complex. Furthermore, it is demonstrated that sites II and III of IL-11 are independent gp130 binding epitopes and that both are essential for gp130 dimerization. We also show that a stable high affinity complex of IL-11, IL-11R, and gp130 can be resolved by nondenaturing polyacrylamide gel electrophoresis, and its composition verified by second dimension denaturing polyacrylamide gel electrophoresis. Results indicate that the three receptor binding sites of IL-11 and the Ig-like domain of gp130 are all essential for this stable receptor complex to be formed. We therefore propose that IL-11 forms a hexameric receptor complex composed of two molecules each of IL-11, IL-11R, and gp130.
Evidence That the Leucine Zipper Is a Coiled Coil (1989)

Recently, a hypothetical structure called a leucine zipper was proposed that defines a new class of DNA binding proteins. The common feature of these proteins is a region spanning approximately 30 amino acids that contains a periodic repeat of leucines every seven residues. A peptide corresponding to the leucine zipper region of the yeast transcriptional activator GCN4 was synthesized and characterized. This peptide associates in the micromolar concentration range to form a very stable dimer of alpha helices with a parallel orientation. Although some features of the leucine zipper model are supported by our experimental data, the peptide has the characteristics of a coiled coil.
Endocrine Therapy, New Biologicals, and New Study Designs for Presurgical Studies in Breast Cancer (2011)

The preoperative setting is increasingly popular for the clinical investigation of hormonal agents and new biological drugs. The effectiveness of endocrine agents is well established for estrogen receptor-positive disease, and the emphasis in preoperative studies is on their combination with agents targeted at resistance mechanisms over 3 or more months. New agents are also being assessed for early evidence of clinical efficacy in shorter-term window-of-opportunity studies. The establishment of Ki67 as an intermediate marker of treatment benefit and of long-term outcome, with endocrine drugs, provides the opportunity for new trial designs with Ki67 as the primary endpoint. The PeriOperative Endocrine Therapy for Individualizing Care (POETIC) trial is randomizing (2:1) 4000 estrogen receptor-positive patients to 2 weeks presurgical treatment with a nonsteroidal aromatase inhibitor or no presurgical treatment. It provides a unique opportunity for detailed study of the determinants of response and resistance to estrogen deprivation as well as testing the role of presurgical therapy for improved biomarker-based estimates of prognosis.
Effects of protein incorporation on calcium phosphate coating (2008)

The incorporation of proteins into calcium phosphate (Ca–P) coatings is expected to alter their properties. The aim of this work is, therefore, to study the effect of protein concentration on the formation of Ca–P film. A biodegradable blend of corn starch/ethylene vinyl alcohol (SEVA-C) was used as substrate and bioactive glass (45S5 Bioglass®) was used as a nucleating agent. Bovine serum albumin (BSA) and α-amylase were added, separately, at a concentration of 0.5, 1, and 5 mg/mLto simulated body fluid (SBF) solutions, at the nucleation stage. The incorporation of protein molecules was shown to affect the properties of Ca–P coatings in terms of morphology, composition and crystallinity. Both proteins seem to inhibit in some extent and/or retard the growth of Ca–P nuclei at 0.5 and 5 mg/mL concentrations. FTIR analyses revealed the presence of phosphate and carbonate groups, confiming the formation of a Ca–P layer. The characteristic groups of protein molecules were also detected on the IR spectra, which indicate the efficient incorporation of the proteins into the coatings. When α-amylase was added to the SBF solution the production of reducing sugars was detected, proving the retention of enzyme activity. These results suggest the carrier potential of Ca–P coatings for the sustained delivery of other biologically active proteins and consequently with a strong potential for inducing bone tissue regeneration.
Fibrosing Interstitial Lung Disease. A Practical High-Resolution Computed Tomography–based Approach to Diagnosis and Management and a Review of the Literature (2013)

Establishing the etiology of fibrosing interstitial lung disease (FILD) remains a clinical challenge. This is because many disorders resulting in lung fibrosis may be similar in their initial clinical and radiographic appearances. High-resolution computed tomography (HRCT) studies are now almost always obtained for patients who present with otherwise nonspecific clinical symptoms and chest radiographic findings. In the majority of cases presenting with FILD, differential diagnosis typically requires differentiating among three most commonly encountered clinical entities: idiopathic pulmonary fibrosis with usual interstitial pneumonia, nonspecific interstitial pneumonia, and chronic hypersensitivity pneumonitis. As a consequence, the development of a simplified diagnostic algorithmic approach initially focusing on the interpretation of HRCT findings may prove of considerable value provided thorough familiarity with optimal HRCT techniques and methods of interpretation. For this purpose, in patients with FILD in whom an underlying etiology is not initially apparent, the recently proposed American Thoracic Society/European Respiratory Society/Japanese Respiratory Society/Latin American Thoracic Association guidelines for the diagnosis of IPF have been modified to create a straightforward, clinically practicable algorithmic approach to clinical management based on the initial interpretation and classification of HRCT findings.
Quantitation of MicroRNAs by Real-Time RT-qPCR (2010)

MicroRNAs (miRNAs) are ∼22 nucleotide regulatory RNA molecules that play important roles in controlling developmental and physiological processes in animals and plants. Measuring the level of miRNA expression is a critical step in methods that study the regulation of biological functions and that use miRNA profiles as diagnostic markers for cancer and other diseases. Even though the quantitation of these small miRNA molecules by RT-qPCR is challenging because of their short length and sequence similarity, a number of quantitative RT-qPCR-based miRNA quantitation methods have been introduced since 2004. The most commonly used methods are stem-loop reverse transcription (RT)-based TaqMan(®) MicroRNA assays and arrays. The high sensitivity and specificity, large dynamic range, and simple work flow of TaqMan(®) MicroRNA assays and arrays have made TaqMan analysis the method of choice for miRNA expression profiling and follow-up validation. Other methods such as poly (A) tailing-based and direct RT-based SYBR miRNA assays are also discussed in this chapter.
Evidence for shutter‐speed variation in CR bolus‐tracking studies of human pathology (2004)

The standard pharmacokinetic model for the analysis of MRI contrast reagent (CR) bolus-tracking (B-T) data assumes that the mean intracellular water molecule lifetime (tau(i)) is effectively zero. This assertion is inconsistent with a considerable body of physiological measurements. Furthermore, theory and simulation show the B-T time-course shape to be very sensitive to the tau(i) magnitude in the physiological range (hundreds of milliseconds to several seconds). Consequently, this standard model aspect can cause significant underestimations (factors of 2 or 3) of the two parameters usually determined: K(trans), the vascular wall CR transfer rate constant, and v(e), the CR distribution volume (the extracellular, extravascular space fraction). Analyses of animal model data confirmed two predicted behaviors indicative of this standard model inadequacy: (1) a specific temporal pattern for the mismatch between the best-fitted curve and data; and (2) an inverse dependence of the curve's K(trans) and v(e) magnitudes on the CR dose. These parameters should be CR dose-independent. The most parsimonious analysis allowing for realistic tau(i) values is the 'shutter-speed' model. Its application to the experimental animal data essentially eliminated the two standard model signature inadequacies. This paper reports the first survey for the extent of this 'shutter-speed effect' in human data. Retrospective analyses are made of clinical data chosen from a range of pathology (the active multiple sclerosis lesion, the invasive ductal carcinoma breast tumor, and osteosarcoma in the leg) that provides a wide variation, particularly of K(trans). The signature temporal mismatch of the standard model is observed in all cases, and is essentially eliminated by use of the shutter-speed model. Pixel-by-pixel maps show that parameter values from the shutter-speed analysis are increased by more than a factor of 3 for some lesion regions. This endows the lesions with very high contrast, and reveals heterogeneities that are often not seen in the standard model maps. Normal muscle regions in the leg allow validation of the shutter-speed model K(trans), v(e), and tau(i) magnitudes, by comparison with results of previous careful rat leg studies not possible for human subjects.
The Vα14 NKT Cell TCR Exhibits High-Affinity Binding to a Glycolipid/CD1d Complex (2002)

Most CD1d-dependent NKT cells in mice have a canonical V alpha 14J alpha 18 TCR rearrangement. However, relatively little is known concerning the molecular basis for their reactivity to glycolipid Ags presented by CD1d. Using glycolipid Ags, soluble forms of a V alpha 14 NKT cell-derived TCR, and mutant and wild-type CD1d molecules, we probed the TCR/CD1d interaction by surface plasmon resonance, tetramer equilibrium staining, and tetramer staining decay experiments. By these methods, several CD1d alpha-helical amino acids could be defined that do not greatly alter lipid binding, but that affect the interaction with the TCR. Binding of the V alpha 14(+) TCR to CD1d requires the agonist alpha-galactosylceramide (alpha-GalCer), as opposed to the nonantigenic beta-galactosylceramide, although both Ags bind to CD1d, indicating that the carbohydrate moiety of the CD1d-bound Ag plays a major role in the TCR interaction. The TCR has a relatively high-affinity binding to the alpha-GalCer/CD1d complex, with a particularly slow off rate. These unique properties are consistent with the coreceptor-independent action of the V alpha 14 TCR and may be related to the intense response to alpha-GalCer by NKT cells in vivo.
Toward ontology-based personalization of a recommender system in social network (2010)

Personalized search, navigation and content delivery techniques have attracted interest in the recommender systems as a means to decrease search ambiguity and return results most relevant to a particular user preferences. In this paper, we study the effect of incorporating user semantic profile derived from past user's behavior and preferences on the accuracy of a recommender system. We present a preliminary work which aims at tackling the most technical issues due to the integration of an ontology-based semantic user profile within a hybrid recommender system based on our early released guided recommender algorithm. A semantic user profile context is represented as an instance of a reference domain ontology in which concepts are annotated by interest scores.
18 Stem Cells and Neurogenesis (2001)

NEURAL DEVELOPMENT DURING EMBRYOGENESIS Neural differentiation is an early embryonic event that occurs soon after germ layer specification. The newly formed ectoderm undergoes further patterning to separate into two identifiable components, the presumptive neural ectoderm and the presumptive epidermis. Neural tissue segregates as a clearly demarcated epithelium termed the neuroepithelium (or neuroectoderm). The neuroepithelium generates the central nervous system (CNS) whereas cells at the margins of the neuroepithelium will generate the peripheral nervous system (PNS). Two groups of cells contribute to the PNS. Neural crest stem cells differentiate at the neuroectodermal/epithelial junction, and placodal precursors differentiate from cranial ectoderm that lies more laterally than the zone that generates neural crest (Fig. 1). Precursors that generate the PNS also contribute to nonneural structures, including pigment cells of the skin and craniofacial mesenchyme (for review, see Le Douarin and Kalchem 1999). Undifferentiated neural precursor cells, whether in the CNS, neural crest, or the placodes, proliferate, differentiate, and migrate to appropriate locations. Cells undergo further maturation and become postmitotic. Neuronal cells go on to project to appropriate targets, make synapses, and acquire the correct rostrocaudal and dorsoventral identity. Seminal work by a number of laboratories has led to rapid advances in our understanding of phenotypic specification (for review, see Rao 1999). An accumulating body of evidence suggests that neurogenesis follows a pattern of development similar to developmental patterns described in the liver, skin, and the hematopoietic system (Edlund and Jessell 1999; Rao 1999; Weissman 2000). In each of these systems, tissue-specific stem cells...
Recent developments in the use of γ -H2AX as a quantitative DNA double-strand break biomarker (2011)

The past year has seen considerable developments in the use of the DNA double-strand breaks (DSBs) to evaluate genome alterations in cells undergoing a variety of genotoxic stresses in vitro and in vivo. When the γ-H2AX foci which mark the DSBs are stained, individual breaks are detectible, making the assay suitable for situations requiring great sensitivity. While the methods for the detection of γ-H2AX foci are still evolving, particularly for in vivo detection, the basic assay has proven to be useful in several diverse areas of research. We will highlight recent developments of the assay in four areas: radiation biodosimetry, the evaluation or validation of new cancer drugs in clinical studies, chronic inflammation, and environmental genotoxicity.
Attenuated Vesicular Stomatitis Viruses as Vaccine Vectors (1999)

We showed previously that a single intranasal vaccination of mice with a recombinant vesicular stomatitis virus (VSV) expressing an influenza virus hemagglutinin (HA) protein provided complete protection from lethal challenge with influenza virus (A. Roberts, E. Kretzschmar, A. S. Perkins, J. Forman, R. Price, L. Buonocore, Y. Kawaoka, and J. K. Rose, J. Virol. 72:4704-4711, 1998). Because some pathogenesis was associated with the vector itself, in the present study we generated new VSV vectors expressing HA which are completely attenuated for pathogenesis in the mouse model. The first vector has a truncation of the cytoplasmic domain of the VSV G protein and expresses influenza virus HA (CT1-HA). This nonpathogenic vector provides complete protection from lethal influenza virus challenge after intranasal administration. A second vector with VSV G deleted and expressing HA (DeltaG-HA) is also protective and nonpathogenic and has the advantage of not inducing neutralizing antibodies to the vector itself.
Lithium‐Salt Effects in Peptide Synthesis. Part II. Improvement of Degree of Resin Swelling and of Efficiency of Coupling in Solid‐Phase Synthesis (1991)

Abstract The course of solid‐phase peptide‐coupling reactions as well as the swelling properties of a peptide‐resin are influenced by the addition of inorganic salts (LiCl, LiBr, LiClO 4 , KSCN). Used as additives, these salts can ( i ) improve coupling yields ( e.g. , for Fmoc‐(Ala) 5 ‐Phe‐resin → Fmoc‐(AIa) 6 ‐Phe‐resin in DMF/CH 2 Cl 2 1:1 from 89.4 to 97.1% (for polyethylene oxide) on polystyrene ( PEO‐PS) resin) or from 77.5 to 93.8% (for poly‐( N , N ′‐dimethylacrylamide) on ‘Kieselgur’ (PDMAA‐KG) resin) without and with 0.4 M LiCl, respectively), ( ii ) increase resin swelling ( e.g. for Fmoc‐(Ala) 5 ‐Phe‐(polystyrene resin) from 2.42‐ to 5.73‐fold in 1‐methylpyrrolidin‐2‐one (NMP) without and with LiCl, (respectively), and ( iii ) change coupling rates. Example;; of coupling reactions and swelling behaviour (degree and rate) in different solvents (DMF, DMF/CH 2 Cl 2 1:1, THF, NMP, N , N ‐dimethylpropyleneurea ( DMPU) with and without salts) using different resins (polystyrene (PS); PEO–PS, and PDMAA‐KG) and an improved analysis of alanine oligomers up to Ala 12 ‐Phe by HPLC and FAB‐MS are reported.
Acute and chronic microsphere loss from canine left ventricular myocardium (1982)

We determined the effects of time, type of anesthesia, and myocardial infarction on loss of radioactive microspheres averaging 9 or 15 micrometers diameter from left ventricular myocardium. The principle used to compute losses was comparison of the number of microspheres injected directly into coronary arteries to the numbers remaining in myocardium, appearing within 2-4 min in the coronary sinus, or trapped in the lungs. Losses of 9-micrometers microspheres within 2 min of injection were significantly greater for halothane (mean 6.3%) than nitrous oxide anesthesia (mean 3.3%), and in the next 2 h increased to 11.7 and 7.9%, respectively. Over 5 wk in conscious dogs losses were as high as 40 and 11% for 9 and 15 micrometers microspheres, respectively. Losses were not greater for infarcted than normal muscle, and negligible radioactivity appeared in paracardiac lymph nodes. Microspheres leaving the heart were almost all below 10.3 micrometers diameter, so that microspheres with diameters 10-14 (mean 12) micrometers might be the best size to use for myocardial studies.
A Phase I, randomized controlled clinical trial to study the reactogenicity and immunogenicity of a new split influenza vaccine derived from a non-tumorigenic cell line. (1999)

We have found that our MDCK-derived cell line (BV-5F1) is non-tumorigenic in tests conducted in accordance with FDA guidelines, and thus may be suitable for producing live, attenuated or inactivated vaccine. The cell line has been extensively tested for the presence of contaminating microorganisms. No infectious agents of viral or other microbial origin were present. Using the BV-5F1 cell line, we have now designed a process for the large-scale production of influenza virus for the manufacture of a vaccine. The production system involves expansion of cells anchored on a microcarrier using stirred fermenters, followed by virus infection. Viral particles are purified in a way similar to the licensed egg-derived vaccine Fluviral SF and mainly involves ultracentrifugation, ultrafiltration and formaldehyde inactivation. The final product is a split inactivated vaccine. A randomized, double-blind clinical study was made in healthy adults using the new split influenza vaccine derived from viruses grown in cell culture (bivalent formulation). The results of this Phase I study have demonstrated that the split influenza vaccine derived from cell culture is highly immunogenic and safe in adults.
Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX (2009)

The oncoproteins MDM2 and MDMX negatively regulate the activity and stability of the tumor suppressor protein p53--a cellular process initiated by MDM2 and/or MDMX binding to the N-terminal transactivation domain of p53. MDM2 and MDMX in many tumors confer p53 inactivation and tumor survival, and are important molecular targets for anticancer therapy. We screened a duodecimal peptide phage library against site-specifically biotinylated p53-binding domains of human MDM2 and MDMX chemically synthesized via native chemical ligation, and identified several peptide inhibitors of the p53-MDM2/MDMX interactions. The most potent inhibitor (TSFAEYWNLLSP), termed PMI, bound to MDM2 and MDMX at low nanomolar affinities--approximately 2 orders of magnitude stronger than the wild-type p53 peptide of the same length (ETFSDLWKLLPE). We solved the crystal structures of synthetic MDM2 and MDMX, both in complex with PMI, at 1.6 A resolution. Comparative structural analysis identified an extensive, tightened intramolecular H-bonding network in bound PMI that contributed to its conformational stability, thus enhanced binding to the 2 oncogenic proteins. Importantly, the C-terminal residue Pro of PMI induced formation of a hydrophobic cleft in MDMX previously unseen in the structures of p53-bound MDM2 or MDMX. Our findings deciphered the structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX, shedding new light on structure-based rational design of different classes of p53 activators for potential therapeutic use.
Molecular basis for allelic polymorphism of the maize Globulin-1 gene. (1991)

An abundant protein in maize (Zea mays L.) embryos is a storage globulin encoded by the polymorphic Glb1 gene. Several Glb1 protein size alleles and a null allele have been described. Here we report the isolation and nucleotide sequence analysis of genomic clones corresponding to two Glb1 size alleles (Glb1-L and Glb1-S) and to the Glb1-0 null allele. The Glb1-L and Glb1-0 alleles differ from Glb1-S by the presence of small nucleotide insertions which are imperfect or perfect duplications, respectively, of adjacent sequences. In the case of Glb1-L, the insertion is in-frame and results in a protein larger than that encoded by Glb1-S, whereas in Glb1-0 the insertion causes a translational frameshift which introduces a premature termination codon. Although steady-state levels of Glb1-0 transcripts are extremely low in Glb1-0/0 embryos, nuclear transcription assays indicate that the Glb1-0 gene is transcribed at a level comparable to that of Glb1-L. This suggests that the low amounts of Glb1-0 transcripts in the cytoplasm may be due to mRNA instability.