gebhart/patrepeval huggingface dataset:
Genetic dissection of a TIR‐NB‐LRR locus from the wild North American grapevine species Muscadinia rotundifolia identifies paralogous genes conferring resistance to major fungal and oomycete pathogens in cultivated grapevine (2013)

The most economically important diseases of grapevine cultivation worldwide are caused by the fungal pathogen powdery mildew (Erysiphe necator syn. Uncinula necator) and the oomycete pathogen downy mildew (Plasmopara viticola). Currently, grapegrowers rely heavily on the use of agrochemicals to minimize the potentially devastating impact of these pathogens on grape yield and quality. The wild North American grapevine species Muscadinia rotundifolia was recognized as early as 1889 to be resistant to both powdery and downy mildew. We have now mapped resistance to these two mildew pathogens in M. rotundifolia to a single locus on chromosome 12 that contains a family of seven TIR-NB-LRR genes. We further demonstrate that two highly homologous (86% amino acid identity) members of this gene family confer strong resistance to these unrelated pathogens following genetic transformation into susceptible Vitis vinifera winegrape cultivars. These two genes, designated resistance to Uncinula necator (MrRUN1) and resistance to Plasmopara viticola (MrRPV1) are the first resistance genes to be cloned from a grapevine species. Both MrRUN1 and MrRPV1 were found to confer resistance to multiple powdery and downy mildew isolates from France, North America and Australia; however, a single powdery mildew isolate collected from the south-eastern region of North America, to which M. rotundifolia is native, was capable of breaking MrRUN1-mediated resistance. Comparisons of gene organization and coding sequences between M. rotundifolia and the cultivated grapevine V. vinifera at the MrRUN1/MrRPV1 locus revealed a high level of synteny, suggesting that the TIR-NB-LRR genes at this locus share a common ancestor.
Inhaled Nitric Oxide and Persistent Pulmonary Hypertension of the Newborn (1997)

Inhaled nitric oxide improves systemic oxygenation in infants with persistent pulmonary hypertension and may reduce the need for more invasive treatments.
Coordinated Cancer Germline Antigen Promoter and Global DNA Hypomethylation in Ovarian Cancer: Association with the BORIS/CTCF Expression Ratio and Advanced Stage (2011)

DNA hypomethylation coordinately affects CG antigen gene promoters and specific repetitive DNA elements in EOC, and correlates with advanced stage disease. The BORIS/CTCF mRNA expression ratio is closely associated with DNA hypomethylation and confers poor prognosis in EOC.
Intraannular Savige–Fontana Reaction: One‐Step Conversion of One Class of Monocyclic Peptides into Another Class of Bicyclic Peptides (2008)

Cyclisation and cross-linking strategies are important for the synthesis of cyclic and bicyclic peptides. These macrolactams are of great interest due to their increased biological activity compared to linear analogues. Herein, we describe the synthesis of a cyclic peptide containing an Hpi toxicophore, reminiscent of phakellistatins and omphalotins. The first intraannular cross-linking of such a peptide is then presented: using neat TFA to catalyse a Savige-Fontana tryptathionylation, the Hpi-containing peptide is converted to a bicyclic amatoxin analogue. As such, this methodology represents an efficient cyclisation method for cross-linking peptides and exposes a heretofore unrealised relationship between two different classes of peptide natural products. This finding increases the degree of potential chemical space for library generation.
Hypothalamic hormones: from neuroendocrinology to cancer therapy. (1994)

The discovery of hypothalamic hormones, especially LH-RH and somatostatin has led to practical clinical use of their analogs in the field of cancer treatment. Bombesin/GRP antagonists can be also considered for the development of new methods for treatment of various tumors. The understanding of functions of these peptide hormones and the availability of their synthetic analogs should permit the clinicians to treat a variety of cancers more successfully than in the past.
A Metal‐Oxide Interconnection Layer for Polymer Tandem Solar Cells with an Inverted Architecture (2010)

A metal-oxide-only interconnecting layer for application in inverted polymer tandem solar cells is reported. Good electrical and optical coupling of the two sub-cells is achieved by using a carefully-designed MoO3/Al/ZnO layer, which leads to a power coversion efficiency of 5.1%. Our results demonstrate that effective connection between polymer bulk heterojunctions can be realized by this facile metal-oxide interlayer.
Superradiance of High Density Frenkel Excitons at Room Temperature (1995)

Superradiance of high density Frenkel excitons in an $R$-phycoerythrin single crystal is observed at room temperature for the first time. No fluorescence is observed except the emission at the sharp exciton band when the superradiance of excitons occurs, and the higher the pump density, the sharper the emission bandwidth. A redshift and a blueshift are observed at the rise time and the fall time of the emission pulse, respectively. The experimental results also imply deformed-boson properties of high density Frenkel excitons.
Expression of interleukin 1 receptors on human peripheral T cells. (1987)

The expression of interleukin 1 receptors (IL 1R) on human peripheral T cells was studied by the binding assay with 125I-labeled recombinant human interleukin 1 (IL 1) alpha and IL 1 beta and by the flow cytofluorometry with the fluorescein isothiocyanate (FITC)-conjugated IL 1 alpha. Peripheral blood lymphocytes expressed only few IL 1R without any stimulations. When they were stimulated with concanavalin A (Con A), IL 1R-positive cells began to increase by 4 hr, reached the maximum level at 48 hr, and then gradually decreased. The kinetics of the expression of IL 1 alpha R and IL 1 beta R showed the same pattern. Furthermore the binding of 125I-labeled IL 1 alpha to IL 1R on T cells was inhibited by the addition of either cold IL 1 alpha or IL beta, but not by interleukin 2 or interferons. The similar results were observed in the binding of 125I-labeled IL 1 beta. These results suggest that IL 1R on human peripheral T cells reactive for IL 1 alpha and IL 1 beta were identical. By Scatchard plot analysis, the numbers of IL 1R were estimated as 40 and 350 molecules per cell before and after Con A stimulation, respectively, and their Kd values were 3.1 X 10(-10) M and 2.8 X 10(-10) M. When purified T cells alone were stimulated with Con A, IL 1R were only marginally expressed. However, by the addition of monocytes, IL 1R were expressed on T cells in a dose-dependent manner. The maximum response was induced in the presence of 10% monocytes. The maximum IL 1R-positive T cells were approximately 30% by the detection of the flow cytofluorometry with FITC-conjugated IL 1 alpha. This enhancing activity of IL 1R expression on T cells by monocytes was inhibited by the addition of an anti-HLA-DR antibody or by the treatment of monocytes with the anti-HLA-DR antibody and complement. Furthermore T cell proliferative responses induced with IL 1 and Con A were also enhanced by the addition of HLA-DR-positive monocytes. These results suggest that IL 1R are expressed as the result of monocyte-T cell interaction in the early stage of T cell activation, and the expression of IL 1R on T cells and the responsiveness of T cells for IL 1 require the accessory function of HLA-DR-positive monocytes.
Phase Detection in Acoustic Microscopy (1990)

The scanning laser acoustic microscope provides a relatively simple means by which speed of sound data can be collected from biological specimens. By employing a phase detection circuit, phase-contour lines can be superimposed on acoustic micrographs and digitized for direct speed of sound calculations. Because of the existence of mild field non-uniformities, the phase reference must be mathematically modeled. This is accomplished by employing a polynomial function and simple linear regression. Scattering can be studied by using a frequency-selective “dark field” approach. Speed of sound maps are readily produced from the phase data by applying the simple geometric relationships of wave propagation; however the theoretical limitations of the technique must be kept in mind. Using this approach, useful data have been obtained.
Minimally invasive aortic valve surgery: state of the art and future directions. (2015)

Minimally invasive aortic valve replacement (MIAVR) is defined as an aortic valve replacement (AVR) procedure that involves a small chest wall incision as opposed to conventional full sternotomy (FS). The MIAVR approach is increasingly being used with the aim of reducing the "invasiveness" of the surgical procedure, while maintaining the same efficacy, quality and safety of a conventional approach. The most common MIAVR techniques are ministernotomy (MS) and right anterior minithoracotomy (RT) approaches. Compared with conventional surgery, MIAVR has been shown to reduce postoperative mortality and morbidity, providing faster recovery, shorter hospital stay and better cosmetics results, requires less rehabilitations resources and consequently cost reduction. Despite these advantages, MIAVR is limited by the longer cross-clamp and cardiopulmonary bypass (CPB) times, which have raised some concerns in fragile and high risk patients. However, with the introduction of sutureless and fast deployment valves, operative times have dramatically reduced by 35-40%, standardizing this procedure. According to these results, the MIAVR approach using sutureless valves may be the "real alternative" to the transcatheter aortic valve implantation (TAVI) procedures in high risk patients "operable" patients. Prospective randomized trials are required to confirm this hypothesis.
Quantitative genetic analysis of biomass and wood chemistry of Populus under different nitrogen levels (2009)

The genetic control of carbon allocation and partitioning in woody perennial plants is poorly understood despite its importance for carbon sequestration, biofuels and other wood-based industries. It is also unclear how environmental cues, such as nitrogen availability, impact the genes that regulate growth, biomass allocation and wood composition in trees. We phenotyped 396 clonally replicated genotypes of an interspecific pseudo-backcross pedigree of Populus for wood composition and biomass traits in above- and below-ground organs. The loci that regulate growth, carbon allocation and partitioning under two nitrogen conditions were identified, defining the contribution of environmental cues to their genetic control. Sixty-three quantitative trait loci were identified for the 20 traits analyzed. The majority of quantitative trait loci are specific to one of the two nitrogen treatments, demonstrating significant nitrogen-dependent genetic control. A highly significant genetic correlation was observed between plant growth and lignin/cellulose composition, and quantitative trait loci co-localization identified the genomic position of potential pleiotropic regulators. Pleiotropic loci linking higher growth rates to wood with less lignin are excellent targets to engineer tree germplasm improved for pulp, paper and cellulosic ethanol production. The causative genes are being identified with a genetical genomics approach.
Explicit B-spline regularization in diffeomorphic image registration (2013)

Diffeomorphic mappings are central to image registration due largely to their topological properties and success in providing biologically plausible solutions to deformation and morphological estimation problems. Popular diffeomorphic image registration algorithms include those characterized by time-varying and constant velocity fields, and symmetrical considerations. Prior information in the form of regularization is used to enforce transform plausibility taking the form of physics-based constraints or through some approximation thereof, e.g., Gaussian smoothing of the vector fields [a la Thirion's Demons (Thirion, 1998)]. In the context of the original Demons' framework, the so-called directly manipulated free-form deformation (DMFFD) (Tustison et al., 2009) can be viewed as a smoothing alternative in which explicit regularization is achieved through fast B-spline approximation. This characterization can be used to provide B-spline "flavored" diffeomorphic image registration solutions with several advantages. Implementation is open source and available through the Insight Toolkit and our Advanced Normalization Tools (ANTs) repository. A thorough comparative evaluation with the well-known SyN algorithm (Avants et al., 2008), implemented within the same framework, and its B-spline analog is performed using open labeled brain data and open source evaluation tools.
Phosphotyrosyl protein phosphatases (1989)

Research Article| January 01 1989 Phosphotyrosyl protein phosphatases K H W Lau; K H W Lau 1Department of Medicine and Biochemistry, Loma Linda University, and Mineral Metabolism Unit (151), Jerry L. Pettis Memorial Veterans' Hospital, Loma Linda, CA 92357, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar J R Farley; J R Farley 1Department of Medicine and Biochemistry, Loma Linda University, and Mineral Metabolism Unit (151), Jerry L. Pettis Memorial Veterans' Hospital, Loma Linda, CA 92357, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar D J Baylink D J Baylink 1Department of Medicine and Biochemistry, Loma Linda University, and Mineral Metabolism Unit (151), Jerry L. Pettis Memorial Veterans' Hospital, Loma Linda, CA 92357, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1989) 257 (1): 23–36. https://doi.org/10.1042/bj2570023 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share MailTo Twitter LinkedIn Cite Icon Cite Get Permissions Citation K H W Lau, J R Farley, D J Baylink; Phosphotyrosyl protein phosphatases. Biochem J 1 January 1989; 257 (1): 23–36. doi: https://doi.org/10.1042/bj2570023 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1989 London: The Biochemical society1989 Article PDF first page preview Close Modal You do not currently have access to this content.
Linkage of a QTL Contributing to Normal Variation in Bone Mineral Density to Chromosome 11q12–13 (1998)

Osteoporosis is a leading public health problem that is responsible for substantial morbidity and mortality. A major determinant of the risk for osteoporosis in later life is bone mineral density (BMD) attained during early adulthood. BMD is a complex trait that presumably is influenced by multiple genes. Recent linkage of three Mendelian BMD-related phenotypes, autosomal dominant high bone mass, autosomal recessive osteoporosis-pseudoglioma, and autosomal recessive osteopetrosis to chromosome 11q12-13 led us to evaluate this region to determine if the underlying gene(s) could also contribute to variation in BMD in the normal population. We performed a linkage study in a sample of 835 premenopausal Caucasian and African-American sisters to identify genes underlying BMD variation. A maximum multipoint LOD score of 3.50 with femoral neck BMD was obtained near the marker D11S987, in the same chromosomal region as the three Mendelian traits mentioned above. Our results suggest that the gene(s) underlying these Mendelian phenotypes also play a role in determining peak BMD in the normal population and are the first using linkage methods to establish a chromosomal location for a gene important in determining peak BMD. These findings support the hypothesis that a gene responsible for one or more of the rare Mendelian BMD traits linked to chromosome 11q12-13 has an important role in osteoporosis in the general population.
Multiphoton Intrapulse Interference. 1. Control of Multiphoton Processes in Condensed Phases (2002)

We explore and demonstrate the use of phase-modulated ultrafast laser pulses for controlling nonlinear optical processes in large molecules, proteins, and solid materials. Our experiments illustrate that in condensed phases, when spectra are broad, the spectrum of the nth-order electric field, determined by multiphoton intrapulse interference, plays a major role in controlling multiphoton excitation. These findings determine key parameters (amplitude, period, and symmetry of the phase function) for coherent femtosecond laser control in condensed phases.
Potent Inhibition of Mammalian Ribonucleases by 3′,5′-Pyrophosphate-linked Nucleotides (1999)

Molecular modeling based on the crystal structure of the complex of bovine pancreatic RNase A with the inhibitor 5'-diphosphoadenosine 3'-phosphate (ppAp) (Leonidas, D. D., Shapiro, R., Irons, L. I., Russo, N., and Acharya, K. R. (1997) Biochemistry 36, 5578-5588) was used to design new inhibitors that extend into unoccupied regions of the enzyme active site. These compounds are dinucleotides that contain an unusual 3',5'-pyrophosphate linkage and were synthesized in solution by a combined chemical and enzymatic procedure. The most potent of them, 5'-phospho-2'-deoxyuridine 3'-pyrophosphate, P' --> 5'-ester with adenosine 3'-phosphate (pdUppAp), binds to RNase A with Ki values of 27 and 220 nM at pH 5.9 and 7, respectively. These values are 6-9-fold lower than those for ppAp and 50-fold lower than that for the transition state analogue, uridine vanadate. pdUppAp has broad specificity; it is an effective inhibitor of at least two other members of the pancreatic RNase superfamily, human RNase-2 (eosinophil-derived neurotoxin) and RNase-4, which share only 36-44% sequence identity with the pancreatic enzyme. The potency of pdUppAp and the other inhibitors described here depends critically on the extended internucleotide linkage; the pyrophosphate group enhances dinucleotide binding to the three RNases by 2.1-2.9 orders of magnitude, as compared with a monophosphate. These data give further insight into the organization of the catalytic centers of the various RNases. Moreover, the new class of inhibitors provides a useful means by which to probe the biological actions of these and other related enzymes.
Online maintenance of very large random samples on flash storage (2008)

Recent advances in flash media have made it an attractive alternative for data storage in a wide spectrum of computing devices, such as embedded sensors, mobile phones, PDA's, laptops, and even servers. However, flash media has many unique characteristics that make existing data management/analytics algorithms designed for magnetic disks perform poorly with flash storage. For example, while random (page) reads are as fast as sequential reads, random (page) writes and in-place data updates are orders of magnitude slower than sequential writes. In this paper, we consider an important fundamental problem that would seem to be particularly challenging for flash storage: efficiently maintaining a very large (100 MBs or more) random sample of a data stream (e.g., of sensor readings). First, we show that previous algorithms such as reservoir sampling and geometric file are not readily adapted to flash. Second, we propose B-FILE, an energy-efficient abstraction for flash media to store self-expiring items, and show how a B-FILE can be used to efficiently maintain a large sample in flash. Our solution is simple, has a small (RAM) memory footprint, and is designed to cope with flash constraints in order to reduce latency and energy consumption. Third, we provide techniques to maintain biased samples with a B-FILE and to query the large sample stored in a B-FILE for a subsample of an arbitrary size. Finally, we present an evaluation with flash media that shows our techniques are several orders of magnitude faster and more energy-efficient than (flash-friendly versions of) reservoir sampling and geometric file. A key finding of our study, of potential use to many flash algorithms beyond sampling, is that "semi-random" writes (as defined in the paper) on flash cards are over two orders of magnitude faster and more energy-efficient than random writes.
Receptor-Mediated Endocytosis of α-Galactosidase A in Human Podocytes in Fabry Disease (2011)

Injury to the glomerular podocyte is a key mechanism in human glomerular disease and podocyte repair is an important therapeutic target. In Fabry disease, podocyte injury is caused by the intracellular accumulation of globotriaosylceramide. This study identifies in the human podocyte three endocytic receptors, mannose 6-phosphate/insulin-like growth II receptor, megalin, and sortilin and demonstrates their drug delivery capabilities for enzyme replacement therapy. Sortilin, a novel α-galactosidase A binding protein, reveals a predominant intracellular expression but also surface expression in the podocyte. The present study provides the rationale for the renal effect of treatment with α-galactosidase A and identifies potential pathways for future non-carbohydrate based drug delivery to the kidney podocyte and other potential affected organs.
Nilotinib versus Imatinib for Newly Diagnosed Chronic Myeloid Leukemia (2010)

Nilotinib at a dose of either 300 mg or 400 mg twice daily was superior to imatinib in patients with newly diagnosed chronic-phase Philadelphia chromosome-positive CML. (ClinicalTrials.gov number, NCT00471497.)
Combination Chemotherapy in the Treatment of Follicular Low-Grade Lymphoma (1993)

The therapeutic approach to patients with follicular low-grade non-Hodgkin's lymphoma is controversial and has varied over a wide spectrum. A "watch and wait" approach in asymptomatic patients has been taken in some studies. In other series, single agent therapy with alkylating agents as cyclophosphamide or chlorambucil has been employed. Response rates including complete responses are high, but relapses inevitably occur. Three-drug combination chemotherapy regimens consisting of cyclophosphamide, vincristine, and prednisone (CVP) have been utilized, in addition to more intensive regimens consisting of four or more drugs. Although responses are commonly achieved, there is no consistent survival advantage conferred by these more aggressive regimens. However, the remission duration may be prolonged in some subsets of patients as those with follicular mixed lymphoma. Due to the prolonged natural history of follicular low-grade lymphoma, a long period of follow-up is necessary to adequately evaluate the impact of a therapeutic regimen on remission duration and overall survival. Future trials may employ more aggressive therapy in combination with growth factors or biologic response modifiers in an effort to improve the outcome of patients with follicular low-grade lymphoma.
Polymyxin B nonapeptide inhibits mating in Saccharomyces cerevisiae (1986)

Polymyxin B nonapeptide enhanced susceptibility of yeast cells to various hydrophobic antibiotics and to mating pheromones. At much lower concentrations, the nonapeptide severely inhibited mating. The inhibition was caused by interference with sexual agglutination.