gebhart/patrepeval huggingface dataset:
A Calcium/Calmodulin-dependent Activation of ERK1/2 Mediates JunD Phosphorylation and Induction of nur77 and20α-hsd Genes by Prostaglandin F2α in Ovarian Cells (2002)

We have previously demonstrated that prostaglandin F(2alpha) (PGF(2alpha)) induces a rapid and transient expression of Nur77 in luteal cells. We have shown that Nur77 plays an important role in ovarian physiology by mediating the PGF(2alpha) induction of 20alpha-HSD, a steroidogenic enzyme involved in the catabolism of progesterone. In this report we established, using luteinized granulosa cells, that PGF(2alpha) stimulates in vitro nur77 expression in a time- and dose-dependent manner. Serial 5'-deletion of the nur77 promoter revealed that the necessary and sufficient elements for PGF(2alpha) induction of Nur77 promoter activity are located between the nucleotides -86 and -33 upstream of the transcription start site, this region containing two AP1 elements. JunD binds to these AP1 sites, but its binding is not stimulated by PGF(2alpha). However, mutation of the AP1 sites as well as a dominant-negative JunD abolished nur77 induction by PGF(2alpha). PGF(2alpha) induces phosphorylation of JunD bound to the nur77 promoter. Stimulation of nur77 expression and JunD phosphorylation were prevented by inhibitors of calcium, calmodulin, or ERK1/2 kinase. PGF(2alpha)-induced ERK1/2 phosphorylation was prevented by calcium/calmodulin inhibitors. We conclude that activation of JunD through a calmodulim-dependent activation of ERK1/2 mediates nur77 induction by PGF(2alpha). Finally, we demonstrated that this molecular mechanism also mediates 20alpha-hsd induction.
Digital Predistortion Based on Combined Feedback in MIMO Transmitters (2012)

An adaptive digital predistortion (PD) technique is proposed for linearization of power amplifiers (PAs) in multiple-input multiple-output (MIMO) transmitters. Instead of constructing a separate feedback path at each PA, we propose a PD technique based on a combined feedback, which adds all the PAs' outputs to form a single feedback. We develop an algorithm for finding the multiple PA characteristics jointly from the combined feedback. The PD parameters are calculated from the identified PA characteristics. Although the proposed method requires more computations for PA identification than the conventional method, its hardware implementation is much simpler and can overcome the crosstalk problem of a radio frequency (RF) selector, which is necessary for multiple feedback selection. The simulation results show that, despite its simple structure, the linearization performance of the proposed method is almost the same as the separate multiple feedback method.
Fatty acids and β-cell toxicity (2009)

The findings have implications for the development of new therapeutic agents designed to minimize beta-cell dysfunction and the loss of beta-cell viability in type 2 diabetes.
Progress of cereal transformation technology mediated by Agrobacterium tumefaciens (2014)

Monocotyledonous plants were believed to be not transformable by the soil bacterium Agrobacterium tumefaciens until two decades ago, although convenient protocols for infection of leaf disks and subsequent regeneration of transgenic plants had been well established in a number of dicotyledonous species by then. This belief was reinforced by the fact that monocotyledons are mostly outside the host range of crown gall disease caused by the bacterium and by the failures in trials in monocotyledons to mimic the transformation protocols for dicotyledons. However, a key reason for the failure could have been the lack of active cell divisions at the wound sites in monocotyledons. The complexity and narrow optimal windows of critical factors, such as genotypes of plants, conditions of the plants from which explants are prepared, tissue culture methods and culture media, pre-treatments of explants, strains of A. tumefaciens, inducers of virulence genes, transformation vectors, selection marker genes and selective agents, kept technical hurdles high. Eventually it was demonstrated that rice and maize could be transformed by co-cultivating cells of callus cultures or immature embryos, which are actively dividing or about to divide, with A. tumefaciens. Subsequently, these initial difficulties were resolved one by one by many research groups, and the major cereals are now transformed quite efficiently. As many as 15 independent transgenic events may be regenerated from a single piece of immature embryo of rice. Maize transformation protocols are well established, and almost all transgenic events deregulated for commercialization after 2003 were generated by Agrobacterium-mediated transformation. Wheat, barley, and sorghum are also among those plants that can be efficiently transformed by A. tumefaciens.
IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis (2018)

Insertions and deletions (indels) have been implicated in dozens of human diseases through the radical alteration of gene function by short frameshift indels as well as long indels. However, the accurate detection of these indels from next-generation sequencing data is still challenging. This is particularly true for intermediate-size indels (≥50 bp), due to the short DNA sequencing reads. Here, we developed a new method that predicts intermediate-size indels using BWA soft-clipped fragments (unmatched fragments in partially mapped reads) and unmapped reads. We report the performance comparison of our method, GATK, PINDEL and ScanIndel, using whole exome sequencing data from the same samples. False positive and false negative counts were determined through Sanger sequencing of all predicted indels across these four methods. The harmonic mean of the recall and precision, F-measure, was used to measure the performance of each method. Our method achieved the highest F-measure of 0.84 in one sample, compared to 0.56 for GATK, 0.52 for PINDEL and 0.46 for ScanIndel. Similar results were obtained in additional samples, demonstrating that our method was superior to the other methods for detecting intermediate-size indels. We believe that this methodology will contribute to the discovery of intermediate-size indels associated with human disease.
Two distinct pathways for essential metabolic precursors for isoprenoid biosynthesis (2012)

Isoprenoids are a diverse group of molecules found in all organisms, where they perform such important biological functions as hormone signaling (e.g., steroids) in mammals, antioxidation (e.g., carotenoids) in plants, electron transport (e.g., ubiquinone), and cell wall biosynthesis intermediates in bacteria. All isoprenoids are synthesized by the consecutive condensation of the five-carbon monomer isopentenyl diphosphate (IPP) to its isomer, dimethylallyl diphosphate (DMAPP). The biosynthetic pathway for the formation of IPP from acetyl-CoA (i.e., the mevalonate pathway) had been established mainly in mice and the budding yeast Saccharomyces cerevisiae. Curiously, most prokaryotic microorganisms lack homologs of the genes in the mevalonate pathway, even though IPP and DMAPP are essential for isoprenoid biosynthesis in bacteria. This observation provided an impetus to search for an alternative pathway to synthesize IPP and DMAPP, ultimately leading to the discovery of the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate pathway. This review article focuses on our significant contributions to a comprehensive understanding of the biosynthesis of IPP and DMAPP.
Effect of Cystic Fibrosis on Inhaled Aerosol Boluses (1989)

An aerosol bolus undergoes changes in shape between its inspiration and expiration. In comparison with the inhaled bolus, the exhaled bolus is more spread because of convective mixing, may have a shift in the location of the mode caused by asymmetries of filling and emptying of lung units, and contains fewer particles because of particle deposition. We hypothesized that the extent of these changes is related to lung health. To examine this, 11 patients with cystic fibrosis (CF) and 11 healthy subjects inhaled 70 cm3 boluses containing 1 micron monodisperse particles that were inspired to volumetric penetrations (Vp) of 100 to 700 cm3. As each bolus was expired, we measured spreading (volumetric width at one-half aerosol concentration peak height), modal shift, and particle deposition. Patients with CF exhaled boluses that were broader than those exhaled by normal subjects at all penetrations examined. At a Vp of 600 cm3, patients had a mean bolus half-width that was 68% greater than that of healthy subjects (p less than 0.0001), and they exhaled the bolus mode 20% earlier (p less than 0.0002). Particle deposition was increased compared with that in normal subjects at all Vp. For example, mean deposition at a Vp of 600 cm3 was 46.2 +/- 2.6% (SE) for the patients versus 25.8 +/- 1.6% for the normal subjects (p less than 0.0001). Among the patients with CF, pulmonary function parameters indicating obstruction were significantly correlated with bolus spreading and aerosol deposition: the percent predicted FEV1/FVC was inversely correlated with spreading (r = -0.88, p less than 0.0004) and deposition (r = -0.84, p less than 0.0008).(ABSTRACT TRUNCATED AT 250 WORDS)
Lack of Mutations in the Thyroid Hormone Receptor (TR) α and β Genes but Frequent Hypermethylation of the TRβ Gene in Differentiated Thyroid Tumors (2007)

Mutation is not common in TR genes, whereas hypermethylation of the TRbeta gene as an alternative gene silencing mechanism is highly prevalent in thyroid cancer, particularly FTC, consistent with a possible tumor suppressor role of this gene for FTC.
Purification and preliminary characterization of a glial growth factor from the bovine pituitary. (1980)

In a normal tissue culture medium containing 10% fetal calf serum, purified rat Schwann cells divide very slowly. We have previously reported that the cells are stimulated to divide by an activity present in extracts of the brain and pituitary (Brockes, J.P., Fields, K.L. and Raff, M.C. (1979) Brain Res. 165, 105-118), and this activity appears to be both novel and restricted in its distribution (Raff, M.C., Abney, E.R., Brockes, J.P. and Hornby-Smith, A. (1978) Cell 15, 813-822). The pituitary activity has been purified over 4000-fold from a pool of 10 kg of frozen glands and 4000 lyophilized anterior lobes. The activity was assayed by the incorporation of 125I-UdR into DNA of Schwann cells growing in microwells. The most purified (phosphocellulose) fraction was analyzed on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and displayed a major band of 3 x 10(4) molecular weight which was approximately 25% of the stained material. When analyzed by native gel electrophoresis at pH 4.5 followed by a second dimension of sodium dodecyl sulfate-gel electrophoresis, the activity was consistently associated with this component. The effect of the phosphocellulose fraction on proliferation of central glial cells in dissociated cultures of the rat corpus callosum was also investigated by using fluorescent antisera to identify the cells and [3H]thymidine autoradiography to assay proliferation. The oligodendrocytes and "macrophage-like" microglia were not significantly stimulated, but the astrocytes were stimulated over the same range of concentration as Schwann cells. The activity against astrocytes and that against Schwann cells co-migrated in native gel electrophoresis at pH 4.5, providing strong evidence that the same molecule acts on both cell types.
A Mathematical Theory of Communication (1948)

In this final installment of the paper we consider the case where the signals or the messages or both are continuously variable, in contrast with the discrete nature assumed until now. To a considerable extent the continuous case can be obtained through a limiting process from the discrete case by dividing the continuum of messages and signals into a large but finite number of small regions and calculating the various parameters involved on a discrete basis. As the size of the regions is decreased these parameters in general approach as limits the proper values for the continuous case. There are, however, a few new effects that appear and also a general change of emphasis in the direction of specialization of the general results to particular cases.
Agent based preprocessing (2007)

The current data mining tools is used to build knowledge based on a huge historical data. At present, businesses are facing with fast growing data that are very valuable in contributing knowledge. Knowledge should be updated regularly in order to ensure its quality and precision thus improve the decision making process. Data mining has shown great potential in extracting valuable knowledge from large databases. However, current data mining algorithms and tools are costly and several are too complex in their operations when dealing with large databases. In recent years, agents have become a popular paradigm in computing, because its autonomous, flexible and provides intelligence. Embedding agents in the current data mining processes and tools are believed to be able to solve the obstacle. One of the most important process in data mining is data preprocessing. It is reported that 60% of the data mining project is on preprocessing. Data preprocessing involves integration, selection, cleaning and transformation of data set that will be used for mining. This paper focuses on an agent-based preprocessing framework. The aims is to provides an auto preprocessing a set of new data, which suite to data mining novice user. The proposed agent based preprocessing framework consists of seven agents: User Interface agents, Coordinator Agent, Identify Agent, CleanMiss Agent, CleanNoisy Agent, Transformation Agent and Discretization Agent. User Interface Agent is designed in such a way to provide interface suite to novice users. Coordinator agent is responsible for coordinating and cooperating with all other agents to achieve the goals. Identify agent responsible to provide an adaptive user data cleaning profiling. CleanMiss Agent, CleanNoisy Agent, Transformation Agent and Discretization Agent provide various types of techniques autonomously, which ended with proposing the best cleaning techniques from various types of techniques to keep in the preprocessing profile. This paper is start by introducing the data mining process problem includes data preprocessing which agent can solve data mining problems. By applying agent in data preprocessing, a tool that intelligence yet flexible can be produced.
Visceral Fat Accumulation Is an Important Determinant of PAI-1 Levels in Young, Nonobese Men and Women (1998)

Increased plasminogen activator inhibitor type-1 (PAI-1) levels, leading to impaired fibrinolysis, are associated with increased visceral fat in middle-aged and obese subjects. It is unknown, however, whether this association is independent of other disturbances clustered in the insulin resistance syndrome. We analyzed this association in young, nonobese transsexual men and women before and after administration of cross-sex steroids, which potentially influence many elements of the insulin resistance syndrome, including PAI-1 levels and visceral fat accumulation. We assessed the visceral fat area (by MRI); total body fat; insulin sensitivity (with a glucose clamp technique); and plasma levels of PAI-1, insulin, and triglycerides in young (<37 years old), nonobese (body mass index <28 kg/m2), healthy men (n=18) and women (n=15) before and after 12 months of cross-sex hormone administration. Men were treated with ethinyl estradiol 100 microgram/d plus cyproterone acetate 100 mg/d, and women were treated with testosterone esters 250 mg IM every 2 weeks. At baseline, only visceral fat area was significantly correlated with plasma PAI-1 levels in both men (r=0.57, P=0.03) and women (r=0.59, P=0.03). In multivariate linear regression analysis, this association was independent of total body fat, insulin sensitivity, and plasma levels of triglycerides and insulin. After 12 months of cross-sex hormone administration, the plasma PAI-1 levels were no longer correlated with visceral fat (which had increased). We conclude that in young, nonobese men and women, visceral fat area is an important determinant of plasma PAI-1 levels. After cross-sex hormone administration, this association was no longer demonstrable.
Fibroblast-specific TGF-β–Smad2/3 signaling underlies cardiac fibrosis (2017)

The master cytokine TGF-β mediates tissue fibrosis associated with inflammation and tissue injury. TGF-β induces fibroblast activation and differentiation into myofibroblasts that secrete extracellular matrix proteins. Canonical TGF-β signaling mobilizes Smad2 and Smad3 transcription factors that control fibrosis by promoting gene expression. However, the importance of TGF-β-Smad2/3 signaling in fibroblast-mediated cardiac fibrosis has not been directly evaluated in vivo. Here, we examined pressure overload-induced cardiac fibrosis in fibroblast- and myofibroblast-specific inducible Cre-expressing mouse lines with selective deletion of the TGF-β receptors Tgfbr1/2, Smad2, or Smad3. Fibroblast-specific deletion of Tgfbr1/2 or Smad3, but not Smad2, markedly reduced the pressure overload-induced fibrotic response as well as fibrosis mediated by a heart-specific, latency-resistant TGF-β mutant transgene. Interestingly, cardiac fibroblast-specific deletion of Tgfbr1/2, but not Smad2/3, attenuated the cardiac hypertrophic response to pressure overload stimulation. Mechanistically, loss of Smad2/3 from tissue-resident fibroblasts attenuated injury-induced cellular expansion within the heart and the expression of fibrosis-mediating genes. Deletion of Smad2/3 or Tgfbr1/2 from cardiac fibroblasts similarly inhibited the gene program for fibrosis and extracellular matrix remodeling, although deletion of Tgfbr1/2 uniquely altered expression of an array of regulatory genes involved in cardiomyocyte homeostasis and disease compensation. These findings implicate TGF-β-Smad2/3 signaling in activated tissue-resident cardiac fibroblasts as principal mediators of the fibrotic response.
A class of sp3 boron-based single-ion polymeric electrolytes for lithium ion batteries (2013)

A class of sp3 boron-based polymeric compounds with highly exposed lithium cations is both thermally and electrochemically stable for use in Li-ion batteries. Syntheses of a variety of the sp3 boron-based polymeric materials can be realized by taking advantage of the well-developed methods used for preparation of metal organic framework compounds.
Conceptual design of reactive dividing wall columns (2006)

Economic and environmental reasons have led to process intensification in the process industries. Reactive distillation is the most prominent example. The integration of further sepn. steps with a reactive distn. column leads to a highly integrated process: a reactive dividing wall column. Within one app., more than two products can be obtained and the capital cost can be reduced drastically. Furthermore, the well-known redn. in energy demand for dividing wall columns compared to a sequence of conventional distn. columns can lead to reduced operating costs. However, the simulation, design and operation of such complex columns is complicated. A novel approach for the conceptual design of reactive dividing wall columns is presented in this work. The methodol. is based on the graphically-based boundary value method. Chem. equil. is assumed on every reactive stage of the column. Four component systems with one reaction are considered in this work.
Characterization of a glycosphingolipid antigen defined by the monoclonal antibody MBr1 expressed in normal and neoplastic epithelial cells of human mammary gland. (1984)

The antigen defined by a monoclonal antibody, MBr1, was found to be expressed in normal human mammary gland epithelia and human mammary carcinoma cells (Ménard, S., Tagliabue, E., Canevari, S., Fossati, G., and Colnaghi, M. I. (1983) Cancer Res. 43, 1295-1300). The antigen has been isolated from breast cancer cell line MCF-7, which was used as immunogen, and its structure was determined by methylation analysis, NMR spectroscopy, direct probe mass spectrometry, and enzymatic degradation as identified below. Fuc alpha 1----2Gal beta 1----3GalNAc beta 1----3Gal alpha 1----4Gal beta 1----4Glc beta 1----1Cer The antibody cross-reacted weakly with fucosylasialo-GM1 (IV2FucGg4), which shares the same terminal sequence, Fuc alpha 1----2Gal beta 1----3GalNAc, with this antigen. However, various other structures, including lacto-series H structure (Fuc alpha 1----2 Gal beta 1----4/or 3GlcNAc beta 1----3Gal), did not show any reactivity with this antibody. Therefore, this antigen represents a blood group H antigen with a globo-series structure which is abundant in human teratocarcinoma (Kannagi, R., Levery, S. B., Ishigami, F., Hakomori, S., Shevinsky, L. H., Knowles, B. B., and Solter, D. (1983) J. Biol. Chem. 258, 8934-8942), although its presence must be limited in normal adult human tissue.
SLE - Rituximab in lupus. (2003)

B cells are essential to the development of systemic lupus erythematosus (SLE). The chimeric monoclonal antibody rituximab depletes B cells by targeting the pan-B-cell surface marker CD20. Preliminary experience with this agent in SLE and other autoimmune diseases has been encouraging. Controlled trials in SLE will be necessary to determine whether rituximab is useful therapy in this disease, and will teach us more about the roles of B cells in its pathogenesis.
Synthesis of isomeric β‐haloethylthienopyrroles (1984)

Abstract The preparation of ethyl 4‐(2‐bromoethyl)thieno[2,3‐ b ]pyrrole‐5‐carboxylate and ethyl 6‐(2‐bromoethyl)thieno[3,2‐ b ]pyrrole‐5‐carboxylate by reaction of t ‐butyl 2‐(2‐thienyl)carbazate and t ‐butyl 2‐(3‐thienyl)carbazate with ethyl‐5‐bromo‐2‐oxopentanoate are described.
Marrow microenvironment transfer by heterotopic transplantation of freshly isolated and cultured cells in porous sponges. (1982)

Cells for study were obtained from mouse bone marrow by three methods: 1) Mechanical dissociation; 2) Trypsin release; and 3) Passage through a syringe and needle. The ratio of the fibroblast colony-forming cells in these suspensions was, respectively, 1:13:1. Of the colonies formed by cells obtained by trypsin release, 70% were alkaline phosphatase positive fibroblasts. Freshly isolated marrow cells and cells harvested, by trypsin treatment, from cultures established from the differently obtained bone marrow cell suspensions, were absorbed into porous sponges for transplantation under the renal capsule of mice. Ossicles containing bone marrow formed after transplantation of either freshly isolated cells, or cultured cells obtained from marrow by trypsin treatment, but not after the transplantation of cells cultured from marrow obtained by mechanical dissociation. The size of the bone marrow "organs" that formed was determined by both the number of cells grafted and the size of the sponge in which they had been absorbed for grafting.