gebhart/patrepeval huggingface dataset:
A role for SOX1 in neural determination (1998)

In vertebrates, the delineation of the neural plate from a region of the primitive ectoderm is accompanied by the onset of specific gene expression which in turn promotes the formation of the nervous system. Here we show that SOX1, an HMG-box protein related to SRY, is one of the earliest transcription factors to be expressed in ectodermal cells committed to the neural fate: the onset of expression of SOX1 appears to coincide with the induction of neural ectoderm. We demonstrate a role for SOX1 in neural determination and differentiation using an inducible expression P19 cell system as an in vitro model of neurogenesis. Misexpression of SOX1 can substitute for the requirement of retinoic acid to impart neural fate to competent ectodermal P19 cells. Using a series of antigenic markers which identify early neural cell types in combination with BrdU labeling, we demonstrate a temporal and spatial correlation between the differentiation of cell types along the dorsoventral axis of the neural tube and the downregulation of SOX1 expression. SOX1, therefore, defines the dividing neural precursors of the embryonic central nervous system (CNS).
A Nonlinear Bayesian Filtering Framework for ECG Denoising (2007)

In this paper, a nonlinear Bayesian filtering framework is proposed for the filtering of single channel noisy electrocardiogram (ECG) recordings. The necessary dynamic models of the ECG are based on a modified nonlinear dynamic model, previously suggested for the generation of a highly realistic synthetic ECG. A modified version of this model is used in several Bayesian filters, including the Extended Kalman Filter, Extended Kalman Smoother, and Unscented Kalman Filter. An automatic parameter selection method is also introduced, to facilitate the adaptation of the model parameters to a vast variety of ECGs. This approach is evaluated on several normal ECGs, by artificially adding white and colored Gaussian noises to visually inspected clean ECG recordings, and studying the SNR and morphology of the filter outputs. The results of the study demonstrate superior results compared with conventional ECG denoising approaches such as bandpass filtering, adaptive filtering, and wavelet denoising, over a wide range of ECG SNRs. The method is also successfully evaluated on real nonstationary muscle artifact. This method may therefore serve as an effective framework for the model-based filtering of noisy ECG recordings.
Type II (tositumomab) anti-CD20 monoclonal antibody out performs type I (rituximab-like) reagents in B-cell depletion regardless of complement activation (2008)

Abstract Anti-CD20 monoclonal antibodies (mAbs) are classified into type I (rituximab-like) or type II (tositumomab-like) based on their ability to redistribute CD20 molecules in the plasma membrane and activate various effector functions. To compare type I and II mAbs directly in vivo and maximize Fc effector function, we selected and engineered mAbs with the same mouse IgG2a isotype and assessed their B-cell depleting activity in human CD20 transgenic mice. Despite being the same isotype, having similar affinity, opsonizing activity for phagocytosis, and in vivo half-life, the type II mAb tositumomab (B1) provided substantially longer depletion of B cells from the peripheral blood compared with the type I mAb rituximab (Rit m2a), and 1F5. This difference was also evident within the secondary lymphoid organs, in particular, the spleen. Failure to engage complement did not explain the efficacy of the type II reagents because type I mAbs mutated in the Fc domain (K322A) to prevent C1q binding still did not display equivalent efficacy. These results give support for the use of type II CD20 mAbs in human B-cell diseases.
Beneficial health effects of modest weight loss. (1992)

The medical effects of modest weight reduction (approximately 10% or less) in patients with obesity-associated medical complications were reviewed. The National Library of Medicine MEDLINE database and the Derwent RINGDOC database were searched to identify English language studies that examined the effects of weight loss in obese patients with serious medical complications commonly associated with obesity (non-insulin dependent diabetes mellitus (NIDDM or type II), hypertension, hyperlipidemia, hypercholesterolemia, and cardiovascular disease). Studies in which patients experienced approximately 10% or less weight reduction were selected for review. Studies indicated that, for obese patients with NIDDM, hypertension or hyperlipidemia, modest weight reduction appeared to improve glycemic control, reduce blood pressure, and reduce cholesterol levels, respectively. Modest weight reduction also appeared to increase longevity in obese individuals. In conclusion, a large proportion of obese individuals with NIDDM, hypertension, and hyperlipidemia experienced positive health benefits with modest weight loss. For patients who are unable to attain and maintain substantial weight reduction, modest weight loss should be recommended; even a small amount of weight loss appears to benefit a substantial subset of obese patients.
Orthodoxy and the New Russia (2007)

This paper examines the contemporary phenomenon of the re-emergence of the Orthodox Church not only as a leading religious institution of post-Soviet Russia, but also as a core marker of identity. The disappearance of the Soviet Union has produced a profound crisis of identity in Russia. Traditional markers of identity, particularly the Orthodox Church, have assumed an importance hardly anticipated before the collapse of the USSR.
Structure-activity relationship of estrogens: receptor affinity and estrogen antagonist activity of certain (E)- and (2)-1,2,3-triaryl-2-propen-2-ones (1985)

(E)- and (Z)-1,2,3-triphenyl-2-propen-1-ones and some of their phenolic and alkoxy analogues, substituted at the para position in one or more of the aromatic rings, were synthesized and assigned geometry on the basis of their spectroscopic data. The structure-activity relationship of the triarylpropenones was studied from the point of view of their estrogen receptor affinity and estrogen agonist and antagonist activities. (E)- as well as (Z)-propenones were found to compete with estradiol for binding with the mouse uterine cytosol receptors, with phenolic analogues usually more potent than the unsubstituted as well as alkoxypropenones. The (E)-propenones, which have now emerged as a new group of estrogen receptor ligands, were found to differ from Z isomers quite markedly in their binding specificities. The uterotrophic and antiuterotrophic assays in immature mice revealed that while some of the compounds were marginally estrogenic, nearly all the isomeric propenones were antiestrogenic to a varying degree.
BMPR2 mutations and survival in pulmonary arterial hypertension: an individual participant data meta-analysis (2016)

Cambridge NIHR Biomedical Research Centre, Medical Research Council, British Heart Foundation, Assistance Publique-Hôpitaux de Paris, INSERM, Université Paris-Sud, Intermountain Research and Medical Foundation, Vanderbilt University, National Center for Advancing Translational Sciences, National Institutes of Health, National Natural Science Foundation of China, and Beijing Natural Science Foundation.
Pressure Buildup and Flow Tests in Wells (1967)

A time-tested classic, Pressure Buildup and Flow Tests in Wells presents a comprehensive study of the creation and analysis of transient pressure responses in wells. Basic principles are reviewed, and the applicability and limitations of the various techniques are critically discussed and illustrated with examples. With its detailed review of literature and extensive bibliography, this book serves as a useful guide and reference to engineers directly engaged in well pressure work.
Oct-1 POU domain-DNA interactions: cooperative binding of isolated subdomains and effects of covalent linkage. (1996)

Structural and biochemical studies of Oct-1 POU domain-DNA interactions have raised important questions about cooperativity and the role of the linker connecting the POU-specific domain and the POU homeo domain. To analyze these interactions, we have studied binding of the isolated domains. Surprisingly, we find that two unlinked polypeptides corresponding to the POU-specific domain and the POU homeo domain bind cooperatively to the octamer site and have a coupling energy of 1.6 kcal/mole. We suggest that overlapping DNA contacts near the center of the octamer site may be the source of this cooperativity, as there are no protein-protein contacts between the domains in the crystal structure of the Oct-1 POU domain-DNA complex. These studies also have allowed us to describe the thermodynamic contribution of the linker (present in the intact POU domain) in terms of an effective concentration (3.6 mM). The broader implications for understanding cooperativity in protein-DNA recognition and gene regulation are discussed.
DNA Origami Nanopillars as Standards for Three-Dimensional Superresolution Microscopy (2013)

Nanopillars are promising nanostructures composed of various materials that bring new functionalities for applications ranging from photovoltaics to analytics. We developed DNA nanopillars with a height of 220 nm and a diameter of ~14 nm using the DNA origami technique. Modifying the base of the nanopillars with biotins allowed selective, upright, and rigid immobilization on solid substrates. With the help of site-selective dye labels, we visualized the structure and determined the orientation of the nanopillars by three-dimensional fluorescence superresolution microscopy. Because of their rigidity and nanometer-precise addressability, DNA origami nanopillars qualify as scaffold for the assembly of plasmonic devices as well as for three-dimensional superresolution standards.
Effects of verapamil on daunomycin cellular retention and cytotoxicity in P388 leukemic cells. (1984)

We have utilized digitized video microscopy to investigate the influence of verapamil, a calcium channel blocker, on the in vitro effects of daunomycin in P388 sensitive and resistant sublines. In this study, verapamil enhanced the uptake of daunomycin and its cytotoxicity in both sublines, but the effect was more pronounced in the resistant cells. Flow cytometry showed a pronounced accumulation of resistant cells at G2-M when treated with daunomycin in the presence of verapamil, with no effects observed in the absence of verapamil. Analysis of individual resistant cells using the digitized video fluorescence microscopy technique demonstrated that the influence of verapamil on daunomycin uptake affected all cells and was not restricted to certain subpopulations of cells.
The STRO-1+ fraction of adult human bone marrow contains the osteogenic precursors (1994)

The monoclonal antibody STRO-1 identifies clonogenic bone marrow stromal cell progenitors (fibroblast colony-forming units [CFU-F]) in adult human bone marrow. These STRO-1+ CFU-F have previously been shown to give rise to cells with the phenotype of fibroblasts, adipocytes, and smooth muscle cells. In this study, the osteogenic potential of CFU-F derived from the STRO-1+ fraction of adult human bone marrow was determined. CFU-F were isolated from normal bone marrow aspirates by fluorescence activated cell sorting, based on their expression of the STRO-1 antigen. Osteogenic differentiation was assessed by the induction of alkaline phosphatase expression, by the formation of a mineralized matrix (hydroxyapatite), and by the production of the bone-specific protein osteocalcin. STRO-1+ cells were cultured in the presence of dexamethasone (DEX; 10(-8) mol/L), ascorbic acid 2-phosphate (ASC-2P; 100 mumol/L), and inorganic phosphate (PO4i; 2.9 mmol/L). After 2 weeks of culture, greater than 90% of the cells in each CFU-F colony stained positive for alkaline phosphatase using a monoclonal antibody specific for bone and liver alkaline phosphatase. Alkaline phosphatase activity was confirmed by histochemistry. A mineralized matrix developed in the CFU-F cultures, after 4 weeks of culture in the presence of DEX, ASC-2P, and PO4i. Mineralization was confirmed by both light and electron microscopy. The mineral was identified as hydroxyapatite by electron dispersive x-ray microanalysis and by x-ray diffraction analysis. In replicate cultures, osteocalcin release was shown after exposure of the cells to 1,25-dihydroxyvitamin D3 (10(-7) mol/L) both by radioimmunoassay and Northern blot analysis. This work provides direct evidence that adult human bone marrow-derived CFU-F are capable of differentiating into functional osteoblasts and that osteoprogenitors are present in the STRO-1+ population.
Novel device isolation technology with selective epitaxial growth (1982)

A fine device isolation technology for small geometry VLSIs using selective epitaxial growth (SEG) is described. The epitaxial silicon layer is selectively grown on a bulk silicon surface surrounded with a SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> isolation wall under reduced pressure using SiH <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> Cl <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> -H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> -HCl systems. Polysilicon gate MOSFETs are successively fabricated on the epitaxial silicon layer. The p-n junction characteristics are reasonable, according to theoretical values, and the leakage current along the lateral SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> wall is negligibly small. The subthreshold characteristics for parasitic devices with submicron geometry gives the same slope value as that for conventional devices.
Clinical manufacturing of CAR T cells: foundation of a promising therapy (2016)

The treatment of cancer patients with autologous T cells expressing a chimeric antigen receptor (CAR) is one of the most promising adoptive cellular therapy approaches. Reproducible manufacturing of high-quality, clinical-grade CAR-T cell products is a prerequisite for the wide application of this technology. Product quality needs to be built-in within every step of the manufacturing process. We summarize herein the requirements and logistics to be considered, as well as the state of the art manufacturing platforms available. CAR-T cell therapy may be on the verge of becoming standard of care for a few clinical indications. Yet, many challenges pertaining to manufacturing standardization and product characterization remain to be overcome in order to achieve broad usage and eventual commercialization of this therapeutic modality.
Simulation of terahertz pulse propagation in biological systems (2004)

Studies in terahertz (THz) imaging have revealed a significant difference between skin cancer (basal cell carcinoma) and healthy tissue. Since water has strong absorptions at THz frequencies and tumor affects the water content of tissue, a likely contrast mechanism is variation in water content. Modeling the propagation of a THz pulse through water is the first step toward understanding the origin of contrast in terahertz pulsed images of skin cancer. In this letter, we develop a finite-difference-time-domain simulation to model the propagation of a THz pulse and incorporate double Debye theory to model the behavior of water subject to THz radiation. Furthermore, we apply this model to skin.
Selective targeting of miRNA‐regulated plant development by a viral counter‐silencing protein (2007)

The cucumber mosaic virus (CMV) 2b protein suppresses RNA silencing and determines viral symptoms. Among Arabidopsis thaliana lines expressing 2b proteins from mild (LS and Q CMV) or severe (Fny CMV) strains, only Fny 2b-transgenic plants displayed strong symptom-like phenotypes in leaves, stems and flowers, together with stunting of main root growth and increased emergence of lateral roots. However, LS and Fny 2b proteins both enhanced lateral root length. Micro (mi)RNA-mediated cellular mRNA turnover was inhibited in Fny 2b-transgenic plants, but there was no evidence for this in LS 2b-transgenic plants. Both 2b proteins efficiently suppressed small interfering (si)RNA-mediated RNA silencing, suggesting that 2b proteins can target the siRNA pathway without disrupting miRNA-regulated RNA turnover. Thus, symptom induction is not an inevitable consequence of RNA silencing suppression. For CMV, strain-specific differences between the 2b silencing proteins determine whether only one or both small RNA-guided RNA destruction pathways are disrupted.
Evidence for Cardiomyocyte Repopulation by Extracardiac Progenitors in Transplanted Human Hearts (2002)

Human myocardium has long been considered to have essentially no intrinsic regenerative capacity. Recent studies in rodent models, however, have suggested the presence of an extracardiac stem cell population, perhaps in bone marrow, that is capable of some reconstitution of cardiomyocytes after injury. To determine whether similar mechanisms exist in the human heart, we evaluated human female allograft hearts transplanted into male patients. The presence of Y chromosomes in cardiomyocytes would indicate these cells arose from the recipient, rather than the donor heart. We identified 5 male patients who had retained a female heart at least 9 months before death and necropsy. Remarkably, in each case, the transplanted heart contained a minute but readily detectable fraction of Y chromosome-positive cardiomyocytes. The mean percentage of cardiomyocytes arising from the host was estimated to be 0.04% with a median of 0.016%. Most Y-positive cardiomyocytes were associated with regions of acute rejection, suggesting such chimerism involves an injury event. Furthermore, the sole patient whose immediate cause of death was allograft rejection showed a much higher percentage of host-derived cardiomyocytes, up to 29% in local, 1-mm(2) "hot spots." Thus, adult humans have extracardiac progenitor cells capable of migrating to and repopulating damaged myocardium, but this process occurs at very low levels.
Molecular cloning of a novel putative G‐protein coupled receptor expressed during rat spermiogenesis (1991)

A cDNA clone encoding a novel putative G-protein coupled receptor has been isolated from a rat testis cDNA library using a PCR-amplified cDNA fragment as a hybridization probe. Northern blot analysis reveals that a corresponding 1.5 kb mRNA is exclusively expressed in testis. By in situ hybridization experiments this mRNA has been localized in spermatocytes and spermatids but not in spermatogonia, Leydig or sertoli cells. Ontogenic studies show that expression of the receptor-encoding mRNA and sexual maturation are correlated reaching highest levels during the second and third months. Although the ligand for this receptor has not yet been identified, this receptor may play a role during reproduction.
Growth of mouse megakaryocyte colonies in vitro. (1975)

Mouse bone marrow and spleen cells formed pure or mixed colonies of up to 80 megakaryocytes in agar cultures after stimulation by medium conditioned by activated mouse lymphoid cells. Megakaryocytes were identified on the basis of their morphology, polyploid mitoses and DNA content, and high cytoplasmic content of acetylcholinesterase. Megakaryocyte colony-forming cells were relatively small with a peak sedimentation velocity of 4.2 mm/hr. Spleen, lymph node, and thymus cells produced the factor stimulating megakaryocyte proliferation after culture in medium containing 2-mercaptoethanol, with or without added mitogens or allogeneic spleen cells. Peak activity in conditioning medium was associated with the small lymphocyte fractions in mouse spleen.
Fidelity of DNA synthesis by the Thermococcus litoralis DNA polymerase—an extremely heat stable enzyme with proofreading activity (1991)

We demonstrate that the DNA polymerase isolated from Thermococcus litoralis (VentTM DNA polymerase) is the first thermostable DNA polymerase reported having a 3'----5' proofreading exonuclease activity. This facilitates a highly accurate DNA synthesis in vitro by the polymerase. Mutational frequencies observed in the base substitution fidelity assays were in the range of 30 x 10(-6). These values were 5-10 times lower compared to other thermostable DNA polymerases lacking the proofreading activity. All classes of DNA polymerase errors (transitions, transversions, frameshift mutations) were assayed using the forward mutational assay (1). The mutation frequencies of Thermococcus litoralis DNA polymerase varied between 15-35 x 10(-4) being 2-4 times lower than the respective values obtained using enzymes without proofreading activity. We also noticed that the fidelity of the DNA polymerase from Thermococcus litoralis responds to changes in dNTP concentration, units of enzyme used per one reaction and the concentration of MgSO4 relative to the total concentration of dNTPs present in the reaction. The high fidelity DNA synthesis in vitro by Thermococcus litoralis DNA polymerase provides good possibilities for maintaining the genetic information of original target DNA sequences intact in the DNA amplification applications.
Holographic Imaging Through a Random Medium (1968)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text H. Kogelnik and K. S. Pennington, "Holographic Imaging Through a Random Medium," J. Opt. Soc. Am. 58, 273-274 (1968) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Controlling Polymer Adhesion with “Pancakes” (2005)

Topographical patterns are used to selectively tune the adhesion of polymers. Although nature has provided guidance, relatively little is known of how topographic patterns can be intelligently used not only to enhance adhesion but, more importantly, to tune adhesion. We demonstrate that properly designed, low-aspect-ratio posts can alter adhesion from 20% to 400% the value of conventional adhesion descriptors for nonpatterned interfaces. This control is not related to the magnitude of interfacial area but, rather, to altering the local separation processes at an interface by geometry. We establish general relationships that govern the interaction between material properties, pattern length scales, and the control of adhesion. These relationships provide insight into the mechanisms of adhesion for examples in nature, such as the gecko, while also providing concrete guidance for the future design of "smart" adhesives and coatings with nanoscale patterns.
IL-6 Is Required for the Development of Th1 Cell-Mediated Murine Colitis (2000)

Proinflammatory cytokines have been demonstrated to play a crucial role in the pathogenesis of Crohn's disease. Among those cytokines, strong expression of IL-6 has been repeatedly demonstrated. To examine the role for IL-6 in the pathogenesis of Crohn's disease, we introduced anti-IL-6R mAb to a murine model of colitis. Colitis was induced in C.B-17-scid mice transferred with CD45RBhigh CD4+ T cells from BALB/c mice. Anti-IL-6R mAb or rat IgG was administered weekly after T cell transfer. ICAM-1 and VCAM-1 expression were analyzed by immunohistochemistry. Colonic cytokine expression was determined by RT-PCR. Mice treated with mAb showed normal growth, whereas controls lost weight. The average colitis score was 0.64 for mAb-treated mice and 1.80 for controls. T cell expansion in treated mice was less remarkable than in the controls. Colonic ICAM-1 and VCAM-1 expression were markedly suppressed by mAb. IFN-gamma, TNF-alpha, and IL-1beta mRNA were reduced by the treatment. The results presented here show a crucial role for IL-6 in the pathogenesis of murine colitis and suggest a therapeutic potential of anti-IL-6R mAb for treatment of human Crohn's disease.