gebhart/patrepeval huggingface dataset:
The Use of 3-D Culture in Peptide Hydrogel for Analysis of Discoidin Domain Receptor 1-Collagen Interaction (2007)

The aim of this study is to examine a novel drop culture model using a biologically inspired self-assembling peptide: hydrogel (RAD16-I, also called PuraMatrix), which produces a nanoscale environment similar to native extracellular matrix (ECM) for a cell line weakly adherent to a plastic surface during cell culture. Our work investigates quantitatively analyzing discoidin domain receptor (DDR) 1-mediated protein interactions between collagen type I and matrix metalloproteinase (MMP)-2 or -9, as well as cell invasion, using, as a scaffold, PuraMatrix, a novel peptide hydrogel. Results demonstrate that the dynamic cell culture technique produced a highly stable reharvesting of cells throughout the constructs with HP-75, human pituitary adenoma cell line when compared to the traditional seeding methods. Secretion of MMP via collagen type I was observed quantitatively in the supernatant (EC50; MMP-2, 50.4 ng/ml: MMP-9, 57.6 ng/ml). In PuraMatrix gel impregnated with 50 ng/ml of collagen type I, transfection of the vector encoding full-length DDR1 or siRNA targeting DDR1 up- or downregulated respectively secretion of MMP-2 and -9, and cell invasion. Our results show that incorporation of this peptide with each ECM component provides a more permissive environment to elucidate ECM to cell signal interaction.
Biopolymer functionalized reduced graphene oxide with enhanced biocompatibility via mussel inspired coatings/anchors (2012)

A green and facile method for preparing biopolymer functionalized reduced graphene oxide (RGO) by using mussel inspired dopamine (DA) as the reducing reagent and the functionalized molecule is proposed. In the study, GO is reduced by DA and DA is adhered to RGO by one-step pH-induced polymerization of DA (polydopamine, PDA), and then heparin or protein is grafted onto the PDA adhered RGO (pRGO) through catechol chemistry. The obtained pRGO, heparin grafted pRGO (Hep-g-pRGO), and BSA grafted pRGO (BSA-g-pRGO) exhibit fine 2D morphology and excellent stability in water and PBS solution. Furthermore, the biocompatibility of the biopolymer functionalized RGO are investigated using human blood cells and human umbilical vein endothelial cells (HUVECs). The biopolymer functionalized RGO exhibits an ultralow hemolysis ratio (lower than 1.8%), and the cellular toxicity assay suggests that the biopolymer functionalized RGO has good cytocompatibility for HUVEC cells, even at a high concentration of 100 μg mL<sup>-1</sup>. Moreover, the high anticoagulant ability of Hep-g-pRGO indicates that the grafted biopolymer could maintain its biological activity after immobilization onto the surface of pRGO. Therefore, the proposed safe and green biomimetic method confers the biopolymer functionalized RGO with great potential for various biological and biomedical applications.
Thrombospondin‐1, vascular endothelial growth factor and fibroblast growth factor‐2 are key functional regulators of angiogenesis in the prostate (2001)

During disease progression in the prostate, production of TSP-1, the major inhibitor, is down-regulated while that of stimulatory FGF-2 and/or VEGF rise, leading to the induction of the new vessels necessary to support tumor growth.
Approximation by rational numbers (2004)

Throughout the present Chapter, we are essentially concerned with the following problem: for which functions Ψ : ℝ≥1 → : ℝ≥0 is it true that, for a given real number ξ, or for all real numbers ξ in a given class, the equation |ξ – p/q| < Ψ (q) has infinitely many solutions in rational numbers p/q? We begin by stating the results on rational approximation obtained by Dirichlet and Liouville in the middle of the nineteenth century. In Section 1.2, we define the continued fraction algorithm and recall the main properties of continued fractions expansions. These are used in Section 1.3 to give a full proof of a metric theorem of Khintchine. The next two Sections are devoted to the Duffin–Schaeffer Conjecture and to some complementary results on continued fractions.
A modern extreme value theory approach to calculating the distribution of the peak-to-average power ratio in OFDM systems (2003)

Orthogonal frequency division multiplexing (OFDM) is a promising framework for future wireless communication systems. One of the main impediments that has limited the applicability of OFDM systems in low-power wireless communication systems is the highly variable amplitude of the baseband transmitted signal; thus, a number of previous analyses have characterized this variation. These analyses have generally employed the following two components: (1) the assumption that the complex envelope of the OFDM signal converges to a Gaussian random process in some sense as the number of subcarriers becomes large, and (2) Rice's (1945) classical results on level-crossing rates for the envelope of Gaussian random processes. In this work, we improve on both of these components to arrive at a simple, accurate, and rigorously-established expression for the peak distribution of the OFDM envelope. In particular, using a rigorous (and non-trivial) proof establishing the convergence in (1) above as justification, the modern extreme value theory for chi-squared processes is applied to the problem. Numerical results for both uncoded and coded systems establish that the simple expression obtained for the distribution of the peaks of the envelope process is extremely accurate, even for a modest number of subcarriers.
The Effects of Human Growth Hormone Administration in Elderly Adults with Recent Weight Loss (1988)

The effects of human GH administration in elderly adults with recent weight loss were investigated in a metabolic ward study. Four patients were studied for 20 days. In addition to a constant caloric and nitrogen-sufficient diet, consisting of the recommended amounts of protein and energy plus 20%, the patients received GH in dosages of 25 and 50 micrograms/kg.day for two 4-day periods (days 5-8 and 13-16, respectively). Significant increases in nitrogen retention of 1.6 (114.2) and 1.4 g/day (100 mmol/day), respectively, occurred compared with that in the control periods. No difference was found between the two GH dosages, but the nitrogen-retaining effect of the higher dose appeared to last for several days after its administration was stopped. Plasma insulin-like growth factor I levels rose during both treatment periods. No important disturbances in carbohydrate metabolism occurred. Body weight increased 2.3 kg during each treatment period, probably due to water retention. We conclude that even during more than adequate nutritional intake, low GH doses cause considerable nitrogen retention in underweight adults.
Editor’s Introduction: American Apocrypha? (2001)

Introduction to the current issue, including editor's picks. Peterson surmises what the assumptions of the forthcoming book American Apocrypha will be. The statements of the Book of Mormon witnesses must be taken seriously, and the work of Royal Skousen reveals a stunningly consistent, systematic, and complex book. Keith Norman's dissertation on deification and Jordan Vajda's master's thesis on divinization note parallels with early doctrines of theosis. Joseph Smith's mission consisted of making clear that which was formerly hidden.
Integrin‐mediated attachment of articular chondrocytes to extracellular matrix proteins (1993)

Chondrocytes can attach to a variety of cartilage and bone proteins; this attachment is mediated via integrins, including members of both the beta 1 and beta 3 subunit families. The modulation of the chondrocyte phenotype during monolayer culture may be related to activation or increased expression of integrins.
Type I interferon suppresses memory Th2 cell cytokine secretion from allergic subjects (2019)

Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Guaranteeing anonymity when sharing medical data, the Datafly system (2018)

We present a computer program named Datafly that maintains anonymity in medical data by automatically generalizing, substituting, and removing information as appropriate without losing many of the details found within the data. Decisions are made at the field and record level at the time of database access, so the approach can be used on the fly in role-based security within an institution, and in batch mode for exporting data from an institution. Often organizations release and receive medical data with all explicit identifiers, such as name, address and phone number, removed in the incorrect belief that patient confidentiality is maintained because the resulting data look anonymous; however, we show the remaining data can often be used to re-identify individuals by linking or matching the data to other databases or by looking at unique characteristics found in the fields and records of the database itself. When these less apparent aspects are taken into account, each released record can be made to ambiguously map to many possible people, providing a level of anonymity determined by the user.
Relationship Between Second Life and the U.S. Economy (2010)

Second Life is a virtual world designed to be a free, laissez-faire market economy in which Linden Dollars are used to buy and sell goods and services. This study investigated the relationship between the economies of Second Life and the United States, using financial data collected from Linden Lab and the Federal Reserve. Partial correlation analyses were computed between two pairs of economic measures, and our results indicated that there was a significant relationship between the two economies.
610. s-Triazolopyrimidines. Part II. Synthesis as potential therapeutic agents (1965)

G. W. Miller and F. L. Rose, J. Chem. Soc., 1965, 3357 DOI: 10.1039/JR9650003357
Expression profiles of voltage‐gated Na+ channel α‐subunit genes in rat and human prostate cancer cell lines (2001)

(1) Several VGSCalpha genes and their splice variants are expressed similarly in both rat and human PC cell lines. (2) Expression levels are much higher in the strongly metastatic (MAT-LyLu/PC-3) cells. (3) Levels of SCN9A mRNA specifically are predominant in MAT-LyLu and PC-3 cells; thus, SCN9A is highly likely to be the main source of the functional VGSC detected.
The C8/144B monoclonal antibody recognizes cytokeratin 15 and defines the location of human hair follicle stem cells (1998)

Stem cells are vital for the homeostasis of self-renewing tissues such as the hair follicle. Epithelial stem cells have been implicated in tumorigenesis and wound healing, and their manipulation may have wide ranging applications including gene therapy and tissue transplantation. Rodent hair follicle stem cells have been localized to an area of the follicle called the bulge, however, the identification and characterization of human hair follicle stem cells has been hampered by a lack of cellular markers for this area. We have determined that the C8/144B monoclonal antibody, originally generated against a short intracytoplasmic peptide of CD8, preferentially immunostains hair follicle bulge keratinocytes without staining the remaining hair follicle. Using expression cloning, we identified cytokeratin 15 as the keratinocyte protein recognized by the C8/144B monoclonal antibody. By delineating the bulge using this antibody, we demonstrated that bulge cells possess a stem cell phenotype characterized by their slowly-cycling nature, preferential proliferation at the onset of new hair follicle growth, high level of beta1 integrin expression, and expression of cytokeratin 19.
Optimal interpolation in helical scan 3D computerized tomography (2003)

A data acquisition scheme combining the axial translation of the object with rotation of the imaging gantry is introduced for three-dimensional computerized tomography (CT), and a reconstruction algorithm for its implementation is explored. A computationally attractive interpolation scheme that converts the data to standard CT format and permits reconstruction by existing algorithms is proposed. The approach is to convert by interpolation the helical-scan projection data into standard planar scan format and then use a standard 2-D reconstruction technique, such as convolution backprojection, on each slice. Optimum interpolation coefficients are derived, minimizing a worst case normalized maximum error magnitude criterion. The theoretical predictions are illustrated by simulation results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Isolation and characterization of the cDNA encoding human DNA methyltransferase (1992)

We have cloned a series of overlapping cDNA clones encoding a 5194 bp transcript for human DNA methyltransferase (DNA MTase). This sequence potentially codes for a protein of 1495 amino acids with a predicted molecular weight of 169 kDa. The human DNA MTase cDNA has eighty percent homology at the nucleotide level, and the predicted protein has seventy-four percent identity at the amino acid level, to the DNA MTase cDNA cloned from mouse cells. Like the murine DNA MTase, the amino terminal two-thirds of the human protein contains a cysteine-rich region suggestive of a metal-binding domain. The carboxy terminal one-third of the protein shows considerable similarity to prokaryotic (cytosine-5)-methyltransferases. The arrangement of multiple motifs conserved in the prokaryotic genes is preserved in the human DNA MTase, including the relative position of a proline-cysteine dipeptide thought to be an essential catalytic site in all (cytosine-5)-methyltransferases. A single 5.2 kb transcript was detected in all human tissues tested, with the highest levels of expression observed in RNA from placenta, brain, heart and lung. DNA MTase cDNA clones were used to screen a chromosome 19 genomic cosmid library. The DNA MTase-positive cosmids which are estimated to span a genomic distance of 93 kb have been localized to 19p13.2-p13.3 by fluorescence in situ hybridization. Isolation of the cDNA for human DNA MTase will allow further study of the regulation of DNA MTase expression, and of the role of this enzyme in establishing DNA methylation patterns in both normal and neoplastic cells.
Mesenchymal Stem Cell Insights: Prospects in Cardiovascular Therapy (2014)

Ischemic heart damage usually triggers cardiomyopathological remodeling and fibrosis, thus promoting the development of heart functional failure. Mesenchymal stem cells (MSCs) are a heterogeneous group of cells in culture, with multipotent and hypoimmunogenic characters to aid tissue repair and avoid immune responses, respectively. Numerous experimental findings have proven the feasibility, safety, and efficiency of MSC therapy for cardiac regeneration. Despite that the exact mechanism remains unclear, the therapeutic ability of MSCs to treat ischemia heart diseases has been tested in phase I/II clinical trials. Based on encouraging preliminary findings, MSCs might become a potentially efficacious tool in the therapeutic options available to treat ischemic and nonischemic cardiovascular disorders. The molecular mechanism behind the efficacy of MSCs on promoting engraftment and accelerating the speed of heart functional recovery is still waiting for clarification. It is hypothesized that cardiomyocyte regeneration, paracrine mechanisms for cardiac repair, optimization of the niche for cell survival, and cardiac remodeling by inflammatory control are involved in the interaction between MSCs and the damaged myocardial environment. This review focuses on recent experimental and clinical findings related to cellular cardiomyoplasticity. We focus on MSCs, highlighting their roles in cardiac tissue repair, transdifferentiation, the MSC niche in myocardial tissues, discuss their therapeutic efficacy that has been tested for cardiac therapy, and the current bottleneck of MSC-based cardiac therapies.
Cloning of rat aorta lysyl oxidase cDNA: complete codons and predicted amino acid sequence. (1990)

Lysyl oxidase cDNA clones were identified by their reactivity with anti-bovine lysyl oxidase in a neonatal rat aorta cDNA lambda gt11 expression library. A 500-bp cDNA sequence encoding four of six peptides derived from proteolytic digests of bovine aorta lysyl oxidase was found from the overlapping cDNA sequences of two positive clones. The library was rescreened with a radiolabeled cDNA probe made from one of these clones, thus identifying an additional 13 positive clones. Sequencing of the largest two of these overlapping clones resulted in 2672 bp of cDNA sequence containing partial 5'- and 3'-untranslated sequences of 286 and 1159 nucleotides, respectively, and a complete open reading frame of 1227 bp encoding a polypeptide of 409 amino acids (46 kDa), consistent with the 48 +/- 3 kDa cell-free translation product of rat smooth muscle cell RNA that was immunoprecipitated by anti-bovine lysyl oxidase. The rat aorta cDNA-derived amino acid sequence contains the sequence of each of the six peptides isolated and sequenced from the 32-kDa bovine aorta enzyme, including the C-terminal peptide with sequence identity of 96%. Northern blots screened with lysyl oxidase cDNA probes identified hybridizing species of 5.8 and 4.5 kb in mRNA of rat aorta and lung, while dot blot analyses were negative for lysyl oxidase mRNA in preparations of rat brain, liver, kidney, and heart. A 258-bp segment of the 3'-untranslated region of lysyl oxidase cDNA is 93% identical with a highly conserved region of the 3'-untranslated sequence of rat elastin cDNA.(ABSTRACT TRUNCATED AT 250 WORDS)
Advances in Neural Information Processing Systems 16: Proceedings of the 2003 Conference (2004)

The annual Neural Information Processing (NIPS) conference is the flagship meeting on neural computation. It draws a diverse group of attendees &amp; physicists, neuroscientists, mathematicians, statisticians, and computer scientists. The presentations are interdisciplinary, with contributions in algorithms, learning theory, cognitive science, neuroscience, brain imaging, vision, speech and signal processing, reinforcement learning and control, emerging technologies, and applications. Only thirty percent of the papers submitted are accepted for presentation at NIPS, so the quality is exceptionally high. This volume contains all the papers presented at the 2003 conference.
SOIL BACTERIAL COMMUNITY STRUCTURE CHANGES FOLLOWING DISTURBANCE OF THE OVERLYING PLANT COMMUNITY (2004)

The effect of plant species identity and diversity on the spatial and temporal differentiation in bacterial community structure in the active root zone was studied at a field site that was treated with herbicide, burned, and then reseeded with native grass species. Treatments were arranged in three blocks. The blocks corresponded to an elevational gradient that was used as a surrogate for moisture differences across the field. Samples were collected before and after devegetation, and eight times thereafter, over the subsequent year. The soil samples were examined for bacterial abundance (direct counts) and bacterial community structure by the genetic fingerprinting techniques randomly amplified polymorphic DNA (RAPD) and denaturing gradient gel electrophoresis (DGGE) of whole-community DNA extracts. The bacterial abundance was relatively constant in both time and space. Discriminant function analysis and the Mantel test revealed clear temporal trends in community structure throughout the entire 2-year study that coincided with the overall development of the grasses in the field. Spatial differentiation of community structure was clear among the blocks, suggesting differences in community structure based on soil moisture content. Significant differences were also observed between control and treated plots. Spatial and temporal change in the bacterial community was evident, and bacterial and plant succession coincided temporally. Differences in the bacterial communities that developed were also affected by the soil moisture.
Kinetic and Structural Characteristics of the Inhibition of Enoyl (Acyl Carrier Protein) Reductase by Triclosan (1999)

Triclosan is used widely as an antibacterial agent in dermatological products, mouthwashes, and toothpastes. Recent studies imply that antibacterial activity results from binding to enoyl (acyl carrier protein) reductase (EACPR, EC 1.3.1.9). We first recognized the ability of triclosan to inhibit EACPR from Escherichia coli in a high throughput screen where the enzyme and test compound were preincubated with NAD(+), which is a product of the reaction. The concentration of triclosan required for 50% inhibition approximates to 50% of the enzyme concentration, indicating that the free compound is depleted by binding to EACPR. With no preincubation or added NAD(+), the degree of inhibition by 150 nM triclosan increases gradually over several minutes. The onset of inhibition is more rapid when NAD(+) is added. Gel filtration and mass spectrometry show that inhibition by triclosan is reversible. Steady-state assays were designed to avoid depletion of free inhibitor and changes in the degree of inhibition. The results suggest that triclosan binds to E-NAD(+) complex, with a dissociation constant around 20-40 pM. Triclosan follows competitive kinetics with respect to NADH, giving an inhibition constant of 38 pM at zero NADH and saturating NAD(+). Uncompetitive kinetics are observed when NAD(+) is varied, giving an inhibition constant of 22 pM at saturating NAD(+). By following regain of catalytic activity after dilution of EACPR that had been preincubated with triclosan and NAD(+), the rate constant for dissociation of the inhibitor (k(off)) is measured as 1.9 x 10(-4) s(-1). The association rate constant (k(on)) is estimated as 2.6 x 10(7) s(-1) M(-1) by monitoring the onset of inhibition during assays started by addition of EACPR. As expected, the ratio k(off)/k(on) = 7.1 pM is similar to the inhibition constants from the steady-state studies. The crystal structure of E. coli EACPR in a complex with coenzyme and triclosan has been determined at 1.9 A resolution, showing that this compound binds in a similar site to the diazaborine inhibitors. The high affinity of triclosan appears to be due to structural similarity to a tightly bound intermediate in catalysis.