gebhart/patrepeval huggingface dataset:
Controlling cell attachment on contoured surfaces with self-assembled monolayers of alkanethiolates on gold. (1996)

This paper describes a method based on experimentally simple techniques--microcontact printing and micromolding in capillaries--to prepare tissue culture substrates in which both the topology and molecular structure of the interface can be controlled. The method combines optically transparent contoured surfaces with self-assembled monolayers (SAMs) of alkanethiolates on gold to control interfacial characteristics; these tailored interfaces, in turn, control the adsorption of proteins and the attachment of cells. The technique uses replica molding in poly(dimethylsiloxane) molds having micrometer-scale relief patterns on their surfaces to form a contoured film of polyurethane supported on a glass slide. Evaporation of a thin (< 12 nm) film of gold on this surface-contoured polyurethane provides an optically transparent substrate, on which SAMs of terminally functionalized alkanethiolates can be formed. In one procedure, a flat poly(dimethylsiloxane) stamp was used to form a SAM of hexadecanethiolate on the raised plateaus of the contoured surface by contact printing hexadecanethiol [HS(CH2)15CH3]; a SAM terminated in tri(ethylene glycol) groups was subsequently formed on the bare gold remaining in the grooves by immersing the substrate in a solution of a second alkanethiol [HS(CH2)11(OCH2CH2)3OH]. Then this patterned substrate was immersed in a solution of fibronectin, the protein adsorbed only on the methyl-terminated plateau regions of the substrate [the tri(ethylene glycol)-terminated regions resisted the adsorption of protein]; bovine capillary endothelial cells attached only on the regions that adsorbed fibronectin. A complementary procedure confined protein adsorption and cell attachment to the grooves in this substrate.
PRIMARY CULTURE OF HUMAN BLADDER CARCINOMAS AND ESTABLISHMENT OF HUMAN BLADDER CARCINOMA CELL LINE BY SERUM-FREE CULTURE (1989)

It was possible to cultivate cells from bladder carcinoma tissues in 4 cases out of 6 without the overgrowth of fibroblast. A new human transitional cell carcinoma cell line (HAMT-1) was established in longterm tissue culture by using serum-free medium (BEM-841) which had been developed by us. The tissue for culture was taken from a 61-year-old Japanese male with grade 3 transitional cell carcinoma of the bladder. The microscopic features of the cell in cultures and of the tumors developed in nude mice resembled closely that of the original tumor. Electron microscopy of the cultured cells and the tumors developed in nude mice revealed characteristics of the epithelial origin of these cells with microvilli, junctional complex and scarce filament formation. Blood TPA level of the nude mouse with the transplanted tumor was equally high as that of the patient from whom the original tumor had been taken. The cells were anchorage independent in the serum-free medium but anchorage dependent in the medium containing 5% FCS. Anchorage dependency could not be restored by the addition of collagen and fibronectin. The doubling time of the cells were 18-20 hours. The chromosome counts of the cell line ranged from 59-78 with a modal count of 74.
Inhibition of Retinal Neovascularization by Intraocular Viral-Mediated Delivery of Anti-angiogenic Agents (2002)

Neovascularization characterizes diabetic retinopathy and choroidal neovascularization associated with age-related macular degeneration, the most common causes of severe visual loss in the developed world. Gene transfer to the eye using adeno-associated viral (AAV) vectors is a promising new treatment for inherited and acquired ocular diseases. We used an AAV vector with rapid onset and high levels of gene expression in the retina to deliver three anti-angiogenic factors (pigment epithelium-derived factor, tissue inhibitor of metalloproteinase-3, and endostatin) to the eyes of mice in a mouse model of retinopathy of prematurity. All three vectors inhibited ischemia-induced neovascularization.
Alzheimer's Turning Point: A Vascular Approach to Clinical Prevention (2016)

Chapter 1 How does Alzheimer’s begin and who gets it? -- Chapter 2 Forming memories -- Chapter 3 Masquerading as dementia -- Chapter 4 Alzheimer’s --then and now -- Chapter 5 Unproven hypotheses on the cause of Alzheimer’s -- Chapter 6 Other hypotheses on the cause of Alzheimer’s disease -- Chapter 7 Alzheimer noise -- Chapter 8 Social contract and Alzheimer’s -- Chapter 9 Genetics of Alzheimer’s -- Chapter 10 Powering the brain -- Chapter 11 Pharmaceuticals and Alzheimer’s -- Chapter 12 Alzheimer vascular risk factors -- Chapter 13 The Good, The Bad and The Ugly of Advanced Aging -- Chapter 14 A Personal Account of How a Scientific Hypothesis Blooms Into a Life of Its Own -- Chapter 15 Clinical tools to detect and predict individuals at risk of Alzheimer’s -- Chapter 16 The turning point for Alzheimer’s -- Chapter 17 How poor brain blood flow promotes Alzheimer’s disease -- Chapter 18 Interventions that may increase cerebral blood flow -- Chapter 19 Great Expectations -- Chapter 20 A road to new thinking.
DNA Sequence and Regional Assignment of the Human Follicle-Stimulating Hormone β-Subunit Gene to the Short Arm of Human Chromosome 11 (1987)

A human genomic DNA fragment in phage lambda containing FSHB, the gene for the beta-subunit of human follicle-stimulating hormone (FSH-beta), was analyzed and the nucleotide sequence of the region of the clone encoding FSH-beta was determined. A subclone of the lambda phage containing 67% of FSH-beta coding sequence was used as hybridization probe to determine the human chromosomal location of FSHB. A panel of mouse-human somatic cell hybrids containing reduced numbers of human chromosomes was screened with the FSHB probe; complete cosegregation of FSHB with human chromosome 11 was observed in all 26 cell hybrids tested. Analysis of a set of cell hybrids containing translocated derivatives of chromosome 11 further localized FSHB to the human chromosome region 11p11.2----11pter. A Hind III restriction fragment length polymorphism (RFLP) detected by another subclone of the lambda phage containing FSHB now provides a genetic marker for this region of the human genome.
Real-time deformation invariant optical pattern recognition using coordinate transformations (1987)

The well-known scale and rotation invariant polar-logarithmic coordinate transformation is used to achieve in-plane distortion invariant pattern recognition. The coordinate transform is produced by a computergenerated hologram on a laser printer. Attention is given to weighting terms in the output and their effect on resolution and the number of input plane pixels removed near the origin. The optically produced coordinate transformed input pattern is interfaced to a correlator by a pocket liquid crystal TV to provide real-time processing. Experimental results are included.
Monoclonal antibody-directed effector cells selectively lyse human melanoma cells in vitro and in vivo. (1983)

Monoclonal antibody 9.2.27 (mAb 9.2.27) directed to a chondroitin sulfate proteoglycan on human melanoma cells was able to suppress tumor growth in athymic (nu/nu) mice more effectively when bound with polyethylene glycol to murine effector cells than when injected alone. These "armed" effector cells also proved more effective than the monoclonal antibody in eliciting antibody-dependent cellular cytotoxicity against human melanoma target cells in vitro.
The oncogenic potential of deregulated homeobox genes. (1993)

Homeobox genes encode DNA-binding proteins that regulate gene expression during embryonic development. Deregulation of homeobox gene expression has been invoked as the molecular basis of a number of leukemias. We now demonstrate, using in vitro and in vivo transformation assays, that the overexpression of homeobox genes is the basis for transformation and tumorigenesis. Thus, clustered homeobox genes related to Drosophila Hom genes (Hoxa-7, Hoxa-5, Hoxa-1, Hoxb-7, and Hoxc-8) as well as the homeobox genes Evx-1 and Cdx-1 constitute a new family of nuclear protooncogenes. This finding suggests that many homeobox genes regulating embryogenesis can--if deregulated--also contribute to tumorigenesis.
Expression and Characterization of Recombinant Type 2 3α-Hydroxysteroid Dehydrogenase (HSD) from Human Prostate: Demonstration of Bifunctional 3α/17β-HSD Activity and Cellular Distribution (1997)

In androgen target tissues, 3alpha-hydroxysteroid dehydrogenase (3alpha-HSD) may regulate occupancy of the androgen receptor (AR) by catalyzing the interconversion of 5alpha-dihydrotestosterone (5alpha-DHT) (a potent androgen) and 3alpha-androstanediol (a weak androgen). In this study, a 3alpha-HSD cDNA (1170 bp) was isolated from a human prostate cDNA library. The human prostatic 3alpha-HSD cDNA encodes a 323-amino acid protein with 69.9%, 84.1%, 99.4%, and 87.9% sequence identity to rat liver 3alpha-HSD and human type 1, type 2, and type 3 3alpha-HSDs, respectively, and is a member of the aldo-keto reductase superfamily. The close homology with human type 2 3alpha-HSD suggests that it is either identical to this enzyme or a structural allele. Surprisingly, when the recombinant protein was expressed and purified from Escherichia coli, the enzyme did not oxidize androsterone when measured spectrophotometrically, an activity previously assigned to recombinant type 2 3alpha-HSD using this assay. Complete kinetic characterization of the purified protein using spectrophotometric, fluorometric, and radiometric assays showed that the catalytic efficiency favored 3alpha-androstanediol oxidation over 5alpha-DHT reduction. Using [14C]-5alpha-DHT as substrate, TLC analysis confirmed that the reaction product was [14C]-3alpha-androstanediol. However, in the reverse reaction, [3H]-3alpha-androstanediol was oxidized first to [3H]-androsterone and then to [3H]-androstanedione, revealing that the expressed protein possessed both 3alpha- and 17beta-HSD activities. The 17beta-HSD activity accounted for the higher catalytic efficiency observed with 3alpha-androstanediol. These findings indicate that, in the prostate, type 2 3alpha-HSD does not interconvert 5alpha-DHT and 3alpha-androstanediol but inactivates 5alpha-DHT through its 3-ketosteroid reductase activity. Levels of 3alpha-HSD mRNA were measured in primary cultures of human prostatic cells and were higher in epithelial cells than stromal cells. In addition, elevated levels of 3alpha-HSD mRNA were observed in epithelial cells derived from benign prostatic hyperplasia and prostate carcinoma tissues. Expression of 3alpha-HSD was not prostate specific, since high levels of mRNA were also found in liver, small intestine, colon, lung, and kidney. This study is the first complete characterization of recombinant type 2 3alpha-HSD demonstrating dual activity and cellular distribution in the human prostate.
Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides (2004)

We present a fast and simple protocol for large-scale preparation and purification of RNA oligonucleotides. RNA oligonucleotides are prepared by in vitro transcription with T7 RNA polymerase from linearized plasmid DNA templates constructed by PCR. In place of denaturing polyacrylamide gel electrophoresis (PAGE), size-exclusion chromatography is employed to purify the RNA oligonucleotide from the transcription mixture yielding >99% pure RNA product. In contrast to PAGE-based purification, the gel filtration method does not require denaturation of the RNA oligonucleotide, which is desirable for larger RNAs, and the product is free of low-molecular-weight acrylamide contaminants, which greatly benefits NMR, crystallographic, and other biophysical studies of large RNAs and RNA-protein complexes.
Synthesis of Ag Nanobars in the Presence of Single-Crystal Seeds and a Bromide Compound, and Their Surface-Enhanced Raman Scattering (SERS) Properties (2012)

This Article describes the synthesis of Ag nanobars with different aspect ratios using a seed-mediated method and evaluation of their use for surface-enhanced Raman scattering (SERS). The formation of Ag nanobars was found to critically depend on the introduction of a bromide compound into the reaction system, with ionic salts being more effective than covalent molecules. We examined single-crystal seeds with both spherical and cubic shapes and found that Ag nanobars grown from spherical seeds had much higher aspect ratios than those grown from cubic seeds. The typical product of a synthesis contained nanocrystals with three different morphologies: nanocubes, nanobars with a square cross section, and nanobars with a rectangular cross section. Their formation can be attributed to the difference in growth rates along the three orthogonal <100> directions. The SERS enhancement factor of the Ag nanobar was found to depend on its aspect ratio, its orientation relative to the laser polarization, and the wavelength of excitation.
Temperature dependence of the fundamental band gap of InN (2003)

The fundamental band gap of InN films grown by molecular beam epitaxy have been measured by transmission and photoluminescence spectroscopy as a function of temperature. The band edge absorption energy and its temperature dependence depend on the doping level. The band gap variation and Varshni parameters of InN are compared with other group III nitrides. The energy of the photoluminescence peak is affected by the emission from localized states and cannot be used to determine the band gap energy. Based on the results obtained on two samples with distinctly different electron concentrations, the effect of degenerate doping on the optical properties of InN is discussed.
TCV 116 prevents progressive renal injury in rats with extensive renal mass ablation. (1994)

These data show that TCV 116 prevents the development of systemic hypertension, glomerular capillary hypertension, proteinuria and glomerulosclerosis in rats with reduced renal mass. We therefore conclude that the renal protection associated with angiotensin I converting enzyme inhibitors and other pharmacologic blockers of the renin-angiotensin system arises chiefly from blockade of AT1 receptor-mediated hemodynamic effects.
Assessing the role of HLA-linked and unlinked determinants of disease. (1987)

The relationship between increased risk in relatives over population prevalence (lambda R = KR/K) and probability of sharing zero marker alleles identical by descent (ibd) at a linked locus (such as HLA) by an affected relative pair is examined. For a model assuming a single disease-susceptibility locus or group of loci tightly linked to a marker locus, the relationship is remarkably simple and general. Namely, if phi R is the prior probability for the relative pair to share zero marker alleles identical by descent, then P (sharing 0 markers/both relatives are affected) is just phi R/lambda R. Alternatively, lambda AR, the increased risk over population prevalence to a relative R due to a disease locus tightly linked to marker locus A, equals the prior probability that the relative pair share zero A alleles ibd divided by the posterior probability that they share zero alleles ibd, given that they are both affected. For example, for affected sib pairs, P (sharing 0 markers/both sibs are affected) = .25/lambda S. This formula holds true for any number of alleles at the disease locus and for their frequencies, penetrances, and population prevalence. Similar formulas are derived for sharing one and two markers. Application of these formulas to several well-studied HLA-associated diseases yields the following results: For multiple sclerosis, insulin-dependent diabetes mellitus, and coeliac disease, a single-locus model of disease susceptibility is rejected, implying the existence of additional unlinked familial determinants. For all three diseases, the effect of the HLA-linked locus on familiality is minor: for multiple sclerosis, it accounts for only a 2.5-fold increased risk to sibs over the population prevalence, compared to an observed value of 20; for coeliac disease, it accounts for approximately a 5.25-fold increased risk to sibs, while the observed value is on the order of 60; for insulin-dependent diabetes mellitus, it accounts for a 3.42-fold increased risk in sibs, while the observed value is 15. In all cases, the secondary determinants must be outside the HLA region. For tuberculoid leprosy, an unlinked familial determinant is also implicated (increased risk to sibs due to HLA = 1.49; observed value = 2.38). For hemochromatosis and Hodgkin's disease, there is little evidence for HLA-unlinked familial determinants. With this formula, it is also possible to examine the hypothesis of pleiotropy versus linkage dis-equilibrium by comparing lambda AS with the increased risk to sibs due to the associated allele(s).(ABSTRACT TRUNCATED AT 400 WORDS)
The packaging signal of influenza viral RNA molecules (2001)

The packaging signal present in influenza viral RNA molecules is shown not to constitute a separate structural element, but to reside within the 5'-bulged promoter structure, as caused by the central unpaired residue A10 in its 5' branch. Upon insertion of two uridine residues in the 3' branch opposite A10, the minus-strand viral RNA (vRNA) promoter is converted into a 3'-bulged structure, whereas the plus-strand cRNA promoter instead adopts the 5'-bulged conformation. In this promoter variant it is exclusively the cRNA that is found packaged in the progeny virions. Upon insertion of only a single uridine nucleotide opposite 5'A10, the two debulged structures of the vRNA and cRNA promoters are rendered identical, and both vRNA and cRNA molecules are packaged indiscriminately, in a 1:1 ratio, but at lower rates. We propose that the binding interactions of viral polymerase with either of the two differently bulged vRNA and cRNA promoter structures result in two different conformations of the enzyme protein. Only the 5' bulged RNA-associated polymerase conformation appears to be recognized for nuclear export, which depends on nuclear matrix protein M1 and nonstructural protein NS2. And the respective wild-type vRNP- or insertion mutant cRNP complex is observed to enter the cytoplasm and hence is included in the viral encapsidation process, which takes place at the plasma membrane.
A self-calibrating 15 bit CMOS A/D converter (1984)

A self-calibrating analog-to-digital converter using binary weighted capacitors and resistor strings is described. Linearity errors are corrected by a simple digital algorithm. A folded cascode CMOS comparator resolves 30 /spl mu/V in 3 /spl mu/s. An experimental converter fabricated using a 6-/spl mu/m-gate CMOS process demonstrates 15-bit resolution and linearity at a 12-kHz sampling rate.
The topology of politics : voting connectivity in the US House of Representatives (2012)

Time-varying topological simplifications of the space of votes in the US House of Representatives (US HoR) display several interesting features unavailable with classical methods of machine learnin ...
Intranasal administration of a detoxified endotoxin vaccine protects mice against heterologous Gram-negative bacterial pneumonia (2008)

When given passively or elicited actively, antibodies induced by a detoxified Escherichia coli J5 mutant lipopolysaccharide (J5dLPS)-group B meningococcal outer membrane protein (-OMP) vaccine previously protected animals from lethal sepsis. To assess the use of this vaccine for the treatment of Gram-negative bacillary pneumonia, we vaccinated mice, with or without the adjuvant CpG, by intranasal (i.n.) or intraperitoneal (i.p.) routes of administration. Local and systemic IgG levels were 2-3 logs higher following i.p. immunization compared to i.n. However, i.n. immunization elicited both local and systemic IgA, unlike i.p. administration. The addition of CpG to the vaccine, by either route of administration, elicited greater levels of antibody. Intranasal immunization protected mice against lethal heterologous Gram-negative bacillary pneumonia and post-immunization serum and broncho-alveolar lavage fluid mediated enhanced bacterial killing with peritoneal and alveolar macrophages in vitro. We conclude that further studies on the use of J5dLPS-OMP for the prevention of nosocomial pneumonia are warranted.
Pharmacological Characterization of the Mechanism of Action of R523062, a Promising Antiviral for Enterovirus D68 (2020)

Enterovirus D68 (EV-D68) is a re-emerging virus that causes moderate to severe respiratory diseases in children. In severe cases, EV-D68 infection can lead to neurological complications called acute flaccid myelitis (AFM). There is currently no antiviral or vaccine available for EV-D68. The goal of this study is to delineate the mechanism of action of a promising antiviral drug candidate <b>R523062</b> that was identified through a phenotypic cytopathic effect (CPE)-based high-throughput screening. <b>R523062</b> inhibits multiple contemporary EV-D68 strains with single-digit micromolar EC<sub>50</sub> values and is less effective against the enterovirus A71 strains. Resistant mutants identified through serial viral passage experiments were mapped to four viral proteins including VP1-G178S, 2A-V112I, 2C-I227L/Q322R, and 3A-V54A. The involvements of VP1-G178S, 2A-V112I, and 3A-V54A mutants in drug resistance were ruled out by the drug time-of-addition experiment, protease enzymatic assay, and the plaque assay with recombinant virus, respectively. In contrast, recombinant virus encoding the 2C-I227L/Q322R double mutants confers significant drug resistance, which is consistent with the result from serial passage experiments. The thermal shift binding assay showed <b>R523062</b> binds to the wild-type EV-D68 2C and 2C-Q322R but not 2C-I227L or 2C-I227L/Q322R, confirming 2C as the direct drug target of <b>R523062</b> and 2C-I227L alone confers drug resistance. The 2C inhibitor <b>R523062</b> also showed additive antiviral activity with the viral 2A protease inhibitor telaprevir as well as the viral capsid VP1 inhibitor <b>R856932</b>. Collectively, this study identified a promising EV-D68 antiviral drug candidate <b>R523062</b> with a confirmed mechanism of action by targeting the viral 2C protein.
Evaluating interface aesthetics: measure of symmetry (2006)

Symmetry is one of the most fundamental principles in design. The choice between symmetry and asymmetry affects the layout and feeling of a design. A symmetrical page gives a feeling of permanence and stability, while informal or asymmetrical balance creates interest. The aim of this paper is to solve the problem of an automatic detection of axial and radial symmetry or lack of it in published documents. Previous approaches to this problem gave only a necessary condition for symmetry. We present a necessary and sufficient criterion for automatic symmetry detection and also introduce a Euclidean-type distance from any layout to the closest symmetrical one [3]. We present mathematical proof that the measure of symmetry we introduce is exact and accurate. It coincides with intuition and can be effectively calculated. Moreover, any other symmetry criterion will be a derivative of this measure.