gebhart/patrepeval huggingface dataset:
Use of a monoclonal antibody to measure the surface expression of thrombospondin following platelet activation (1988)

The radiolabelled monoclonal antibody, 5G11, directed against native thrombospondin, has been used to assess the surface expression of secreted thrombospondin on human blood platelets. Emphasis has been placed on studying the role of fibrinogen in this process. Unstimulated platelets bound low amounts of 5G11 (about 2000 molecules/platelet). Binding increased 2-fold and 5-7-fold after stimulation of platelets with ADP or thrombin (or ionophore A23187) respectively. Unstimulated platelets from patients deficient in alpha-granule proteins (gray platelet syndrome) bound baseline levels of 5G11. However, binding was not increased after activation. Thrombospondin expression on thrombin-stimulated normal platelets was for a large part divalent-cation-dependent and was not affected by AP-2, a monoclonal antibody to GPIIb-IIIa complexes. However, binding of 5G11 was some 50% lower when platelets were stimulated in the presence of Fab fragments of a polyclonal rabbit antibody to fibrinogen. This suggested either a direct binding of thrombospondin to surface-bound fibrinogen or a steric inhibition due to a close proximity of the two proteins. The fact that binding of 5G11 was at the lower limit of the normal range to the stimulated platelets of an afibrinogenaemic patient specifically lacking detectable fibrinogen favoured the latter explanation. Thus, a major fibrinogen-independent pathway for thrombospondin expression must exist.
Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data (2005)

Hyperspectral scanning together with multivariate analysis offers a unique and detailed understanding of the sources of microarray emissions after hybridization. This opportunity to simultaneously identify and quantitate contaminant and background emissions in microarrays markedly improves the reliability and accuracy of the data and permits a level of quality control of microarray emissions previously unachievable. Using these tools, we can not only quantify the extent and contribution of extraneous emission sources to the signal, but also determine the consequences of failing to account for them and gain the insight necessary to adjust preparation protocols to prevent such problems from occurring.
Fabrication of thin-film InGaN light-emitting diode membranes by laser lift-off (1999)

Indium–gallium nitride (InGaN) multiple-quantum-well (MQW) light-emitting diode (LED) membranes, prefabricated on sapphire growth substrates, were created using pulsed-excimer laser processing. The thin-film InGaN MQW LED structures, grown on sapphire substrates, were first bonded onto a Si support substrate with an ethyl cyanoacrylate-based adhesive. A single 600 mJ/cm2, 38 ns KrF (248 nm) excimer laser pulse was directed through the transparent sapphire, followed by a low-temperature heat treatment to remove the substrate. Free-standing InGaN LED membranes were then fabricated by immersing the InGaN LED/adhesive/Si structure in acetone to release the device from the supporting Si substrate. The current–voltage characteristics and room-temperature emission spectrum of the LEDs before and after laser lift-off were unchanged.
Discovering New Ordered Phases of Block Copolymers (2000)

We propose a new and general method for discovering novel ordered phases of block copolymer melts. The method involves minimizing a free energy functional in an arbitrary unit cell with respect to the composition profile and the dimensions of the unit cell, without any prior assumption of the microphase symmetry. Varying the initial conditions allows to search for different stable and metastable structures. Application of this method to ABC star and linear triblock copolymers using an approximate free energy reveals new morphologies not yet observed in experiment.
Promoter elements required for sugar‐repression of the RAmy3D gene for α‐amylase in rice (1998)

There is increasing evidence showing that cereal alpha-amylase gene expression is controlled not only by the classical hormonal regulation, but also by feed-back sugar repression. We demonstrated by in situ hybridization that the sugar repression of rice alpha-amylase gene RAmy3D takes place in scutellar epithelium cells of callus-forming rice embryos. We also used a transient expression system to study the cis-acting elements involved in the sugar repression of the RAmy3D promoter activity. Site-directed mutagenesis of the 50-bp nucleotide sequence from -172 to -123 revealed that consensus sequences of G motif (TACGTA) and TATCCA T/C motif (GATA motif as its antisense sequence) are responsible for sugar repression. The promoter sequences required for sugar repression are reported and discussed.
Identification of three forms of human myelin basic protein by cDNA cloning. (1986)

We have isolated cDNA clones encoding three separate forms of human myelin basic protein (MBP), 21.5, 18.5, and 17.2 kDa, and have determined the nucleotide sequence of each. The three forms share a common sequence but differ by the inclusion of a 26-residue amino acid sequence near the N terminus of the 21.5-kDa protein or by the absence of an 11-residue amino acid sequence near the C terminus of the 17.2-kDa protein. The sequences either added to or deleted from the major 18.5-kDa MBP correspond exactly to exons 2 and 5 of the mouse MBP gene, suggesting that the human and mouse genes have similar exon structures. We have also identified the 21.5-kDa human MBP on immunoblots using antisera raised to a peptide encoded by the mouse exon 2 sequence. Southern blotting studies of human genomic DNA reveal a simple pattern consistent with a single human MBP gene. Thus, the three MBP mRNAs are likely to arise from alternative splicing of a primary human MBP transcript. Conservation of the 26 amino acid mouse exon 2 sequence in human MBP suggests an important role for this sequence in myelination.
Epidemiology as a Framework for Large-Scale Mobile Application Accessibility Assessment (2017)

Mobile accessibility is often a property considered at the level of a single mobile application (app), but rarely on a larger scale of the entire app "ecosystem," such as all apps in an app store, their companies, developers, and user influences. We present a novel conceptual framework for the accessibility of mobile apps inspired by epidemiology. It considers apps within their ecosystems, over time, and at a population level. Under this metaphor, "inaccessibility" is a set of diseases that can be viewed through an epidemiological lens. Accordingly, our framework puts forth notions like risk and protective factors, prevalence, and health indicators found within a population of apps. This new framing offers terminology, motivation, and techniques to reframe how we approach and measure app accessibility. It establishes how app accessibility can benefit from multi-factor, longitudinal, and population-based analyses. Our epidemiology-inspired conceptual framework is the main contribution of this work, intended to provoke thought and inspire new work enhancing app accessibility at a systemic level. In a preliminary exercising of our framework, we perform an analysis of the prevalence of common determinants or accessibility barriers. We assess the health of a stratified sample of 100 popular Android apps using Google's Accessibility Scanner. We find that 100% of apps have at least one of nine accessibility errors and examine which errors are most common. A preliminary analysis of the frequency of co-occurrences of multiple errors in a single app is also presented. We find 72% of apps have five or six errors, suggesting an interaction among different errors or an underlying influence.
Effects of the lethal yellow (AY) mutation in mouse aggregation chimeras (1990)

The Ay allele is a recessive lethal mutation at the mouse agouti locus, which results in embryonic death around the time of implantation. In the heterozygous state, Ay produces several dominant pleiotropic effects, including an increase in weight gain and body length, a susceptibility to hepatic, pulmonary and mammary tumors, and a suppression of the agouti phenotype, which results in a yellow coat color. To investigate the cellular action of Ay with regard to its effects upon embryonic viability and adult-onset obesity, we generated a series of aggregation chimeras using embryos that differ in their agouti locus genotype. Embryos derived from Ay/a x Ay/a matings were aggregated with those derived from A/A x A/A matings, and genotypic identification of the resultant chimeras was accomplished using a molecular probe at the Emv-15 locus that distinguishes among the three different alleles, Ay, A, and a. Among 50 chimeras, 25 analyzed as liveborns and 25 as 9.5 day embryos, 29 were a/a in equilibrium A/A and 21 were Ay/a in equilibrium A/A. The absence of Ay/Ay in equilibrium A/A chimeras demonstrates that Ay/Ay cells cannot be rescued in a chimeric environment, and the relative deficiency of Ay/a in equilibrium A/A chimeras suggests that, under certain conditions, Ay heterozygosity may partially affect cell viability or proliferation. In the 25 liveborn chimeras, Ay/a in equilibrium A/A animals became obese as adults and a/a in equilibrium A/A animals did not. There was no correlation between genotypic proportions and rate of weight gain, which shows that, with regard to its effects on weight gain, Ay heterozygosity is cell non-autonomous.
Structure and expression of human IFN-α genes (1982)

Copy DNA (cDNA) was prepared from induced leucocyte poly(A) RNA and cloned in Escherichia coli. IFN-alpha cDNA clones were isolated by subculture cloning with the use of a translation hybridization assay. Definitive identification of the clones was based on the production of an interferon-like protein by the transformed bacteria. Different IFN-alpha cDNAs, with characteristic target cell specificities, were identified. The cloned cDNAs typically encode a mature polypeptide of 166 (or, for IFN-alpha 2, 165) amino acids and a signal sequence of 23 amino acids. A human chromosomal library was screened with IFN cDNA and 17 distinct IFN-alpha-related sequences were isolated and identified, of which 7 proved to be nonallelic authentic genes and 4 pseudogenes; 6 sequences remain to be elucidated. Taking into account the work of Goeddel and his colleagues, 13 non-allelic authentic genes and 6 pseudogenes can be distinguished. In addition, 9 genes believed to be allelic to the 13 authentic genes have been sequenced. The IFN-alpha genes may be classified into two major subfamilies, which diverged at least 33 Ma ago, but perhaps much earlier, if sequence rectification occurred. At least one IFN-alpha gene appears to have resulted by a recombinational event between members of the subfamily I and II. IFN-beta is distantly related to IFN-alpha's and may have diverged from a common ancestor at least 500 Ma ago. Both IFN-alpha and IFN-beta genes differ from most other genes of higher organisms by being devoid of introns. The mouse was found to possess an IFN-alpha gene family of a size similar to that of man; the murine genes also do not have introns. IFN-alpha genes devoid of their signal sequence were joined to prokaryotic promoters to produce the mature interferons in E. coli in high yield. IFN-alpha 2, purified to homogeneity, has been crystallized by T. Unge and B. Strandberg (Uppsala). Hybrid genes consisting of IFN-alpha 1 and IFN-alpha 2 segments were constructed and expressed in E. coli; the target cell specificities of such hybrids were dependent on the arrangement of the segments and were different from those of either parent. The chromosomal gene for HuIFN-alpha 1 was introduced into mouse L cells to study the mechanism of its expression. Correct transcription was only detected after induction (with Newcastle disease virus); expression was transient, with the same kinetics as those of the endogenous mouse IFN mRNA. Natural murine IFNs and human IFN-beta and IFN-gamma are glycosylated. Because E. coli cells transformed with the genes of eukaryotic glycoproteins are not expected to yield correctly glycosylated polypeptides, we prepared lines of hamster cells permanently transformed with hybrid plasmids, which contained an IFN gene linked to the SV40 early promoter, as well as dihydrofolate reductase as a selective marker. After intracellular amplification of the introduced genes, cell lines were obtained which constitutively produced IFN at about 40 000 units ml-1 and could be propagated for at least several months.
An injectable collagen/poly(γ-glutamic acid) hydrogel as a scaffold of stem cells and α-lipoic acid for enhanced protection against renal dysfunction (2016)

Mesenchymal stem cells (MSCs) can ameliorate renal injury and accelerate repair of acute kidney injury. Herein, we developed a collagen/poly(γ-glutamic acid) (γ-PGA) hydrogel as an injectable scaffold for the delivery of mouse MSCs (mMSCs) and anti-oxidant drugs into injured sites. By the introduction of γ-PGA into conventional collagen, the viscosity of collagen was reduced at ambient temperature for easy handling, while the elastic and viscous moduli of collagen were increased and a new porous structure was generated near body temperature. When in situ gel-forming collagen/γ-PGA hydrogels loaded with mMSCs and α-lipoic acid (LA) were administered to a mouse model of renal dysfunction, they significantly attenuated the level of blood urea nitrogen and creatinine, which resulted from the increased retention of therapeutic mMSCs and the controlled release of anti-oxidant drugs at the injured site. These findings suggested that this novel type of hydrogel could be applied as an injectable scaffold for use in regenerative medicine.
Sample aware embedded feature selection for reinforcement learning (2012)

Reinforcement learning (RL) is designed to learn optimal control policies from unsupervised interactions with the environment. Many successful RL algorithms have been developed, however, none of them can efficiently tackle problems with high-dimensional state spaces due to the "curse of dimensionality," and so their applicability to real-world scenarios is limited. Here we propose a Sample Aware Feature Selection algorithm embedded in NEAT, or SAFS-NEAT, to help address this challenge. This algorithm builds upon the powerful evolutionary policy search algorithm NEAT, by exploiting data samples collected during the learning process. This data permits feature selection techniques from the supervised learning domain to be used to help RL scale to problems with high-dimensional state spaces. We show that by exploiting previously observed samples, on-line feature selection can enable NEAT to learn near optimal policies for such problems, and also outperform an existing feature selection algorithm which does not explicitly make use of this available data.
Comparison of resolution in microemulsion EKC and MEKC employing suppressed electroosmosis: Application to bisphenol‐A‐diglycidyl ether and its derivatives (2007)

The resolution (R(s)) of hydrophobic analytes in microemulsion EKC (MEEKC) and MEKC with suppressed electroosmosis was investigated using bisphenol-A-diglycidyl ether and its derivatives (BADGEs) as test analytes. Separation scales were compared using our equation for the resolution, R(s)= (square rootN/4)(alpha-1)/(1+K(2)),where k is the retention factor, alpha the selectivity (alpha = k(2)/k(1) for k(2) > or = k(1)>0), and N the average efficiency. At given concentrations of SDS and organic cosolvent in the buffer, in comparison with MEKC, MEEKC was found to provide better resolution of BADGEs, mainly due to the significantly smaller k in MEEKC, but not the greater alpha in MEEKC, while a comparable range of N. Significantly improved resolution of BADGEs was obtained with increase in the concentration of organic cosolvent in the MEEKC and MEKC buffers, while small change in R(s) with the SDS concentration in a range of 100-180 mM. In addition, a decrease in temperature or voltage resulted in slightly better R(s).
Hypersensitivity Pneumonitis (2002)

Hypersensitivity pneumonitis (HP) is a group of immunologically mediated lung diseases caused by the inhalation of environmental agents in susceptible individuals. Most HP patients are non-smokers and have been exposed to organic dusts from vegetable or animal products. Some HP cases are associated with exposures to relatively simple chemical compounds. HP may present as an acute, subacute, or chronic disease and may follow various clinical courses. The type of exposure is thought to be more important in the clinical outcome than the nature of the antigen. A diagnosis of HP is often considered on the basis of clinical history of exposure with resulting respiratory symptoms, but the definitive diagnosis requires a constellation of clinical, radiologic, laboratory, and pathologic findings. The characteristic histologic triad in HP includes bronchiolitis, interstitial lymphocytic infiltration, and granulomas; however, biopsy in HP cases may lack the diagnostic triad and manifest as nonspecific interstitial pneumonia (NSIP). Avoiding exposure to the offending antigen(s) is usually sufficient to resolve symptoms and physiological abnormalities. Pulmonary fibrosis and physiological abnormalities occurring in chronic HP may be irreversible. Steroid therapy is helpful for symptomatic relief, but probably does not affect the long-term prognosis. Type III and type IV hypersensitivity reactions are involved in the pathogenesis; alveolar macrophages and T cells (Th-1 type) play a central role in the immune responses after antigen exposure via their increased interaction and secretion of regulatory mediators.
Local increase in the number of mast cells and expression of nerve growth factor in the bronchus of asthmatic patients after repeated inhalation of allergen at low‐dose (2001)

Our study shows that the increase in the number of mast cells and in the expression of NGF induced by allergen exposure in the bronchus of asthmatic patients is occurring before the onset of symptoms. In addition, our finding of the presence of the TrkA receptor on the membrane of the infiltrated mast cell in situ brings evidence of the mast cell as a target cell for the growth factor activity of NGF in the airways in asthma.
ELECTROCHEMICAL THERAPY OF PELVIC PAIN : Effects of PEMF on Tissue Trauma (1994)

￻ Unusually effective and long-lasting relief of pelvic pain of gynecological origin has been obtained consistently by short exposures of affected areas to irradiation by a magnetic induction device producing short, sharp, magnetic-field pulses of a minimal 1amplitude to initiate the electrochemical phenomenon of Electroporation within a 25 cm. focal area. Treatments are short, fast-acting, economical and in many instances have obviated surgery. This report includes typical cases such as dysmenorrhoea, endometriosis, ruptured ovarian cyst, acute lower urinary tract infection, post-operative hematoma, and persistent dyspareunia in which pulsed magnetic field treatment has not, in most cases, been supplemented by analgesic medication. Of 17 female patients presenting with acute (n=13) and/or chronic (n=9) pelvic pain, 16 (89.8%) experienced marked, even dramatic relief and 2 (10.2%) less than complete pain relief after an average of three 15-minute treatments.
Virogenic BrdU and BrdU-sensitive DNA sequences are disproportionately concentrated in the template-active chromatin of rat embryo cells (1979)

In order to characterize the molecular mechanism responsible for the BrdU-mediated activation of endogenous retrovirus from normal rat embryo cells, the previously reported selective distribution of bromouracil in DNA was correlated with the corresponding organization of the nucleo-protein complex in regard to nucleosome structure and template - active and -inactive chromatin. Following micrococcal nuclease digestion of chromatin labeled with either [(3)H]thymidine or [(3)H]BrdU, the amount and specific activities of the respective nucleosomal DNA were indistinguishable. Comparable findings were obtained following direct examination of the nuclease-sensitive, "spacer" DNA. However, when each chromatin type was fractionated into template-active and -inactive components, it was evident that [(3)H]bromouracil was nonrandomly more concentrated in the template-active portion in comparison to the random distribution of [(3)H]thymine moieties. Furthermore, it was apparent that the template-active chromatin fraction was substantially enriched in the nucleotide sequences of rat DNA known to be sensitive to the virogenic action of BrdU.
Detection of a primitive megakaryocyte progenitor cell in human fetal bone marrow. (1996)

Ontogeny-related changes in megakaryocyte (MK) progenitor cells were a analyzed to further define the cellular hierarchy occurring during human MK development. CD34+ cells were selected from human low-density adult bone marrow (ABM) or unfractionated fetal bone marrow (FBM) and assayed for MK colony formation in a serum-depleted fibrin clot assay system. At days 3, 7, 12, 16, 21, and 28 of incubation, MK colonies were analyzed for colony number, size and number of foci of development. Unifocal CFU-MK-derived colonies cloned from FBM formed after fewer days of in vitro culture and were 2.6-fold larger than those colonies cloned from ABM, However, the frequency of CFU-MK derived colonies cloned from ABM was significantly greater. the MK colonies cloned from FBM morphologically consisted of both pure MK colonies and mixed MK-containing colonies, in which a core of CD41- cells were surrounded by CD41+MKs. Large colonies resembling the primitive burst-forming unit-MK (BFU-MK) also were assayable from both FBM and ABM. These BFU-MK-derived colonies appeared after fewer days of incubation when FBM was assayed compared to ABM, but at a significantly lower frequency. In addition, large unifocal MK colonies consisting of >300 cells (300-1000) appeared from cells cloned from FBM but not ABM. This type of colony, which appears to represent a unique type of MK progenitor cell, was termed a high proliferative potential cell-MK (HPPC-MK). such colonies represent a relatively rare MK progenitor. We conclude that there are a significant ontologic changes in human MK progenitor cell development. The kinetics of MK colony formation from ABM differs significantly from that of FBM. Furthermore, the proliferative capacity of fetal MK progenitor cells appear to be far greater than that of ABM. In addition, a more primitive lineage-restricted MK progenitor cell with extensive proliferative capacity, the HPPC-MK, was assayable exclusively from FBM.
Synergistic Post-Transcriptional Regulation of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) by miR-101 and miR-494 Specific Binding (2011)

microRNAs (miRNAs) are a class of regulatory small non-coding molecules that control gene expression at post-transcriptional level. Deregulation of miRNA functions affects a variety of biological processes also involved in the etiology of several human mendelian and complex diseases. Recently, aberrant miRNA expression has been observed in Cystic Fibrosis (CF), an autosomal-recessive genetic disorder caused by mutations in the CFTR gene, in which a genotype-phenotype correlation is not always found. In order to determine miRNA role in CFTR post-transcriptional regulation, we searched for miR-responsive elements in the CFTR 3'-UTR. In silico analysis, performed using different computational on-line programs, identified some putative miRNAs. Both miR-101 and miR-494 synthetic mimics significantly inhibited the expression of a reporter construct containing the 3'-UTR of CFTR in luciferase assays. Interestingly, miR-101/miR-494 combination was able to markedly suppress CFTR activity by approximately 80% (p<0.001). This is one of the first in vitro studies implicating microRNAs as negative regulators of the CFTR gene expression. miRNA aberrant expression and function might explain the wide phenotypic variability observed among CF patients.