gebhart/patrepeval huggingface dataset:
Storage Stability of Saponified Starch‐g‐Polyacrylonitrile and Related Absorbents (1982)

Abstract Use of methanol as a precipitant to isolate saponified starch‐ g ‐polyacrylonitrile from an aqueous alkaline saponification mixture gives a product with a higher water absorbency and better storage stability than that from precipitation with either ethanol, acetone, or isopropanol. Storage stability of the material is strongly dependent on moisture content of the polymer and is enhanced if excess alkali is neutralized before the product is isolated. Absorbent polymers prepared from flour suffer a greater absorbency loss on storage than starch‐based polymers. Storage stabilities of drum dried‐, freeze dried‐, and tray dried products are also examined.
The Radioprotective 105/MD-1 Complex Links TLR2 and TLR4/MD-2 in Antibody Response to Microbial Membranes (2005)

Low-affinity IgG3 Abs to microbial membranes are important for primary immune defense against microbes, but little is known about the importance of TLRs in their production. IgG3 levels were extremely low in mice lacking radioprotective 105 (RP105), a B cell surface molecule structurally related to TLRs. RP105(-/-) B cells proliferated poorly in response to not only the TLR4 ligand LPS but also TLR2 ligand lipoproteins, both of which mediate the immunostimulatory activity of microbial membranes. RP105(-/-) mice were severely impaired in hapten-specific Ab production against LPS or lipoproteins. CD138 (syndecan-1)-positive plasma cells were detected after lipid A injection in wild-type spleen but much less in RP105(-/-) spleen. RP105 ligation in vivo induced plasma cell differentiation. RP105 expression was approximately 3-fold higher on marginal zone B cells than on follicular and B1 cells and was down-regulated on germinal center cells. These results demonstrate that a signal via RP105 is uniquely important for regulating TLR-dependent Ab production to microbial membranes.
Partial uracil–DNA–glycosylase treatment for screening of ancient DNA (2014)

The challenge of sequencing ancient DNA has led to the development of specialized laboratory protocols that have focused on reducing contamination and maximizing the number of molecules that are extracted from ancient remains. Despite the fact that success in ancient DNA studies is typically obtained by screening many samples to identify a promising subset, ancient DNA protocols have not, in general, focused on reducing the time required to screen samples. We present an adaptation of a popular ancient library preparation method that makes screening more efficient. First, the DNA extract is treated using a protocol that causes characteristic ancient DNA damage to be restricted to the terminal nucleotides, while nearly eliminating it in the interior of the DNA molecules, allowing a single library to be used both to test for ancient DNA authenticity and to carry out population genetic analysis. Second, the DNA molecules are ligated to a unique pair of barcodes, which eliminates undetected cross-contamination from this step onwards. Third, the barcoded library molecules include incomplete adapters of short length that can increase the specificity of hybridization-based genomic target enrichment. The adapters are completed just before sequencing, so the same DNA library can be used in multiple experiments, and the sequences distinguished. We demonstrate this protocol on 60 ancient human samples.
A Model for Antiplasticization in Polystyrene (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Model for Antiplasticization in PolystyreneS. L. Anderson, E. A. Grulke, P. T. DeLassus, P. B. Smith, C. W. Kocher, and B. G. LandesCite this: Macromolecules 1995, 28, 8, 2944–2954Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/ma00112a047https://doi.org/10.1021/ma00112a047research-articleACS PublicationsRequest reuse permissionsArticle Views930Altmetric-Citations99LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Signaling mechanisms of the epithelial-mesenchymal transition (2014)

The epithelial-mesenchymal transition (EMT) is an essential mechanism in embryonic development and tissue repair. EMT also contributes to the progression of disease, including organ fibrosis and cancer. EMT, as well as a similar transition occurring in vascular endothelial cells called endothelial-mesenchymal transition (EndMT), results from the induction of transcription factors that alter gene expression to promote loss of cell-cell adhesion, leading to a shift in cytoskeletal dynamics and a change from epithelial morphology and physiology to the mesenchymal phenotype. Transcription program switching in EMT is induced by signaling pathways mediated by transforming growth factor β (TGF-β) and bone morphogenetic protein (BMP), Wnt-β-catenin, Notch, Hedgehog, and receptor tyrosine kinases. These pathways are activated by various dynamic stimuli from the local microenvironment, including growth factors and cytokines, hypoxia, and contact with the surrounding extracellular matrix (ECM). We discuss how these pathways crosstalk and respond to signals from the microenvironment to regulate the expression and function of EMT-inducing transcription factors in development, physiology, and disease. Understanding these mechanisms will enable the therapeutic control of EMT to promote tissue regeneration, treat fibrosis, and prevent cancer metastasis.
Proteolytic activity in sheep lung lymph as marker of lung capillary injury. (1987)

Intravenous infusions of Escherichia coli endotoxin into sheep caused the appearance in lung lymph of high levels of an enzyme with trypsinlike activity. The time course of appearance of the enzyme and the extent of its increase corresponded to the known events of endotoxin-induced capillary injury. Accordingly, activity was low in the first phase of endotoxin-induced increased lung lymph flow caused by increased pressure filtration but was high in the second phase of increased lung lymph flow caused by increased permeability filtration. Recovery was associated with a decrease of activity to preinfusion levels. Capillary damage and increased permeability filtration induced by air emboli or oleic acid led to a similar increase in lung lymph proteolytic activity. By contrast lung lymph proteolytic activity remained virtually unchanged during increased pressure filtration induced by inflation of a balloon in the left atrium. Activity also remained unchanged in thoracic duct lymph, indicating that the increased activity in lung lymph is not an expression of a generalized response to endotoxin. The enzyme, a serine protease with a molecular weight of about 70,000 to 75,000 and a pH optimum between 7.3 and 7.6, was not related to lymph clotting and was not capable of correcting the clotting defects of plasmas deficient in enzymes of the clotting cascade. These results together with specificity studies indicate that the enzyme represents a new, hitherto unidentified, protease. Measurements of its activity in lung lymph represent a sensitive marker of lung capillary injury.
Interaction of peptide fragment 828-848 of the envelope glycoprotein of human immunodeficiency virus type I with lipid bilayers (1993)

The interaction of the peptide fragment 828-848, called P828, from the carboxy-terminal region of the envelope glycoprotein gp41 of HIV-I with model membranes composed of phosphatidylcholine (PC) and phosphatidylglycerol (PG) was investigated using microelectrophoretic mobility of liposomes, fluorescence polarization of labeled lipids, NMR, and differential scanning calorimetry. The peptide binds to negatively charged lipid surfaces. No interaction between P828 and neutral PC surfaces is observed. The interaction between the peptide and the lipid is exclusively electrostatic with the six positively charged arginines of P828 acting as binding sites for PG. Circular dichroism measurements of P828 indicate that the peptide undergoes a transition from a random coil to an ordered conformation upon binding to negatively charged PG bilayers or SDS micelles, but not in the presence of neutral PC bilayers. The ordered structure has an apparent helical content of 60%. IN DOPG/DOPC mixtures containing 20 mol % DOPG, the peptide causes the formation of lipid domains enriched in DOPG, as assessed by measurement of fluorescence energy transfer between labeled PG and PC. The formation of these domains requires energy and therefore reduces the strength of peptide binding to the lipid matrix. Our data support and quantitate the results from antibody binding studies [Haffar, O.K., Dowbenko, D. J., & Berman, P. W. (1988) J. Cell Biol. 107, 1677-1687] that the carboxy-terminal segment of the envelope glycoprotein gp41 interacts with microsomal membranes.
A Novel Surfactant Nanoemulsion with Broad‐Spectrum Sporicidal Activity againstBacillusSpecies (1999)

Two nontoxic, antimicrobial nanoemulsions, BCTP and BCTP 401, have been developed. These emulsions are composed of detergents and oils in 80% water. BCTP diluted up to 1:1000 inactivated>90% of Bacillus anthracis spores in 4 h and was also sporicidal against three other Bacillus species. This sporicidal activity is due to disruption of the spore coat after initiation of germination without complete outgrowth. BCTP 401 diluted 1:1000 had greater activity than BCTP against Bacillus spores and had an onset of action of <30 min. Mixing BCTP or BCTP 401 with Bacillus cereus prior to subcutaneous injection in mice reduced the resulting skin lesion by 99%. Wound irrigation with BCTP 1 h after spore inoculation yielded a 98% reduction in skin lesion size, and mortality was reduced 3-fold. These nanoemulsion formulas are stable, easily dispersed, nonirritant, and nontoxic compared with other available sporicidal agents.
MegaTevs: single-chain dual nucleases for efficient gene disruption (2014)

Targeting gene disruptions in complex genomes relies on imprecise repair by the non-homologous end-joining DNA pathway, creating mutagenic insertions or deletions (indels) at the break point. DNA end-processing enzymes are often co-expressed with genome-editing nucleases to enhance the frequency of indels, as the compatible cohesive ends generated by the nucleases can be precisely repaired, leading to a cycle of cleavage and non-mutagenic repair. Here, we present an alternative strategy to bias repair toward gene disruption by fusing two different nuclease active sites from I-TevI (a GIY-YIG enzyme) and I-OnuI E2 (an engineered meganuclease) into a single polypeptide chain. In vitro, the MegaTev enzyme generates two double-strand breaks to excise an intervening 30-bp fragment. In HEK 293 cells, we observe a high frequency of gene disruption without co-expression of DNA end-processing enzymes. Deep sequencing of disrupted target sites revealed minimal processing, consistent with the MegaTev sequestering the double-strand breaks from the DNA repair machinery. Off-target profiling revealed no detectable cleavage at sites where the I-TevI CNNNG cleavage motif is not appropriately spaced from the I-OnuI binding site. The MegaTev enzyme represents a small, programmable nuclease platform for extremely specific genome-engineering applications.
Nitric oxide in the inner ear (2002)

During the past year significant advances have been made in our understanding of the functional significance of nitric oxide (NO) in the inner ear. NO synthase and the NO production site have now been localized using immunohistochemistry and a new fluorescence indicator for NO. The functional significance of NO in the inner ear, in particular as a neurotransmitter, is becoming increasingly clear. Increasing evidence suggests that excessive NO production may play an essential role in inner ear disorders. The production of an inducible form of NO synthase may be closely related to this phenomenon. Based on the mechanisms of inner ear disorders, new pharmacological strategies for preventing or treating inner ear disorders have been suggested.
Remote Toehold: A Mechanism for Flexible Control of DNA Hybridization Kinetics (2011)

Hybridization of DNA strands can be used to build molecular devices, and control of the kinetics of DNA hybridization is a crucial element in the design and construction of functional and autonomous devices. Toehold-mediated strand displacement has proved to be a powerful mechanism that allows programmable control of DNA hybridization. So far, attempts to control hybridization kinetics have mainly focused on the length and binding strength of toehold sequences. Here we show that insertion of a spacer between the toehold and displacement domains provides additional control: modulation of the nature and length of the spacer can be used to control strand-displacement rates over at least 3 orders of magnitude. We apply this mechanism to operate displacement reactions in potentially useful kinetic regimes: the kinetic proofreading and concentration-robust regimes.
Representing shape with a spatial pyramid kernel (2007)

The objective of this paper is classifying images by the object categories they contain, for example motorbikes or dolphins. There are three areas of novelty. First, we introduce a descriptor that represents local image shape and its spatial layout, together with a spatial pyramid kernel. These are designed so that the shape correspondence between two images can be measured by the distance between their descriptors using the kernel. Second, we generalize the spatial pyramid kernel, and learn its level weighting parameters (on a validation set). This significantly improves classification performance. Third, we show that shape and appearance kernels may be combined (again by learning parameters on a validation set).
Salt and Blood Pressure: Time to Challenge (2005)

Hypertension is a worldwide epidemic and its control is costly, but still inadequate. The mechanisms underlying the development of primary hypertension remain elusive. Several observations point to the kidney as a primary actor and sodium as the main culprit for development of hypertension. Over the last few decades, experimental, observational and clinical data have continuously indicated that excess salt intake is positively associated with elevated blood pressure and that blood pressure can be significantly reduced with substantial reductions in dietary sodium. This review highlights the pathophysiological mechanisms linking sodium to elevated blood pressure, synthesizes available evidence for the effect of reducing salt intake in controlling blood pressure. It specifically analyzes 6 recent meta-analyses and dietary approaches to stop hypertension.
Anticancer effects of thiazolidinediones are independent of peroxisome proliferator-activated receptor gamma and mediated by inhibition of translation initiation. (2001)

The thiazolidinedione (TZD) class of peroxisome proliferator-activated receptor (PPAR) gamma ligands, known for their ability to induce adipocyte differentiation and increase insulin sensitivity, also exhibits anticancer properties. Currently, TZDs are being tested in clinical trials for treatment of human cancers expressing high levels of PPARgamma because it is assumed that activation of PPARgamma mediates their anticancer activity. Using PPARgamma(-/-) and PPARgamma(+/+) mouse embryonic stem cells, we report here that inhibition of cell proliferation and tumor growth by TZDs is independent of PPARgamma. Our studies demonstrate that these compounds block G(1)-S transition by inhibiting translation initiation. Inhibition of translation initiation is the consequence of partial depletion of intracellular calcium stores and the resulting activation of protein kinase R that phosphorylates the alpha subunit of eukaryotic initiation factor 2 (eIF2), thus rendering eIF2 inactive. PPARgamma-independent inhibition of translation initiation most likely accounts for the anticancer properties of thiazolidinediones.
Direct Growth of Semiconducting Single-Walled Carbon Nanotube Array (2009)

By introducing the UV beam into our homemade chemical vapor deposition system, we had obtained a well aligned SWNT array on an ST-cut quartz substrate. After transfer onto a SiO(2)/Si substrate, the SWNT array was detected by Raman spectroscopy and electrical measurement, which showed that over 95% of the SWNTs were semiconducting ones. It is proposed that the selection process took place at the very beginning of the SWNT formation rather than destroying the metallic SWNTs after growth. This approach has solved one of the most important problems in SWNT application.
Adjuvant Properties of CpG Oligonucleotides in Primates (2006)

Unlike mammalian DNA, bacterial, plasmid, and synthetic DNA containing unmethylated CpG dinucleotides in specific sequence contexts are recognized by the Toll-like receptor 9 expressed by B cells and plasmacytoid dendritic cells, and trigger the activation of the innate and adaptive immune system. Upon signaling, CpG DNA induces B cells, natural killer cells, macrophages, and dendritic cells to proliferate, differentiate, take up, and present antigen and secrete a variety of immunoglobulins, chemokines, and predominantly Th1-type cytokines. Preclinical studies in mice and primates show that DNA sequences containing CpG motifs can selectively promote cellular and/or humoral immune responses in vivo. Early results from ongoing clinical studies indicate that CpG oligonucleotides (ODN) are well tolerated and improve the immune response to microbial vaccines. This work examines the progress in utilizing CpG ODN as adjuvants in conventional and DNA vaccines.
Approaching a Million-Fold Sensitivity Increase in Capillary Electrophoresis with Direct Ultraviolet Detection:  Cation-Selective Exhaustive Injection and Sweeping (2000)

A novel method that combines two on-line concentration techniques in capillary electrophoresis (CE), namely, sample stacking with electrokinetic injection (field-enhanced sample injection, FESI) and sweeping, afforded the detection of positively chargeable analytes in parts per trillion (ppt) levels. The main idea is to selectively introduce by FESI as many molecules of cationic analytes as possible from a very dilute sample solution and focus the resulting zone by sweeping. Limit of detection values (signal-to-noise ratio 3) of 4.1 and 8.0 ppt-the lowest concentration reported by direct UV detection in CE-with average plate numbers of 3.6 x 10(5) and 4.4 x 10(5) are obtained for laudanosine and naphthylamine (standard solutions), respectively. This translates to improvements in peak heights compared with usual injection approaching a million-fold. Optimization schemes and application to quantitative and qualitative analyses are also investigated.
Amplification of Epidermal Growth Factor Receptor Gene in Gliomas: Histopathology and Prognosis (1992)

In order to evaluate the incidence and prognostic significance of gene amplification in primary brain neoplasms we measured the number of gene copies per cell of three oncogenes (epidermal growth factor receptor [EGFR] gene, N-myc, C-myc) and syntenic control genes in 40 specimens using quantitative DNA dot blots. We observed EGFR gene amplification in astrocytomas and anaplastic astrocytomas with approximately the same incidence as in glioblastoma multiforme (33%), although large amplifications were only seen in glioblastoma multiforme. Fourteen patients had a supratentorial glioblastoma multiforme; six had EGFR gene amplification and eight had either normal EGFR gene copy number or elevated EGFR copy number attributable to extra copies of chromosome 7. Patients with gene amplification had shorter survival than patients without gene amplification (p = 0.01). The observed difference in survival was not likely to be due to group differences in age, sex, treatment, or histopathology.
DNA-Binding Specificity of GATA Family Transcription Factors (1993)

GATA-binding proteins constitute a family of transcription factors that recognize a target site conforming to the consensus WGATAR (W = A or T and R = A or G). Here we have used the method of polymerase chain reaction-mediated random site selection to assess in an unbiased manner the DNA-binding specificity of GATA proteins. Contrary to our expectations, we show that GATA proteins bind a variety of motifs that deviate from the previously assigned consensus. Many of the nonconsensus sequences bind protein with high affinity, equivalent to that of conventional GATA motifs. By using the selected sequences as probes in the electrophoretic mobility shift assay, we demonstrate overlapping, but distinct, sequence preferences for GATA family members, specified by their respective DNA-binding domains. Furthermore, we provide additional evidence for interaction of amino and carboxy fingers of GATA-1 in defining its binding site. By performing cotransfection experiments, we also show that transactivation parallels DNA binding. A chimeric protein containing the finger domain of areA and the activation domains of GATA-1 is capable of activating transcription in mammalian cells through GATA motifs. Our findings suggest a mechanism by which GATA proteins might selectively regulate gene expression in cells in which they are coexpressed.
More efficient genetic algorithm for solving optimization problems (2002)

Genetic algorithms (GA) are stochastic search techniques based on mechanics of natural selection and natural genetics. By using genetic operators and cumulative information, genetic algorithms prune the search space and generate a set of plausible solutions. This paper describes an efficient genetic algorithm defined as modified genetic algorithms (MGA). The proposed algorithms is developed by hybridising simple genetic algorithms (SGA) with simulated annealing (SA). In this proposed algorithm, all the conventional genetic operators, such as, selection, reproduction, crossover, mutation, have been used. But they have been modified by a set of new functions such as a selection function 1, a selection function 2, a mutation function, etc., which utilizes the concept of successive descent as seen in simulated annealing. In this way, MGA can be implemented to solve various optimization problems more accurately and quickly.
A Human Gene Responsible for Zellweger Syndrome That Affects Peroxisome Assembly (1992)

The primary defect arising from Zellweger syndrome appears to be linked to impaired assembly of peroxisomes. A human complementary DNA has been cloned that complements the disease's symptoms (including defective peroxisome assembly) in fibroblasts from a patient with Zellweger syndrome. The cause of the syndrome in this patient was a point mutation that resulted in the premature termination of peroxisome assembly factor-1. The homozygous patient apparently inherited the mutation from her parents, each of whom was heterozygous for that mutation.