gebhart/patrepeval huggingface dataset:
Effect of intermixing on self-propagating exothermic reactions in Al/Ni nanolaminate foils (2000)

Exothermic reactions can self-propagate rapidly in multilayered foils, and the properties of these reactions depend strongly on the heat of reaction, the average atomic diffusion distance, and the degree of intermixing at the layer interfaces prior to ignition. By performing low-temperature anneals on sputter-deposited Al/Ni nanolaminate foils, the thickness of the intermixed region between layers was increased and its effects on the heats and velocities of reactions were measured. The intermixed region consisted of the metastable Al9Ni2 phase while the final phase of the foil was Al3Ni2. Analytical and empirical models were used to predict reaction velocities as a function of bilayer thickness and intermixing thickness, and the predictions are in good agreement with the experimental results. Increasing the average thickness of the intermixed region from 2.4 to 18.3 nm reduced the reaction velocity for all of the foils but was most significant for the foils with bilayer thicknesses less than 25 nm. The results indicate that the reaction velocity can be separated into two distinct regimes. The first regime occurs for thicker bilayers in which the average atomic diffusion distance is large. In this regime, reaction temperatures are high and reducing the bilayer thickness increases the reaction velocity. The second regime occurs for thinner bilayers where reaction velocity is dominated by the reduction in available energy due to intermixing. In this regime, reducing bilayer thickness results in a decrease in reaction velocity.
Drosophila Kelch Is an Oligomeric Ring Canal Actin Organizer (1997)

Drosophila kelch has four protein domains, two of which are found in kelch-family proteins and in numerous nonkelch proteins. In Drosophila, kelch is required to maintain ring canal organization during oogenesis. We have performed a structure-function analysis to study the function of Drosophila kelch. The amino-terminal region (NTR) regulates the timing of kelch localization to the ring canals. Without the NTR, the protein localizes precociously and destabilizes the ring canals and the germ cell membranes, leading to dominant sterility. The amino half of the protein including the BTB domain mediates dimerization. Oligomerization through the amino half of kelch might allow cross-linking of ring canal actin filaments, organizing the inner rim cytoskeleton. The kelch repeat domain is necessary and sufficient for ring canal localization and likely mediates an additional interaction, possibly with actin.
A UniqueMycobacteriumSpecies Isolated from an Epizootic of Striped Bass (Morone saxatilis) (2001)

We isolated a Mycobacterium sp. resembling Mycobacterium marinum and M. ulcerans from diseased striped bass (Morone saxatilis) during an epizootic of mycobacteriosis in the Chesapeake Bay. This isolate may represent an undescribed Mycobacterium species, based on phenotypic characteristics and comparative 16S rRNA gene sequence.
Nonlinear Optical Microscopy of Single Nanostructures (2013)

We review recent advances in nonlinear optical (NLO) microscopy studies of single nanostructures. NLO signals are intrinsically sensitive to the electronic, vibrational, and structural properties of such nanostructures. Ultrafast excitation allows for mapping of energy relaxation pathways at the single-particle level. The strong nonlinear response of nanostructures makes them highly attractive for applications as novel NLO imaging agents in biological and biomedical research. NLO modalities based on harmonic generation, multiphoton photoluminescence, four-wave mixing, and pump-probe processes are discussed in detail.
Leaf Senescence Is Delayed in Tobacco Plants Expressing the Maize Homeobox Gene knotted1 under the Control of a Senescence-Activated Promoter (1999)

Naomi Ori, Michelle T. Juarez, David Jackson, Judy Yamaguchi, Gary M. Banowetz, Sarah Hake, Leaf Senescence Is Delayed in Tobacco Plants Expressing the Maize Homeobox Gene knotted1 under the Control of a Senescence-Activated Promoter, The Plant Cell, Vol. 11, No. 6 (Jun., 1999), pp. 1073-1080
Long-Term Administration of Highly Purified Eicosapentaenoic Acid Provides Improvement of Psoriasis (1991)

Nine patients with chronic stable psoriasis (4 males and 5 females) were entered in this trial. Eicosapentaenoic acid (EPA) ethylester (90% pure) without docosahexaenoic acid (DHA) in gelatin-coated capsules at a daily dose of 3.6 g was administered to 9 patients for 3 months, 7 patients for 6 months and 6 patients for 12 months. The clinical changes of skin lesions of the patients with 12 months of treatment were as follows: marked improvement 1, improvement 3, relative improvement 1, no change 1. A clinical improvement of skin lesions was first observed 2-3 months after EPA treatment. The supplementation of highly purified EPA caused a significant increase in the content of plasma EPA and docosapentaenoic acid without affecting that of arachidonic acid (AA) and DHA. EPA decreased the production of leukotriene B4 (LTB4) and increased the formation of leukotriene B5 (LTB5) and 5-hydroxyeicosapentaenoic acid significantly in A23187-stimulated neutrophils. The LTB5/LTB4 ratio positively correlated with the plasma EPA/AA ratio and was directionally related to the clinical score, although the directional data were not statistically significant. We could not observe any side effects of EPA over 1 year. Although its effects are modest, it is nontoxic and its favorable effect appears to continue for the duration of its usage, indicating that EPA could be beneficial for the long-term treatment of psoriasis.
Distinction by radioisotope technique of a subgroup with increased thrombophilic potential among patients submitted to major abdominal surgery. (1986)

Deep vein thrombosis (DVT) detectable by the 99mTechnetium-labeled plasmin test developed in 13 (37%) of 35 sequentially studied patients, all above 40 years, undergoing elective major abdominal surgery. Ten of the 13 patients with DVT had an abnormal pulmonary perfusion scintigram, suggesting pulmonary embolism (PE), but only three had clinical evidence of thrombotic disease.
Massive Idiosyncratic Exon Skipping Corrects the Nonsense Mutation in Dystrophic Mouse Muscle and Produces Functional Revertant Fibers by Clonal Expansion (2000)

Conventionally, nonsense mutations within a gene preclude synthesis of a full-length functional protein. Obviation of such a blockage is seen in the mdx mouse, where despite a nonsense mutation in exon 23 of the dystrophin gene, occasional so-called revertant muscle fibers are seen to contain near-normal levels of its protein product. Here, we show that reversion of dystrophin expression in mdx mice muscle involves unprecedented massive loss of up to 30 exons. We detected several alternatively processed transcripts that could account for some of the revertant dystrophins and could not detect genomic deletion from the region commonly skipped in revertant dystrophin. This, together with exon skipping in two noncontiguous regions, favors aberrant splicing as the mechanism for the restoration of dystrophin, but is hard to reconcile with the clonal idiosyncrasy of revertant dystrophins. Revertant dystrophins retain functional domains and mediate plasmalemmal assembly of the dystrophin-associated glycoprotein complex. Physiological function of revertant fibers is demonstrated by the clonal growth of revertant clusters with age, suggesting that revertant dystrophin could be used as a guide to the construction of dystrophin expression vectors for individual gene therapy. The dystrophin gene in the mdx mouse provides a favored system for study of exon skipping associated with nonsense mutations.
Converting a Peptide into a Drug: Strategies to Improve Stability and Bioavailability (2002)

The discovery of peptide hormones, growth factors and neuropeptides implicated in vital biological functions of our organism has increased interest in therapeutic use of short peptides. However, the development of peptides as clinically useful drugs is greatly limited by their poor metabolic stability and low bioavailability, which is due in part to their inability to readily cross membrane barriers such as the intestinal and blood-brain barriers. The aim of peptide medicinal chemistry is, therefore, to develop strategies to overcome these problems. Recent progress in chemical synthesis and design have resulted in several strategies for producing modified peptides and mimetics with lower susceptibility to proteolysis and improved bioavailability, which has increased the probability of obtaining useful drugs structurally related to parent peptides. This review describes different experimental approaches to transforming a peptide into a potential drug and provides examples of the usefulness of these strategies.
Ribonomic approaches to study the RNA‐binding proteome (2014)

Gene expression is controlled through a complex interplay among mRNAs, non-coding RNAs and RNA-binding proteins (RBPs), which all assemble along with other RNA-associated factors in dynamic and functional ribonucleoprotein complexes (RNPs). To date, our understanding of RBPs is largely limited to proteins with known or predicted RNA-binding domains. However, various methods have been recently developed to capture an RNA of interest and comprehensively identify its associated RBPs. In this review, we discuss the RNA-affinity purification methods followed by mass spectrometry analysis (AP-MS); RBP screening within protein libraries and computational methods that can be used to study the RNA-binding proteome (RBPome).
Scalar and Tensor Holographic Artificial Impedance Surfaces (2010)

We have developed a method for controlling electromagnetic surface wave propagation and radiation from complex metallic shapes. The object is covered with an artificial impedance surface that is implemented as an array of sub-wavelength metallic patches on a grounded dielectric substrate. We pattern the effective impedance over the surface by varying the size of the metallic patches. Using a holographic technique, we design the surface to scatter a known input wave into a desired output wave. Furthermore, by varying the shape of the patches we can create anisotropic surfaces with tensor impedance properties that provide control over polarization. As an example, we demonstrate a tensor impedance surface that produces circularly polarized radiation from a linearly polarized source.
Enzymatic Cleavage of Peptide-Linked Radiolabels from Immunoconjugates (1999)

We have incorporated peptides selected by combinatorial library [Peterson, J. J., and Meares, C. F. (1998) Bioconjugate Chem. 9, 618-626) into peptide-linked radiolabeled immunoconjugates of the form DOTA-peptide-antibody. Decapeptide linkers -GFQGVQFAGF- and -GFGSVQFAGF-, selected for cleavage by human liver cathepsin B, were rapidly digested in vitro when compared to the simple model tetrapeptide motif of the prototype -GGGF- [Li, M., and Meares, C. F. (1993) Bioconjugate Chem. 4, 275-283]. Cleavage properties of these library-selected substrates for cathepsin B compared favorably with decapeptide linkers -GLVGGAGAGF- and -GGFLGLGAGF-, which incorporate two of the most labile extended cathepsin B substrates from the literature. The decapeptide linker -GFGSTFFAGF-, selected from the library for cleavage by human liver cathepsin D, was rapidly digested by cathepsin D while the others were not.
The c-met/HGF receptor in human tumours (1992)

Giordano, S; di Renzo, M F; Olivero, M; Mondino, A; Zhen, Z; Medico, E; Comoglio, P M Author Information
Efficient CRISPR-rAAV engineering of endogenous genes to study protein function by allele-specific RNAi (2015)

Gene knockout strategies, RNAi and rescue experiments are all employed to study mammalian gene function. However, the disadvantages of these approaches include: loss of function adaptation, reduced viability and gene overexpression that rarely matches endogenous levels. Here, we developed an endogenous gene knockdown/rescue strategy that combines RNAi selectivity with a highly efficient CRISPR directed recombinant Adeno-Associated Virus (rAAV) mediated gene targeting approach to introduce allele-specific mutations plus an allele-selective siRNA Sensitive (siSN) site that allows for studying gene mutations while maintaining endogenous expression and regulation of the gene of interest. CRISPR/Cas9 plus rAAV targeted gene-replacement and introduction of allele-specific RNAi sensitivity mutations in the CDK2 and CDK1 genes resulted in a >85% site-specific recombination of Neo-resistant clones versus ∼8% for rAAV alone. RNAi knockdown of wild type (WT) Cdk2 with siWT in heterozygotic knockin cells resulted in the mutant Cdk2 phenotype cell cycle arrest, whereas allele specific knockdown of mutant CDK2 with siSN resulted in a wild type phenotype. Together, these observations demonstrate the ability of CRISPR plus rAAV to efficiently recombine a genomic locus and tag it with a selective siRNA sequence that allows for allele-selective phenotypic assays of the gene of interest while it remains expressed and regulated under endogenous control mechanisms.
Salicylic Acid Interferes with Tobacco Mosaic Virus Replication via a Novel Salicylhydroxamic Acid-Sensitive Mechanism. (1997)

Salicylic acid (SA) induces resistance to all plant pathogens, including bacteria, fungi, and viruses, but the mechanism by which SA engenders resistance to viruses is not known. Pretreatment of tobacco mosaic virus (TMV)-susceptible (nn genotype) tobacco tissue with SA reduced the levels of viral RNAs and viral coat protein accumulating after inoculation with TMV. Viral RNAs were not affected equally, suggesting that SA treatment interferes with TMV replication. Salicylhydroxamic acid (SHAM), an inhibitor of the mitochondrial alternative oxidase, antagonized both SA-induced resistance to TMV in nn genotype plants and SA-induced acquired resistance in resistant (NN genotype) tobacco. SHAM did not inhibit induction of the PR-1 pathogenesis-related protein or induction of resistance to Erwinia carotovora or Botrytis cinerea by SA. This indicates that SA induces resistance to TMV via a novel SHAM-sensitive signal transduction pathway (potentially involving alternative oxidase), which is distinct from that leading to resistance to bacteria and fungi.
Some Aspects of the Biological Role of Adenosine 3',5'-monophosphate (Cyclic AMP) (1968)

Cyclic AMP (adenosine 3',5'-monophosphate or cyclic adenylate) has now been established as a second messenger mediating many of the effects of a variety of hormones. Several of the metabolic effects mediated by cyclic AMP are discussed, and it is suggested that certain other ("functional" or "mechanical") hormonal effects may be similarly mediated. In particular, the evidence presented supports the hypothesis that the positive inotropic response to the catecholamines is mediated by cyclic AMP. Although knowledge of the biological role of cyclic AMP has not been widely applied clinically, sufficient knowledge has now accumulated to make research in this area desirable.
Functional characterization of the rat growth hormone promoter elements required for induction by thyroid hormone with and without a co-transfected β type thyroid hormone receptor (1989)

We have extensively characterized the sequences of the rat growth hormone (rGH) promoter required for induction by T3 (thyroid hormone, 3,5,3'-L-triiodothyronine) in a transient transfection system. Oligonucleotides containing portions of the rGH promoter sequence with various deletions and point mutations were placed upstream of the first 137 base pairs of the rGH promoter or the heterologous herpes virus thymidine kinase promoter in chloramphenicol acetyltransferase expression vectors. The rGH137 and thymidine kinase promoters show no or minimal response to T3 in the basal state. The constructs were tested in GH4C1 rat pituitary cells and COS cells (functionally deficient in thyroid hormone receptor) with and without a co-transfected plasmid expressing a beta type c-erbA gene coding for a functional T3 receptor. Oligonucleotides containing the T3 receptor binding site confer hormone-dependent induction in a manner that is independent of either orientation or variation in position on the helix relative to the promoter. Point mutations in the sequence -189 to -173 result in loss of T3 induction, and bases between -173 and -167 were also required for a full T3 response. The minimal length to confer T3 induction to the rGH promoter was 23 base pairs (-190 to -167). Point mutations creating a perfect duplication of 7 base pairs within the receptor binding site conferred 12-fold T3 response to the rGH137 promoter, 3-fold greater than the wild type rGH237 construct. T3 inductibility was also transferred to the thymidine kinase promoter by an oligonucleotide containing the sequence -200 to -157, demonstrating that cell type specific elements located 3' to 157 of the rGH promoter are not required for thyroid hormone responsiveness.
Quality of long-term survival in young children with medulloblastoma (1994)

The reported success of treatment for children with medulloblastoma must be balanced against the effect that treatment has on the quality of life of long-term survivors. The outcome of long-term survivors reported in previous studies has been conflicting. The authors evaluate the mental and behavioral skills of a group of medulloblastoma survivors from their institution, all of whom had survived for more than 5 years postdiagnosis. A review of the institutional records yielded 32 patients. Twenty-three families were interviewed by telephone and, of these, 13 subjects came to the hospital for detailed neuropsychological and neurological evaluations. Intelligence quotient (IQ) was less than 90 for all participants tested, and patients diagnosed before the age of 3 years had lower IQ scores on average than those diagnosed later. Mean IQ and achievement test scores in reading, spelling, and mathematics were all higher in survivors who had undergone shunting. Achievement test results were often not in accord with intellectual potential, and individual intellectual skills varied widely. Perceptual-motor task performance was below average in more than 50% of the participants, but motor dexterity was more severely affected than perception. Problems in learning and a delay in both physical growth and development were seen in a majority of participants. This study directs attention to the serious difficulties faced by long-term survivors of medulloblastoma and their families, and underscores the importance of routine neuropsychological testing. Moreover, the study provides further impetus to seek alternatives to irradiation in the treatment of malignant brain tumors.
Cost-Effectiveness of Colorectal Cancer Screening (2001)

PURPOSE: To determine the most cost-effective colorectal cancer screening strategy costing less than $100,000 per life-year saved and to determine how available strategies compare with each other. MATERIALS AND METHODS: Standardized methods were used to calculate incremental cost-effectiveness ratios (ICERs) from published estimates of cost and effectiveness of colorectal cancer screening strategies, and the direction and magnitude of any effect on the ratio from parameter estimate adjustments based on literature values were estimated. RESULTS: Strategies in which double-contrast barium enema examination was performed emerged as optimal from all studies included. In average-risk individuals, screening with double-contrast barium enema examination every 3 years, or every 5 years with annual fecal occult blood testing, had an ICER of less than $55,600 per life-year saved. However, double-contrast barium enema examination screening every 3 years plus annual fecal occult blood testing had an ICER of more than $100,000 per life-year saved. Colonoscopic screening had an ICER of more than $100,000 per life-year saved, was dominated by other screening strategies, and offered less benefit than did double-contrast barium enema examination screening. CONCLUSION: Double-contrast barium enema examination can be a cost-effective component of colorectal cancer screening, but further modeling efforts are necessary.
Genistein inhibits proliferation similarly in estrogen receptor-positive and negative human breast carcinoma cell lines characterized by P21WAF1/CIP1 induction, G2/M arrest, and apoptosis (1998)

Genistein has been proposed to be responsible for lowering the rate of breast cancer in Asian women but the mechanism for this chemopreventive effect in vivo is unknown. In this study, we present in vitro evidence that genistein inhibits cell proliferation similarly in ER-positive and ER-negative human breast carcinoma cell lines. This inhibition is associated with specific G2/M arrest and induction of p21WAF1/CIP1 expression. Genistein results in a five-to six-fold increase in p21WAF1/CIP1 mRNA levels and a three- to four-fold increase in protein levels, only a 1.5-fold increase in p21WAF1/CIP1 transcription but a three- to six-fold increase in p21WAF1/CIP1 mRNA stability. The increase in p21WAF1/CIP1 is followed by increased apoptosis. The similar effects of genistein on a number of breast carcinoma cell lines with different ER and p53 status suggest that the actions of genistein reported here are mediated through ER and p53 independent mechanisms. The chemopreventive effects of genistein in vivo could be mediated along an identical or similar anti-proliferative pathway.
Airfoil performance studies with a trailing edge jet flap (2014)

This paper discusses the concept of simple blowing directly from the trailing edge of the wing of an aircraft to provide increased lift, especially during the take-off and landing maneuvers. Although a noticeable increment in coefficient of lift has been obtained to replace or even augment the effect of classic flaps, its application as a means to exert immediate and instantaneous control on stability and control would be an added benefit. Indeed, if such a concept could truly be optimized to replace the physical presence of traditional flaps in an aircraft, the benefits in weight savings and comparative simplicity in design and operational adoptability would be enormous. The jet blowing has been applied at the trailing edge of an airfoil and a 3-D wing at a variety of jet-ejection vector angles with respect to the chord line; a noticeable increase in lift has been recorded using both configurations.
V antigen-polyhistidine fusion peptide: binding to LcrH and active immunity against plague (1996)

The structural gene for V antigen (lcrV) is known to be encoded within the lcrGVH-yopBD operon of the approximately 70-kb low-calcium-response or Lcr plasmid of Yersinia pestis. This 37-kDa monomeric peptide was reported to provide active immunity in mice, suppress inflammatory cytokines, and regulate expression of the low calcium response (Lcr+). Here we describe pVHB62, encoding a polyhistidine-V antigen fusion peptide (Vh) and linked LcrH. Vh underwent degradation from both the C terminus and N terminus during classical chromatographic fractionation but remained intact within two compartments during Ni2+ affinity chromatography. The first was homogeneous, capable of active immunization (mouse intravenous 50% lethal dose, > 10(7) bacteria), and stable at 4 degrees C. The second remained bound to the affinity column but could be eluted as a mixture of Vh, LcrH, and low-molecular-weight material by application of 6 M guanidine HCl. This mixture was dialyzed, denatured in 8 M urea, and again applied to the affinity column, which then hound Vh but not LcrH. The latter was recovered and renatured, and low-molecular-weight material was removed by biochemical fractionation. The resulting homogeneous LcrH bound protein AN antigen fusion peptide but not protein A in a sandwich enzyme-linked immunosorbent assay, and this reaction was inhibited by Vh. These observations indicate that LcrH normally binds V antigen in bacterial cytoplasm and suggest that only free LcrH down-regulates expression of the low calcium response.