gebhart/patrepeval huggingface dataset:
A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E" motif. (1994)

The transposon-like elements TBE1, Tec1, and Tec2 of hypotrichous ciliated protozoa appear to encode a protein that belongs to the IS630-Tc1 family of transposases. The Anabaena IS895 transposase also is placed in this family. We note that most family members transpose into the dinucleotide target, TA, and that members with eukaryotic hosts have a tendency for somatic excision that is carried to an extreme by the ciliate elements. Alignments including the additional members, and also mariner elements, show that transposases of this family share strongly conserved residues in a large C-terminal portion, including a fully conserved dipeptide, Asp-Glu (DE), and a block consisting of a fully conserved Asp and highly conserved Glu, separated by 34 or 35 residues (D35E). This D35E motif likely is homologous to the previously characterized D35E motif of the family of retroviral-retrotransposon integrases and IS3-like transposases. Because it is known that the IS3-retroposon D35E region is a critical portion of a domain capable of various in vitro transposition-related reactions, the results suggest that the two families share homologous catalytic transposase domains and that members of both families may share a common transposition mechanism.
[Research progress on preservation of severed limbs]. (2000)

After the severed limbs are reasonably preserved, the period of replantation may be prolonged.
Ordered indium-oxide nanowire arrays and their photoluminescence properties (2001)

Ordered semiconductor In2O3 nanowire arrays are uniformly assembled into hexagonally ordered nanochannels of anodic alumina membranes (AAMs) by electrodeposition and oxidizing methods. Their microstructures were characterized by x-ray diffraction, scanning electron microscopy, and transmission electron microscopy. A blue-green photoluminescence (PL) band in the wavelength range of 300–650 nm was observed in the In2O3/AAM assembly system. The PL intensity and peak position depend on the annealing temperature, which is mainly attributed to the singly ionized oxygen vacancy in the In2O3 nanowire array system.
Three-year outcome after balloon aortic valvuloplasty. Insights into prognosis of valvular aortic stenosis. (1994)

Long-term survival after balloon aortic valvuloplasty is poor with 1- and 3-year survival rates of 55% and 23%, respectively. Although survivors report fewer symptoms, early restenosis and recurrent hospitalization are common.
Advancing high-throughput gene synthesis technology (2009)

The emerging field of synthetic biology is generating insatiable demands for synthetic genes, which far exceed existing gene synthesis capabilities. This review discusses the current methods of chemical DNA synthesis and gene assembly, as well as the latest engineering tools, technologies and trends which could potentially lead to breakthroughs in the development of accurate, low-cost and high-throughput gene synthesis technology. The capability of generating unlimited supplies of DNA molecules of any sequence or size will transform biomedical research in the near future.
Edge descriptors for robust wide-baseline correspondence (2008)

This paper describes a method for finding wide-baseline correspondences between images at locations along gradient edges. We find edges in scale space using established methods and develop invariant descriptors for these edges based on orientation and scale histograms. Because edges are often found on occluding boundaries, we calculate and store two descriptors per edge, one on each side, for robustness to occlusions. We demonstrate the effectiveness of edge matching in the applications of wide-baseline correspondence, structure from motion from line segments, and object category recognition on the Caltech 101 dataset.
A modest reduction in c-myc expression has minimal effects on cell growth and apoptosis but dramatically reduces susceptibility to Ras and Raf transformation. (2001)

Dergulation of c-myc and mutation of ras genes is commonly found in many human tumors. Several lines of evidence indicate that c-Myc and oncogenic Ras cooperate in causing malignant transformation, but the mechanism of this cooperation is not understood. We set out to investigate the effect on transformation of a modest reduction in endogenous c-Myc expression, which was achieved using a c-myc heterozygous cell line constructed by targeted homologous recombination. In contrast to previous reports where c-Myc expression or activity was ablated using antisense or dominant-defective methods, use of c-myc +/- cells provides a stable and homogeneous cell culture system with a precisely defined c-Myc expression level. In addition, this approach does not suffer from nonspecific artifacts such as antisense oligonucleotide toxicity or interference of dominant-defective proteins with multiple (and often undefined) target proteins. The striking and unexpected finding communicated here is that the relatively modest 50% reduction in c-Myc expression resulted in a greater than 10-fold reduction in susceptibility to transformation by oncogenic Ras or Raf proteins. This very significant defect in transformation potential cannot be explained on the basis of a generalized cell-cycle defect, because c-myc +/- cells exhibit only a minimal (20%) reduction in proliferation. Genetic epistasis analysis indicated that c-Myc and Ras acted by independent pathways that converged to regulate the abundance of the cyclin-dependent kinase inhibitor protein p27Kip1. Anchorage deprivation elicited a strong up-regulation of p27, and a 50% reduction in c-Myc expression significantly compromised the ability of Ras to down-regulate p27. We propose that Ras and c-Myc signals cooperate to regulate the activity of cyclin D-Cdk4/6 complexes: the former by up-regulating the expression of cyclin D1 and the latter by affecting the activity of the complexes. Ectopic expression of cyclin A restored the transformation potential of c-myc +/- cells, implicating it as a downstream genetic component in the pathway. From a therapeutic standpoint, it is of interest that, although transformation appears to be very sensitive to c-Myc expression levels, much larger reductions can be tolerated without causing any significant cell cycle defects.
Intron-exon organization of the NF-Y genes. Tissue-specific splicing modifies an activation domain. (1992)

NF-Y is a highly conserved transcription factor which recognizes CCAAT motifs in a variety of genes. We report here the genomic organization of the genes encoding both subunits, which gives interesting clues about the functional organization of the proteins. We also report the existence of isoforms of NF-YA which result from differential splicing. These alternative splicing events map within a glutamine-rich activation domain and show a marked cell- and tissue-specific bias.
Crystallization-induced asymmetric transformation: stereospecific synthesis of a potent peripheral CCK antagonist (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystallization-induced asymmetric transformation: stereospecific synthesis of a potent peripheral CCK antagonistPaul J. Reider, Paul Davis, David L. Hughes, and Edward J. J. GrabowskiCite this: J. Org. Chem. 1987, 52, 5, 955–957Publication Date (Print):March 1, 1987Publication History Published online1 May 2002Published inissue 1 March 1987https://pubs.acs.org/doi/10.1021/jo00381a052https://doi.org/10.1021/jo00381a052research-articleACS PublicationsRequest reuse permissionsArticle Views1199Altmetric-Citations77LEARN 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
Cantor network, control algorithm, two-dimensional compact structure and its optical implementation (1995)

A compact integrating module technique for packaging a optical multistage Cantor network with a polarization multiplex technique is suggested. The modules have a unique configuration, which is the solid-state combination of a polarization rotator, double birefringent slabs, and a 2 × 2 switch array. The design and the fabrication of an eight-channel optical nonblocking Cantor network are demonstrated, and a fast-setup control algorithm is developed. The network systems are easy to assemble and insensitive to environment disturbance.
Cavity QED in a molecular ion trap (2011)

We propose a class of experiments using rotational states of dipolar molecular ions trapped near an on-chip superconducting microwave cavity. Molecular ions have several advantages over neutral molecules for such cavity quantum electrodynamics experiments. In particular, ions can be loaded easily into deep rf traps and are held independent of their internal state. An analysis of the detection efficiency for, and coherence properties of, the molecular ions is presented. We discuss approaches for manipulating quantum information and performing high-resolution rotational spectroscopy using this system.
Direct measurement of mass fragmentograms for eluents from a micro‐liquid chromatograph using an improved nebulizing interface (1980)

Abstract An improved vacuum nebulizing interface with a very short counter nozzle was developed for direct coupling of a micro‐LC and a quadrupole MS with CI‐chamber. With the LC‐MS system using the nebulizing interface, it became possible to take mass fragmentograms for various less volatile compounds such as glutamic acid, steroids, aromatic amines and chlorine‐containing insecticides.
Fast and robust super-resolution (2004)

In the last two decades, many papers have been published, proposing a variety methods of multiframe resolution enhancement. These methods are usually very sensitive to their assumed model of data and noise, which limits their utility. This paper reviews some of these methods and addresses their shortcomings. We propose a different implementation using L/sub 1/ norm minimization and robust regularization to deal with different data and noise models. This computationally inexpensive method is robust to errors in motion and blur estimation, and results in sharp edges. Simulation results confirm the effectiveness of our method and demonstrate its superiority to other robust super-resolution methods.
Growth and differentiation factors: role in bone induction and potential application in craniofacial surgery. (1990)

Repair of craniofacial bone often requires autogenous or allogeneic bone. Natural materials deliver bone-inducing substances to wound beds and provide scaffolding for osteoconduction, but not without risk of morbidity. We are developing a synthetic material consisting of proteins which stimulate bone repair encased within a moldable, biodegradable delivery system. The stages of bone induction include chemoattraction of stem cells, proliferation and differentiation of these cells to competent chondrocytes and osteoblasts, angiogenesis, mineralization, and remodeling. Bovine osteogenin induces bone formation in soft tissue in rats, and accelerates bone repair in cranial defects. The protein has been purified and partially sequenced. Growth factors may augment the inductive effects of osteogenin by attracting preosteoblasts, accelerating their proliferation, and stimulating angiogenesis. A composite material of osteogenin and growth factors released from a biodegradable delivery system in a time-dependent fashion is proposed to decrease the necessity for autogenous and allogeneic bone implants.
Synthetic biology (2005)

Chemistry is a broadly powerful discipline in contemporary science because it has the ability to create new forms of the matter that it studies. By doing so, chemistry can test models that connect molecular structure to behaviour without having to rely on what nature has provided. This creation, known as 'synthesis', began to be applied to living systems in the 1980s as recombinant DNA technologies allowed biologists to deliberately change the molecular structure of the microbes that they studied, and automated chemical synthesis of DNA became widely available to support these activities. The impact of the information that has emerged has made biologists aware of a truism that has long been known in chemistry: synthesis drives discovery and understanding in ways that analysis cannot. Synthetic biology is now setting an ambitious goal: to recreate in artificial systems the emergent properties found in natural biology. By doing so, it is advancing our understanding of the molecular basis of genetics in ways that analysis alone cannot. More practically, it has yielded artificial genetic systems that improve the healthcare of some 400,000 Americans annually. Synthetic biology is now set to take the next step, to create artificial Darwinian systems by direct construction. Supported by the National Science Foundation as part of its Chemical Bonding program, this work cannot help but generate clarity in our understanding of how biological systems work.
Management of allergic rhinitis. (2004)

Rhinitis is characterised by the presence of two or more of the following symptoms: nasal blockage, sneezing, rhinorrhoea (a persistent watery mucous discharge from the nose) and nasal itching which last for an hour or more on most days. Allergy is the commonest cause of chronic symptoms. Patients with allergic rhinitis often have a clear relationship between symptoms and allergen exposure, for example, during the tree/grass pollen season. Viral or bacterial infection is the commonest acute cause of symptoms and is usually self-limiting.
Human embryonic stem cells (2000)

Embryonic stem (ES) cells are cells derived from the early embryo that can be propagated indefinitely in the primitive undifferentiated state while remaining pluripotent; they share these properties with embryonic germ (EG) cells. Candidate ES and EG cell lines from the human blastocyst and embryonic gonad can differentiate into multiple types of somatic cell. The phenotype of the blastocyst-derived cell lines is very similar to that of monkey ES cells and pluripotent human embryonal carcinoma cells, but differs from that of mouse ES cells or the human germ-cell-derived stem cells. Although our understanding of the control of growth and differentiation of human ES cells is quite limited, it is clear that the development of these cell lines will have a widespread impact on biomedical research.
A haptic model of a bone-cutting burr (2003)

We describe a strategy for collecting experimental data and validating a bone-burr haptic contact model developed in a virtual surgical training system for middle ear surgery. The validation strategy is based on the analysis of data acquired during virtual and real burring sessions. Our approach involves intensive testing of the surgical simulator by expert surgeons and trainees as well as experimental data acquisition in a controlled environment.
Calpain Upregulation in Spinal Cords of Mice with 1‐Methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP)‐induced Parkinson's Disease (2000)

1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), a heroin analogue, is a neurotoxin that undergoes in vivo oxidation by monoamine oxidase-B (MAO-B) to 1-methyl-4-phenylpyridinium ion (MPP+) which preferentially exerts its toxic effects on the dopaminergic neurons of the substantia nigra in brain. Spinal interneuronal pathways are also likely to be affected in the course of MPP+ neurotoxicity. The primary effect of MPP+ is mediated by irreversible inhibition of mitochondrial complex I, releasing free radicals. MPP+ may also activate N-methyl-D-aspartate (NMDA) receptors, increasing the cytosolic concentration of free Ca2+. Intracellular free radicals indirectly and free Ca2+ directly can activate Ca2+-dependent proteases such as calpain. We investigated involvement of calpain in spinal cord degeneration due to neurotoxin by subjecting male C57BL/6N mice (17 months old) to MPTP administration (12.5 mg/kg for 0.5 h; 25 mg/kg for 0.25 h; and 50 mg/kg for 0.25, 0.5, 1, 2, and 24 h). RT-PCR and Western blot analysis were performed using the thoracic segment of spinal cords from control and MPTP-administered mice. The administration of MPTP caused calpain upregulation at the mRNA and protein levels to various extents, compared to control mice. Calpain activity was measured by 68 kDa neurofilament protein (NFP) degradation, which was increased in MPTP-induced PD mice. These results suggest that calpain may play a role in spinal cord degeneration in mice with MPTP-induced PD.
Millimeter Wave Thickness Evaluation of Thermal Barrier Coatings (TBCs) Using Open-Ended Waveguide Probes (2023)

ABSTRACTNondestructive testing (NDT) of thermal barrier coatings (TBCs) is a critical and ongoing topic of research and development. In particular, inspection techniques that determine the thickness of ceramic topcoat and thermally grown oxide (TGO) are of interest. This work investigates the utility of open-ended rectangular waveguide probes in the millimeter wave frequency range of 26.5–110 GHz for evaluation of topcoat and TGO thicknesses through a compressive set of electromagnetic (EM) simulations. In addition, these EM simulations are used to illustrate the influence of probe size and TBC substrate curvature on the complex reflection coefficient properties and the subsequent thickness estimation. The impact of volumetric porosity level on the same is also investigated. A standing-wave probe at V-band (50–75 GHz) is constructed and used to measure the topcoat thickness on three button-type TBC samples. This probe eliminates the need for using expensive and bulky vector network analyzers (VNA), which is quite desirous from a practical point-of-view. The experimental results indicate the capability of estimating the topcoat thickness to within ±15 μm (0.6 mils).KEYWORDS: Thermal barrier coating (TBC)millimeter wave NDTopen-ended waveguideselectromagnetic modelingthickness evaluation AcknowledgmentsThis work was supported in part by the Center for Nondestructive Evaluation (CNDE) Membership Funds at Iowa State University (ISU). The authors wish to thank Mr Aaron McCarville for assisting with the measurements.Disclosure statementNo potential conflict of interest was reported by the author(s).
Effect of Hf metal predeposition on the properties of sputtered HfO2/Hf stacked gate dielectrics (2002)

The electrical and physical properties of reactively sputtered HfO2 thin films on predeposited Hf metal layer were investigated. Compared with a conventional deposition process, i.e., direct deposition of HfO2 on a Si substrate, the HfO2/Hf stacked capacitor exhibits excellent electrical characteristics such as capacitance equivalent thickness (CET) as thin as 1.3 nm with lower leakage current of 2×10−5 (A/cm2) at −1 V gate bias. Based on the structural analysis as well as the electrical characteristics, the interfacial layer thickness is found to be controllable with minimum CET and higher permittivity by optimizing the thickness ratio between HfO2 and Hf. This improvement in electrical characteristics can be explained by the blocking of oxygen diffusion through HfO2 films into the Si substrate due to oxidation of the Hf metal layer itself.
Improved detection of nitric oxide radical (NO•) production in an activated macrophage culture with a radical scavenger, car☐y PTIO, and Griess reagent (1995)

An improved method for the detection of nitric oxide radicals (NO. in cultures of activated macrophages was developed, involving a nitric oxide radical scavenger, 2-(4-carboxyphenyl)-4,4,5,5- tetramethylimidazoline-3-oxide-1-oxyl (carboxy PTIO) and Griess reagent. A murine macrophage-like cell line, J774.1, was activated with interferon-gamma (IFN-gamma) and bacterial lipopolysaccharide (LPS), which induced the production and secretion of NO2- into the culture supernatant. Addition of carboxy PTIO to the activated macrophages increased the amount of NO2- to 4- to 5-fold without cell damages, probably because carboxy PTIO rapidly reacted with NO. to form NO2-, which was finally assayed by the Griess reaction.
A recombinant minigene vaccine containing a nonameric cytotoxic-T-lymphocyte epitope confers limited protection against Listeria monocytogenes infection (1996)

We have previously shown that vaccines expressing virus-derived cytotoxic-T-lymphocyte (CTL) epitopes as short minigenes can confer effective protection against virus challenges, and here we extend these studies to the bacterium Listeria monocytogenes. Host defense against this important human pathogen appears largely T cell mediated, and a nonamer CTL epitope from the listeriolysin O (LLO) protein has been identified in BALB/c mice. We have synthesized this nonamer as a minigene, expressed it in a recombinant vaccinia virus (VV-list), and used this to immunize mice. Memory CTLs cultured from VV-list-immunized mice specifically lyse target cells pulsed with a nonamer peptide identified at LLO amino acid residues 91 to 99. Four weeks postimmunization, mice were challenged with L. monocytogenes. By day 6 following challenge with a sublethal dose of L. monocytogenes, mice immunized with VV-list showed a approximately 2,000- to 6,000-fold reduction in bacteria CFU in the spleen and liver. At this time point, with control mice, bacterial were readily detectable by Gram stain of the liver but were undetectable in the VV-list-immunized animals. Additionally, when a normally lethal dose of bacteria was given, death was delayed in VV-list-immunized animals. This study has demonstrated that a single immunization with a recombinant vaccinia virus bearing only nine amino acids from a bacterial pathogen can induce specific CTLs able to confer partial protection against bacterial challenge.
Development of a Bacteria-Independent Model of the Multiple Organ Failure Syndrome (1989)

Criteria that allow definition of the multiple organ failure syndrome include pulmonary, hepatic, renal, and gut barrier dysfunction along with characteristic histopathologic changes. It has been difficult to study multiple organ failure due to lack of a satisfactory experimental model that would reproduce the pathophysiologic and histopathologic characteristics, would be stable enough to allow study over several days, and would be free of exogenous primary bacterial infection. We have studied pathophysiologic and histopathologic alterations in a potential model of multiple organ failure. Wistar rats received one of the following solutions by intraperitoneal injection: 4 mL of saline, 4 mL of mineral oil, or 1 mg per gram of body weight of zymosan A in 4 mL of mineral oil. Animals that received zymosan developed hypoxia, decreased creatinine clearance, and changes in hepatic microsomal cytochrome P450 content and aniline hydroxylase activity. Bacterial translocation occurred in the zymosan group. The lungs, liver, and kidneys of the animals that received zymosan exhibited histopathologic changes. We conclude that this model fulfills our criteria for a model of multiple organ failure.