gebhart/patrepeval huggingface dataset:
3-D sequence interpretation of seismic instantaneous attributes from the Gorgon Field (1998)

Michaelangelo once described the act of sculpting as simply freeing the form he saw locked inside a block of marble. Increasingly, geoscientists are viewing their interpretation work with 3-D seismic data volumes in somewhat the same manner. So much information is locked inside our data, we have only to free it with the right tools. A profusion of seismic attributes has been defined in the past decade, challenging the intrepid interpreter with many problems; foremost is understanding what these attributes mean as well as working efficiently with multiple displays of the same data volume.
Translocation-Specific Conformation of Adenylate Cyclase Toxin from Bordetella pertussis Inhibits Toxin-Mediated Hemolysis (2001)

Bordetella pertussis adenylate cyclase (AC) toxin belongs to the RTX family of toxins but is the only member with a known catalytic domain. The principal pathophysiologic function of AC toxin appears to be rapid production of intracellular cyclic AMP (cAMP) by insertion of its catalytic domain into target cells (referred to as intoxication). Relative to other RTX toxins, AC toxin is weakly hemolytic via a process thought to involve oligomerization of toxin molecules. Monoclonal antibody (MAb) 3D1, which binds to an epitope (amino acids 373 to 399) at the distal end of the catalytic domain of AC toxin, does not affect the enzymatic activity of the toxin (conversion of ATP into cAMP in a cell-free system) but does prevent delivery of the catalytic domain to the cytosol of target erythrocytes. Under these conditions, however, the ability of AC toxin to cause hemolysis is increased three- to fourfold. To determine the mechanism by which the hemolytic potency of AC toxin is altered, we used a series of deletion mutants. A mutant toxin, DeltaAC, missing amino acids 1 to 373 of the catalytic domain, has hemolytic activity comparable to that of wild-type toxin. However, binding of MAb 3D1 to DeltaAC enhances its hemolytic activity three- to fourfold similar to the enhancement of hemolysis observed with 3D1 addition to wild-type toxin. Two additional mutants, DeltaN489 (missing amino acids 6 to 489) and DeltaN518 (missing amino acids 6 to 518), exhibit more rapid hemolysis with quicker onset than wild-type toxin does, while DeltaN549 (missing amino acids 6 to 549) has reduced hemolytic activity compared to wild-type AC toxin. These data suggest that prevention of delivery of the catalytic domain or deletion of the catalytic domain, along with additional amino acids distal to it, elicits a conformation of the toxin molecule that is more favorable for hemolysis.
Specimen Preparation for Transmission Electron Microscopy of Materials (1988)

The view of species as entities subjected to natural selection and amenable to change put forth by Charles Darwin and Alfred Wallace laid the conceptual foundation for understanding speciation. Initially marred by a rudimental understanding of hereditary principles, evolutionists gained appreciation of the mechanistic underpinnings of speciation following the merger of Mendelian genetic principles with Darwinian evolution. Only recently have we entered an era where deciphering the molecular basis of speciation is within reach. Much focus has been devoted to the genetic basis of intrinsic postzygotic isolation in model organisms and several hybrid incompatibility genes have been successfully identified. However, concomitant with the recent technological advancements in genome analysis and a newfound interest in the role of ecology in the differentiation process, speciation genetic research is becoming increasingly open to non-model organisms. This development will expand speciation research beyond the traditional boundaries and unveil the genetic basis of speciation from manifold perspectives and at various stages of the splitting process. This review aims at providing an extensive overview of speciation genetics. Starting from key historical developments and core concepts of speciation genetics, we focus much of our attention on evolving approaches and introduce promising methodological approaches for future research venues.
Purification and characterization of a protein-tyrosine kinase from bovine thymus. (1986)

A protein-tyrosine kinase has been isolated from a soluble extract of bovine thymus based on its ability to phosphorylate the tyrosine-containing peptide angiotensin I. The purification procedure employs sequential chromatography on columns of DEAE-cellulose, heparin-agarose, casein-agarose, butyl-agarose, and Sephadex G-75. The purified enzyme (p40) is a monomer of Mr = 40,000. The p40 kinase contains an ATP-binding site as determined by photoaffinity labeling experiments and catalyzes an intramolecular autophosphorylation reaction that leads to its modification on tyrosine. Of several proteins tested only the cytoplasmic domain of the erythrocyte band 3 protein serves as a good substrate for p40 (Km = 12 microM). Increasing concentrations of NaCl stimulate the phosphorylation of angiotensin I, inhibit the phosphorylation of band 3, and have no effect on the autophosphorylation of p40. At low concentrations of NaCl, Mn2+ is the preferred divalent cation. Peptide mapping experiments indicate that p40 is distinct from pp60src and from the major phosphotyrosine containing proteins of T and B lymphocyte membranes.
Cooperation between Wnt and Notch signalling in human breast cancer (2007)

The Wnt and Notch signalling pathways play major roles in mammary gland development and tumourigenesis. During development, these pathways have opposing effects. However, in a recent paper Ayyanan and coworkers show that expression of Wnt1 is sufficient to transform primary human mammary epithelial cells, and that this is in part due to activation of the Notch pathway. This indicates that during tumourigenesis the two pathways cooperate. Here we ask why activation of Wnt signalling alone is sufficient to cause transformation; whether there is evidence for inhibitory crosstalk between the pathways during tumourigenesis; and whether cooperation between these pathways occurs in other forms of cancer.
Stereo video inpainting (2011)

As the production of stereoscopic content increases, so does the need for post-production tools for that content. Video inpainting has become an important tool for rig removal but there has been little consideration of the problem in stereo. This paper presents an algorithm for stereo video inpainting that builds on existing exemplar-based video completion and also considers the issues of view consistency. Given user selected regions in the sequence which may be in the same location in several frames and in both views, the objective is to fill in this area using all the available picture information. Existing algorithms lack temporal consistency, causing flickering and other artefacts. This paper explores the use of long-term picture information across many frames in order to achieve temporal consistency at the same time as exploiting inter-view dependencies within the same framework.
Neurogenesis in the 3‐month‐old rat visual cortex (1981)

Newly formed neurons in the adult mammalian neocortex have been reported by several investigators using light microscopic radioautography, but these reports have not been confirmed by electron microscopy--probably because their rarity precludes any reasonable chance of observing these cells with electron microscopic radioautography. To overcome this problem I have used a recently developed method that allows serial thin sectioning and subsequent electron microscopic examination of plastic-embedded sections previously prepared for light microscopic radioautography. Ninety-day-old rats were injected with 4.3 microCi per gm body weight of [H3] thymidine and allowed to survive for 30 days. In the light radioautographs, labeled cells were found in layer IV of the visual cortex, and analysis of electron micrographs of selected examples of these labeled cells clearly demonstrated their neuronal nature wit synapses along their cell bodies and dendrites. In order to quantify the relative frequency of labeled neurons, the number of labeled cells seen in the light microscopic sections was expressed as a percentage of the total number of neurons found in sections through the entire thickness of the visual cortex; the percentage was 0.011%, or about 1 in 10,000. The results of this study are in agreement with evidence of neurogenesis of granular neurons in the adult rat olfactory bulb and dentate gyrus (Kaplan and Hinds, '77). Thus, it has now been confirmed that relatively small labeled neurons and their synapses are found in at least 3 brain regions (olfactory bulb, dentate gyrus, and visual cortex) in a normal adult rodent.
Early Delineation of Ischemic Tissue in Rat Brain Cryosections by High-Contrast Staining (1999)

In contrast to other staining methods, SIS allows a reliable delineation of ischemic brain tissue (core plus penumbra) from nonischemic white and gray matter of rat brain cryosections as soon as 2 hours after MCAO.
Iterated WKB method of normalization and phase shifts of the nonrelativistic continuum wave function (1993)

In this paper, we discuss the normalization of nonrelativistic continuum wave functions by using an iterated WKB method and suggest a numerical procedure of evaluating the phase shifts of the continuum wave functions. To illustrate the efficiency and accuracy of the procedure, we calculate the phase shifts of a free electron in the ``polarization'' Yukawa potential. The results are in very good agreement with other exact values. The hybrid grid mesh \ensuremath{\rho}=\ensuremath{\alpha}r+\ensuremath{\beta} ln(Zr), which is appropriate to the computation of continuum wave functions, is used in the calculation.
Modulation of Hepatitis C Virus RNA-dependent RNA Polymerase Activity by Structure-based Site-directed Mutagenesis (2002)

The hepatitis C virus (HCV) encodes an RNA-dependent RNA polymerase (NS5B), which is indispensable for the viral genome replication. Although structural comparison among HCV NS5B, poliovirus 3D-pol, and human immunodeficiency virus-reverse transcriptase RNA-dependent polymerase reveals the canonical palm, fingers, and thumb domains, the crystal structure of HCV NS5B highlights the presence of a unique A1-loop, which extends from the fingers to the thumb domain (amino acids 12-46), providing many contact points for the proposed "closed" conformation of the enzyme. The polymerase also possesses a tunnel, which starts at the active site and terminates on the back surface of the enzyme. This tunnel of 19 A contains five basic amino acids, which may be engaged in NTP trafficking. In the present study, we exploited the crystal structure of the enzyme to elucidate the involvement of these two structural motifs in enzyme activity by site-directed mutagenesis. As predicted, the replacement of leucine 30 located in the Lambda 1-loop is detrimental to the NS5B activity. Heparin-Sepharose column chromatography and analytical ultracentrifugation experiments strongly suggest a local alteration in the structure of the Leu-30 mutant. An analysis of amino acid substitutions in Arg-222 and Lys-151 within the putative NTP tunnel indicates that Arg-222 was critical in delivering NTPs to the active site, whereas Lys-151 was dispensable. Interestingly, the substitution of lysine 151 for a glutamic acid resulted in an enzyme that was consistently more active in de novo synthesis as well as by "copy-back" mechanism of a self-primed substrate when compared with the wild type NS5B enzyme. Burst kinetic analyses indicate that the gain in function of K151E enzyme was primarily the result of the formation of more productive pre-initiation complexes that were used for the elongation reaction. In contrast to the recent observations, both the wild type and mutant enzymes were monomeric in solution, whereas molecules of higher order were apparent in the presence of RNA template.
CS-1 Re-Directed Central Memory T Cell Therapy for Multiple Myeloma (2014)

Abstract Multiple myeloma (MM), a plasma cell malignancy, accounts for approximately 1 percent of all cancers and slightly more than 10 percent of hematologic malignancies in the United States. Approximately 20,000 new cases will be diagnosed this year and over 11,000 people will die from this disease. Current therapies for MM often induce remission, but nearly all patients eventually relapse and die. T-cell mediated anti-tumor therapies using genetically modify T cells with specific chimeric antigen receptors (CARs) have non-overlapping activity, toxicity and tumor resistance profiles compared to conventional chemotherapeutic agents. The main challenge in designing a CAR T cell immunotherapeutic approach is identifying the best antigen for tumor targeting. CS-1 is a cell surface glycoprotein of the signaling lymphocyte activation molecule (SLAM) receptor family that is highly and selectively expressed on normal plasma cells and MM cells, with lower expression on NK cells and little or no expression on normal tissues. This unique expression pattern and proven clinical benefit of CS-1 monoclonal antibody for the treatment of relapsed MM makes CS-1 a good target for CAR T cell therapy. Central memory T cells (TCM) from PBMC were isolated using a two-step process on the AutoMACS device to first deplete CD14+, CD45RA+ and CD25+ cells, then to positively select CD62L+ cells. These TCM undergo anti-CD3/CD28 bead stimulation and transduction with a lentiviral vector encoding CS-1 CAR containing a CD28 co-stimulatory domain and two mutations on IgG4 linker CH-2 portion to ensure enhanced potency and persistence after adoptive transfer. Gene modified CS-1 CAR T cells specifically lysed MM.1S, a MM cell line, in 4-hour 51Cr release assays and all the CAR+ cells expressed 107a upon co-cultured with the MM.1S cells. To investigate the potency of the CS-1CAR T cells, 2x106 MM.1S cells that were engineered to express GFP firefly luciferase were inoculated into NSG mice by tibia injection. 7 days post tumor engraftment, 1x106 CS-1 CAR T cells were intravenously injected into the tumor bearing mice. In contrast to untreated and mock cell treated mice in which tumor progressed rapidly systemically, single intravenous infusion of CS-1 CAR T cells induced dramatic tumor regression and significantly prolonged survival. In addition to CS-1, CD44v6 and BCMA are antigens that have also been shown to be over-expressed on MM tumor cells. We therefore compared the two CARs with CS-1 CAR for their anti-MM activity. Based on our studies, targeting CS-1 resulted in the best efficacy (Figure 1) and would be an attractive strategy for development of a clinical trial. Disclosures No relevant conflicts of interest to declare.
Guest Editor's Introduction (1996)

China's economy has been booming since the beginning of the economic reform in the late 1970s. Between 1978 and 1995, the gross domestic product (GDP) of China grew at an average annual rate of 9.8 percent (see Chen, this issue). If this trend continues, as many analysts have projected, China could overtake the United States and Japan to become the world's largest economy some time between 2020 and 2030.
Mail-order microfluidics: evaluation of stereolithography for the production of microfluidic devices (2014)

The vast majority of microfluidic devices are developed in PDMS by molding ("soft lithography") because PDMS is an inexpensive material, has physicochemical properties that are well suited for biomedical and physical sciences applications, and design cycle lengths are generally adequate for prototype development. However, PDMS molding is tediously slow and thus cannot provide the high- or medium-volume production required for the commercialization of devices. While high-throughput plastic molding techniques (e.g. injection molding) exist, the exorbitant cost of the molds and/or the equipment can be a serious obstacle for device commercialization, especially for small startups. High-volume production is not required to reach niche markets such as clinical trials, biomedical research supplies, customized research equipment, and classroom projects. Crucially, both PDMS and plastic molding are layer-by-layer techniques where each layer is produced as a result of physicochemical processes not specified in the initial photomask(s) and where the final device requires assembly by bonding, all resulting in a cost that is very hard to predict at the start of the project. By contrast, stereolithography (SL) is an automated fabrication technique that allows for the production of quasi-arbitrary 3D shapes in a single polymeric material at medium-volume throughputs (ranging from a single part to hundreds of parts). Importantly, SL devices can be designed between several groups using CAD tools, conveniently ordered by mail, and their cost precisely predicted via a web interface. Here we evaluate the resolution of an SL mail-order service and the main causes of resolution loss; the optical clarity of the devices and how to address the lack of clarity for imaging in the channels; and the future role that SL could play in the commercialization of microfluidic devices.
Preparation of Silicon-CNT (Carbon Nano Tube) Composites for Anode in Lithium Secondary Batteries (2006)

Abstract not Available.
Direct observation of electron emission site on boron-doped polycrystalline diamond thin films using an ultra-high-vacuum scanning tunneling microscope (1999)

Surface morphology characteristics and electron emission properties of boron-doped polycrystalline diamond thin films grown by microwave plasma-assisted chemical-vapor deposition were investigated using an ultra-high-vacuum scanning tunneling microscope. Small secondary grains with average size less than 10 nm were observed to be on top of the isolated crystal surfaces. The current imaging tunneling spectroscopy (CITS) study revealed that high electron emission occurred at some crystalline facets while others showed relatively no measurable electron emission. The CITS study at high magnification also indicated that the electron emission was initiated at the grain boundaries rather than at the top of the grains. This observation suggests that the electrons transport through the grain-boundary conductive channels and preferentially emit at the low electron affinity facets.
Clinical pharmacology of nabilone, a cannabinol derivative (1975)

Nabilone is a modified cannabinol derivative with central nervous system activity. Administration of nabilone in single doses of 1 to 5 mg results in dose-related pharmacologic effects in man. One and 2.5 mg doses of nabilone induced relaxant and sedative effects in all subjects. No euphoria, dry mouth, tachycardia, or postural hypotension was seen after 1 mg, minimal effects were seen after 2.5 mg, and marked effects were seen after 5 mg. Effects were evident within 60 to 90 min and persisted for 8 to 12 hr. Nabilone produced no significant tachycardia. There were no changes in supine blood pressure; however, marked postural hypotension occurred after the 5-mg dose. The administration of nabilone at doses of 1 mg or 2 mg two times daily resulted in euphoria and dry mouth during the first two days of drug; thereafter tolerance developed to these effects but there was no apparent decrease in relaxation. Subjects challenged with a single 5-mg dose of nabilone showed a 66% reduction in symptoms and signs after the 7-day drug period compared to that of the same dose after 1 wk of placebo. Comparison of nabilone with other cannabinol derivatives suggests that some of the undesirable pharmacologic effects can be separated within the group.
Characterization of Structure and Cellular Components of Aspirated and Excised Adipose Tissue (2009)

The authors' results indicate the differential structure and cellular composition of the two tissues, and significant tissue damage and progenitor yield deficiency in aspirated adipose tissue.
Determining the Resolution Limits of Electron-Beam Lithography: Direct Measurement of the Point-Spread Function (2014)

One challenge existing since the invention of electron-beam lithography (EBL) is understanding the exposure mechanisms that limit the resolution of EBL. To overcome this challenge, we need to understand the spatial distribution of energy density deposited in the resist, that is, the point-spread function (PSF). During EBL exposure, the processes of electron scattering, phonon, photon, plasmon, and electron emission in the resist are combined, which complicates the analysis of the EBL PSF. Here, we show the measurement of delocalized energy transfer in EBL exposure by using chromatic aberration-corrected energy-filtered transmission electron microscopy (EFTEM) at the sub-10 nm scale. We have defined the role of spot size, electron scattering, secondary electrons, and volume plasmons in the lithographic PSF by performing EFTEM, momentum-resolved electron energy loss spectroscopy (EELS), sub-10 nm EBL, and Monte Carlo simulations. We expect that these results will enable alternative ways to improve the resolution limit of EBL. Furthermore, our approach to study the resolution limits of EBL may be applied to other lithographic techniques where electrons also play a key role in resist exposure, such as ion-beam-, X-ray-, and extreme-ultraviolet lithography.
Geothermal technology development at Sandia (1987)

Geothermal technology development at Sandia consists of work in two major project areas - Hard Rock Penetration and Magma Energy Extraction. The Hard Rock Penetration Program is directed at reducing drilling costs for geothermal wells. Current activities are focused in three areas: borehole mechanics, rock penetration mechanics, and industry cost-shared research. The Magma Energy Extraction Program is investigating the engineering feasibility of utilizing crustal magma bodies as a source of energy. Work is divided into four major areas: geophysics, geochemistry/materials, drilling, and energy extraction.
A recursive algebra and query optimization for nested relations (1989)

The nested relational model provides a better way to represent complex objects than the (flat) relational model, by allowing relations to have relation-valued attributes. A recursive algebra for nested relations that allows tuples at all levels of nesting in a nested relation to be accessed and modified without any special navigational operators and without having to flatten the nested relation has been developed. In this algebra, the operators of the nested relational algebra are extended with recursive definitions so that they can be applied not only to relations but also to subrelations of a relation. In this paper, we show that queries are more efficient and succinct when expressed in the recursive algebra than in languages that require restructuring in order to access subrelations of relations. We also show that most of the query optimization techniques that have been developed for the relational algebra can be easily extended for the recursive algebra and that queries are more easily optimizable when expressed in the recursive algebra than when they are expressed in languages like the non-recursive algebra.
Molecular Mechanisms of Axon Guidance (2002)

Axons are guided along specific pathways by attractive and repulsive cues in the extracellular environment. Genetic and biochemical studies have led to the identification of highly conserved families of guidance molecules, including netrins, Slits, semaphorins, and ephrins. Guidance cues steer axons by regulating cytoskeletal dynamics in the growth cone through signaling pathways that are still only poorly understood. Elaborate regulatory mechanisms ensure that a given cue elicits the right response from the right axons at the right time but is otherwise ignored. With such regulatory mechanisms in place, a relatively small number of guidance factors can be used to generate intricate patterns of neuronal wiring.