gebhart/patrepeval huggingface dataset:
Manipulating corn germplasm to increase recombinant protein accumulation (2011)

Using plants as biofactories for industrial enzymes is a developing technology. The application of this technology to plant biomass conversion for biofuels and biobased products has potential for significantly lowering the cost of these products because of lower enzyme production costs. However, the concentration of the enzymes in plant tissue must be high to realize this goal. We describe the enhancement of the accumulation of cellulases in transgenic maize seed as a part of the process to lower the cost of these dominant enzymes for the bioconversion process. We have used breeding to move these genes into elite and high oil germplasm to enhance protein accumulation in grain. We have also explored processing of the grain to isolate the germ, which preferentially contains the enzymes, to further enhance recovery of enzyme on a dry weight basis of raw materials. The enzymes are active on microcrystalline cellulose to release glucose and cellobiose.
DISN: Deep Implicit Surface Network for High-quality Single-view 3D Reconstruction (2019)

Reconstructing 3D shapes from single-view images has been a long-standing research problem. In this paper, we present DISN, a Deep Implicit Surface Network which can generate a high-quality detail-rich 3D mesh from an 2D image by predicting the underlying signed distance fields. In addition to utilizing global image features, DISN predicts the projected location for each 3D point on the 2D image, and extracts local features from the image feature maps. Combining global and local features significantly improves the accuracy of the signed distance field prediction, especially for the detail-rich areas. To the best of our knowledge, DISN is the first method that constantly captures details such as holes and thin structures present in 3D shapes from single-view images. DISN achieves the state-of-the-art single-view reconstruction performance on a variety of shape categories reconstructed from both synthetic and real images. Code is available at https://github.com/xharlie/DISN The supplementary can be found at https://xharlie.github.io/images/neurips_2019_supp.pdf
Evolution of Mutation Rates: Phylogenomic Analysis of the Photolyase/Cryptochrome Family (2009)

Photoreactivation, one of the first DNA repair pathways to evolve, is the direct reversal of premutagenic lesions caused by ultraviolet (UV) irradiation, catalyzed by photolyases in a light-dependent, single-enzyme reaction. It has been experimentally shown that photoreactivation prevents UV mutagenesis in a broad range of species. In the absence of photoreactivation, UV-induced photolesions are repaired by the more complex and much less efficient nucleotide excision repair pathway. Despite their obvious beneficial effects, several lineages, including placental mammals, lost photolyase genes during evolution. In this study, we ask why photolyase genes have been lost in those lineages and discuss the significance of these losses in the context of the evolution of the genomic mutation rates. We first perform an extensive phylogenomic analysis of the photolyase/cryptochrome family, to assess what species lack each kind of photolyase gene. Then, we estimate the ratio of nonsynonymous to synonymous substitution rates in several groups of photolyase genes, as a proxy of the strength of purifying natural selection, and we ask whether less evolutionarily constrained photolyase genes are more likely lost. We also review functional data and compare the efficiency of different kinds of photolyases. We find that eukaryotic photolyases are, on average, less evolutionarily constrained than eubacterial ones and that the strength of natural selection is correlated with the affinity of photolyases for their substrates. We propose that the loss of photolyase genes in eukaryotic species may be due to weak natural selection and may result in a deleterious increase of their genomic mutation rates. In contrast, the loss of photolyase genes in prokaryotes may not cause an increase in the mutation rate and be neutral in most cases.
Morphologies of Bottle-Brush Block Copolymers (2014)

We investigate the self-assembly of bottle-brush block copolymers into well-defined periodic morphologies by using molecular dynamics simulations of a bead-spring model. The microphase separation is driven by the chemical incompatibility between the different blocks of side chains leading to the formation of two- and three-domain lamellae and hexagonally packed cylinders. The molecular asymmetry required for the formation of cylindrical domains is not introduced by the difference in volume fractions, but by the asymmetry of the side chain lengths. Such behavior deviates significantly from what is typically known for linear block copolymers. The obtained morphology maps provide a genuine way of understanding the role of molecular architecture in achieving experimentally desired structures for nanoporous and photonic materials based on the self-assembly of bottle-brush block copolymers.
Configuring Networks and Devices with Simple Network Management Protocol (SNMP) (2003)

This document is written for readers interested in the Internet Standard Management Framework and its protocol, the Simple Network Management Protocol (SNMP).In particular, it offers guidance in the effective use of SNMP for configuration management.This information is relevant to vendors that build network elements, management application developers, and those that acquire and deploy this technology in their networks.
Monster Trucks on the Go (2017)

This book outlines what a monster truck is, who can drive a monster truck, what the monster truck stadiums are like, and how the racing works. Even at such a simple level of understanding, the reader is taught the multi-faceted elements of monster trucks. All the facts presented in this book are easy to understand and make it an exciting read for those with a zeal for engines and trucks. There is a glossary at the end explaining each "big word" with pictures. Monster Trucks on the Go is the perfect book for any child with an interest in any type of machinery. Big photographs of trucks, drivers, and stadiums are included on every page to allow even the youngest child a good experience with this book. It is a great resource for parents who have children interested in monster trucks, but may not live close enough to experience an actual event. Additionally, parents whose children struggle with reading, but find this topic interesting, may become motivated to read independently. Overall, readers will love this book!
Antibiotic elution profile and physical properties of a novel calcium phosphate cement material (2016)

Calcium phosphate cement (CPC) is an injectable, self-setting artificial bone material that has recently been used as a drug delivery system for bone infection therapy because of its high capacity for antibiotic elution. Despite this advantageous property, the mechanical strength of CPC dramatically decreases upon impregnation with certain types of antibiotics. A novel CPC material (CPC-A) with four-fold higher initial compression strength than that of conventional CPC (CPC-B) was developed by decreasing the median particle size of alpha-tricalcium phosphate powder in CPC from 6.34 to 2.30 µm. However, the elution profile and mechanical strength of the material following antibiotic impregnation remain unclear. In the present study, we compared the elution profiles and physical properties of CPC-A and CPC-B impregnated with vancomycin hydrochloride (VCM) and gentamicin sulfate (GM). CPC-A showed 3.6-fold higher initial (1 h after hardening) compression strength than CPC-B, even when impregnated with VCM. Scanning electron microscopy and porosimetry analyses revealed that the high compression strength of CPC-A was attributable to the densely arranged micro-porous structure. The small pores, which had a median size of 11.3 nm and served as passages for antibiotic elution, reduced the VCM elution rate and promoted long-term (18-week) antibiotic release compared to CPC-B, which contained larger pores (19.6 nm) and did not release VCM beyond 16 weeks. In contrast to VCM, GM impregnation did not markedly affect the compression strength of either material, and the GM elution profiles from CPC-A and CPC-B were nearly identical throughout the measurement period. Taken together, these findings demonstrate that the novel CPC material CPC-A has higher initial compression strength than conventional CPC and the potential for prolonged antibiotic release, suggesting that CPC-A would be an effective bone substitute material, particularly for bone infection therapy.
The design and evolution of the UberBake light baking system (2020)

We describe the design and evolution of UberBake, a global illumination system developed by Activision, which supports limited lighting changes in response to certain player interactions. Instead of relying on a fully dynamic solution, we use a traditional static light baking pipeline and extend it with a small set of features that allow us to dynamically update the precomputed lighting at run-time with minimal performance and memory overhead. This means that our system works on the complete set of target hardware, ranging from high-end PCs to previous generation gaming consoles, allowing the use of lighting changes for gameplay purposes. In particular, we show how to efficiently precompute lighting changes due to individual lights being enabled and disabled and doors opening and closing. Finally, we provide a detailed performance evaluation of our system using a set of production levels and discuss how to extend its dynamic capabilities in the future.
Transmission electron microscopic observations of membrane effects of antibiotic cecropin B on <i>Escherichia coli</i> (2003)

Abstract The pathway of cell membrane lysis by the peptide antibiotic cecropin B (CB), which contains both a hydrophobic and an amphipathic α‐helix, was analysed by assessing the morphological changes of Escherichia coli following treatment with the peptide. Exposure of green fluorescent protein (GFP)‐expressing E. coli to CB does not lead to an efflux of GFP. Moreover, transmission electron microscopic (TEM) examination of cecropin B‐treated cells showed that severe swelling precedes cell death and that the outer membrane becomes distended away from the plasma membrane. Using immuno‐gold staining and TEM of E. coli expressing the maltose‐binding protein in the cytoplasm, it was apparent that the protein remains restricted to the cytoplasmic compartment. These observations suggest that CB causes gross disruption of the outer membrane of Gram‐negative bacteria. Circular dichroism measurements of CB in the presence of cell membrane‐mimicking liposomes showed that CB forms secondary structure dependent on the ratio of [lipid]/[peptide]. These observations from this study are important for the future design of custom antimicrobial peptides. Microsc. Res. Tech. 62:423–430, 2003. © 2003 Wiley‐Liss, Inc.
Synthesis of 3-substituted pyrazolo(1,5-a)pyridine derivatives with inhibitory activity on platelet aggregation. II. (1986)

The structure-activity relationship of 3-(p-substituted benzoyl)pyrazolo[1, 5-a]pyridine derivatives as inhibitors of rabbit platelet aggregation in vitro have been examined. The cluster analysis approach to hte selection of substituents on the phenyl ring of 2-isopropyl-3-(p-substituted benzoyl)pyrazolo[1, 5-a]pyridine was used, and the effect of substituents was investigated by quantitative regression analysis. The p-dimethylamino group was found to be the most effective p-substituent on the phenyl ring for antiaggregant activity.
Index-guided operation in narrow stripe InGaAs-GaAs strained-layer quantum well heterostructure lasers by MeV oxygen implantation (1991)

Stable index-guided operation of variable stripe strained-layer InGaAs-GaAs-AlGaAs lasers achieved by MeV oxygen implantation-induced disorder of the active region is demonstrated. Well-behaved near- and far-field patterns for lasers implanted with 5×1016 cm−2 and 1×1017 cm−2 oxygen are observed to be stable with increasing drive current. Comparison with unimplanted, oxide-defined stripe lasers fabricated from the same wafer indicates a dramatic improvement in emission characteristics as a result of the presence of a lateral real-index waveguide in the oxygen-disordered regions which is stronger than the carrier-induced antiguide present in unimplanted InGaAs-GaAs strained-layer lasers.
<title>Novel technique for fabrication of multi-layered microcoils in microelectromechanical systems (MEMS) applications</title> (2002)

A novel planarization technique, compressive molding planarization (CMP) is developed for implementation of a multi-layered micro coil device. Applying CMP and other micromachining techniques, a multi-layered micro coil device has been designed and fabricated, and its use in the magnetic micro actuators for hard disk drive applications has been demonstrated, showing that it can produce milli-Newton of magnetic force suitable for driving a micro actuator. The novel CMP technique can be equally applicable in other MEMS devices fabrication to ease the process integration for the complicated structure.
Fluorescence properties of autofluorescent granules generated by cultured human RPE cells. (1998)

Autofluorescent granules accumulated in cultured RPE cells, regardless of the presence of an exogenous substrate or the nature of the substrate. The rate of accumulation of autofluorescent granules was greatest in cells fed ROS. The autofluorescent material generated in cultured RPE cells had some spectral similarities with RPE lipofuscin but differed in solubility and chromatographic mobility of their constituent fluorophores. CONCLUSIONS. The autofluorescent granules generated by cultured RPE, even with different specific substrates, differ from lipofuscin granules in vivo, suggesting that additional properties of RPE cells or of the materials they phagocytose are required to produce autofluorescent materials with the characteristics of lipofuscin.
Cover Picture: Nanoparticle PCR: Nanogold‐Assisted PCR with Enhanced Specificity (Angew. Chem. Int. Ed. 32/2005) (2005)

Favorable binding of gold nanoparticles to single‐stranded DNA decreases the likelihood of mispair formation during annealing and clearly increases the specificity and yield of PCR, one of the most important standard methods of molecular biology. In their Communication on pp. 5100 ff., Z. Zhang, C. Fan, J. Hu, and co‐workers report on this promising field of biotechnology. (Xiaobin Wang assisted in the production of this image.)
Impact of Ozone Depletion on Skin Cancers (1988)

Because of recent growth in the uses and production of certain chlorofluorocarbon compounds, the ozone layer is at risk of diminishing. The major effect of a decrease in ozone will be an increase in the amount of UV-B radiation in sunlight. Even a small increase in UV-B radiation will almost certainly affect human health. The most obvious effect of increased UV-B radiation will be an increase in the incidence of basal and squamous cell carcinomas. Other possible effects include a contribution to the development of cutaneous melanoma, ocular changes leading to the formation of cataracts, and immunologic perturbations.
DEVELOPMENT OF HIGH SPEED OPTICAL LAN FOR IN-VEHICLE SYSTEM (1997)

In-vehicle information systems, which include car navigation systems, emergency, and information services, are progressing to the stage of diversified features and higher performance wherein the rapid evolution of in-vehicle consumer devices, particularly DVD and DVD-ROM, has created new requirements for a high-speed in-vehicle LAN to accommodate the installation of a wide range of in-vehicle electronics. This paper describes the High Speed Optical LAN (HSO LAN) for in-vehicle systems which provides high speed transmission and offers excellent EMI characteristics. The HSO LAN uses a newly developed protocol, plastic optical fiber (POF), and a burst mode operation optical transceiver. The HSO LAN transfers asynchronous data (equipment control data), bulk data (CD ROM data as digital map data), and isochronous data (audio and video data). The transfer rate of the HSO LAN is 54Mbps. Thus, it provides the backbone for the multimedia systems in the car. For the covering abstract, see IRRD 490001.
A method of matrix addressing polarization rotating or retarding light-valve arrays (1970)

A geometrical arrangement is described that allows matrix-addressed arrays of light valves to be built out of optically active materials which do not possess a switching threshold. Such arrays can be used for optical selectors, composers, and displays. Unlike classical coincident matrix addressing, this new scheme does not impose any limitation on addressing speed nor is it critically dependent on uniformity of switching properties within the material. The basic scheme consists of forming the rows of the matrix on one piece of material, the columns on another, and separating the two pieces with suitably oriented polarizers. This scheme can be applied to ferromagnetic, ferroelectric, and electrooptic solids and optically active liquids. A modified form of the separated matrix scheme, employing no polarizers, can be used with light scattering, absorbing, or reflecting materials which have no switching threshold.
Separations with Fluorous Silica Gel and Related Materials (2004)

This chapter contains sections titled: Introduction Fluorous Silica Gel Types and Sources of Fluorous Silica Gel Materials and Products Fluorous Solid Phase Extraction (FSPE) Fluorous Solid Phase Extraction and its Relationship to Chromatography and Liquid/Liquid Extraction Examples of Fluorous Solid Phase Extractions Reverse Fluorous Synthesis with Solid Phase Extractions Fluorous Flash Chromatography Fluorous HPLC Structure/Retention Trends in Fluorous Chromatography Uses of Fluorous HPLC Analysis and Purification of Organofluorine Compounds Method Development for Preparative Fluorous Chromatographies and SPEs Demixing in Fluorous Mixture Synthesis Derivatization for Chemical Analysis Separation of Fluorous Compounds on Non-Fluorous Media Biphasic Reactions with Fluorous Silica Gel Conclusion
Componentxchange: An E-Exchange for Software Components. (2002)

A key challenge in Component-Based Software Engineering (CBSE) is finding appropriate software components for reuse. A component broker that allows component vendors to make available their modules, and also allows component integrators to search and select components matching their requirements will help solve this problem. In this paper, we describe an E-Exchange for buying and selling of software components over the World Wide Web. The ComponentXchange uses an XML based specification language for components, which is a semi-formal specification language that can describe a rich and an extensible set of component properties including functional properties, non-functional attributes and licensing aspects. ComponentXchange supports two models of component trading. A component can be used either by downloading it and integrating it into the client application or by accessing it remotely over the network. It has a licensing server that enforces the licensing terms and conditions. ComponentXchange can be easily extended to support different payment models like pay-per-use, pay-per-user, etc.
Pain-Induced Analgesia Mediated by Mesolimbic Reward Circuits (1999)

We tested the hypothesis that noxious stimuli induce pain modulation by activation of supraspinal structures. We found that intense noxious stimuli (i.e., subdermal injection of capsaicin or paw immersion in hot water) induced profound attenuation of the jaw-opening reflex in the anesthetized rat; forepaw subdermal capsaicin also elevated the mechanical hindpaw-withdrawal threshold in the awake rat. These antinociceptive effects were blocked by previous injection of either a dopamine antagonist (flupentixol) or an opioid antagonist (naloxone) into the nucleus accumbens. Additional experiments in anesthetized animals showed that the antinociceptive effect of noxious stimulation by either capsaicin (>/=100 micrograms) or hindpaw immersion in hot water (>/=45 degrees C for 4 min) correlated with the intensity of the stimulus. The maximal antinociceptive effect of capsaicin was similar in magnitude to that of a high dose of morphine (10 mg/kg) injected subcutaneously. Injection of the GABA(A)-receptor agonist muscimol, but not naloxone, into the rostroventral medulla, a major component of descending pain modulation systems, blocked capsaicin-induced antinociception. Although it is widely thought that painful stimuli may induce analgesia by activating forebrain structures, this is the first demonstration that such a mechanism exists. Furthermore, this mechanism can be engaged by naturalistic stimuli in awake animals. These observations imply that painful stimuli might under certain conditions be rewarding.
Fabrication of Large-Area Graphene Using Liquid Gallium and Its Electrical Properties (2010)

We demonstrated a new process for synthesizing a graphene sheet at the interface between solid amorphous carbon and liquid gallium. The insolubility of carbon in gallium strongly restricted the depth of graphitization, but a multilayered graphene sheet having four to six layers of graphene was produced over the entire area of the interface immediately beneath the liquid gallium. We also demonstrated the operation of an electric-field-effect device fabricated on the multilayered graphene with a back-gated configuration, and a maximum conductance modulation of 40% was observed for an applied gate voltage ranging from -100 to +100 V.
Platelet‐Derived Growth Factor: Its Potential Roles in Wound Healing, Atherosclerosis, Neoplasia, and Growth and Development (1985)

Platelet-derived growth factor (PDGF) has been found to be derived not only from platelets that have been induced to release their contents, but also from a number of transformed cells (including cells transformed by both DNA and RNA viruses, spontaneous transformation, and cells from various human tumours), from activated macrophages, from embryonic rat aortic smooth muscle cells, and from rat aortic smooth muscle cells derived from experimentally induced intimal proliferative lesions. The studies discussed demonstrate the potential role of platelets and macrophages in atherosclerosis and in wound repair, and indicate the ability of anti-PDGF IgG to inhibit proliferative responses in vitro. With the demonstration that the transforming protein derived from the oncogene from the simian sarcoma virus is highly homologous with PDGF, it was possible to show that a number of transformed cells secrete PDGF and show markedly decreased binding of PDGF. The same is true for embryonic rat aortic smooth muscle cells and for cells from experimentally induced proliferative lesions in the rat carotid artery. All these findings point to the role of PDGF in the formation of these lesions and can be correlated with the capacity of the cells noted above, as well as injured endothelial cells, to secrete PDGF or PDGF-like molecules. The biological significance of these observations is discussed and a model for atherogenesis is proposed.