gebhart/patrepeval huggingface dataset:
Cloning of reiterated and nonreiterated herpes simplex virus 1 sequences as BamHI fragments. (1980)

Over 95% of the herpes simplex virus type 1 (strain F) DNA sequences have been cloned as BamHI fragments in the pBR322 plasmid. With one exception, all of the cloned fragments have the same electrophoretic mobilities and restriction enzyme cleavage sites as do the authentic fragments derived from the BamHI digests of the viral genome. The exception is the BamHI B fragment mapping at the right end of L component in the prototype arrangement of the DNA. Thus, a small deletion mapping near the left end of the fragment was present in two independently derived plasmids. Included in the collection of plasmids are several clones containing DNA sequences that span the junction between the L and S components of the virus DNA. Several plasmids containing the junction fragment were found to be sufficiently stable to permit the preparation of large amounts of the DNA fragment for fine-structure mapping of the restriction enzyme cleavage sites. Preliminary studies on one cloned fragment (BamHI G) have shown that it is biologically active in marker rescue of a temperature-sensitive mutation and in transfer of a plaque morphology marker.
Second-Generation Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Non-Small Cell Lung Cancer (2007)

Inhibiting epidermal growth factor receptor (EGFR) signaling has proven to be an effective strategy for treating non-small cell lung cancer (NSCLC) patients and the first generation of agents developed for this purpose, gefitinib and erlotinib, stimulated a unique escalation in both biologic and clinical research within the field. Second-generation EGFR-targeted agents that aim to further improve patient outcomes are now in preclinical and clinical trials. This review discusses four promising agents that are currently being studied in NSCLC: EKB-569, HKI-272, CI-1033, and ZD6474.
Activatable cell penetrating peptides and their use in clinical contrast agent and therapeutic development (2009)

Activatable cell penetrating peptides (ACPPs) are polycationic cell penetrating peptides (CPPs) whose cellular uptake is minimized by a polyanionic inhibitory domain and then restored upon proteolysis of the peptide linker connecting the polyanionic and polycationic domains. Local activity of proteases able to cut the linker causes amplified retention in tissues and uptake into cells. This ACPP platform has been specifically designed to meet 3 major criteria for contrast and therapeutic agent development. The first criterion was to target a wide spread disease process and mechanism that is inherent to cancer progression, in this case, matrix metalloprotease activity. Secondly, the platform was designed with an amplification mechanism that can deliver multiple molecules per target; in this case the targets are cancer proteases. Thirdly, the ACPP platform is not limited to a single enzyme target, imaging modality, or therapeutic playload. We show the validation of the ACPP concept from tissue culture to systemic administration in tumor bearing mice. ACPPs have enhanced biodistribution compared to the CPP counterpart and they yield MMP dependent contrast in multiple tumors and in metastases. ACPPs can be conjugated to macromolecular weight carriers to further enhance the biodistribution profile by prolonging plasma half-life resulting in enhanced tumor uptake and providing clinically significant contrast as an 111-In radiotracer. The second part of the dissertation focuses on translation from imaging agents into therapeutic agents. We describe the challenges of cell penetration, drug conjugation, stability, and the resulting animal testing using doxorubicin conjugated dendrimers that yielded some promising results. Lastly, we describe the simple attachment of ACPPs to clinically approved therapeutic nanoparticles. This approach has resulted in ACPP based targeted doxorubicin liposomes that have significant anti-tumor activity compared to untargeted liposomes. We conclude that because of preclinical successes, ACPPs have significant potential in the development of a targeting portfolio of imaging and therapeutic agents that could one day be useful in the clinic
Genetic engineering of taxol biosynthetic genes in Saccharomyces cerevisiae (2005)

Baccatin III, an intermediate of Taxol biosynthesis and a useful precursor for semisynthesis of the anti-cancer drug, is produced in yew (Taxus) species by a sequence of 15 enzymatic steps from primary metabolism. Ten genes encoding enzymes of this extended pathway have been described, thereby permitting a preliminary attempt to reconstruct early steps of taxane diterpenoid (taxoid) metabolism in Saccharomyces cerevisiae as a microbial production host. Eight of these taxoid biosynthetic genes were functionally expressed in yeast from episomal vectors containing one or more gene cassettes incorporating various epitope tags to permit protein surveillance and differentiation of those pathway enzymes of similar size. All eight recombinant proteins were readily detected by immunoblotting using specific monoclonal antibodies and each expressed protein was determined to be functional by in vitro enzyme assay, although activity levels differed considerably between enzyme types. Using three plasmids carrying different promoters and selection markers, genes encoding five sequential pathway steps leading from primary isoprenoid metabolism to the intermediate taxadien-5alpha- acetoxy-10beta-ol were installed in a single yeast host. Metabolite analysis showed that yeast isoprenoid precursors could be utilized in the reconstituted pathway because products accumulated from the first two engineered pathway steps (leading to the committed intermediate taxadiene); however, a pathway restriction was encountered at the first cytochrome P450 hydroxylation step. The means of overcoming this limitation are described in the context of further development of this novel approach for production of Taxol precursors and related taxoids in yeast.
Sequence of gene and cDNA encoding murine major histocompatibility complex class II gene A beta 2. (1985)

The murine major histocompatibility complex is known to express two class II molecules, A and E. They are composed of one alpha- and one beta-polypeptide chain. Recently, we reported the finding of an additional beta-chain second domain exon tentatively designated A beta 2. We describe here the nucleotide sequence of the A beta 2 gene and an A beta 2 cDNA clone. A beta 2 displays the same exon organization as the known expressed beta-chain genes, and the predicted A beta 2 polypeptide shows all the characteristic features of the expressed beta-chains. The predicted A beta 2 polypeptide shows 49-56% amino acid sequence identity to A beta and E beta chains and to the human DP, DQ, and DR beta-chains. These are 63-79% homologous to each other, indicating that A beta 2 is the most divergent member of the beta-chain family. The A beta 2 gene seems to be transcribed in the same types of cells as other class II genes. Detection of incompletely spliced A beta 2 mRNA and the finding of a cDNA clone containing an intron segment suggest that A beta 2 transcripts are processed slowly. Hybridizations with A beta 2 probes to restriction enzyme-digested genomic DNA indicate that the A beta 2 gene displays lower allelic polymorphism than the A beta gene.
Formation of monolayer films by the spontaneous assembly of organic thiols from solution onto gold (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFormation of monolayer films by the spontaneous assembly of organic thiols from solution onto goldColin D. Bain, E. Barry Troughton, Yu Tai Tao, Joseph Evall, George M. Whitesides, and Ralph G. NuzzoCite this: J. Am. Chem. Soc. 1989, 111, 1, 321–335Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/ja00183a049https://doi.org/10.1021/ja00183a049research-articleACS PublicationsRequest reuse permissionsArticle Views19008Altmetric-Citations2931LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Organic photovoltaic films (2002)

Organic electronic materials are of interest for future applications in solar cells. Although results for single layer organic materials have been disappointing, high photocurrent quantum efficiencies can be achieved in composite systems including both electron donating and electron accepting components. Efficiencies of over 2% have now been reported in four different types of organic solar cell. Performance is limited by the low red absorption of organic materials, poor charge transport, and low stability. These problems are being tackled by the synthesis of new materials, the use of new materials combinations, and optimization of molecular design, self-assembly, and processing conditions to control morphology. Power conversion efficiencies of over 5% are within reach, but the fundamental physics of organic donor-acceptor solar cells remains poorly understood. The last two years have seen an unprecedented growth of interest in solar cells made from organic electronic materials. This is partly due to the rapid growth of the photovoltaic market1, which has stimulated research into longer term, more innovative photovoltaic technologies, and partly to the development of organic electronic materials for display applications. The rapid progress in optoelectronic molecular materials has introduced a range of potential new photovoltaic materials, as well as an improved understanding of the capabilities of such materials and confidence in their application2.
L’església catòlica i el pagament del ICIO a Espanya (2017)

Un tema no pacific que cueja en els debats politics es el de l’obligatorietat o la
exempcio del pagament del ICIO (Impost sobre construccions, instal·lacions
i obres) per l’Esglesia catolica. A mes, afecta tambe a les cases de les ordres
religioses, les escoles, els centres educatius, hospitals, residencies de la
tercera edat i a altres immobles i instal·lacions dedicades a serveis educatius,
culturals, sanitaries o de labor social de l’Esglesia catolica a Espanya.
Effects of Prolonged Food Deprivation on the Ultradian Growth Hormone Rhythm and Immunoreactive Somatostatin Tissue Levels in the Rat* (1979)

The effects of prolonged food deprivation on plasma GH, pituitary GH, and tissue somatostatin levels were investigated in the male rat. Six-hour GH secretory profiles obtained from normal animals bearing chronic intracardiac venous cannulae showed the typical ultradian GH rhythm, with most peak GH values being >600 ng/ml. Exposure to 24-h food deprivation resulted in a significant depression in amplitude of GH pulses, with peak values not exceeding 300 ng/ml. The amplitude and duration of the GH secretory episodes declined progressively after 48 and 72-h food deprivation, and normal periodicity was not evident. The mean 6-h GH level in each of the food-deprived groups was significantly less than that of normal animals. A rebound response was observed in rats allowed to refeed for 3 days after 72-h food deprivation, as evidenced by an increased number of GH secretory episodes and a shorter period of the GH rhythm. In a second series of experiments, pituitary GH and tissue levels of somatostatin-like immunoreactivity (SLI) were measured in two groups of rats which were subjected to either 72-h food deprivation or ad libitum feeding. Starvation resulted in a significant increase in pituitary GH concentration when compared to fed controls (88.7 ± 3.2 vs. 66.0 ± 2.4 μg/mg wet wt; P < 0.01), but did not significantly alter medial basal hypothalamic SLI concentration. A significant elevation of the SLI concentration of starved rats was observed in the pancreas, jejunum, and colon. These results indicate that the GH secretory episodes are markedly suppressed in response to prolonged food deprivation via decreased release from the pituitary gland. The finding of an alteration in pancreatic and gastrointestinal SLI concentration in response to deprivation of exogenous nutrients is compatible with the view that somatostatin may play a role in nutrient homeostasis.
WORLD'S LARGEST TEST OF DYNAMIC ROUTE GUIDANCE. ADVANCE OPENING (1994)

Illinois is conducting the largest test of dynamic route guidance ever attempted. Advance (Advanced Driver and Vehicle Advisory Navigation Concept) uses differential global positioning system navigation, dead reckoning, and map matching to guide drivers in route selection. Based on real-time travel data, volunteer drivers have an in-vehicle computer with display screen (mobile navigation assistant) mounted on the dashboard, which supplies information regarding traffic conditions. More than 3,000 vehicles are participating in this 3-year field test sponsored in part by the Federal Highway Administration. This article discusses the challenging issues that Advance investigators face, including insurance questions, leased and financed vehicles, and privacy. Also provided is a lessons learned column from the contracting and audit phases and a list of Advance participants.
Lean management, group support systems, and hypermedia: a combination whose time has come (2002)

The TeamGlobal team support system (TSS) is implemented in a multimedia product, HyperNet, for users with workstations linked world-wide over INTERNET. The use of object-oriented technology coupled with the HyperNet communications environment enables these TSSs to span varied platforms without apparent restraint upon the users. The interactive richness of the resulting class of TSS opens many opportunities for extending applied research and selected actual applications in useful ways. The present study demonstrates that information technology can now support an organization which chooses to move into the practices of lean management, and that this support is practical for selected organizations regardless of how distributed their human resources may be and what assortment of computing platforms may be involved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Discovery of Shared Semantic Spaces for Multiscene Video Query and Summarization (2016)

The growing rate of public space closed-circuit television (CCTV) installations has generated a need for automated methods for exploiting video surveillance data, including scene understanding, query, behavior annotation, and summarization. For this reason, extensive research has been performed on surveillance scene understanding and analysis. However, most studies have considered single scenes or groups of adjacent scenes. The semantic similarity between different but related scenes (e.g., many different traffic scenes of a similar layout) is not generally exploited to improve any automated surveillance tasks and reduce manual effort. Exploiting commonality and sharing any supervised annotations between different scenes is, however, challenging due to the following reason: some scenes are totally unrelated and thus any information sharing between them would be detrimental, whereas others may share only a subset of common activities and thus information sharing is only useful if it is selective. Moreover, semantically similar activities that should be modeled together and shared across scenes may have quite different pixel-level appearances in each scene. To address these issues, we develop a new framework for distributed multiple-scene global understanding that clusters surveillance scenes by their ability to explain each other's behaviors and further discovers which subset of activities are shared versus scene specific within each cluster. We show how to use this structured representation of multiple scenes to improve common surveillance tasks, including scene activity understanding, cross-scene query-by-example, behavior classification with reduced supervised labeling requirements, and video summarization. In each case, we demonstrate how our multiscene model improves on a collection of standard single-scene models and a flat model of all scenes.
Rich Feature Hierarchies for Accurate Object Detection and Semantic Segmentation (2014)

Object detection performance, as measured on the canonical PASCAL VOC dataset, has plateaued in the last few years. The best-performing methods are complex ensemble systems that typically combine multiple low-level image features with high-level context. In this paper, we propose a simple and scalable detection algorithm that improves mean average precision (mAP) by more than 30% relative to the previous best result on VOC 2012 -- achieving a mAP of 53.3%. Our approach combines two key insights: (1) one can apply high-capacity convolutional neural networks (CNNs) to bottom-up region proposals in order to localize and segment objects and (2) when labeled training data is scarce, supervised pre-training for an auxiliary task, followed by domain-specific fine-tuning, yields a significant performance boost. Since we combine region proposals with CNNs, we call our method R-CNN: Regions with CNN features. We also present experiments that provide insight into what the network learns, revealing a rich hierarchy of image features. Source code for the complete system is available at http://www.cs.berkeley.edu/~rbg/rcnn.
Advancing process‐based watershed hydrological research using near‐surface geophysics: a vision for, and review of, electrical and magnetic geophysical methods (2008)

Abstract We want to develop a dialogue between geophysicists and hydrologists interested in synergistically advancing process based watershed research. We identify recent advances in geophysical instrumentation, and provide a vision for the use of electrical and magnetic geophysical instrumentation in watershed scale hydrology. The focus of the paper is to identify instrumentation that could significantly advance this vision for geophysics and hydrology during the next 3–5 years. We acknowledge that this is one of a number of possible ways forward and seek only to offer a relatively narrow and achievable vision. The vision focuses on the measurement of geological structure and identification of flow paths using electrical and magnetic methods. The paper identifies instruments, provides examples of their use, and describes how synergy between measurement and modelling could be achieved. Of specific interest are the airborne systems that can cover large areas and are appropriate for watershed studies. Although airborne geophysics has been around for some time, only in the last few years have systems designed exclusively for hydrological applications begun to emerge. These systems, such as airborne electromagnetic (EM) and transient electromagnetic (TEM), could revolutionize hydrogeological interpretations. Our vision centers on developing nested and cross scale electrical and magnetic measurements that can be used to construct a three‐dimensional (3D) electrical or magnetic model of the subsurface in watersheds. The methodological framework assumes a ‘top down’ approach using airborne methods to identify the large scale, dominant architecture of the subsurface. We recognize that the integration of geophysical measurement methods, and data, into watershed process characterization and modelling can only be achieved through dialogue. Especially, through the development of partnerships between geophysicists and hydrologists, partnerships that explore how the application of geophysics can answer critical hydrological science questions, and conversely provide an understanding of the limitations of geophysical measurements and interpretation. Copyright © 2008 John Wiley &amp; Sons, Ltd.
The Rush to Measure Performance (1998)

This article examines the concept of performance measurement and identifies several major performance measurement initiatives that have implications for the human services. Each of these initiatives is briefly discussed and their similarities and differences noted. The article points out that little coordination appears to be taking place between these initiatives which raises the specter of human service agencies having to contend with multiple potentially incompatible performance measurement systems. The implications of performance measurement for human services agencies is then discussed. The article closes by suggesting that agency administrators, advocacy groups, clients and others concerned about the human services need to become informed and knowledgeable about performance measurement.
Non‐Covalent Functionalization of Graphene Using Self‐Assembly of Alkane‐Amines (2011)

Abstract A simple, versatile method for non‐covalent functionalization of graphene based on solution‐phase assembly of alkane‐amine layers is presented. Second‐order Møller–Plesset (MP2) perturbation theory on a cluster model (methylamine on pyrene) yields a binding energy of ≈220 meV for the amine–graphene interaction, which is strong enough to enable formation of a stable aminodecane layer at room temperature. Atomistic molecular dynamics simulations on an assembly of 1‐aminodecane molecules indicate that a self‐assembled monolayer can form, with the alkane chains oriented perpendicular to the graphene basal plane. The calculated monolayer height (≈1.7 nm) is in good agreement with atomic force microscopy data acquired for graphene functionalized with 1‐aminodecane, which yield a continuous layer with mean thickness ≈1.7 nm, albeit with some island defects. Raman data also confirm that self‐assembly of alkane‐amines is a non‐covalent process, i.e., it does not perturb the sp 2 hybridization of the graphene. Passivation and adsorbate n‐doping of graphene field‐effect devices using 1‐aminodecane, as well as high‐density binding of plasmonic metal nanoparticles and seeded atomic layer deposition of inorganic dielectrics using 1,10‐diaminodecane are also reported.
MBARS: mini bone‐attached robotic system for joint arthroplasty (2005)

A report on a new active, miniature bone-attached, robotic system including its design, high level and low level control, is given together with a description of the system implementation and first experimental use. The system is capable of preparing the bone cavity for an implant during joint arthroplasty procedures. Without loss of generality, the report describes the implementation of the system for a Patellofemoral Joint Replacement procedure. The system is image-free and all planning is performed intra-operatively in the robot coordinate system, eliminating the need for external tracking systems in the operating room. Experiments were conducted using the first robot prototype and the results supported the feasibility of the concept. The methodology which is presented can be modified to other orthopaedic procedures and could improve the results in terms of accuracy and operational time. Moreover, it enables minimally invasive procedures and use of the next generation of more anatomically shaped implants.