gebhart/patrepeval huggingface dataset:
Real Space and Cyberspace: A Comparison of Museum Maps and Electronic Publication Maps. (1997)

It is well known that a floor plan helps the visitor explore the museum space and locate particular objects or collections of interest. This paper discusses models for creating maps to guide visitors through museum spaces, both real and electronic. We describe two examples of printed museum floor plans, comparing two- and three-dimensional depiction of architectural space, and illustrating varying approaches to the representation of architectural and collection details. Finding one's way in cyberspace is a more challenging task than moving through a physical structure. The content of electronic publications is typically seen one screen at a time and the overall scope remains invisible to the user. We illustrate how interactive timelines, tables of contents, virtual room plans as well as printed maps are used to guide users through CD ROM and Web site collections.
UK CropNet (2000)

This review explores the UK CropNet site. The project is aimed at aiding the comparative mapping of cereal and other crop genomes. The site provides software tools for use by those working on genome mapping, and access to an array of databases that will be of interest to all members of the plant genomics research community, using several ACeDB interfaces. All screen views from the website are reproduced with the kind permission of Dr Sean May, Director, Nottingham Arabidopsis Stock Centre (NASC).
Designing and Engineering Complex Behavior in Living Machines (2011)

Living organisms exhibit many fascinating behaviors that profoundly impact the world surrounding us. Some of these functions have been harnessed within biotechnology and redirected towards solving problems of industrial relevance, e.g. the microbial synthesis of pharmaceuticals and biofuels. However, these behaviors tend to be encoded by relatively simple genetics and constrained to a handful of lab-friendly organisms. To gain access to diverse, more complex behaviors, I have developed a number of methods for understanding and reprogramming sophisticated genetic networks inside cells. First, I reverse engineered and predictively modified the control of the Type III secretion system in Salmonella using mathematical modeling and high-throughput gene expression measurements in single cells. Next, a "refactoring" methodology was developed to entirely reconstruct and specify the genetics of a complex behavior using synthetic parts. I applied this strategy to reprogram and modularize the agriculturally relevant behavior of nitrogen fixation from Klebsiella. Then, classical engineering methods for nonlinear systems optimization were adapted to guide the selection of parts and optimize performance in well-specified genetic systems. Finally, orthogonal genetic wires were developed to engineer multiple behaviors in a single cell. I utilized these wires to construct orthogonal networks for sensing environmental conditions, performing computation, and synthesizing red and green pigments in E. coli. Together, these techniques and engineering principles represent a major step towards the design and synthesis of entire genomes based solely on genetic information found in sequence databases.
Intramolecular Schmidt Reactions of Alkyl Azides with Ketones: Scope and Stereochemical Studies (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIntramolecular Schmidt Reactions of Alkyl Azides with Ketones: Scope and Stereochemical StudiesGregory L. Milligan, Craig J. Mossman, and Jeffrey AubeCite this: J. Am. Chem. Soc. 1995, 117, 42, 10449–10459Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/ja00147a006https://doi.org/10.1021/ja00147a006research-articleACS PublicationsRequest reuse permissionsArticle Views3169Altmetric-Citations178LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
Shape groups of the electronic isodensity surfaces for small molecules: Shapes of 10‐electron hydrides (1993)

Abstract An algorithm for a detailed 3‐D characterization of the shapes of molecular charge distributions is implemented in the form of a comprehensive package of computer programs, GSHAPE, and applied to a series of 10‐electron hydrides to critically evaluate the methodology. Attention is paid to the effects of nuclear geometry and the size of basis on the molecular shape. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend on two continuous parameters: a density value defining the density contour and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is calculated at the ab initio level using basis sets ranging from STO‐3G to 6‐31G**. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visualization of the results is one option of our program using Application Visualization Software (AVS). For a given molecule, in a given nuclear geometry, the technique provides a 2‐D shape map, displaying the distribution of the shape gruops as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis automatically. This feature makes it potentially useful in the context of computer‐aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, a variety of 2‐D shape maps are discussed. © John Wiley &amp; Sons, Inc.
Architectural and multiprocessor design verification of the PowerPC 604 data cache (2002)

The PowerPC 604 microprocessor has high performance 32-bit implementation, which is optimized to produce compact code while adhering to RISC philosophy. The PowerPC 604 microprocessor can sustain a maximum issue rate of 4 instructions per cycle. The data cache of the 604 is a 16 KB four-way set-associative non-blocking cache which contains MESI states (M: Modified, E: Exclusive-unmodified, S: Shared, I: Invalid), a reservation bit with its reservation address register, an independent snoop port, WIMG (W: cache write policy, I: cacheability, M: coherency mode, G: protection against speculative access) support logic, and parity bits. The 604 has an on-chip phase-locked loop to provide different Processor/Bus clock ratios to simplify the system design while using a 100 MHz processor clock. The data cache to BIU (Bus Interface Unit) interface can handle different Processor/Bus clock ratios. The architecture and multiprocessor verification for the PowerPC 604 data cache systematically checks the data cache architecture, logic, and implementation correctness and provides the assurance that the PowerPC 604 microprocessor's aggressive hardware and software implementation is carried out correctly in the uniprocessor and multiprocessor environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
p53 Antibodies in the sera of patients with various types of cancer: a review. (2000)

p53 antibodies (p53-Abs) were discovered 20 years ago during the course of tumor-associated antigens screening. The discovery of p53 mutation and accumulation of p53 in human tumors shed new light on the p53 humoral response. In the present review, we have compiled more than 130 papers published in this specific field since 1992. We demonstrate that p53-Abs are found predominantly in human cancer patients with a specificity of 96%. Such antibodies are predominantly associated with p53 gene missense mutations and p53 accumulation in the tumor, but the sensitivity of such detection is only 30%. It has been demonstrated that this immune response is due to a self-immunization process linked to the strong immunogenicity of the p53 protein. The clinical value of these antibodies remains subject to debate, but consistent results have been observed in breast, colon, oral, and gastric cancers, in which they have been associated with high-grade tumors and poor survival. The finding of p53-Abs in the sera of individuals who are at high risk of cancer, such as exposed workers or heavy smokers, indicates that they have promising potential in the early detection of cancer.
Impaired lymphocyte blastogenic response in patients with colon adenocarcinoma: Effects of disease and age (1977)

The in vitro blastogenic response of 76 patients with colon adenocarcinoma and 29 age-matched normal healthy volunteers was compared. An age-related decline in cellular immunocompetence was observed in both the patient and control group. Within each age interval, the patients' blastogenic responses were lower than the controls' and the rate of decline of the blastogenic response in the patient group was greater in magnitude, suggesting that their disease state also contributed to loss of cellular immunocompetence. Thus, both increasing age and presence of tumor are factors that contribute to the decline the immunocompetence in patients with colon adenocarcinoma.
Decorated Electrospun Fibers Exhibiting Superhydrophobicity (2007)

Hierarchically roughened nonwoven fabrics that exhibit superhydrophobic behavior (see figure) are obtained by decorating electrospun fibers (diameter ca. 1 μm) with pores or particles of a diameter of ca. 100 nm, followed by surface hydrophobization. The enhanced hydrophobicity, due to a second level of roughness originating from the introduction of pores or particles, is evidenced by higher contact angles and lower contact-angle hysteresis.
A Method to Integrate Business Registries by Using OWL-S Ontologies (2006)

WWW is currently undergoing a remarkable change from a collection of pages to a collection of services that interoperate through the Internet. The most successful types of these services are XML Web services and ebXML, which are emerging as significant e-Business application frameworks. However, both ebXML and Web services use different registries each other for the purpose of publishing and discovering services. And this discrepancy of registries has given rise to a demand for integrated query when adopting the frameworks. Furthermore, these registries support only keyword-based search, which does not make use of semantic information, and which does not address the problem of matching service capabilities and allowing service location based on the functionalities sought. In the literature of semantic Web, the problem of creating ontologies from legacy information has been also arisen. In this paper, we show how service descriptions, written in OWL-S, can be mapped into UDDI and ebXML registry entries, and can be migrated from registries. Therefore, it provides not only a way to support integrated queries for registry entries but also a way to build a foundation of semantic service discovery. Also, migrated OWL-S can be updated periodically while registry entries are being modified by using replication APIs of the registries.
The μ Switch Region Tandem Repeats Are Important, but Not Required, for Antibody Class Switch Recombination (2001)

Class switch DNA recombinations change the constant (C) region of the antibody heavy (H) chain expressed by a B cell and thereby change the antibody effector function. Unusual tandemly repeated sequence elements located upstream of H chain gene exons have long been thought to be important in the targeting and/or mechanism of the switch recombination process. We have deleted the entire switch tandem repeat element (Sμ) from the murine μ H chain gene. We find that the Sμ tandem repeats are not required for class switching in the mouse immunoglobulin H-chain locus, although the efficiency of switching is clearly reduced. Our data demonstrate that sequences outside of the Sμ tandem repeats must be capable of directing the class switch mechanism. The maintenance of the highly repeated Sμ element during evolution appears to reflect selection for a highly efficient switching process rather than selection for a required sequence element.
Streptococcus pneumoniae-associated Hemolytic Uremic Syndrome Among Children in North America (2011)

North American children with SP-HUS had severe clinical manifestations and significant morbidity. In this series, nearly all cases were caused by serotypes that are not in PCV7 but are included in PCV13.
Switching Control of Expression ofptsGfrom the Mlc Regulon to the NagC Regulon (2008)

The Mlc and NagC transcriptional repressors bind to similar 23-bp operators. The sequences are weakly palindromic, with just four positions totally conserved. There is no cross regulation observed between the repressors in vivo, but there are no obvious bases which could be responsible for operator site discrimination. To investigate the basis for operator recognition and to try to understand what differentiates NagC sites from Mlc sites, we have undertaken mutagenesis experiments to convert ptsG from a gene regulated by Mlc into a gene regulated by NagC. There are two Mlc operators upstream of ptsG, and to switch ptsG to the NagC regulon, it was necessary to change two different characteristics of both operators. Firstly, we replaced the AT base pair at position +/-11 from the center of symmetry of the operators with a GC base pair. Secondly, we changed the sequence of the CG base pairs in the central region of the operator (positions -4 to +4 around the center of symmetry). Our results show that changes at either of these locations are sufficient to lose regulation by Mlc but that both types of changes in both operators are necessary to convert ptsG to a gene regulated by NagC. In addition, these experiments confirmed that two operators are necessary for regulation by NagC. We also show that regulation of ptsG by Mlc involves some cooperative binding of Mlc to the two operators.
ChemInform Abstract: The Properties of Resin Supports and Their Effects on Solid‐Phase Organic Synthesis (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The Mycobacterium avium complex (1993)

Mycobacterium avium complex (MAC) disease emerged early in the epidemic of AIDS as one of the common opportunistic infections afflicting human immunodeficiency virus-infected patients. However, only over the past few years has a consensus developed about its significance to the morbidity and mortality of AIDS. M. avium was well known to mycobacteriologists decades before AIDS, and the MAC was known to cause disease, albeit uncommon, in humans and animals. The early interest in the MAC provided a basis for an explosion of studies over the past 10 years largely in response to the role of the MAC in AIDS opportunistic infection. Molecular techniques have been applied to the epidemiology of MAC disease as well as to a better understanding of the genetics of antimicrobial resistance. The interaction of the MAC with the immune system is complex, and putative MAC virulence factors appear to have a direct effect on the components of cellular immunity, including the regulation of cytokine expression and function. There now is compelling evidence that disseminated MAC disease in humans contributes to both a decrease in the quality of life and survival. Disseminated disease most commonly develops late in the course of AIDS as the CD4 cells are depleted below a critical threshold, but new therapies for prophylaxis and treatment offer considerable promise. These new therapeutic modalities are likely to be useful in the treatment of other forms of MAC disease in patients without AIDS. The laboratory diagnosis of MAC disease has focused on the detection of mycobacteria in the blood and tissues, and although the existing methods are largely adequate, there is need for improvement. Indeed, the successful treatment of MAC disease clearly will require an early and rapid detection of the MAC in clinical specimens long before the establishment of the characteristic overwhelming infection of bone marrow, liver, spleen, and other tissue. Also, a standard method of susceptibility testing is of increasing interest and importance as new effective antimicrobial agents are identified and evaluated. Antimicrobial resistance has already emerged as an important problem, and methods for circumventing resistance that use combination therapies are now being studied.
Characterization of a Novel Influenza A Virus Hemagglutinin Subtype (H16) Obtained from Black-Headed Gulls (2005)

In wild aquatic birds and poultry around the world, influenza A viruses carrying 15 antigenic subtypes of hemagglutinin (HA) and 9 antigenic subtypes of neuraminidase (NA) have been described. Here we describe a previously unidentified antigenic subtype of HA (H16), detected in viruses circulating in black-headed gulls in Sweden. In agreement with established criteria for the definition of antigenic subtypes, hemagglutination inhibition assays and immunodiffusion assays failed to detect specific reactivity between H16 and the previously described subtypes H1 to H15. Genetically, H16 HA was found to be distantly related to H13 HA, a subtype also detected exclusively in shorebirds, and the amino acid composition of the putative receptor-binding site of H13 and H16 HAs was found to be distinct from that in HA subtypes circulating in ducks and geese. The H16 viruses contained NA genes that were similar to those of other Eurasian shorebirds but genetically distinct from N3 genes detected in other birds and geographical locations. The European gull viruses were further distinguishable from other influenza A viruses based on their PB2, NP, and NS genes. Gaining information on the full spectrum of avian influenza A viruses and creating reagents for their detection and identification will remain an important task for influenza surveillance, outbreak control, and animal and public health. We propose that sequence analyses of HA and NA genes of influenza A viruses be used for the rapid identification of existing and novel HA and NA subtypes.
Distinct frontal and amygdala correlates of change detection for facial identity and expression (2015)

Recruitment of 'top-down' frontal attentional mechanisms is held to support detection of changes in task-relevant stimuli. Fluctuations in intrinsic frontal activity have been shown to impact task performance more generally. Meanwhile, the amygdala has been implicated in 'bottom-up' attentional capture by threat. Here, 22 adult human participants took part in a functional magnetic resonance change detection study aimed at investigating the correlates of successful (vs failed) detection of changes in facial identity vs expression. For identity changes, we expected prefrontal recruitment to differentiate 'hit' from 'miss' trials, in line with previous reports. Meanwhile, we postulated that a different mechanism would support detection of emotionally salient changes. Specifically, elevated amygdala activation was predicted to be associated with successful detection of threat-related changes in expression, over-riding the influence of fluctuations in top-down attention. Our findings revealed that fusiform activity tracked change detection across conditions. Ventrolateral prefrontal cortical activity was uniquely linked to detection of changes in identity not expression, and amygdala activity to detection of changes from neutral to fearful expressions. These results are consistent with distinct mechanisms supporting detection of changes in face identity vs expression, the former potentially reflecting top-down attention, the latter bottom-up attentional capture by stimulus emotional salience.
Probabilistic Independent Component Analysis for Functional Magnetic Resonance Imaging (2004)

We present an integrated approach to probabilistic independent component analysis (ICA) for functional MRI (FMRI) data that allows for nonsquare mixing in the presence of Gaussian noise. In order to avoid overfitting, we employ objective estimation of the amount of Gaussian noise through Bayesian analysis of the true dimensionality of the data, i.e., the number of activation and non-Gaussian noise sources. This enables us to carry out probabilistic modeling and achieves an asymptotically unique decomposition of the data. It reduces problems of interpretation, as each final independent component is now much more likely to be due to only one physical or physiological process. We also describe other improvements to standard ICA, such as temporal prewhitening and variance normalization of timeseries, the latter being particularly useful in the context of dimensionality reduction when weak activation is present. We discuss the use of prior information about the spatiotemporal nature of the source processes, and an alternative-hypothesis testing approach for inference, using Gaussian mixture models. The performance of our approach is illustrated and evaluated on real and artificial FMRI data, and compared to the spatio-temporal accuracy of results obtained from classical ICA and GLM analyses.
Protection of rats from adjuvant arthritis by immunization with naked dna encoding for mycobacterial heat shock protein 65 (1997)

We have demonstrated for the first time that naked DNA delivery is feasible in controlling experimental autoimmune disease. Although the actual mechanism of protection has not been fully elucidated, this simple and versatile approach could represent a useful tool in dissecting basic autoimmune mechanisms.
Discrimination of temperature and strain with a single FBG based on the birefringence effect (2004)

We will demonstrate a new technique to discriminate the temperature and strain effects using a single fiber Bragg grating (FBG). The birefringence is typically induced during FBG inscription, and it is manifested as polarization-dependent loss (PDL), and it is defined as the maximum change in the transmitted power for polarizations. Two independent measurements of the resonance wavelength shift and the changes of PDL can discriminate those effects.