gebhart/patrepeval huggingface dataset:
WOODSS and the Web (2005)

This paper discusses ongoing research on scientific workflows at the Institute of Computing, University of Campinas (IC - UNICAMP) Brazil. Our projects with bio-scientists have led us to develop a scientific workflow infrastructure named WOODSS. This framework has two main objectives in mind: to help scientists to specify and annotate their models and experiments; and to document collaborative efforts in scientific activities. In both contexts, workflows are annotated and stored in a database. This "annotated scientific workflow" database is treated as a repository of (sometimes incomplete) approaches to solving scientific problems. Thus, it serves two purposes: allows comparison of distinct solutions to a problem, and their designs; and provides reusable and executable building blocks to construct new scientific workflows, to meet specific needs. Annotations, moreover, allow further insight into methodology, success rates, underlying hypotheses and other issues in experimental activities.The many research challenges faced by us at the moment include: the extension of this framework to the Web, following Semantic Web standards; providing means of discovering workflow components on the Web for reuse; and taking advantage of planning in Artificial Intelligence to support composition mechanisms. This paper describes our efforts in these directions, tested over two domains - agro-environmental planning and bioinformatics.
Electroluminescence from Localized Defects in Zinc Oxide: Toward Electrically Driven Single Photon Sources at Room Temperature (2015)

Single photon sources are required for a wide range of applications in quantum information science, quantum cryptography, and quantum communications. However, the majority of room temperature emitters to date are only excited optically, which limits their proper integration into scalable devices. In this work, we overcome this limitation and present room temperature electrically driven light emission from localized defects in zinc oxide (ZnO) nanoparticles and thin films. The devices emit in the red spectral range and show excellent rectifying behavior. The emission is stable over an extensive period of time, providing an important prerequisite for practical devices. Our results open possibilities for building new ZnO-based quantum integrated devices that incorporate solid-state single photon sources for quantum information technologies.
77. Efficient Transduction and Therapy of Malignant Glioma by Lentiviral Vectors Pseudotyped with LCMV Glycoproteins (2005)

Hrvoje Miletic,1 Yvonne Fischer,2 Harald Neumann,3 Tsanan Giroglou,2 Manuel M. Hermann,1 Werner Stenzel,1 Maria A. Rueger,4 Yannic Waerzeggers,4 Uwe Himmelreich,5 Mathias Hoehn,5 Andreas H. Jacobs,4 Martina Deckert,1 Dorothee von Laer,2
Intradermal Delivery of Interleukin-12 Plasmid DNA by <i>in vivo</i> Electroporation (2001)

Gene therapy depends on safe and efficient gene delivery. The skin is an attractive target for gene delivery because of its accessibility. Recently, in vivo electroporation has been shown to enhance expression after injection of plasmid DNA. In this study, we examined the use of electroporation to deliver plasmid DNA to cells of the skin in order to demonstrate that localized delivery can result in increased serum concentrations of a specific protein. Intradermal injection of a plasmid encoding luciferase resulted in low levels of expression. However, when injection was combined with electroporation, expression was significantly increased. When performing this procedure with a plasmid encoding interleukin-12, the induced serum concentrations of gamma-interferon were as much as 10 fold higher when electroporation was used. The results presented here demonstrate that electroporation can be used to augment the efficiency of direct injection of plasmid DNA to skin.
Analyze-NOW-an environment for collection and analysis of failures in a network of workstations (1996)

This paper describes Analyze-NOW, an environment for the collection and analysis of failures/errors in a network of workstations. Descriptions cover the data collection methodology and the tool implemented to facilitate this process. Software tools used for analysis are described, with emphasis on the details of the implementation of the Analyzer, the primary analysis tool. Application of the tools is demonstrated by using them to collect and analyze failure data (for 32-week period) from a network of 69 SunOS-based workstations. Classification based on the source and effect of faults is used to identify problem areas. Different types of failures encountered on the machines and network are highlighted to develop a proper understanding of failures in a network environment. The results from the analysis tool should be used to pinpoint the problem areas in the network. The results obtained from using Analyze-NOW on failure data from the monitored network reveal some interesting behavior of the network. Nearly 70% of the failures were network-related, whereas disk errors were few. Network-related failures were 75% of all hard-failures (failures that make a workstation unusable). Half of the network-related failures were due to servers not responding to clients, and half were performance-related and others. Problem areas in the network were found using this tool. The authors' approach was compared to the method of using the network architecture to locate problem areas. This comparison showed that locating problem areas using network architecture over-estimates the number of problem areas.
SARHA – Development of a Sensor-Augmented GPS/EGNOS/Galileo Receiver for Urban and Indoor Environments (2007)

The main objective of the project âSARHA - Sensor-Augmented EGNOS/Galileo Receiver for Handheld Applications in Urban and Indoor Environmentsâ is the development of a modern satellite navigation receiver with autonomous sensor augmentation. Additionally, the hybrid navigation system will be enhanced by a transponder capable of receiving absolute position updates from transmitters installed inside buildings. The transponder will allow the SARHA system to significantly increase reliability and accuracy of the positioning solutions indoors. The hybrid navigation software is split up into two parts. The first one will be implemented directly on the GPS receiver, whereas the second part will run on a microcontroller. Thus, a small, low-performance microcontroller can be used, representing the first step towards the reduction of size, weight and power consumption of the mobile system. This paper provides an overview on personal mobility and typical applications related to the system, describes the system architecture and the hybrid navigation software in detail. Furthermore, emphasis is laid on a comparison of different step detection algorithms, showing their advantages and disadvantages. Based on the Galileo signal definition, additional analysis set up to explore the signal characteristics in comparison to the GPS signals, are provided. Improvements due to the Galileo signal availability in urban and indoor environments are assessed and will later ensure seamless integration of enhanced technologies into the continuous developments.
Increased Intestinal Permeability in Endotoxic Pigs (1991)

Infusing pigs with lipopolysaccharide (LPS) decreases superior mesenteric artery blood flow (Qsma), suggesting that mesenteric hypoperfusion may be responsible for LPS-induced alterations in gut mucosal permeability. To test this hypothesis, we studied four groups of anesthetized swine. Group 1 animals (N = 6) were infused with LPS (250 micrograms/kg over 1 hour beginning at 60 minutes) and continuously resuscitated with Ringer's lactate (48 mL/kg per hour). In group 2 (N = 5), Qsma was decreased by 50% by means of a mechanical occluder to mimic the LPS-induced alterations in Qsma observed in group I. Group 3 (N = 5) was included to document our ability to detect ischemia/reperfusion-induced alterations in mucosal permeability; in these pigs, Qsma was decreased in steps to zero flow (at 150 to 210 minutes) and then perfusion was restored (at 210 to 270 minutes). Pigs in group 4 (N = 6) served as normal controls; these animals were resuscitated with Ringer's lactate at the same rate as in group 1 but were not infused with LPS. To assess mucosal permeability, we measured plasma-to-lumen clearances for two markers, chromium 51-labeled edetic acid monohydrate (EDTA) and urea. Loading and maintenance infusions of the markers were given intravenously, and a 20-cm isolated segment of small intestine was continuously perfused at 2 mL/min with Ringer's lactate at 37 degrees C. Results were expressed as the ratio of the clearances for the two probes (CEDTA/CUREA). In group 3, CEDTA/CUREA was 999% +/- 355% of baseline at 270 minutes. In group 1, CEDTA/CUREA was 572% +/- 235% of baseline at 270 minutes. In groups 2 and 4, however, CEDTA/CUREA did not change significantly from the baseline value over the duration of the study. These data suggest that increased mucosal permeability after LPS is due to factors other than (or in addition to) mesenteric hypoperfusion.
Model-driven Visual Analytics (2008)

We describe a visual analytics (VA) infrastructure, rooted on techniques in machine learning and logic-based deductive reasoning that will assist analysts to make sense of large, complex data sets by facilitating the generation and validation of models representing relationships in the data. We use logic programming (LP) as the underlying computing machinery to encode the relations as rules and facts and compute with them. A unique aspect of our approach is that the LP rules are automatically learned, using Inductive Logic Programming, from examples of data that the analyst deems interesting when viewing the data in the high-dimensional visualization interface. Using this system, analysts will be able to construct models of arbitrary relationships in the data, explore the data for scenarios that fit the model, refine the model if necessary, and query the model to automatically analyze incoming (future) data exhibiting the encoded relationships. In other words it will support both model-driven data exploration, as well as data-driven model evolution. More importantly, by basing the construction of models on techniques from machine learning and logic-based deduction, the VA process will be both flexible in terms of modeling arbitrary, user-driven relationships in the data as well as readily scale across different data domains.
Genomic Insights into the Immune System of the Sea Urchin (2006)

Comparative analysis of the sea urchin genome has broad implications for the primitive state of deuterostome host defense and the genetic underpinnings of immunity in vertebrates. The sea urchin has an unprecedented complexity of innate immune recognition receptors relative to other animal species yet characterized. These receptor genes include a vast repertoire of 222 Toll-like receptors, a superfamily of more than 200 NACHT domain-leucine-rich repeat proteins (similar to nucleotide-binding and oligomerization domain (NOD) and NALP proteins of vertebrates), and a large family of scavenger receptor cysteine-rich proteins. More typical numbers of genes encode other immune recognition factors. Homologs of important immune and hematopoietic regulators, many of which have previously been identified only from chordates, as well as genes that are critical in adaptive immunity of jawed vertebrates, also are present. The findings serve to underscore the dynamic utilization of receptors and the complexity of immune recognition that may be basal for deuterostomes and predicts features of the ancestral bilaterian form.
Substituent effects in the pyrolysis of aryl n-propyl sulfoxides (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSubstituent effects in the pyrolysis of aryl n-propyl sulfoxidesDavid W. Emerson and Thomas J. KorniskiCite this: J. Org. Chem. 1969, 34, 12, 4115–4118Publication Date (Print):December 1, 1969Publication History Published online1 May 2002Published inissue 1 December 1969https://doi.org/10.1021/jo01264a076RIGHTS & PERMISSIONSArticle Views148Altmetric-Citations38LEARN 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 InReddit PDF (571 KB) Get e-Alerts Get e-Alerts
A One Pot Procedure for the Synthesis of α-Hydroxyamides from the Corresponding α-Hydroxyacids (1992)

Abstract α-Hydroxyamides are synthesized from the cooresponding α-hydroxyacids by generation of the bis-trimethylsilyl derivative and treating it with oxalyl chloride. Following addition of the appropriate amine, the TMS ether is hydrolyzed in the workup to provide the desired α-hydroxyamide. As summarized in Table I, this reaction has proven to be general and compatible with chiral α-hydroxyacids affording the desired α-hydroxyamides in excellent yield (77–99%).
Can External Monitoring Affect Corporate Financial Reporting and Disclosure? Evidence from Earnings and Expectations Management (2014)

SYNOPSIS This study examines whether financial analysts and institutional investors play a disciplinary role in monitoring corporate financial reporting and disclosure. Using a sample of firms that meet or marginally beat analysts' forecasts, likely through upward earnings management and downward expectations management, this study shows that managers' use of the two tactics is associated with monitoring measures, including analyst following, analyst experience and independence, institutional ownership, and institutional investors' experience and investment style. Managers under more effective monitoring by analysts and institutional investors are more likely to manage expectations downward than to manage earnings upward. Overall, the findings are consistent with financial analysts and institutional investors playing a monitoring role in constraining distortions in reported earnings and inducing timely disclosure of bad news. Data Availability: All data are from public sources.
Novel Avidin-like Protein from a Root Nodule Symbiotic Bacterium, Bradyrhizobium japonicum (2005)

Bradyrhizobium japonicum is an important nitrogenfixing symbiotic bacterium, which can form root nodules on soybeans. These bacteria have a gene encoding a putative avidin- and streptavidin-like protein, which bears an amino acid sequence identity of only about 30% over the core regions with both of them. We produced this protein in Escherichia coli both as the full-length wild type and as a C-terminally truncated core form and showed that it is indeed a high affinity biotin-binding protein that resembles (strept)avidin structurally and functionally. Because of the considerable dissimilarity in the amino acid sequence, however, it is immunologically very different, and polyclonal rabbit and human antibodies toward (strept)avidin did not show significant cross-reactivity with it. Therefore this new avidin, named bradavidin, facilitates medical treatments such as targeted drug delivery, gene therapy, and imaging by offering an alternative tool for use if (strept)avidin cannot be used, because of a deleterious patient immune response for example. In addition to its medical value, bradavidin can be used both in other applications of avidin-biotin technology and as a source of new ideas when creating engineered (strept)avidin forms by changing or combining the desired parts, interface patterns, or specific residues within the avidin protein family. Moreover, the unexpected discovery of bradavidin indicates that the group of new and undiscovered bacterial avidin-like proteins may be both more diverse and more common than hitherto thought.
A Conserved HPD Sequence of the J-domain Is Necessary for YDJ1 Stimulation of Hsp70 ATPase Activity at a Site Distinct from Substrate Binding (1996)

The 46-kDa protein YDJ1 is one of several known yeast homologues of the Escherichia coli DnaJ protein. Like all J homologues, it shares homology with the highly conserved NH2-terminal "J-domain" of DnaJ. A component of the DnaK (Hsp70) chaperone machinery that mediates protein folding, DnaJ is necessary for survival at elevated temperatures. It stimulates ATP hydrolysis by DnaK and effects the release of DnaK-bound polypeptides. Previous genetic and biochemical studies indicate that the J-domain is necessary for these functions. Using peptides corresponding to J-domain sequence, we show that a peptide containing the highly conserved His-Pro-Asp sequence at positions 34-36 in the J-domain competes off YDJ1 stimulation of Hsp70 ATPase activity. Inhibitory concentrations of peptide do not prevent binding of folding substrates, therefore YDJ1 must interact with Hsp70 at a site distinct from that for substrate binding. This interaction is critical for Hsp70 activity, since a mutant YDJ1 protein harboring a H34Q change (ydj1Q34) stimulates neither Hsp70 ATPase nor substrate release. The importance of the proper function of this region of the protein is supported by the poor growth and temperature-sensitive phenotype of yeast expressing ydj1Q34.
Quantitative detection of E. coli, E. coli O157 and other shiga toxin producing E. coli in water samples using a culture method combined with real-time PCR (2006)

Recent water related outbreaks of shiga toxin producing E. coli O157 have resulted in increased attention of the water industry to this potentially deadly pathogen. Current methods to detect E. coli O157 and its virulence genes are laborious and time-consuming. Specificity, sensitivity and simple use of a real-time PCR method makes it an attractive alternative for the detection of STEC E. coli O157. This study describes the development and application of real-time PCR methods for the detection of E. coli O157, shiga toxin genes (Stx1 and Stx2) and E. coli. The specificity of the methods was confirmed by performing colony-PCR assays on characterized bacterial isolates, demonstrating the applicability of these assays as rapid tests to confirm the presence of E. coli or E. coli O157 colonies on culture plates. Sensitive culture-PCR methods were developed by combining culture enrichment with real-time PCR detection. This rapid method allowed detection of low concentrations of E. coli O157 in the presence of high concentrations of non-O157-E. coli (1:104). Culture-PCR methods were applied to 27 surface water and 4 wastewater samples. E. coli O157 and both Stx genes were detected in two wastewater samples, whereas only E. coli O157 was detected in two surface water samples. Culture-PCR methods were not influenced by matrix effects and also enabled quantitative (MPN) detection of E. coli in these samples.
Distribution of specific serum IgE to recombinant pollen allergens (rPhlp1, rPhlp2, rPhlp5, and rBetv2) and their relationship to each other and to their natural counterparts in patients allergic to grass pollen (2000)

Recombinant pollen allergens rPhlp1, rPhlp2, rPhlp5, and rBetv2 may function as effective markers of atopy and account for a substantial proportion of grass pollen-specific IgE. The purpose of the present study was to determine the frequency of IgE antibodies to rPhlp1, rPhlp2, rPhlp5 and rBetv2 in patients allergic to grass pollen. Blood was taken from 436 patients, aged 4-70 years, with allergy to grass. The sample was stratified by 10-year age groups. Specific serum IgE were measured by the immunoenzymatic CAP Fluoroenzyme Immunoassay System. Specific IgE binding to rPhlp1, rPhlp5, rPhlp2, was, respectively, detected in 388 (88.9%), 353 (80.9%) and 265 (60.7%) of 436 patients. Sera from 252 patients (57.7%) showed IgE binding to rPhlp1, rPhlp2 and rPhlp5; sera from 102 patients (23.3%) reacted to rPhlp1 and rPhlp5, but not rPhlp2; 30 sera (6.8%) reacted to rPhlp1 but not rPhlp2 and rPhlp5; 22 sera (5.1%) reacted only to rPhlp5; one serum reacted to rPhlp2 (0.2%); and nine sera (2%) did not react to recombinant allergens. It was found that patients in the age group 0-20 years had higher IgE levels to timothy grass and rPhlp1, rPhlp2 and rPhlp5, than patients in the older age group (41-60 years). We found, as expected, seasonal variation of IgE levels to recombinant allergens and natural allergen. Allergens rPhlp1, rPhlp2 and rPhlp5 were extremely positively correlated with timothy grass and rBetv2, but not rBetv1. These results encourage the use of recombinant pollen allergens for diagnosis and to improve specific immunotherapy in the near future.
The Effect of AlPO[sub 4]-Coating Layer on the Electrochemical Properties in LiCoO[sub 2] Thin Films (2006)

-coated thin films showed electrochemical properties superior to those of bare film. Moreover, the electrochemical properties of the coated films were affected by the nanostructures of the -coating layer, which was deposited at various deposition temperatures. In particular, coated with deposited at showed optimal capacity retention. It was found that the -coating layer effectively suppressed the increase in the charge-transfer resistance during cycling, as measured by electrochemical impedance spectroscopy. This dependence on the deposition temperature was attributed to the nanostructures of the -coating layer, and to interdiffusion at the interface between the and the nanoscale-coating layer.
Impact of 5-fluorouracil metabolizing enzymes on chemotherapy in patients with resectable colorectal cancer (2014)

Although 5-fluorouracil (5-FU) is an important drug for colorectal cancer (CRC) treatment, no useful biomarker is currently available to predict treatment response. Since 5-FU is converted into active or inactive forms by orotate phosphoribosyltransferase (OPRT) or dihydropyrimidine dehydrogenase (DPD), a correlation between these enzymes and response to 5-FU has been suggested. However, such a correlation has not been investigated prospectively. Therefore, in the present study, we aimed to prospectively evaluate whether OPRT and DPD were predictive factors of the response to 5-FU treatment in patients with resectable CRC. The present investigation was designed as a multicenter prospective cohort study. OPRT and DPD activities were assessed in biopsy samples, obtained surgically from patients with resectable CRC. The OPRT/DPD ratio was calculated and the cut-off values for this ratio were determined for 5-year disease-free survival (DFS) and overall survival (OS). Patients were treated with 5-FU/leucovorin (LV) regimens and oral 5-FU. The endpoint of this study was the correlation between the OPRT/DPD ratio and 5-year DFS and OS. The cut-off value for the OPRT/DPD ratio was determined by using the maximum χ2 statistic method against 5-year DFS and OS. Sixty-eight patients were enrolled from July 2003 to May 2005. The median follow-up period was 1925 days. The OPRT/DPD ratio cut-off values for 5-year DFS and OS were 0.015 and 0.013, respectively. During the 5-year DFS and OS periods, patients with higher cut-off values had a better prognosis than those with lower ratios (P=0.03 and 0.02, respectively). In conclusion, our results suggest that the OPRT/DPD ratio could be a predictive factor for response to 5-FU/LV adjuvant chemotherapy.