gebhart/patrepeval huggingface dataset:
Single-Copy Green Fluorescent Protein Gene FusionsAllow Accurate Measurement of <i>Salmonella</i> Gene Expression InVitro and during Infection of MammalianCells (2003)

We developed a reliable and flexible green fluorescent protein (GFP)-based system for measuring gene expression in individual bacterial cells. Until now, most systems have relied upon plasmid-borne gfp gene fusions, risking problems associated with plasmid instability. We show that a recently developed GFP variant, GFP+, is suitable for assessing bacterial gene expression. Various gfp+ transcriptional fusions were constructed and integrated as single copies into the chromosome of Salmonella enterica serovar Typhimurium. A comparison of the expression levels of proU-lacZ and proU-gfp+ fusions showed that GFP+ reported proU activity in individual Salmonella cells as accurately as beta-galactosidase reported activity for entire populations. The single-copy gfp+ fusions were ideal for monitoring up- and downregulation of Salmonella virulence genes. We discovered that in vitro induction of the SPI1gene prgH occurs only in a portion of the population and that the proportion varies with the growth phase. We determined the level of expression of the SPI2 gene ssaG in bacteria released from murine macrophages. Our results demonstrate for the first time that single-copy GFP+ fusions reliably report gene expression in simple and complex environments. This approach promises to allow accurate measurement of gene expression in individual bacteria during animal infection.
Combined Inhibition of CCL2, CX3CR1, and CCR5 Abrogates Ly6C <sup>hi</sup> and Ly6C <sup>lo</sup> Monocytosis and Almost Abolishes Atherosclerosis in Hypercholesterolemic Mice (2008)

CCL2, CX3CR1, and CCR5 play independent and additive roles in atherogenesis. Signals mediated through these pathways critically determine the frequency of circulating monocyte subsets and thereby account for almost all macrophage accumulation into atherosclerotic arteries.
Bootstrapping higher-order program transformers from interpreters (1996)

Article Free Access Share on Bootstrapping higher-order program transformers from interpreters Authors: Michael Sperber Wilhelm-Schickard-Institut, Universität Tübingen, Sand 13, 72076 Tübingen, Germany Wilhelm-Schickard-Institut, Universität Tübingen, Sand 13, 72076 Tübingen, GermanyView Profile , Robert Glück DIKU, Department of Computer Science, University of Copenhagen, Universitetsparken 1, DK-2100 Copenhagen East, Denmark DIKU, Department of Computer Science, University of Copenhagen, Universitetsparken 1, DK-2100 Copenhagen East, DenmarkView Profile , Peter Thiemann Wilhelm-Schickard-Institut, Universität Tübingen, Sand 13, 72076 Tübingen, Germany Wilhelm-Schickard-Institut, Universität Tübingen, Sand 13, 72076 Tübingen, GermanyView Profile Authors Info & Claims SAC '96: Proceedings of the 1996 ACM symposium on Applied ComputingFebruary 1996 Pages 408–413https://doi.org/10.1145/331119.331417Published:18 February 1996Publication History 6citation212DownloadsMetricsTotal Citations6Total Downloads212Last 12 Months11Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Selective Hydrolysis of Fish Oil by Lipase to Concentrate n-3 Polyunsaturated Fatty Acids (1990)

Journal Article Selective Hydrolysis of Fish Oil by Lipase to Concentrate n-3 Polyunsaturated Fatty Acids Get access Tamotsu Hoshino, Tamotsu Hoshino Laboratory of Bioreaction Engineering, Department of Food Science and Technology, School of Agriculture, Nagoya University, Chikusa-ku, Nagoya, 464-01, Japan Search for other works by this author on: Oxford Academic Google Scholar Tsuneo Yamane, Tsuneo Yamane Laboratory of Bioreaction Engineering, Department of Food Science and Technology, School of Agriculture, Nagoya University, Chikusa-ku, Nagoya, 464-01, Japan Corresponding author. Search for other works by this author on: Oxford Academic Google Scholar Shoichi Shimizu Shoichi Shimizu Laboratory of Bioreaction Engineering, Department of Food Science and Technology, School of Agriculture, Nagoya University, Chikusa-ku, Nagoya, 464-01, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 54, Issue 6, 1 June 1990, Pages 1459–1467, https://doi.org/10.1080/00021369.1990.10870149 Published: 01 June 1990 Article history Published: 01 June 1990 Received: 20 December 1990
Whispering gallery mode carousel – a photonic mechanism for enhanced nanoparticle detection in biosensing (2009)

Individual nanoparticles in aqueous solution are observed to be attracted to and orbit within the evanescent sensing ring of a Whispering Gallery Mode micro-sensor with only microwatts of driving power. This Carousel trap, caused by attractive optical gradient forces, interfacial interactions, and the circulating momentum flux, considerably enhances the rate of transport to the sensing region, thereby overcoming limitations posed by diffusion on such small area detectors. Resonance frequency fluctuations, caused by the radial Brownian motion of the nanoparticle, reveal the radial trapping potential and the nanoparticle size. Since the attractive forces draw particles to the highest evanescent intensity at the surface, binding steps are found to be uniform.
PhylloTrees: Phyllotactic Patterns for Tree Layout (2006)

Motivations for drawing hierarchical structures are probably as diverse as datasets to visualize. This ubiquity of tree structures has lead to a manifold of tree layout algorithms and tree visualization systems. While many tree layouts exist, increasingly massive data sets, expanding computational power, and still relatively limited display space make tree layout algorithms a topic of ongoing interest. We explore the use of natures phyllotactic patterns to inform the layout of hierarchical data. These naturally occurring patterns provide a non-overlapping, optimal packing when the total number of nodes is not known a priori. We present PhylloTrees, a family of expandable tree layouts based on these patterns.
Real-time keyframe extraction towards video content identification (2009)

Keyframe extraction constitutes a fundamental unit in many video retrieval-related applications. In the emerging research field of content-based video copy detection, efficient representation of video content at keyframe level is crucial, due to the fact that similarity search is mainly performed between content-representative frames. In this paper a sequential search algorithm that bypasses the process of temporal video segmentation is proposed for keyframe extraction in MPEG videos. We aim at providing an efficient, real-time and fully-automatic way of extracting keyframes in videos, where not only the laborious task of offline video database indexing is avoided, but also query video processing is performed in the same manner as the reference video database. Significant reduction in computational cost is achieved by exploiting DCT coefficients in feature extraction. The effectiveness of the proposed scheme is evaluated in terms of quality and speed on the manually annotated TRECVid 2007 test video dataset.
An unsupervised method for multilingual word sense tagging using parallel corpora (2000)

With an increasing number of languages making their way to our desktops everyday via the Internet, researchers have come to realize the lack of linguistic knowledge resources for scarcely represented/studied languages. In an attempt to bootstrap some of the required linguistic resources for some of those languages, this paper presents an unsupervised method for automatic multilingual word sense tagging using parallel corpora. The method is evaluated on the English Brown corpus and its translation into three different languages: French, German and Spanish. A preliminary evaluation of the proposed method yielded results of up to 79% accuracy rate for the English data on 81.8% of the SemCor manually tagged data.
Automated lung segmentation in digital chest tomosynthesis (2012)

The method achieved relatively high accuracy for lung segmentation and will be useful for computer-aided detection of lung nodules in digital tomosynthesis.
Interspecific crossing among the new world lupin species for Lupinus mutabilis crop improvement. (2008)

There are as many as 300 New World lupin species, distributed from Alaska to the extreme south of South America. Only one species among these, Lupinus mutabilis has achieved crop status while several other species have been used as ornamentals or for land rehabilitation. L. mutabilis has considerable potential as a high protein and oil legume and it is phylogenetically related to the western North and South American lupins most of which share the chromosome number 2n = 48. The genetic variation in these species may provide useful traits for L. mutabilis breeding and a series of crosses was attempted to initiate an introgression program. We have obtained hybrids between L. mutabilis and each of L. mexicanus (both a germplasm accession and a horticultural accession listed as ‘L. hartwegii ’), L. arizonicus and a South American species, L. tomentosus . Pod retention and immature seed growth after hand crossing and pollen viability data from F 1 hybrids indicated a moderate degree of compatibility between L. mutabilis and the other species. Embryo rescue was not required for the cross combinations: L. hartwegii × L. mutabilis and L. mutabilis × L. tomentosus however L. mutabilis × L. mexicanus, L. hartwegii , and L. arizonicus each required embryo rescue to produce F 1 plants. Additional species are being crossed to L. mutabilis and the results reported in this paper. Hybrids show intermediate morphological characters and reduced pollen viability from flowers produced on F 1 interspecific plants. Tripping and backcrossing is being carried out to improve hybrid fertility and BC 1 progeny will be advanced as potential parents in the crop improvement of L. mutabilis .
Mass Spectrometry in the Biological Sciences (1996)

Leading practitioners describe in detail advanced methods of mass spectrometry used in structural characterization of biomacromolecules of both natural and recombinant origin. They demonstrate by exam
A 250-MHz skewed-clock pipelined dual-port embedded DRAM (2002)

A special-purpose dual-port dynamic memory suitable for use in a variety of digital switching and signal processing applications is described. The memory design is based on a dual-port three-transistor (3T) cell that occupies less than half the area of a conventional dual-port SRAM cell. Hamming error correction coding (ECC) is used to improve the memory's immunity to soft errors, as well as enhance its fabrication yield. Skewed-clock pipelining permits operation at clock rates as high as 250 MHz, and a compact low power sense amplifier circuit allows the use of a wide data bus to increase the memory's bandwidth.
Efficient Receive Beamformers for Secure Spatial Modulation Against a Malicious Full-Duplex Attacker With Eavesdropping Ability (2021)

In this paper, we consider a new secure spatial modulation scenario with a full-duplex (FD) malicious attacker Mallory owning eavesdropping capacity, where Mallory works on FD model and transmits a malicious jamming such as artificial noise (AN) to interfere with legitimate user Bob. To suppress the malicious jamming on Bob from Mallory, a conventional maximum receive power (Max-RP) at Bob is presented firstly. Subsequently, to exploit the colored property of noise plus interference at Bob, a whitening-filter-based Max-RP (Max-WFRP) is proposed with an obvious performance enhancement over Max-RP. To completely remove the malicious jamming from Mallory, a Max-RP with a constraint of forcing the malicious jamming from Mallory to zero at Bob is proposed. To further improve secrecy rate (SR) by removing the zero-forcing contraint (ZFC), the maximum signal-to-jamming-plus-noise ratio (Max-SJNR) is proposed. Our proposed methods have closed-form expressions. Simulation results show that the four receive beamforming methods have an increasing order in performance: Max-RP, Max-RP with ZFC, and Max-SJNR ≈ Max-WFRP. Additionally, the latter two harvest a substantial performance gains over Max-RP and Max-RP with ZFC in the low and medium signal-to-noise ratio regions.
Electronic Records and Signatures under the Federal E-Sign Legislation and the UETA (2000)

PELD has reliable efficacy and safety in the treatment of LDH linked with PRAS.
Human Interferon Production: Superinduction by 5,6-Dichloro-1-β-D-Ribofuranosylbenzimidazole (1975)

Polyinosinic.polycytidylic acid [poly(I.C)] induced production of interferon by a strain of diploid human fibroblasts (FS-4), measured between 5 and 24 hours from induction, is enhanced up to 128-fold by 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), a reversible inhibitor of nuclear heterogeneous RNA synthesis. A normalized dose-effect plot shows a close correlation between the superinducing effect of DRB and inhibition of RNA synthesis. Cultures that contained DRB continue to produce interferon for up to 4 days. Removal of the drug at any time during this period leads to a prompt shutoff of interferon production.
Expression Profile of Amylolytic Genes in<i>Aspergillus nidulans</i> (2006)

Aspergillus nidulans possessed 16 putative amylolytic genes consisting of 7 alpha-glucosidase (agdA-F), 7 alpha-amylase (amyA-F), and 2 glucoamylase (glaA and B) genes on the genome. Among them, the agdA, agdB, agdE, agdF, amyA, amyB, amyF, and glaB genes were induced by isomaltose. AmyR, a Zn(II)(2)Cys(6) transcription factor, was required for the induction. The isomaltose-inducible genes possessed at least one consensus sequence for AmyR binding, 5'-CGGN(8)CGG, on each promoter region. None of the amylolytic genes was induced by maltose. The mRNA levels of the amylolytic genes except for agdC, amyD, and amyG increased under carbon-starved conditions. Release from CreA-dependent carbon catabolite repression was the main cause of the increase, but, the mRNA levels of agdB, agdF, amyB, amyF, and glaB increased to some extent even in a creA mutant. Therefore, both CreA-dependent and -independent mechanisms are involved in the up-regulation of the amylolytic genes under carbon-starved conditions.
Time-resolved extreme ultraviolet emission from a highly ionized lithium capillary discharge (1989)

A fast discharge current pulse (50 ns FWHM) was used to create a highly ionized plasma in a 500-μm-diam lithium hydride capillary 3.8 cm in length. Time-resolved extreme ultraviolet spectra of the capillary plasma show simultaneous line emission from highly ionized (O VI) and singly ionized (O II) species, indicating the existence of a hot-core plasma (Te&gt;25 eV) surrounded by a significantly cooler plasma near the walls. The intensity of the 72.9 nm emission corresponding to the Li III 3–2 transition was observed to increase during the decay of the current pulse, consistent with excitation by electron-ion recombination. The results are relevant to the possibility of amplification of extreme ultraviolet radiation in a discharge-pumped device.
Quantitative high-throughput screening: A titration-based approach that efficiently identifies biological activities in large chemical libraries (2006)

High-throughput screening (HTS) of chemical compounds to identify modulators of molecular targets is a mainstay of pharmaceutical development. Increasingly, HTS is being used to identify chemical probes of gene, pathway, and cell functions, with the ultimate goal of comprehensively delineating relationships between chemical structures and biological activities. Achieving this goal will require methodologies that efficiently generate pharmacological data from the primary screen and reliably profile the range of biological activities associated with large chemical libraries. Traditional HTS, which tests compounds at a single concentration, is not suited to this task, because HTS is burdened by frequent false positives and false negatives and requires extensive follow-up testing. We have developed a paradigm, quantitative HTS (qHTS), tested with the enzyme pyruvate kinase, to generate concentration-response curves for >60,000 compounds in a single experiment. We show that this method is precise, refractory to variations in sample preparation, and identifies compounds with a wide range of activities. Concentration-response curves were classified to rapidly identify pyruvate kinase activators and inhibitors with a variety of potencies and efficacies and elucidate structure-activity relationships directly from the primary screen. Comparison of qHTS with traditional single-concentration HTS revealed a high prevalence of false negatives in the single-point screen. This study demonstrates the feasibility of qHTS for accurately profiling every compound in large chemical libraries (>10(5) compounds). qHTS produces rich data sets that can be immediately mined for reliable biological activities, thereby providing a platform for chemical genomics and accelerating the identification of leads for drug discovery.
Shear-induced reaction-limited aggregation kinetics of Brownian particles at arbitrary concentrations (2010)

The aggregation of interacting brownian particles in sheared concentrated suspensions is an important issue in colloid and soft matter science per se. Also, it serves as a model to understand biochemical reactions occurring in vivo where both crowding and shear play an important role. We present an effective medium approach within the Smoluchowski equation with shear which allows one to calculate the encounter kinetics through a potential barrier under shear at arbitrary colloid concentrations. Experiments on a model colloidal system in simple shear flow support the validity of the model in the concentration range considered. By generalizing Kramers' rate theory to the presence of shear and collective hydrodynamics, our model explains the significant increase in the shear-induced reaction-limited aggregation kinetics upon increasing the colloid concentration.
Endogenous Growth Factors as Cosmeceuticals (2005)

These data, as well as other studies of growth factors in wound healing, demonstrate positive cosmetic and clinical outcomes of topical application of growth factors for the treatment of photodamaged skin.
A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics (2011)

Shotgun proteomics data analysis usually relies on database search. However, commonly used protein sequence databases do not contain information on protein variants and thus prevent variant peptides and proteins from been identified. Including known coding variations into protein sequence databases could help alleviate this problem. Based on our recently published human Cancer Proteome Variation Database, we have created a protein sequence database that comprehensively annotates thousands of cancer-related coding variants collected in the Cancer Proteome Variation Database as well as noncancer-specific ones from the Single Nucleotide Polymorphism Database (dbSNP). Using this database, we then developed a data analysis workflow for variant peptide identification in shotgun proteomics. The high risk of false positive variant identifications was addressed by a modified false discovery rate estimation method. Analysis of colorectal cancer cell lines SW480, RKO, and HCT-116 revealed a total of 81 peptides that contain either noncancer-specific or cancer-related variations. Twenty-three out of 26 variants randomly selected from the 81 were confirmed by genomic sequencing. We further applied the workflow on data sets from three individual colorectal tumor specimens. A total of 204 distinct variant peptides were detected, and five carried known cancer-related mutations. Each individual showed a specific pattern of cancer-related mutations, suggesting potential use of this type of information for personalized medicine. Compatibility of the workflow has been tested with four popular database search engines including Sequest, Mascot, X!Tandem, and MyriMatch. In summary, we have developed a workflow that effectively uses existing genomic data to enable variant peptide detection in proteomics.
A memory efficient method for fast transposing run-length encoded images (1999)

We present a memory efficient method for transposing a run-length encoded bi-level image. Image transposing is a commonly used operation for affine transformations such as document image deskewing. The best existing method for transposing a run-length image is the pxy table based method. For images of typical engineering drawings, which are large, crowded and noisy, this method requires an exorbitant amount of memory. The method proposed uses a very compact representation of run-length encoded images. Also, it bypasses certain steps from the pxy table based method. Consequently, the saving in memory use is proportional to the number of horizontal runs and the number of vertical (transposed) runs. The computation time for both the methods is almost identical.
Ultrashort pulse generation from a Q-switched AlGaAs laser with CW injection (1991)

International audience
The role of thrombin's Tyr-Pro-Pro-Trp motif in the interaction with fibrinogen, thrombomodulin, protein C, antithrombin III, and the Kunitz inhibitors. (1993)

When amino acids Pro60B, Pro60C, and Trp60D are deleted from thrombin, the resulting mutant (des-PPW) exhibits (compared to the wild-type enzyme): a similar second order rate constant of inhibition (k(on)) for diisopropyl fluorophosphate, and a comparable inhibition constant (K(i)) for benzamidine, suggesting that the charge stabilizing system and the primary binding pocket are little altered, if at all, by the mutation. As predicted from the x-ray structure, des-PPW is remarkably sensitive to the bovine pancreatic trypsin inhibitor, with a K(i) over 3 x 10(3) times tighter relative to thrombin, but des-PPW is also markedly less susceptible to inactivation by antithrombin III, with a k(on) that is over 100-fold lower. The catalytic constant (kcat) for most p-nitroanilide substrates tested is preserved or even increased, but the Michaelis constant (Km) increases. In contrast, the Km for the fibrinogen A alpha-chain is essentially unchanged, whereas kcat decreases approximately 50-fold. Unlike thrombin, the rate of fibrinopeptide B release becomes, following a lag phase, comparable to that of fibrinopeptide A. Inasmuch as des-PPW cleaves an additional peptide bond in the bovine fibrin alpha-chain, it remains a highly specific serine protease, which releases a single peptide from denatured casein (versus two with thrombin). Protein C activation by des-PPW is approximately 30 times slower than by thrombin in the absence, as well as in the presence, of calcium and thrombomodulin. Although this study confirms that the B-insertion restricts access to the active site cleft, it also suggests that other motifs and/or discrete amino acids are mainly responsible for the narrow specificity of thrombin.
Why watermarking is nonsense (2002)

The ease with which early watermarking algorithms were broken has given rise to a new set of schemes that are usually robust to a wide variety of attacks. We argue that this has created an illusion of progress, when in reality there is none. Most published watermarking algorithms, like their predecessors, protect all objects in a neighborhood surrounding the marked object. We point out that while this is necessary, it is very far from being sufficient. To withstand adversarial attack, a watermarking scheme would have to protect all valuable variations of an object, not merely ones that are close to it.