gebhart/patrepeval huggingface dataset:
Site-directed mutagenesis of lysine 58 in a putative ATP-binding domain of the calmodulin-sensitive adenylate cyclase from Bordetella pertussis abolishes catalytic activity (1989)

A 2.7-kb cya A gene fragment encoding the amino-terminal end of the calmodulin-sensitive adenylate cyclase from Bordetella pertussis has been placed under the control of the lac promoter for expression in Escherichia coli. Following induction with isopropyl beta-D-thiogalactoside, calmodulin-sensitive adenylate cyclase activity was detected in a cell extract from E. coli. The expression vector directed the synthesis of a 90-kDa polypeptide that was recognized by rabbit polyclonal antibodies raised against the catalytic subunit of B. pertussis adenylate cyclase. Inspection of the deduced amino acid sequence of the cya A gene product revealed a sequence with homology to consensus sequences for an ATP-binding domain found in many ATP-binding proteins. On the basis of the analysis of nucleotide binding proteins, a conserved lysine residue has been implicated in the binding of ATP. A putative ATP-binding domain in the B. pertussis adenylate cyclase possesses an analogous lysine residue at position 58. To test whether lysine 58 of the B. pertussis adenylate cyclase is a crucial residue for enzyme activity, it was replaced with methionine by oligonucleotide-directed mutagenesis. E. coli cells were transformed with the mutant cya A gene, and the expressed gene product was characterized. The mutant protein exhibited neither basal nor calmodulin-stimulated enzyme activity, indicating that lysine 58 plays a critical role in enzyme catalysis.
Photoelectrochemistry with p-Si electrodes: Effects of inversion (1980)

Reduction of chemical species with redox potentials above the apparent conduction band edge of p-Si were found to be possible with illuminated p-Si in contact with nonaqueous electrolytes. Analysis of the wavelength dependence of the photoreduction current and capacitance data as a function of electrode potential, ac signal frequency, and light intensity shows that this supra-conduction-band-edge reduction is the result of band-edge unpinning, rather than the result of a hot-electron injection process. The band-edge unpinning is caused by the formation of an inversion layer in illuminated p-Si.
Selective blocking of T cell-mediated in vitro cytotoxicity to a xenogeneic tumour by anti-immunoglobulin sera. (1978)

Rejection of a xenograft by BALB/c mice results in a highly potent immune peritoneal population. When these immune cells are analysed by using two in vitro assays in parallel, at least two active cytotoxic mechanisms can be demonstrated. Target cells can be labelled with [125I]iododeoxyuridine (IUdR) before the effector cells are added and the detachment of the DNA from plastic can be used to detect cell-mediated immunity. This is referred to as the direct cytotoxicity test. This assay is largely dependent on T-cell function and evidence is presented here that it can be inhibited by anti-immunoglobulin (anti-Ig) antisera. The second test, which reflects the inhibition of incorporation of IUdR by previously mixed effector and target cells, is called the cytostatic assay. This test, although presumably affected by cytotoxic T cells, also reflects a T-independent mechanism which is not inhibited by anti-Ig sera.
ChemInform Abstract: ZINC SELENIDE PHOTOELECTRODES. EFFICIENT RADIATIVE RECOMBINATION IN A STABLE PHOTOELECTROCHEMICAL CELL (1984)

Abstract Das Photo‐ und Elektrolumineszenzverhalten einkristalliner n‐ZnSe:Al‐Elektroden werden untersucht.
On the Use and Limits of Mass Spectrometry for the Characterization of Fluorocarbon Emission during Plasma Processing (2002)

This paper deals with the quadrupole mass spectrometric evaluation of fluorocompound emissions during plasma processing. A critical discussion of the analytical procedure including the estimation of quantification limits, detection limits, and t-Student test, is reported. The utilization of positive and negative chemical ionization as the ionization source to reduce the interference due to peak overlapping is also examined. © 2002 The Electrochemical Society. All rights reserved.
Active Queue Management of TCP/IP Networks Using Rule-Based Predictive Control (2007)

Model predictive controllers, due to their capability to control the time variant and delayed systems, are considered for congestion control in computer networks. To extend the application of these controllers as an active queue management (AQM) system in dynamic TCP/IP networks, a new rule-based predictive controller is proposed. This controller uses the small signal linearized fluid-flow model of the TCP/IP networks and simulates the future behavior of control system by applying few candidate control sequences. Using the extremes of the resulted predicted output sequences, optimal control signal is determined based on some appropriate rules. This approach benefits from the mentioned capabilities of the model predictive controllers while the computational complexity is reduced compared to the commonly used MPC schemes. Low queue fluctuation, fast response and good disturbance rejection are the features of the proposed controller which are compared via simulations with those of PI and RED, the two well-known AQM methods.
A Zero Error Propagation Extension to H264 for Low Delay Video Communications Over Lossy Channels (2006)

In this paper, we introduce a method for video transmission over lossy channels. The proposed method is similar to NEWPRED and uses feedback information to stop error propagation. Main operational difference is replication of packet loss and error concealment process at the encoder and using the possibly error concealed frames as reference frames in the motion prediction loop. We have studied the optimization of the proposed method under moderate error rates where ACK/NACK mode NEWPRED does not efficiently solve the problem. The proposed solution is an adaptive method that optimizes the operation based on the expected error propagation. We present comparison results with NEWPRED under various channel conditions and video sources.
A Quantitative In Vitro Potency Assay for Adeno-Associated Virus Vectors Encoding for the UGT1A1 Transgene (2020)

Potency assessment of clinical-grade vector lots is crucial to support adeno-associated virus (AAV) vector release and is required for future marketing authorization. We have developed and validated a cell-based, quantitative potency assay that detects both transgenic expression and activity of an AAV8-h<i>UGT1A1</i> vector, which is currently under clinical evaluation for the treatment of Crigler-Najjar syndrome. Potency of AAV8-h<i>UGT1A1</i> was evaluated <i>in vitro</i>. After transduction of human hepatoma 7 (Huh7) cells, transgene-positive cells were quantified using flow cytometry and transgenic activity by a bilirubin conjugation assay. The <i>in vitro</i> potency of various AAV8-hUGT1A1 batches was compared with their potency <i>in vivo</i>. After AAV8-h<i>UGT1A1</i> transduction, quantification of UGT1A1-expressing cells shows a linear dose-response relation (R<sup>2</sup> = 0.98) with adequate intra-assay and inter-day reproducibility (coefficient of variation [CV] = 11.0% and 22.6%, respectively). In accordance, bilirubin conjugation shows a linear dose-response relation (R<sup>2</sup> = 0.99) with adequate intra- and inter-day reproducibility in the low dose range (CV = 15.7% and 19.7%, respectively). Both <i>in vitro</i> potency assays reliably translate to <i>in vivo</i> efficacy of AAV8-h<i>UGT1A1</i> vector lots. The described cell-based potency assay for AAV8-h<i>UGT1A1</i> adequately determines transgenic UGT1A1 expression and activity, which is consistent with <i>in vivo</i> efficacy. This novel approach is suited for the determination of vector lot potency to support clinical-grade vector release.
Smart materials for energy storage in Li-ion batteries (2016)

Advanced lithium-ion batteries contain smart materials having the function of insertion electrodes in the form of powders with specific and optimized electrochemical properties. Different classes can be considered: the surface modified active particles at either positive or negative electrodes, the nano-composite electrodes and the blended materials. In this paper, various systems are described, which illustrate the improvement of lithium-ion batteries in term of specific energy and power, thermal stability and life cycling.
Inactivation of Zika virus in plasma with amotosalen and ultraviolet A illumination (2015)

In this study we demonstrate that amotosalen combined with UVA light inactivates ZIKV in fresh-frozen plasma. This inactivation process is of particular interest to prevent plasma transfusion-transmitted ZIKV infections in areas such as French Polynesia, where several arboviruses are cocirculating.
Using Muzzle Pattern Recognition as a Biometric Approach for Cattle Identification (2007)

Arising from the current need for positive identification for cattle traceability, the objective of this work was to investigate the feasibility of using muzzle pattern as a biometric-based identifier for cattle by acquiring muzzle patterns through lifted ink prints and through digital images. A three-stage matching algorithm was evaluated for scanned muzzle ink prints and performed successfully in all cases. Digital imaging of muzzles was far simpler than the ink print lifting method. For these digital images, the techniques of principal component analysis and Euclidean distance classifier were used. The algorithm training was performed independently on a different number of normalized muzzle images from 29 cattle (sets of 2, 4, 6, 8, and 10 training images per animal). The performance of this technique was assessed on a separate set of images (3 normalized muzzle images per animal). Results showed that when using 230 eigenvectors (out of 290), the recognition rate was 98.85%, and that additional eigenvectors did not improve the recognition rate. As expected, fewer principal components (less than 230) reduced the recognition rate, while a higher number of training images per animal improved it. Although the results have demonstrated the potential of muzzle pattern recognition as a non-invasive, inexpensive, and accurate biometric identifier of cattle, further research towards automation is necessitated.
Novel Rhamnogalacturonan I and Arabinoxylan Polysaccharides of Flax Seed Mucilage (2008)

The viscous seed mucilage of flax (Linum usitatissimum) is a mixture of rhamnogalacturonan I and arabinoxylan with novel side group substitutions. The rhamnogalacturonan I has numerous single nonreducing terminal residues of the rare sugar l-galactose attached at the O-3 position of the rhamnosyl residues instead of the typical O-4 position. The arabinoxylan is highly branched, primarily with double branches of nonreducing terminal l-arabinosyl units at the O-2 and O-3 positions along the xylan backbone. While a portion of each polysaccharide can be purified by anion-exchange chromatography, the side group structures of both polysaccharides are modified further in about one-third of the mucilage to form composites with enhanced viscosity. Our finding of the unusual side group structures for two well-known cell wall polysaccharides supports a hypothesis that plants make a selected few ubiquitous backbone polymers onto which a broad spectrum of side group substitutions are added to engender many possible functions. To this end, modification of one polymer may be accompanied by complementary modifications of others to impart functions to heterocomposites not present in either polymer alone.
Efficient Transfection of Hepatocytes Mediated by mRNA Complexed to Galactosylated Cyclodextrins (2012)

In this study, we aimed at specific targeting of polycationic amphiphilic cyclodextrins (paCDs) to HepG2 cells via the asialoglycoprotein receptor (ASGPr). The transfection efficiencies of paCDs modified with galactose moieties were evaluated. In preliminary experiments, attempts to transfect HepG2 cells with pDNA complexed with different modified paCDs resulted in very low transfection levels. In additional series of experiments, we found out that nucleic acid/cyclodextrin complexes (CDplexes) were efficiently taken up by the cells and that photochemical internalization, which facilitates release from endosomes, did not improve transfection. Further experiments showed that pDNA can be readily released from the CDplexes when exposed to negatively charged vesicles. These observations imply that the lack of transfection cannot be attributed to a lack of internalization, release of CDplexes from the endosomal compartment, or release of free pDNA from the CDplexes. This in turn suggests that the nuclear entry of the pDNA represents the main limiting factor in the transfection process. To verify that HepG2 cells were transfected with targeted CDplexes containing mRNA, which does not require entry into the nucleus for being translated. With mRNA encoding the green fluorescent protein, fractions of GFP-positive cells of up to 31% were obtained. The results confirmed that the galactosylated complexes are specifically internalized via the ASGPr.
Reaction of 1,4,5,6-tetrahydronicotinamide with hydroxylamine [isoxazolinones and aminocyanopentanoic acid] (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of 1,4,5,6-tetrahydronicotinamide with hydroxylamine [isoxazolinones and aminocyanopentanoic acid]Louis D. Quin and Dallas O. PinionCite this: J. Org. Chem. 1970, 35, 9, 3130–3134Publication Date (Print):September 1, 1970Publication History Published online1 May 2002Published inissue 1 September 1970https://pubs.acs.org/doi/10.1021/jo00834a058https://doi.org/10.1021/jo00834a058research-articleACS PublicationsRequest reuse permissionsArticle Views117Altmetric-Citations9LEARN 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-Alertsclose Get e-Alerts
Imaging Three-Dimensional Cardiac Function (2000)

The three-dimensional (3-D) nature of myocardial deformations is dependent on ventricular geometry, muscle fiber architecture, wall stresses, and myocardial-material properties. The imaging modalities of X-ray angiography, echocardiography, computed tomography, and magnetic resonance (MR) imaging (MRI) are described in the context of visualizing and quantifying cardiac mechanical function. The quantification of ventricular anatomy and cavity volumes is then reviewed, and surface reconstructions in three dimensions are demonstrated. The imaging of myocardial wall motion is discussed, with an emphasis on current MRI and tissue Doppler imaging techniques and their potential clinical applications. Calculation of 3-D regional strains from motion maps is reviewed and illustrated with clinical MRI tagging results. We conclude by presenting a promising technique to assess myocardial-fiber architecture, and we outline its potential applications, in conjunction with quantification of anatomy and regional strains, for the determination of myocardial stress and work distributions. The quantification of multiple components of 3-D cardiac function has potential for both fundamental-science and clinical applications.
KapI, a non-essential member of the Pse1p/Imp5 karyopherin family, controls colonial and asexual development in Aspergillus nidulans (2009)

Asexual development in the filamentous fungus Aspergillus nidulans is governed by the timely expression and cellular localization of multiple transcription factors. Hence, factors mediating import and export across the nuclear pore complexes (karyopherins) are expected to play a key role in coordinating the developmental programme. Here we characterize KapI, a putative homologue of the Saccharomyces cerevisiae Kap121/Pse1p karyopherin. KapI is a non-essential importin-beta-like protein located in the nucleus during vegetative growth and conidiophore development. The DeltakapI phenotype is aconidial with many aerial hyphae. This phenotype can be suppressed under abiotic stress. In this regard, it resembles that of the null allele of the bZIP transcription factor FlbB. However a DeltaflbB; DeltakapI double mutant exhibited an additive phenotype with totally impaired conidiation, unresponsive to abiotic stress. In contrast to DeltaflbB, the null kapI mutant is not a fluffy-low-bristle expression mutant. Taken together the findings indicate that KapI is required during asexual development, mediating the nuclear transport of factors acting in a different pathway(s) from those involving the upstream developmental activators.
Respiratory Tract Colonization and Infection in Patients With Chronic Tracheostomy. A One-Year Study in Patients Living at Home (1996)

The high rate of complications, especially respiratory tract infection (RTI), reported in patients with chronic tracheostomy (CT) has discouraged physicians from using this method. However, previous studies of CT have concerned mainly hospitalized patients. We have followed the bacterial colonization patterns of the upper and lower respiratory tract and recorded all RTIs in 39 outpatients with CT during a 12-mo period. Patients were colonized with one or more potential pathogens at the stomal site and in the trachea in 95% and 83%, respectively, of all sampling occasions. Staphylococcus aureus, gram-negative enteric bacteria (GNEB), and Pseudomonas aeruginosa were the most common colonizing bacteria at these sites. Seventy percent of bronchial-protected brush cultures were negative, despite simultaneous heavy colonization of the stomal site or the trachea. Only 18 of 39 (46%) patients were treated with antibiotics because of RTIs on a total of 30 occasions during the study year. Of these, only five episodes of pneumonia in four patients were registered, corresponding to an incidence of about 10 per 100 person years. We conclude that outpatients with chronic tracheostomy can be managed with a low risk for developing severe RTIs, despite massive airway colonization with potentially pathogenic bacteria.
Personal workflows: Modeling and management (2003)

Abstract. As mobile devices are getting powerful, reliable, and inexpensive, more and more personal services have been introduced to individuals via their mobile devices. These services enable users to perform a broad range of activities at any time and anywhere. While a lot of research and development effort has been focusing on extending the scope of activities that can be carried out on mobile devices, little attempt has been made to provide process-oriented services. In this paper, we propose a model for specifying and querying personal processes. This model is equipped with a set of operations that allow mobile users to express queries on their personal processes. Answers of these queries will help mobile users in planning their activities while they are on the move. We have designed and implemented a prototyped personal workflow system on Palm Pilot PDA based on the proposed model. Experiences with this implementation are provided. 1
Epithelial Antimicrobial Peptides: Guardian of the Oral Cavity (2014)

Gingival epithelium provides first line of defence from the microorganisms present in dental plaque. It not only provides a mechanical barrier but also has an active immune function too. Gingival epithelial cells participate in innate immunity by producing a range of antimicrobial peptides to protect the host against oral pathogens. These epithelial antimicrobial peptides (EAPs) include the β-defensin family, cathelicidin (LL-37), calprotectin, and adrenomedullin. While some are constitutively expressed in gingival epithelial cells, others are induced upon exposure to microbial insults. It is likely that these EAPs have a role in determining the initiation and progression of oral diseases. EAPs are broad spectrum antimicrobials with a different but overlapping range of activity. Apart from antimicrobial activity, they participate in several other crucial roles in host tissues. Some of these, for instance, β-defensins, are chemotactic to immune cells. Others, such as calprotectin are important for wound healing and cell proliferation. Adrenomedullin, a multifunctional peptide, has its biological action in a wide range of tissues. Not only is it a potent vasodilator but also it has several endocrine effects. Knowing in detail the various bioactions of these EAPs may provide us with useful information regarding their utility as therapeutic agents.
Factors in Tissue Handling and Processing That Impact RNA Obtained From Formalin-fixed, Paraffin-embedded Tissue (2008)

Formalin-fixed, paraffin-embedded (FFPE) tissue is the most common specimen available for molecular assays on tissue after diagnostic histopathological examination. RNA from FFPE tissue suffers from strand breakage and cross-linking. Despite excellent extraction methods, RNA quality from FFPE material remains variable. To address the RNA quality factors within FFPE tissues, we studied RNA quality, isolating individual elements of the tissue fixation and processing including length of fixation in formalin and the type of buffer incorporated in the fixative. We examined the impact of the length of the tissue processing cycle as well. The optimal fixation period of 12-24 hr in phosphate-buffered formalin resulted in better-quality RNA. Longer tissue processing times were associated with higher quality RNA. We determined that the middle region of gene suffers less damage by these processes as shown by real-time quantitative RT-PCR. These data provide key information for the development of methods of analysis of gene expression in archival FFPE tissues and contribute to the establishment of objective standards for the processing and handling of tissue in surgical pathology. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.
Effect of gender and obesity on electrical current thresholds (2011)

We suggest that both gender and obesity factors should be carefully considered in the design of rational ES treatments.
Development of Biological Approaches to Improve Muscle Healing After Injury and Disease (2012)

Unique among adult tissues, skeletal muscle possesses a robust regeneration capacity dependent upon satellite cells (SC), the professional muscle stem cell. SCs are normally quiescent in a niche located within the basal lamina but outside the muscle membrane, or sarcolemma. Activated SCs proliferate and migrate to the site of injury. Through asymmetric division, a portion of SCs return to quiescence while daughter cells committed to the myogenic lineage, termed myoblasts, fuse and eventually form new muscle fibers. Yet, despite this potential, severely damaged muscle requires medical intervention. In addition to injuries resulting from blunt trauma, work, or sports-related accidents, there are a number of muscle diseases, both inherited, and acquired. At this time, there are no pharmaceutical drugs that can be used to effectively accelerate muscle healing following injury. Here, we discuss new biological approaches to improve muscle healing such as growth factor delivery, myoblast transfer therapy, stem cell-based therapy, gene therapy, and combining biological therapeutics.