gebhart/patrepeval huggingface dataset:
Technology evaluation: HIV ribozyme gene therapy, Gene Shears Pty Ltd. (2000)

Ribozymes (catalytic RNAs) can be made to specifically cleave target RNAs that are involved in disease conditions and therefore have potential as therapeutic agents. Gene Shears Pty Ltd is developing hammerhead ribozyme technology for therapy against HIV infection, targeting either the tat gene or the RNA packaging sequence (Psi) of HIV. These ribozymes have been expressed from constructs that were introduced into hematopoietic cells in culture, thereby protecting the cells against viral infection. Two phase I clinical trials are underway to test the safety and feasibility of the approach with the anti-tat ribozyme in human subjects.
Anatomical Outcomes of Surgery for Idiopathic Macular Hole as Determined by Optical Coherence Tomography (2002)

The postoperative closure of idiopathic macular holes following vitreous surgery was related to the preoperative macular hole diameter determined by OCT, with lesions smaller than 400 microm demonstrating higher success rates. A trend toward greater visual acuity improvement was demonstrated for idiopathic macular holes smaller than 400 microm. Late reopening was only seen in macular holes that were 400 microm or larger measured by OCT. Preoperative analysis and measurement of idiopathic macular holes with OCT may help delineate postoperative expectations for successful anatomical closure of the macular hole, visual acuity, and long-term closure.
Speech recognition with prediction-adaptation-correction recurrent neural networks (2015)

We propose the prediction-adaptation-correction RNN (PAC-RNN), in which a correction DNN estimates the state posterior probability based on both the current frame and the prediction made on the past frames by a prediction DNN. The result from the main DNN is fed back to the prediction DNN to make better predictions for the future frames. In the PAC-RNN, we can consider that, given the new, current frame information, the main DNN makes a correction on the prediction made by the prediction DNN. Alternatively, it can be viewed as adapting the main DNN's behavior based on the prediction DNN's prediction. Experiments on the TIMIT phone recognition task indicate that the PAC-RNN outperforms DNN, RNN, and LSTM with 2.4%, 2.1%, and 1.9% absolute phone accuracy improvement, respectively. We found that incorporating the prediction objective and including the recurrent loop are both important to boost the performance of the PAC-RNN.
A highly sensitive pressure sensor using a Au-patterned polydimethylsiloxane membrane for biosensing applications (2013)

We report on the fabrication and characterization of a highly sensitive pressure sensor using a Au film patterned on a polydimethylsiloxane (PDMS) membrane. The strain-induced change in the film resistance was utilized to perform the quantitative measurement of absolute pressure. The highest sensitivity obtained for a 200 µm thick PDMS film sensor was 0.23/KPa with a range of 50 mm Hg, which is the best result reported so far, over that range, for any pressure sensor on a flexible membrane. The noise-limited pressure resolution was found to be 0.9 Pa (0.007 mm Hg), and a response time of ∼200 ms, are the best reported results for these sensors. The ultrahigh sensitivity is attributed to the strain-induced formation of microcracks, the effect of which on the resistance change was found to be highly reversible within a certain pressure range. A physical model correlating the sensitivity with the sensor parameters and crack geometry has been proposed.
Effects of Allopurinol on Renal Stone Formation and Osteopontin Expression in a Rat Urolithiasis Model (2001)

Allopurinol was effective in preventing calcium oxalate stone formation and reduced OPN expression in rats. Our results suggest that allopurinol prevents renal stone formation by acting against not only the control of oxalate but also OPN expression.
GENERAL MICROBIOLOGY OF recA: Environmental and Evolutionary Significance (1990)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
Pathology of benign prostatic hyperplasia. Insight into etiology. (1990)

Morphometric studies of prostates with benign hyperplasia (BPH) have revealed features that may help clarify the disease's natural history and biologic behavior. Hyperplasia arises within a small anatomic region having precise boundaries and containing an unusual juxtaposition of glandular and stromal elements. Diffuse non-nodular enlargement of the transition zone is the commonest morphologic feature of BPH, but nodules show a greater potential for growth and comprise most of the tissue in large (more than 50-gm) resection specimens. Most nodules are predominantly glandular, with features that suggest a pathogenetic role of induction of embryonic-type stroma.
Glycocalicin: a new assay--the normal plasma levels and its potential usefulness in selected diseases (1994)

Platelet glycocalicin (GC) is the extramembranous portion of GPIb alpha that can be rapidly cleaved by enzymes such as calpain, plasmin, trypsin, elastase, etc. Quantitative cleavage will ultimately result in an acquired Bernard-Soulier-like bleeding disorder, and circulating GC may act as a potential inhibitor of platelet adhesion. We have developed and standardized a new enzyme-linked immunosorbent assay (ELISA), which uses two monoclonal antibodies (mAbs), both of which bind to the amino-terminal 45-kD fragment of GC and inhibit platelet-von Willebrand interactions and the streptavidin-biotin system. First, the methodology was evaluated and standardized with special emphasis on the anticoagulant and the inhibitors (EDTA, prostaglandin E1 [PGE1], aprotinin, N-ethyl-maleimide), the mode of high-speed centrifugation (to avoid platelet microparticles), and the standards used (purified GPIb and GC). This assay was then used to analyze the GC levels of healthy subjects (2.04 +/- 0.46 micrograms/mL) and of patients with selected diseases. The results of patients with aplastic anemia and thrombocytosis confirmed that GC levels are clearly dependent on the platelet count, which was the basis for the introduction of the GC index, the standardization of GC for a platelet count of 250 x 10(9)/L. The GC index discriminates reliably patients with active immune thrombocytopenic purpura from those in remission. GC levels are elevated in patients on hemodialysis (3.62 +/- 0.75 micrograms/mL, P < .001). The high GC index (6.93 +/- 4.21, P < .001) in cirrhosis patients suggests an increased platelet turnover and/or abnormal proteolysis. In contrast to other groups, we have not found that recombinant tissue plasminogen activator (rtPA) treatment of patients with myocardial infarction increases GC levels. However, concentrations are elevated in leukemia and the highest levels found are approximately 40 micrograms/mL. These studies suggest that GC is a useful platelet marker in certain diseases, which directly reflects platelet damage and possibly platelet dysfunction.
A packaging cell line for propagation of recombinant adenovirus vectors containing two lethal gene-region deletions. (1995)

A cell line that provides the E1 as well as the E4 gene functions of human adenovirus 5 has been established by introduction of the full-length Ad5 E4 region into 293 cells. To avoid the E1A transactivation of the E4 gene expression, the E4 promoter was replaced by the mouse alpha inhibin promoter containing a cAMP response element. This cell line was used to generate E1/E4-deleted adenovirus vectors containing a lacZ gene in the E1 region under the control of mouse pgk promoter. The titer and the lacZ gene expression of E1/E4-deleted adenovirus vector were comparable to those of E1-deleted vectors. Evidence of cytopathic effect was absent following infection of nonpermissive cell lines with E1/E4-deleted adenovirus in vitro. Establishment of the 293-E4 cell line and the generation of E1/E4-deleted adenovirus vectors may prolong gene expression in vivo and significantly improve the safety of adenovirus vectors for human gene therapy.
Poling of Ferroelectric Crystals by Using Interdigital Electrodes and Its Application to Bulk-Wave Transducers (1983)

The planar transducer, which uses interdigital electrodes on the surface of a ferroelectric ceramic block for both poling and excitation, can generate bulk waves propagating in the direction normal to the surface. If it is possible to fabricate a similar transducer on a ferroelectric single crystal, such as LiNbOg and LiTa03, It would be useful as a high-frequency bulk-wave transducer for various acousto-optic devices, because of its widebandwidth and bording-less structure. In this paper it is demonstrated that an array of alternating polarity antiparallel domains can be formed under the surface of a LiTa03 crystal by cooling the crystal through the Curie temperature under ar. appiied DC vcltage to interdlgital electrodes on the crystal surface. The characteristics of planar transducers exploiting the domain array are also described.
PLP-Dependent Enzymes: a Potent Therapeutic Approach for Cancer and Cardiovascular Diseases (2011)

The evolution on the field of biotechnology and proteomics create a novel therapeutic field (Enzymo-therapy) for treatment of various types of disease, particularly in the last fifty years. Exploitation of enzymes as anticancer, anti-cardiovascular, anticoagulants, antimicrobials and antioxidants Practically, almost of tumor cells were reported to be auxotrophs for L-methionine, glutamine, asparagine and arginine, due to the absence of intrinsic enzymatic systems synthesizing these amino acids, thus it depends for their growth and proliferation on the exogenous supply of these amino acids, that usually from diets Consequently, L-methioninase, L-glutaminase, L-asparaginase and arginine deiminase were frequently used as common anticancer agents by sequestering their corresponding amino acids from the blood plasma Additionally, hyperaccumulation of certain metabolic intermediates as homocysteine and cystathionine usually associated with various cardiovascular diseases and complex disorders Cystathionine -synthase and cystathionine -lyase are potential for sequestering homocysteine and cystathionine via transsulfuration metabolic pathways for production of glutathione and other antioxidants, so, these enzymes were described as anti-cardiovascular agents Unlike traditional approaches, Enzymo-therapy seems to be the promising therapeutic technology for their great specificity and affinity towards a clue substrate on specific metabolic pathway. However, the structural and conformational complexity of these enzymes makes it more vulnerable to extrinsic parameters, modulators, immunogenicity and proteolysis In addition, purification and formulation of these therapeutic enzymes, due to the economic expenses may add further complications. Therefore, the various approaches for stabilization of these enzymes in situ and decreasing their immunogenicity were the objective of this context. The structural and catalytic identity of pyridoxal phosphate enzymes, molecular aspects to enhance their therapeutic potentiality, in addition to our prospectives will be exploited.
Replication and Plaque Assay of Influenza Virus in an Established Line of Canine Kidney Cells (1968)

A plaque assay system has been developed for types A and B influenza viruses in an established line of canine kidney cells (MDCK-USD). In addition to a homogeneous susceptible cell, consistent plaque production depends on the use of highly purified agar (Agarose). This quantitative system was used to determine the rate of adsorption, synthesis, and thermal inactivation of influenza viruses, as well as to determine a dose response curve. Plaque assays on the MDCK-USD line and the parent MDCK line showed that the latter was more sensitive to A/Swine and A(2)/Japan 305 viruses. Titration of standard virus pools in embryonated eggs and MDCK-USD indicated that the cell culture system was as sensitive as the in ovo assay.
Antibody catalysis of bimolecular amide formation (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAntibody catalysis of bimolecular amide formationK. D. Janda, R. A. Lerner, and Alfonso. TramontanoCite this: J. Am. Chem. Soc. 1988, 110, 14, 4835–4837Publication Date (Print):July 1, 1988Publication History Published online1 May 2002Published inissue 1 July 1988https://pubs.acs.org/doi/10.1021/ja00222a056https://doi.org/10.1021/ja00222a056research-articleACS PublicationsRequest reuse permissionsArticle Views244Altmetric-Citations52LEARN 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
Serrate-mediated activation of Notch is specifically blocked by the product of the gene fringe in the dorsal compartment of the Drosophila wing imaginal disc (1997)

In the developing imaginal wing disc of Drosophila, cells at the dorsoventral boundary require localized Notch activity for specification of the wing margin. The Notch ligands Serrate and Delta are required on opposite sides of the presumptive wing margin and, even though activated forms of Notch generate responses on both sides of the dorsoventral boundary, each ligand generates a compartment-specific response. In this report we demonstrate that Serrate, which is expressed in the dorsal compartment, does not signal in the dorsal regions due to the action of the fringe gene product. Using ectopic expression, we show that regulation of Serrate by fringe occurs at the level of protein and not Serrate transcription. Furthermore, replacement of the N-terminal region of Serrate with the corresponding region of Delta abolishes the ability of fringe to regulate Serrate without altering Serrate-specific signaling.
Supporting All Service Classes in ATM : A Novel Traffic Control Framework (1999)

This paper presents a general traffic control framework for Asynchronous Transfer Mode (ATM) networks with its performance evaluation. The proposed traffic control scheme can incorporate all the recently considered ATM service classes including Constant Bit Rate (CBR), real time Variable Bit Rate (rtVBR), non-real time Variable Bit Rate (nrVBR), Available Bit Rate (ABR) and Unspecified Bit Rate (UBR) services. The control is based on a complete buffer partitioning architecture and on the associated buffer scheduling rule with adaptive weighting functions. We present the formulation of the traffic control as an optimization problem in a 3-dimensional Quality of Service (QoS) state space. A solution approach based on dynamic programming is also suggested. A comprehensive performance evaluation of the method has been performed based on simulations and results are presented with several examples. The QoS dependence on CBR load, VBR load, VBR burstiness, UBR load are investigated and results are demonstrated with explanations. 1 Introduction Since ATM networks are to support CBR, rtVBR, nrVBR, ABR and UBR service classes, the simplest 2-level priority based control policies become inadequate [11, 19]. Furthermore, within these service classes different VCs may require different cell loss, cell delay and cell delay variation parameters. It is therefore essential that the traffic control strategies be capable for the provision of the negotiated QoS parameters and for high network utilization by statistical multiplexing traffic classes with strict (CBR and VBR) or limited (ABR) QoS guarantees with a pure best effort type service class (UBR). Indeed, one of the key issues in the success of ATM is the traffic integration, and specifically, the design and analysis of control stra...
Accessing the Kabat antibody sequence database by computer (1996)

The Kabat antibody sequence database has for many years been the primary site for depositing sequence information on antibodies and other proteins of immunological interest. The chief drawback of this database has been that it has only been available in the form of a printed book (Kabat et al., Sequences of Proteins of Immunological Interest, 1991). These data have recently become available on the global computer Internet, but no method of searching the data has, as yet, been provided. Here, the development of a specialized database program for accessing the antibody data is described. This database software has been made accessible over the World Wide Web, together with a program which allows a novel antibody sequence to be tested against the Kabat sequence database, to identify unusual features of an antibody sequence which may represent cloning artifacts or sequencing errors.
Phosphorylation and inactivation of glycogen synthase kinase 3 by protein kinase A (2000)

Glycogen synthase kinase 3 (GSK-3) is implicated in multiple biological processes including metabolism, gene expression, cell fate determination, proliferation, and survival. GSK-3 activity is inhibited through phosphorylation of serine 21 in GSK-3 alpha and serine 9 in GSK-3 beta. These serine residues of GSK-3 have been previously identified as targets of protein kinase B (PKB/Akt), a serine/threonine kinase located downstream of phosphatidylinositol 3-kinase. Here, we show that serine 21 in GSK-3 alpha and serine 9 in GSK-3 beta are also physiological substrates of cAMP-dependent protein kinase A. Protein kinase A physically associates with, phosphorylates, and inactivates both isoforms of GSK-3. The results indicate that depending on the stimulatory context, the activity of GSK-3 can be modulated either by growth factors that work through the phosphatidylinositol 3-kinase-protein kinase B cascade or by hormonal stimulation of G protein-coupled receptors that link to changes in intracellular cAMP levels.
Hypoxia Leads to Na,K-ATPase Downregulation via Ca2+ Release-Activated Ca2+ Channels and AMPK Activation (2011)

To maintain cellular ATP levels, hypoxia leads to Na,K-ATPase inhibition in a process dependent on reactive oxygen species (ROS) and the activation of AMP-activated kinase α1 (AMPK-α1). We report here that during hypoxia AMPK activation does not require the liver kinase B1 (LKB1) but requires the release of Ca(2+) from the endoplasmic reticulum (ER) and redistribution of STIM1 to ER-plasma membrane junctions, leading to calcium entry via Ca(2+) release-activated Ca(2+) (CRAC) channels. This increase in intracellular Ca(2+) induces Ca(2+)/calmodulin-dependent kinase kinase β (CaMKKβ)-mediated AMPK activation and Na,K-ATPase downregulation. Also, in cells unable to generate mitochondrial ROS, hypoxia failed to increase intracellular Ca(2+) concentration while a STIM1 mutant rescued the AMPK activation, suggesting that ROS act upstream of Ca(2+) signaling. Furthermore, inhibition of CRAC channel function in rat lungs prevented the impairment of alveolar fluid reabsorption caused by hypoxia. These data suggest that during hypoxia, calcium entry via CRAC channels leads to AMPK activation, Na,K-ATPase downregulation, and alveolar epithelial dysfunction.
Triblock Copolymer Based on Poly(propylene oxide) and Poly(1‐[11‐acryloylundecyl]‐3‐methyl‐imidazolium bromide) (2011)

The controlled atom transfer radical polymerization of an ionic liquid, 1-(11-acryloylundecyl)-3-methyl imidazolium bromide (ILBr), from both ends of a telechelic poly(propylene oxide) (PPO) macroinitiator, end-functionalized with bromoisobutyryloyl is reported. The resulting highly water-soluble triblock, poly(ILBr-b-PO-b-ILBr) is multistimuli responsive. This new class of triblocks exhibits classical surface activity in lowering surface tension at the air-water interface and in modifying wetting in waterborne coatings. It also immunizes model colloids against coagulation induced by Debye-Hückel (indifferent electrolyte) electrostatic screening. Further, sol-gel thermoreversibility is unexpectedly found as an additional form of stimuli responsiveness.
UPSNet: A Unified Panoptic Segmentation Network (2019)

In this paper, we propose a unified panoptic segmentation network (UPSNet) for tackling the newly proposed panoptic segmentation task. On top of a single backbone residual network, we first design a deformable convolution based semantic segmentation head and a Mask R-CNN style instance segmentation head which solve these two subtasks simultaneously. More importantly, we introduce a parameter-free panoptic head which solves the panoptic segmentation via pixel-wise classification. It first leverages the logits from the previous two heads and then innovatively expands the representation for enabling prediction of an extra unknown class which helps better resolve the conflicts between semantic and instance segmentation. Additionally, it handles the challenge caused by the varying number of instances and permits back propagation to the bottom modules in an end-to-end manner. Extensive experimental results on Cityscapes, COCO and our internal dataset demonstrate that our UPSNet achieves state-of-the-art performance with much faster inference. Code has been made available at: https://github.com/uber-research/UPSNet
A negative regulator mediates quorum-sensing control of exopolysaccharide production in Pantoea stewartii subsp. stewartii (1998)

Classical quorum-sensing (autoinduction) regulation, as exemplified by the lux system of Vibrio fischeri, requires N-acyl homoserine lactone (AHL) signals to stimulate cognate transcriptional activators for the cell density-dependent expression of specific target gene systems. For Pantoea stewartii subsp. stewartii, a bacterial pathogen of sweet corn and maize, the extracellular polysaccharide (EPS) stewartan is a major virulence factor, and its production is controlled by quorum sensing in a population density-dependent manner. Two genes, esaI and esaR, encode essential regulatory proteins for quorum sensing. EsaI is the AHL signal synthase, and EsaR is the cognate gene regulator. esaI, DeltaesaR, and DeltaesaI-esaR mutations were constructed to establish the regulatory role of EsaR. We report here that strains containing an esaR mutation produce high levels of EPS independently of cell density and in the absence of the AHL signal. Our data indicate that quorum-sensing regulation in P. s. subsp. stewartii, in contrast to most other described systems, uses EsaR to repress EPS synthesis at low cell density, and that derepression requires micromolar amounts of AHL. In addition, derepressed esaR strains, which synthesize EPS constitutively at low cell densities, were significantly less virulent than the wild-type parent. This finding suggests that quorum sensing in P. s. subsp. stewartii may be a mechanism to delay the expression of EPS during the early stages of infection so that it does not interfere with other mechanisms of pathogenesis.