gebhart/patrepeval huggingface dataset:
A model for DNA polymerase switching involving a single cleft and the rim of the sliding clamp (2009)

The actions of Escherichia coli DNA Polymerase IV (Pol IV) in mutagenesis are managed by its interaction with the beta sliding clamp. In the structure reported by Bunting et al. [EMBO J (2003) 22:5883-5892], the C-tail of Pol IV contacts a hydrophobic cleft on the clamp, while residues V303-P305 reach over the dimer interface to contact the rim of the adjacent clamp protomer. Using mutant forms of these proteins impaired for either the rim or the cleft contacts, we determined that the rim contact was dispensable for Pol IV replication in vitro, while the cleft contact was absolutely required. Using an in vitro assay to monitor Pol III*-Pol IV switching, we determined that a single cleft on the clamp was sufficient to support the switch, and that both the rim and cleft contacts were required. Results from genetic experiments support a role for the cleft and rim contacts in Pol IV function in vivo. Taken together, our findings challenge the toolbelt model and suggest instead that Pol IV contacts the rim of the clamp adjacent to the cleft that is bound by Pol III* before gaining control of the same cleft that is bound by Pol III*.
<title>A visual tracking system using an RFID tag</title> (2005)

We propose a visual tracking system that uses RFID-tags to identify objects. The system firstly identifies an object in front of the camera, and pulls up data of the object from the database. The data includes a cad model of the object that is used for estimating 3D motion relative to the camera and a set of image features that is used for detecting the object in the initial image. The set of image features is generated based on the cad model by means of the AdaBoost algorithm and distinguishes the object in images from the backgrounds efficiently. Identifying the object, the system processes images using models that are specialized in the object in front of the camera.
BCR/ABL inhibition by an escort/phosphatase fusion protein (2000)

Cellular transformation by the BCR/ABL oncogene depends on the ABL-encoded tyrosine kinase activity. To block BCR/ABL function, we created a unique tyrosine phosphatase by fusing the catalytic domain of SHP1 (SHP1c) to the ABL binding domain (ABD) of RIN1, an established binding partner and substrate for c-ABL and BCR/ABL. This fusion construct (ABD/SHP1c) binds to BCR/ABL in cells and functions as an active phosphatase. ABD/SHP1c effectively suppressed BCR/ABL function as judged by reductions in transformation of fibroblast cells, growth factor independence of hematopoietic cell lines, and proliferation of primary bone marrow cells. In addition, the leukemogenic properties of BCR/ABL in a murine model system were blocked by coexpression of ABD/SHP1c. Both the "escort" function provided by ABD and the inhibitor function provided by the phosphatase of SHP1c were necessary for effective BCR/ABL interference. Expression of ABD/SHP1c also reversed the transformed phenotype of K562, a human leukemia-derived cell line. These results have direct implications for leukemia therapeutics and suggest an approach to block aberrant signal transduction in other pathologies through the use of appropriately designed escort/inhibitors.
Efficient multi-V<inf>T</inf> FDSOI technology with UTBOX for low power circuit design (2010)

For the first time, Multi-V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> UTBOX-FDSOI technology for low power applications is demonstrated. We highlight the effectiveness of back biasing for short devices in order to achieve I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</inf> current improvement by 45% for LVT options at an I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</inf> current of 23nA/µm and a leakage reduction by 2 decades for the HVT one. In addition, fully functional 0.299um <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> bitcells with 290mV SNM at 1.1V and Vb=0V operation were obtained. We also demonstrate on ring oscillators and 0.299µm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> SRAM bitcells the effectiveness (ΔV <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> versus V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</inf> ∼ 208mV/V) of the conventional bulk reverse and forward back biasing approaches to manage the circuit static power and the dynamic performances.
Mycoplasmas in apple trees infected with the proliferation disease (1972)

A mycoplasma-like microorganism was identified on electron micrographs of ultrathin sections of roots and abnormal underground sprouts growing from roots of young apple trees artificially infected with the proliferation disease. Specimens taken in November, contained mycoplasmas at various stages of reproduction in sieve tubes of the host. Mycoplasma-like bodies occurred especially in abnormal underground sprouts, and rarely also in lateral roots.
A Regularization Parameter in Discrete Ill-Posed Problems (1996)

The Tikhonov regularization method for discrete ill-posed problems is considered. For the practical choice of the regularization parameter $\alpha $, some authors use a plot of the norm of the regularized solution versus the norm of the residual vector for all $\alpha $ considered. This paper contains an analysis of the shape of this plot and gives atheoretical justification for choosing the regularization parameter so it is related to the “{\bf L ” of the plot considered in the logarithmic scale. Moreover, a new criterion for choosing a is introduced (independent of the shape of the plot) which gives a new interpretation of the “corner criterion” mentioned above. The existence of “L-corner” is discussed.
THE DIETARY RECOMMENDATIONS OF THE AMERICAN ACADEMY OF PEDIATRICS (1995)

The AAP cannot logically embrace two contradictory positions put forward by their 1992 Committee on Nutrition: 1) recommending 30% of energy from fat but 2) not one percentile less. Although a population nutrient goal of 30% of energy from fat is reasonable for adults, because ingestion of this amount of energy from fat will not jeopardize their growth, this guideline developed from studies of adults (mostly males) does not and should not apply to children. Because this goal was recommended for children by the 1992 Committee on Nutrition it is obvious that, if implemented, some children will be at risk for growth failure. The pediatricians in Canada have solved this problem by recommending a tapering decrease of fat intake from 50% of energy from fat at age 2 years to 30% by the time of the conclusion of linear growth (ie, adolescence) (11).
Generalized Domain-Adaptive Dictionaries (2013)

Data-driven dictionaries have produced state-of-the-art results in various classification tasks. However, when the target data has a different distribution than the source data, the learned sparse representation may not be optimal. In this paper, we investigate if it is possible to optimally represent both source and target by a common dictionary. Specifically, we describe a technique which jointly learns projections of data in the two domains, and a latent dictionary which can succinctly represent both the domains in the projected low-dimensional space. An efficient optimization technique is presented, which can be easily kernelized and extended to multiple domains. The algorithm is modified to learn a common discriminative dictionary, which can be further used for classification. The proposed approach does not require any explicit correspondence between the source and target domains, and shows good results even when there are only a few labels available in the target domain. Various recognition experiments show that the method performs on par or better than competitive state-of-the-art methods.
Scalable Production of HPV16 L1 Protein and VLPs from Tobacco Leaves (2016)

Cervical cancer is the most common malignancy among women particularly in developing countries, with human papillomavirus (HPV) 16 causing 50% of invasive cervical cancers. A plant-based HPV vaccine is an alternative to the currently available virus-like particle (VLP) vaccines, and would be much less expensive. We optimized methods to express HPV16 L1 protein and purify VLPs from tobacco (Nicotiana benthamiana) leaves transfected with the magnICON deconstructed viral vector expression system. L1 proteins were extracted from agro-infiltrated leaves using a series of pH and salt mediated buffers. Expression levels of L1 proteins and VLPs were verified by immunoblot and ELISA, which confirmed the presence of sequential and conformational epitopes, respectively. Among three constructs tested (16L1d22, TPL1d22, and TPL1F), TPL1F, containing a full-length L1 and chloroplast transit peptide, was best. Extraction of HPV16 L1 from leaf tissue was most efficient (> 2.5% of total soluble protein) with a low-salt phosphate buffer. VLPs were purified using both cesium chloride (CsCl) density gradient and size exclusion chromatography. Electron microscopy studies confirmed the presence of assembled forms of HPV16 L1 VLPs. Collectively; our results indicated that chloroplast-targeted transient expression in tobacco plants is promising for the production of a cheap, efficacious HPV16 L1 VLP vaccine. Studies are underway to develop plant VLPs for the production of a cervical cancer vaccine.
Identification of the plasmid‐encoded immunity protein for colicin El in the inner membrane of <i>Escherichia coli</i> (1985)

A set of plasmids containing portions of the Col E1 plasmid were transformed into recA- cells. These cells, after UV irradiation, only incorporate labelled amino acids into plasmid-encoded proteins. UV-irradiated cells label a 14.5 kDa band if they are phenotypically immune to colicin E1, and do not contain this band if they are sensitive to colicin E1. We conclude that the 14.5 kDa protein is the colicin E1 immunity protein. When the inner and outer membranes of these cells are fractionated, the labelled band appears in the inner membrane. The immunity protein must be an intrinsic inner membrane protein, confirming the predictions made by hydrophobicity calculations from primary sequence data.
Extensible Provisioning Protocol (EPP) Host Mapping (2009)

This document describes an Extensible Provisioning Protocol (EPP) mapping for the provisioning and management of Internet host names stored in a shared central repository. Specified in XML, the mapping defines EPP command syntax and semantics as applied to host names. This document obsoletes RFC 4932.
No past - no future: the political advantages of an ever-present organizational identity (2007)

In this paper we contend that the temporal elements of organizational identity serve to both constrain and enable an organization's ability to act. We support this thesis through an analysis of the identities of, and the relationships between, a front organization and its membe organizations during a major societal debate. In undertaking this research we identified a significant gap in the organizational identity literature in relation to temporary organizations, including front organizations; a gap which this study begins to address. We argue that by existing only in what we term a 'packaged present' and by maintaining a strategically ambiguous relationship with their members, front organizations are able to resolve the identity-related constraints on societal action experienced by other types of organizations.
Angiopoietin-1/Tie2 Signal Augments Basal Notch Signal Controlling Vascular Quiescence by Inducing Delta-Like 4 Expression through AKT-mediated Activation of β-Catenin (2011)

Angiopoietin-1 (Ang1) regulates both vascular quiescence and angiogenesis through the receptor tyrosine kinase Tie2. We and another group previously showed that Ang1 and Tie2 form distinct signaling complexes at cell-cell and cell-matrix contacts. We further demonstrated that the former up-regulates Notch ligand delta-like 4 (Dll4) only in the presence of cell-cell contacts. Because Dll4/Notch signal restricts sprouting angiogenesis and promotes vascular stabilization, we investigated the mechanism of how the Ang1/Tie2 signal induces Dll4 expression to clarify the role of the Dll4/Notch signal in Ang1/Tie2 signal-mediated vascular quiescence. Under confluent endothelial cells, the basal Notch signal was observed. Ang1, moreover, induced Dll4 expression and production of the Notch intracellular domain (NICD). Ang1 stimulated transcriptional activity of β-catenin through phosphoinositide 3-kinase (PI3K)/AKT-mediated phosphorylation of glycogen synthase kinase 3β (GSK3β). Correspondingly, the GSK3β inhibitor up-regulated Dll4, whereas depletion of β-catenin by siRNA blocked Ang1-induced Dll4 expression, indicating the indispensability of β-catenin in Ang1-mediated up-regulation of Dll4. In addition, Dll4 expression by the GSK3β inhibitor was only observed in confluent cells, and was impeded by DAPT, a γ-secretase inhibitor, implying requirement of the Notch signal in β-catenin-dependent Dll4 expression. Consistently, we found that either Ang1 or NICD up-regulates Dll4 through the RBP-J binding site within intron 3 of the DLL4 gene and that β-catenin forms a complex with NICD/RBP-J to enhance Dll4 expression. Ang1 induced the deposition of extracellular matrix that is preferable for basement membrane formation through Dll4/Notch signaling. Collectively, the Ang1/Tie2 signal potentiates basal Notch signal controlling vascular quiescence by up-regulating Dll4 through AKT-mediated activation of β-catenin.
Dense fibrillar collagen matrices for tissue repair (2010)

The preparation of dense fibrillar collagen matrices, through a sol/gel transition at variable concentrations, offers routes to produce a range of simple, non toxic materials. Concentrated hydrogels entrapping cells show enhanced properties in terms of reduced contraction and enhanced cell proliferation . Dense fibrillar matrices attain tissue like mechanical properties and show ultrastructures described in connective tissues, namely liquid crystalline cholesteric geometries. Their colonization by cells and possible association with a mineral phase in a tissue like manner validate their use as biomimetic materials for regenerative medicine.
Lansoprazole as a rescue agent in chemoresistant tumors: a phase I/II study in companion animals with spontaneously occurring tumors (2011)

high dose proton pump inhibitors have been shown to induce reversal of tumor chemoresistance as well as improvement of the quality of life in pets with down staged cancer and in the majority of the treated animals PPI were well tolerated. Further studies are warranted to assess the efficacy of this strategy in patients with advanced cancers in companion animals as well as in humans.
Human models of acute lung injury (2011)

Acute lung injury (ALI) is a syndrome that is characterised by acute inflammation and tissue injury that affects normal gas exchange in the lungs. Hallmarks of ALI include dysfunction of the alveolar-capillary membrane resulting in increased vascular permeability, an influx of inflammatory cells into the lung and a local pro-coagulant state. Patients with ALI present with severe hypoxaemia and radiological evidence of bilateral pulmonary oedema. The syndrome has a mortality rate of approximately 35% and usually requires invasive mechanical ventilation. ALI can follow direct pulmonary insults, such as pneumonia, or occur indirectly as a result of blood-borne insults, commonly severe bacterial sepsis. Although animal models of ALI have been developed, none of them fully recapitulate the human disease. The differences between the human syndrome and the phenotype observed in animal models might, in part, explain why interventions that are successful in models have failed to translate into novel therapies. Improved animal models and the development of human in vivo and ex vivo models are therefore required. In this article, we consider the clinical features of ALI, discuss the limitations of current animal models and highlight how emerging human models of ALI might help to answer outstanding questions about this syndrome.
Diffusion maps for PLDA-based speaker verification (2013)

During the last few years, i-vectors have become an important component in most state-of-the-art speaker recognition systems. I-vector extraction is based on an assumption that GMM supervectors reside on a low dimensional space, which is modeled using Factor Analysis. In this paper we replace the above assumption with an assumption that the GMM supervectors reside on a low dimensional manifold and propose to use Diffusion Maps to learn that manifold. The learnt manifold implies a mapping of spoken sessions into a modified i-vector space which we call d-vector space. D-vectors can further be processed using standard techniques such as LDA, WCCN, cosine distance scoring or Probabilistic Linear Discriminant Analysis (PLDA). We demonstrate the usefulness of our approach on the telephone core conditions of NIST 2010, and obtain significant error reduction.
Polyphosphates: a link between platelet activation, intrinsic coagulation and inflammation? (2010)

Early evidence has already shown that activated platelets play a role in the intrinsic pathway of coagulation, but the mechanism remained unclear. The finding that the dense granules of platelets contain polyphosphate (polyP), which has procoagulant effects, resolved this missing link between activated platelets and coagulation. PolyP secreted from platelets leads via activation of Factor XII to in vivo thrombin and fibrin formation. The relative importance of polyP in the process and stages of thrombus formation will require further investigation. In addition to its role in coagulation, polyP-induced Factor XII activation mediates the release of the inflammatory mediator bradykinin by activating the kallikrein-kinin system. This results in vascular leakage and edema formation in vivo. Together, polyP release from platelets has a physiological role in the thrombus-forming process, as well as in inflammatory reactions.
Individualization of bypassing agent treatment for haemophilic patients with inhibitors utilizing thromboelastography (2006)

The treatment of bleeding for haemophilic patients with inhibitors relies on the use of the bypassing agents, recombinant factor VIIa and factor eight inhibitor bypass activity (FEIBA). While both therapies are effective in the majority of bleeding episodes, there is a significant amount of interindividual variability when it comes to the response to therapy. As of yet, there is no reliable laboratory parameter that can predict the response to therapy in the same manner that factor VIII and factor IX levels predict response in non-inhibitor patients. Developing such a laboratory parameter is vital in order to maximize the clinical efficacy of these agents. Thromboelastography (TEG) is a device, which assesses clot formation over time in whole blood and has several characteristics which suggest it may be an effective way to monitor bypass agent therapy. We studied the ability of TEG to individualize the treatment regimens of three patients with high titre inhibitors assessing the response to recombinant factor VIIa, FEIBA, and when both were used sequentially. The TEG allowed for individualization of treatment for each of the three patients and resulted in more effective, convenient and less expensive treatment regimens. We thus believe that TEG is a promising device for monitoring of bypass agent therapy and should be studied further.
Limulus Gelation Test: Laboratory Considerations (1977)

Journal Article Limulus Gelation Test: Laboratory Considerations Get access Linda Riegle, M.P.H., M(ASCP), RM(AAM), Linda Riegle, M.P.H., M(ASCP), RM(AAM) Section of Infectious Disease, Department of Child Health, University of Missouri Medical Center, Columbia. Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael S. Cooperstock, M.D., M.P.H. Michael S. Cooperstock, M.D., M.P.H. Section of Infectious Disease, Department of Child Health, University of Missouri Medical Center, Columbia. Search for other works by this author on: Oxford Academic PubMed Google Scholar Laboratory Medicine, Volume 8, Issue 9, 1 September 1977, Pages 28–30, https://doi.org/10.1093/labmed/8.9.28 Published: 01 September 1977
Adriamycin-enhanced membrane lipid peroxidation in isolated rat nuclei. (1985)

Isolated rat liver nuclei enzymatically activated Adriamycin to the electron spin resonance-detectable semiquinone free radical in the presence of reduced nicotinamide adenine dinucleotide phosphate (NADPH). This process resulted in the enhancement of oxyradical-mediated peroxidation of the nuclear envelope membrane unsaturated phospholipids, measured as malonaldehyde equivalents by the thiobarbituric acid method. Peroxidation required the inclusion of NADPH and catalytically active protein, presumably NADPH:cytochrome P-450 reductase, and was enhanced more than 5-fold by Adriamycin. It was observed that Adriamycin-stimulated nuclear membrane peroxidation was diminished by superoxide dismutase, reduced glutathione, the hydroxyl radical scavenger, 1,3-dimethylurea, and by the metal ion chelator, diethylenetriaminepentaacetic acid, indicating that multiple species of reactive oxygen and trace amounts of metal ions (iron) were required in the peroxidation reaction. The generation of superoxide and hydroxyl radicals was confirmed by 5,5-dimethyl-1-pyrroline-N-oxide spin trap electron spin resonance spectroscopy. Calf thymus DNA added to incubations containing nuclei and NADPH caused a pronounced concentration-dependent inhibition of Adriamycin-stimulated lipid peroxidation. It was found that nuclei incubated with Adriamycin (300 microM) accumulated 128 nmol of the drug per mg of nuclear protein within 1 h, apparently because the Adriamycin was internalized and bound to the DNA and nuclear protein. These results suggest that some of the toxic effects of Adriamycin observed in the nucleus could result, directly or indirectly, through the peroxidation of the unsaturated lipids of the nuclear membrane.
Exclusion probabilities of 22 bovine microsatellite markers in fluorescent multiplexes for semiautomated parentage testing (1997)

Six multiplexes developed for semiautomated fluorescence genotyping were evaluated for parentage testing. These multiplexes contained primer pairs for the amplification of 22 microsatellites on 17 bovine autosomes. Exclusion probabilities were determined from genotypes of 1022 Holstein cattle and 311 beef cattle belonging to five breeds. Two cases were considered: case 1, genotypes are known for an alleged parent and an offspring but genotypes of a confirmed parent are unknown; and case 2, genotypes are known for an alleged parent, a confirmed parent and an offspring. If the alleged parent is not the true parent, then the 22 markers will exclude the alleged parent with a probability of > 0.9986 for case 1 and with a probability of > 0.99999 for case 2. On the basis of these exclusion probabilities, the probability that an alleged parent will be falsely included as a parent is in the range of 1/716 to 1/2845 for case 1 and 1/1.2 million to 1/159753 for case 2. In addition to these results, a rapid and efficient non-organic method for extraction of DNA from semen is described.