gebhart/patrepeval huggingface dataset:
Integrated genetic and epigenetic analysis of childhood acute lymphoblastic leukemia (2013)

Acute lymphoblastic leukemia (ALL) is the commonest childhood malignancy and is characterized by recurring structural genetic alterations. Previous studies of DNA methylation suggest epigenetic alterations may also be important, but an integrated genome-wide analysis of genetic and epigenetic alterations in ALL has not been performed. We analyzed 137 B-lineage and 30 T-lineage childhood ALL cases using microarray analysis of DNA copy number alterations and gene expression, and genome-wide cytosine methylation profiling using the HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) assay. We found that the different genetic subtypes of ALL are characterized by distinct DNA methylation signatures that exhibit significant correlation with gene expression profiles. We also identified an epigenetic signature common to all cases, with correlation to gene expression in 65% of these genes, suggesting that a core set of epigenetically deregulated genes is central to the initiation or maintenance of lymphoid transformation. Finally, we identified aberrant methylation in multiple genes also targeted by recurring DNA copy number alterations in ALL, suggesting that these genes are inactivated far more frequently than suggested by structural genomic analyses alone. Together, these results demonstrate subtype- and disease-specific alterations in cytosine methylation in ALL that influence transcriptional activity, and are likely to exert a key role in leukemogenesis.
RELION: Implementation of a Bayesian approach to cryo-EM structure determination (2012)

RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. Whereas alternative approaches often rely on user expertise for the tuning of parameters, RELION uses a Bayesian approach to infer parameters of a statistical model from the data. This paper describes developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined. A so-called gold-standard Fourier shell correlation (FSC) procedure to prevent overfitting is also described. The resulting implementation yields high-quality reconstructions and reliable resolution estimates with minimal user intervention and at acceptable computational costs.
Ku and DNA-dependent Protein Kinase Dynamic Conformations and Assembly Regulate DNA Binding and the Initial Non-homologous End Joining Complex (2009)

DNA double strand break (DSB) repair by non-homologous end joining (NHEJ) is initiated by DSB detection by Ku70/80 (Ku) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) recruitment, which promotes pathway progression through poorly defined mechanisms. Here, Ku and DNA-PKcs solution structures alone and in complex with DNA, defined by x-ray scattering, reveal major structural reorganizations that choreograph NHEJ initiation. The Ku80 C-terminal region forms a flexible arm that extends from the DNA-binding core to recruit and retain DNA-PKcs at DSBs. Furthermore, Ku- and DNA-promoted assembly of a DNA-PKcs dimer facilitates trans-autophosphorylation at the DSB. The resulting site-specific autophosphorylation induces a large conformational change that opens DNA-PKcs and promotes its release from DNA ends. These results show how protein and DNA interactions initiate large Ku and DNA-PKcs rearrangements to control DNA-PK biological functions as a macromolecular machine orchestrating assembly and disassembly of the initial NHEJ complex on DNA.
Stereocontrolled synthesis of dinucleoside boranophosphates by an oxazaphospholidine method (2005)

Stereodefined dinucleoside boranophosphates were synthesized from diastereopure nucleoside 3'-oxazaphospholidine derivatives. The new method is based on the stereospecific formation of dinucleoside phosphite intermediates catalyzed by a non-nucleophilic acidic activator, N-(cyanomethyl)pyrrolidinium triflate, and the boronation of the intermediates.
Kalman Filtering With Intermittent Observations (2004)

Motivated by navigation and tracking applications within sensor networks, we consider the problem of performing Kalman filtering with intermittent observations. When data travel along unreliable communication channels in a large, wireless, multihop sensor network, the effect of communication delays and loss of information in the control loop cannot be neglected. We address this problem starting from the discrete Kalman filtering formulation, and modeling the arrival of the observation as a random process. We study the statistical convergence properties of the estimation error covariance, showing the existence of a critical value for the arrival rate of the observations, beyond which a transition to an unbounded state error covariance occurs. We also give upper and lower bounds on this expected state error covariance.
Use of Mycorrhizae in Agriculture (1987)

Types de mycorhizes. Mycorhizes a vesicules et a arbuscules. Ectomycorhizes. Rendements ameliores pour les cultures et reduction des apports d'engrais. Tolerance accrue au stress hydrique. Resistance aux pathogenes. Autres avantages. Production d'inoculums (selection de souches, cultures en masse, essais sur le terrain)
Impact of high-order aberrations on the performance of the aberration monitor (2000)

The aberration ring test is used to determine the low and high order lens aberrations. The method is based on two key elements: the linear response of ART to aberrations and the use of multiple imaging conditions. Once the model parameters are determined by means of simulations, the Zernike coefficients are solved from a set of linear equations. The Zernike coefficients thus obtained are correlated to interferometric lens data and to line width measurements.
A low-noise and wide-band ac boosting current-to-voltage amplifier for scanning tunneling microscopy (2005)

A compact, fast, and low-noise current-to-voltage amplifier is built for scanning tunneling microscopy. The amplifier consists of two amplification stages. The first stage performs low-noise transimpedance amplification by using a high performance FET operational amplifier together with a high-ohm feedback resistor of 1GΩ and a parallel trimming capacitor. The ac boosting amplifier in the second stage recovers the higher frequency above the 3dB cutoff of the first stage to extend the maximum bandwidth up to 100kHz. This two-stage current-to-voltage amplifier shows a low current noise below sub-pA rms when tuned to have the bandwidth of around 1kHz. It also guarantees stable frequency response in the presence of 1000pF input capacitance.
Human dendritic Langerhans cells generated in vitro from CD34+ progenitors can prime naive CD4+ T cells and process soluble antigen (1995)

Earlier studies have concluded that fresh Langerhans cells (LC) are able to capture and process native Ags, whereas cultured LC have lost these functions while acquiring the capacity to prime naive T cells. Herein we studied the functions of human dendritic/Langerhans cells (d-Lc) generated in vitro by culturing CD34+ hemopoietic progenitor cells in the presence of granulocyte-macrophage CSF (GM-CSF) + TNF-alpha. Less than 50 d-Lc were found to strongly stimulate the proliferation of 2.5 x 10(4) allogeneic naive CD4+ T cells. Furthermore, six to 50 d-Lc induced half-maximal proliferation of naive syngeneic CD4+ cord blood T cells, in the presence of picomolar concentrations of superantigens. During the alloreaction, the CD4+ T cells were expanded up to 100-fold within two successive stimulation cycles with the same d-Lc, and the recovered T cells were specific for the d-Lc alloantigen. HLA-matched tetanus toxoid (TT)-specific T cell clones were found to proliferate in response to TT presented by CD1a+ d-Lc. Finally, electron microscopy demonstrated that CD1a+ d-Lc were able to capture an Ag (gold-labeled Igs) through receptor-mediated endocytosis. Thus, in vitro generated d-Lc can prime naive T cells and process native Ags, a property that might eventually prove useful for priming Ag-specific naive T cells for cellular immunotherapy.
Comparison of selective enrichment media for the detection of Salmonella in poultry faeces (2001)

The International Standard method ISO 6579, including RV and selenite cystine broth as selective enrichment media, is most frequently used for the isolation of Salmonella from poultry faeces. This study reveals that there are more suitable combinations of selective enrichment media.
Labelling of mammalian cells for visualisation by MRI (2009)

Through labelling of cells with magnetic contrast agents it is possible to follow the fate of transplanted cells in vivo with magnetic resonance imaging (MRI) as has been demonstrated in animal studies as well as in a clinical setting. A large variety of labelling strategies are available that allow for prolonged and sensitive detection of the labelled cells with MRI. The various protocols each harbour specific advantages and disadvantages. In choosing a particular labelling strategy it is also important to ascertain that the labelling procedure does not negatively influence cell functionality, for which a large variety of assays are available. In order to overcome the challenges still faced in fully exploiting the benefits of in vivo cell tracking by MRI a good understanding and standardisation of the procedures and assays used will be crucial.
Molecular Imaging Secondary Ion Mass Spectrometry for the Characterization of Patterned Self-Assembled Monolayers on Silver and Gold (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Imaging Secondary Ion Mass Spectrometry for the Characterization of Patterned Self-Assembled Monolayers on Silver and GoldGreg. Gillen, Joe. Bennett, Michael J. Tarlov, and Donald R. F. BurgessCite this: Anal. Chem. 1994, 66, 13, 2170–2174Publication Date (Print):July 1, 1994Publication History Published online1 May 2002Published inissue 1 July 1994https://pubs.acs.org/doi/10.1021/ac00085a036https://doi.org/10.1021/ac00085a036research-articleACS PublicationsRequest reuse permissionsArticle Views323Altmetric-Citations68LEARN 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
Growth of transplanted rat tumors following administration of cell-free tumor antigens. (1978)

The variable effect of immunizations with cell-free tumor extract (TE) in a weakly antigenic (Morris hepatoma 3924a) and a highly antigenic (glioma 9L) inbred rat model system was described. Tumor enhancement was noted with the weakly antigenic tumor following either immunization with a low dose of TE admixed with Freund's adjuvant or immunization with high doses of TE. Enhancement was observed at four tumor cell challenge levels. Tumor enhancement with the highly antigenic tumor was found at only one level and was seen following immunization with intermediate doses of TE and a high tumor cell challenge. Tumor protection was only detected with the weakly antigenic tumor following immunizations with an intermediate dose of TE and challenge with a tumor cell dose 5-fold over threshold. This protection was tumor specific, as judged by an amputation and rechallenge experiment.
An easy colorimetric assay for screening and qualitative assessment of deiodination and dehalogenation by bacterial cultures (1999)

Halogenated organic substances are among the main environmental concerns. A number of micro-organisms are able to dehalogenate these compounds. However, the methods for the assessment of micro-organismal ability to dehalogenate are expensive and require complex instrumentation. Here, an easy colorimetric assay for the screening and assessment of the ability of bacterial cultures to deiodinate, and potentially dehalogenate, chemical substances is proposed. The method is based on the oxidation of iodide, released due to biotransformation, to iodine followed by a subsequent detection of iodine by a classical reaction with starch.
Notebook satcom terminal technology development (1995)

Comsat Mobile Communications and Comsat Laboratories have an ongoing multi-year development effort begun in 1992 to evaluate and develop the critical technologies required to meet future generation satellite systems offering handheld and laptop/notebook computer-sized satellite terminals. A critical assumption in the economic success of these future systems is the availability of a low cost terminal in a size and weight that can be targeted to a mass market. Some of the critical technologies identified, that were not readily available in a miniaturized form or at a low cost, included the antenna, diplexer, and intermediate frequency converter. An overview of these technologies is provided as well as the measured test results for the antenna and diplexer. While originally developed for notebook satcom terminals operating in the L-band Inmarsat system, the same design concepts can easily be scaled for other frequency bands, such as UHF or S-band. Thus, the technologies discussed are applicable to a broad range of digital satellite terminals and applications.
Analysis of a tunable multichannel two-mode-interference wavelength-division-multiplexer/demultiplexer (1989)

An integrated optical multichannel wavelength-division multiplexer/demultiplexer for a single-mode fiber system is investigated by the beam propagation method (BPM). Important wavelength characteristics of dual-channel two-mode-interference (TMI) multiplexer/demultiplexer waveguide with and without electrode are studied and general design guidelines for realizing multichannel multiplexer/demultiplexer are given. Design and simulation of four-channel TMI multiplexer/demultiplexer are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Binding Reactivity of Monoclonal Anti-Carcinoembryonic Antigen (CEA) Antibodies with Cell Membrane-Bound CEA and with Free CEA in Solution (1996)

Binding reactivities of 62 anti-CEA MAbs from 10 different research groups with cell membrane-bound CEA and with free CEA in solution were compared by inhibition of MAb binding to CEA-expressing tumor cells by free CEA. Bindings of 30 MAbs to the cell membrane-bound CEA (280 ng CEA/2 x 10(5) cells) were inhibited by approximately equal amounts of free CEA, indicating that binding affinities of about half the MAbs for cell membrane-bound CEA are similar to those for free CEA, respectively. Bindings of 15 MAbs to the cell membrane-bound CEA were easily inhibited by free CEA of less than half the amount of the cell membrane-bound CEA, while inhibition of bindings of the remaining 17 MAbs required twice more free CEA than the amount of cell membrane-bound CEA, showing that about one-fourth of the MAbs have higher affinities for free CEA and the remaining about one-fourth of the MAbs possess higher affinities for cell membrane-bound CEA. These results help form the basis for selecting the anti-CEA MAbs for use in clinical applications, such as serum CEA assay, tumor imaging and immunotherapy.
Immunophilins:  Beyond Immunosuppression (1998)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTImmunophilins: Beyond ImmunosuppressionG. S. Hamilton and J. P. SteinerView Author Information Department of Research, Guilford Pharmaceuticals, Inc., 6611 Tributary Street, Baltimore, Maryland 21224 Cite this: J. Med. Chem. 1998, 41, 26, 5119–5143Publication Date (Web):December 17, 1998Publication History Received15 May 1998Published online17 December 1998Published inissue 1 December 1998https://doi.org/10.1021/jm980307xCopyright © 1998 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views850Altmetric-Citations128LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (333 KB) Get e-AlertsSUBJECTS:Central nervous system,Ligands,Peptides and proteins,Receptors,Rodent models Get e-Alerts
Mannose 6-Phosphate/Insulin-like Growth Factor–II Receptor Targets the Urokinase Receptor to Lysosomes via a Novel Binding Interaction (1998)

The urokinase-type plasminogen activator receptor (uPAR) plays an important role on the cell surface in mediating extracellular degradative processes and formation of active TGF-beta, and in nonproteolytic events such as cell adhesion, migration, and transmembrane signaling. We have searched for mechanisms that determine the cellular location of uPAR and may participate in its disposal. When using purified receptor preparations, we find that uPAR binds to the cation-independent, mannose 6-phosphate/insulin-like growth factor-II (IGF-II) receptor (CIMPR) with an affinity in the low micromolar range, but not to the 46-kD, cation-dependent, mannose 6-phosphate receptor (CDMPR). The binding is not perturbed by uPA and appears to involve domains DII + DIII of the uPAR protein moiety, but not the glycosylphosphatidylinositol anchor. The binding occurs at site(s) on the CIMPR different from those engaged in binding of mannose 6-phosphate epitopes or IGF-II. To evaluate the significance of the binding, immunofluorescence and immunoelectron microscopy studies were performed in transfected cells, and the results show that wild-type CIMPR, but not CIMPR lacking an intact sorting signal, modulates the subcellular distribution of uPAR and is capable of directing it to lysosomes. We conclude that a site within CIMPR, distinct from its previously known ligand binding sites, binds uPAR and modulates its subcellular distribution.
Constructing services with interposable virtual hardware (2004)

Virtual machine monitors (VMMs) have enjoyed a resurgence in popularity, since VMMs can help to solve di#cult systems problems like migration, fault tolerance, code sandboxing, intrusion detection, and debugging. Recently, several researchers have proposed novel applications of virtual machine technology, such as Internet Suspend/Resume [25, 31] and transparent OS-level rollback and replay [13]. Unfortunately, current VMMs do not export enough functionality to budding developers of such applications, forcing them either to reverse engineer pieces of a black-box VMM, or to reimplement significant portions of a VMM. In this paper,
The use of demineralized bone matrix in the repair of segmental defects. Augmentation with extracted matrix proteins and a comparison with autologous grafts. (1986)

A soluble protein component of bone, bone morphogenetic protein, and decalcified bone matrix have been shown to induce the formation of bone in extraosseous tissue. Clinical and animal studies investigating the use of these materials as bone grafts have shown radiographic and histological evidence of formation of bone, but the clinical usefulness of these grafts remains unknown. This study compared the healing processes when plasma-coated demineralized bone matrix and autologous cancellous bone were used to graft segmental defects of bone. A standard procedure was used to make a two-centimeter defect bilaterally in the ulna of forty-eight skeletally mature New Zealand White rabbits. In each rabbit, one ulnar defect was grafted with autologous citrated plasma-coated demineralized bone matrix while the other defect served as a control and was grafted with either autologous cancellous bone from the iliac crest, demineralized bone matrix, or demineralized bone matrix augmented with bone proteins that had been extracted with guanidinium hydrochloride. The ulnar defect was stabilized by the intact radius, and no supplemental device was necessary for fixation. To examine spontaneous healing in this model, one group of rabbits had a control defect that was not grafted. The grafts were periodically evaluated by radiographs, and twelve weeks after surgery the grafts were harvested and tested to failure in a standard torsion-test machine. The mechanical parameters were calculated, and histological examination of major fragments of the grafts was performed. The results of the radiographic and histological evaluation showed that all of the grafted ulnae healed, with fusion of the graft to the cut ends of the defect and reformation of approximately normal anatomy. No ungrafted ulnar defects healed. The results from the mechanical tests were evaluated by comparing the defect that was grafted with plasma-coated demineralized bone matrix with the control graft in each animal. These data showed that: twelve weeks after grafting, the normal ulnae were significantly stronger than the ulnae that had been grafted with plasma-coated demineralized bone matrix; the ulnae that had been grafted with plasma-coated demineralized bone matrix and those that had been grafted with autologous bone were equivalent in strength; and twelve weeks after grafting, grafts of demineralized bone matrix that were augmented with extracted bone proteins were significantly stronger than those that had not been so augmented.
Dislodging Patriarchal and Academic Boundaries: Dialoguing on Trauma Through Text (2001)

In this article, we, two feminist teacher educators who are professional colleagues and friends, use our personal correspondence outside of the academy to help explain how we bridge and navigate our authentic whole selves as teacher educators.These dialogic narratives break from traditional academic texts and their focus on logic and objectivity as they are written from intimate voices and include deep emotions, detailed descriptions of personal anecdotes, and imagery and references to art, music, literature and our general interactions of reading the world (Freire & Macedo, 1987).Through examples from our personal daily correspondence (text, messenger, Facebook, and email) during the Kavanaugh hearings, we explore the following questions: How can we push the boundaries of academic writing to write for our authentic selves?What are the spaces where we can do this?How do we bring in our real-world experiences of sexism, misogyny, and rage into our academic writing as teacher educators?