gebhart/patrepeval huggingface dataset:
Characterization of a high-sensitivity micromachined tunneling accelerometer with micro-g resolution (1998)

A new high-sensitivity bulk-silicon-micromachined tunneling accelerometer with micro-g resolution has been successfully fabricated and tested at Stanford University. This accelerometer is a prototype intended for underwater acoustics applications and is required to feature micro-g resolution at frequencies between 5 Hz and 1 kHz and can be packaged with circuitry in an 8-cm/sup 3/ volume with a total mass of 8 g. This paper briefly describes the mechanical design of this tunneling accelerometer and focuses on the experiments carried out in our laboratory to test the tunneling transducer as well as on the experimental determination of accelerometer resolution. The exponential relationship between tunneling gap and tunneling current is verified and results in an effective tunneling barrier height of about 0.2 eV. The goal of this paper is to outline the measurements which are necessary to verify that the sensor is actually tunneling and to confirm that the accelerometer performance is consistent with what should be expected from a tunneling accelerometer.
A new version of the RDP (Ribosomal Database Project) (1999)

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.
Protransglutaminase E from guinea pig skin. Isolation and partial characterization. (1990)

We have isolated protransglutaminase E, the zymogen form of epidermal transglutaminase E, from the skin of the adult guinea pig. This zymogen is the source of the large majority of soluble transglutaminase activity of skin. A molecular weight value for protransglutaminase E of 77,800 +/- 700, estimated by sedimentation equilibrium, is in close agreement with the apparent values determined by exclusion chromatography and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Treatment of the proenzyme with dispase, proteinase K, trypsin, or thrombin produces active enzyme. The enzyme, transglutaminase E, formed by the action of dispase, was observed to exist in the native state as a molecule indistinguishable in size from the zymogen. Under denaturing conditions, however, the enzyme dissociates into two fragments with molecular weights of 50,000 and 27,000. The observation that reducing agents are not needed for this dissociation suggests a noncovalent association of the two peptide chains in the native enzyme. Evidence that the catalytically essential -SH group of the enzyme residues in the Mr 50,000 fragment and that only the Mr 27,000 fragment possesses an unmasked amino terminus provides the basis for a proposed model of zymogen activation. Whether the noncatalytic fragment plays a role in catalysis is not known because separation of the fragments of native enzyme was not achieved.
Engineering antibody fragments to fold in the absence of disulfide bonds (2009)

Disulfide bonds play a critical role in the stabilization of the immunoglobulin beta-sandwich sandwich. Under reducing conditions, such as those that prevail in the cytoplasm, disulfide bonds do not normally form and as a result most antibodies expressed in that compartment (intrabodies) accumulate in a misfolded and inactive state. We have developed a simple method for the quantitative isolation of antibody fragments that retain full activity under reducing conditions from large mutant libraries. In E. coli, inactivation of the cysteine oxidoreductase DsbA abolishes protein oxidation in the periplasm, which leads to the accumulation of scFvs and other disulfide-containing proteins in a reduced form. Libraries of mutant scFvs were tethered onto the inner membrane of dsbA cells and mutants that could bind fluorescently labeled antigen in the reducing periplasm were screened by Anchored Periplasmic Expression (APEx; Harvey et al., Proc Natl Acad Sci USA 2004;101:9193-9198.). Using this approach, we isolated scFv antibody variants that are fully active when expressed in the cytoplasm or when the four Cys residues that normally form disulfides are substituted by Ser residues.
Hereditary nonpolyposis colorectal cancer (2000)

Hereditary nonpolyposis colorectal cancer (HNPCC), or Lynch syndrome, is the most common form of hereditary colorectal cancer (CRC). A well-orchestrated cancer family history is essential for its diagnosis since, unlike its familial adenomatous polyposis (FAP) hereditary cancer counterpart, HNPCC lacks distinguishing clinical stigmata of its cancer genetic risk. Discoveries in the 1990s of germ-line mutations, the most common of which are hMSH2 and hMLH1, have added enormous power to the diagnosis of Lynch syndrome. Its medical management is contingent upon its natural history. For example, approximately 70% of CRCs occur proximal to the splenic flexure, with one-third of the cancers occurring in the cecum, thereby mandating full colonoscopy. A high rate of metachronous CRCs indicates the need for no less than a subtotal colectomy for the management of initial CRC. Genetic counseling is essential prior to DNA testing, and at the time of disclosure of the results. Education of patients as well as physicians about all facets of this disorder is extremely important. If patients are to show compliance with germ-line testing, screening, and management options, they must understand the natural history and the significance of their genetic risk status. Physicians must also be aware of clinical nuances of this disorder to provide the necessary care.
Prevention of ventilator-associated pneumonia: Do not forget to disinfect the mouth* (2007)

Surgical Intensive Care Unit, University Hospital of Poitiers, Poitiers, France The authors have not disclosed any potential conflicts of interest.
Membrane-Anchored β2-Microglobulin Stabilizes a Highly Receptive State of MHC Class I Molecules (2005)

The magnitude of response elicited by CTL-inducing vaccines correlates with the density of MHC class I (MHC-I)-peptide complexes formed on the APC membrane. The MHC-I L chain, beta2-microglobulin (beta2m), governs complex stability. We reasoned that genetically converting beta2m into an integral membrane protein should exert a marked stabilizing effect on the resulting MHC-I molecules and enhance vaccine efficacy. In the present study, we show that expression of membranal human beta2m (hbeta2m) in mouse RMA-S cells elevates MHC-I thermal stability. RMA-S transfectants bind an exogenous peptide at concentrations 10(4)- to 10(6)-fold lower than parental RMA-S, as detected by complex-specific Abs and by T cell activation. Moreover, saturation of the transfectants' MHC-I by exogenous peptide occurs within 1 min, as compared with approximately 1 h required for parental cells. At saturation, however, level of peptide bound by modified cells is only 3- to 5-fold higher. Expression of native hbeta2m only results in marginal effect on the binding profile. Soluble beta2m has no effect on the accelerated kinetics, but the kinetics of transfectants parallel that of parental cells in the presence of Abs to hbeta2m. Ab inhibition and coimmunoprecipitation analyses suggest that both prolonged persistence of peptide-receptive H chain/beta2m heterodimers and fast heterodimer formation via lateral diffusion may contribute to stabilization. In vivo, peptide-loaded transfectants are considerably superior to parental cells in suppressing tumor growth. Our findings support the role of an allosteric mechanism in determining ternary MHC-I complex stability and propose membranal beta2m as a novel scaffold for CTL induction.
Cloning and characterization of a binding subunit of the interleukin 13 receptor that is also a component of the interleukin 4 receptor. (1996)

Interleukins 4 (IL-4) and 13 (IL-13) have been found previously to share receptor components on some cells, as revealed by receptor cross-competition studies. In the present study, the cloning is described of murine NR4, a previously unrecognized receptor identified on the basis of sequence similarity with members of the hemopoietin receptor family. mRNA encoding NR4 was found in a wide range of murine cells and tissues. By using transient expression in COS-7 cells, NR4 was found to encode the IL-13 receptor alpha chain, a low-affinity receptor capable of binding IL-13 but not IL-4 or interleukins 2, -7, -9, or -15. Stable expression of the IL-13 receptor alpha chain (NR4) in CTLL-2 cells resulted in the generation of high-affinity IL-13 receptors capable of transducing a proliferative signal in response to IL-13 and, moreover, led to competitive cross-reactivity in the binding of IL-4 and IL-13. These results suggest that the IL-13 receptor alpha chain (NR4) is the primary binding subunit of the IL-13 receptor and may also be a component of IL-4 receptors.
CENTERS OF DOMESTICATION FOR CHINESE, SPANISH, AND BEANCAP SNAP BEAN POPULATIONS (2017)

INTRODUCTION: Snap beans were primarily developed in Europe after the Columbian Exchange through selection for low fiber pods, thicker pod walls, and pod stringlessness (Myers & Baggett, 1999). Abundant evidence supports separate domestications of dry beans in the Andean and Mesoamerican centers, and the best available evidence suggests that snap beans were derived from dry bean from both centers, although the majority descend from the Andean gene pool (Gepts, 1998). While most snap beans were developed in Europe, they are not exclusively found there. Snap beans may have also been developed in China, and there is evidence that at least one bean with low fiber pod traits may have been developed by Native Americans, viz. ‘Trail of Tears.’ Three unique bean populations from China, Spain, and North America have the potential to shed light on the broader development of snap beans and their dissemination pathways out of the Americas using modern molecular tools. The first of these populations is an uncatalogued collection of Chinese snap beans assembled from a trip in 1991 by Michael Dickson (Cornell Univ.) consisting of 58 genotypes. The second consists of a selection of 11 Spanish genotypes from the Misión Biológica de Galicia – CSIC (Pontevedra, Spain) collection. These are a subset of lines selected from this collection that possess edible pod traits (de Ron, personal communication). The last population, the BeanCAP diversity panels, consists 149 snap beans mostly from commercial bean lines in North America and Europe.
Steric Stabilization of Nanocrystals in Supercritical CO2 Using Fluorinated Ligands (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSteric Stabilization of Nanocrystals in Supercritical CO2 Using Fluorinated LigandsParag S. Shah, Justin D. Holmes, R. Christopher Doty, Keith P. Johnston, and Brian A. KorgelView Author Information Department of Chemical Engineering and Texas Materials Institute The University of Texas, Austin, Texas 78712-1062 Cite this: J. Am. Chem. Soc. 2000, 122, 17, 4245–4246Publication Date (Web):April 13, 2000Publication History Received15 December 1999Published online13 April 2000Published inissue 1 May 2000https://pubs.acs.org/doi/10.1021/ja9943748https://doi.org/10.1021/ja9943748rapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1035Altmetric-Citations102LEARN 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 SUBJECTS:Ketones,Ligands,Nanocrystals,Nanoparticles,Silver Get e-Alerts
Differentiation of embryonic stem cells into adipocytes in vitro (1997)

ABSTRACT Embryonic stem cells, derived from the inner cell mass of murine blastocysts, can be maintained in a totipotent state in vitro. In appropriate conditions embryonic stem cells have been shown to differentiate in vitro into various derivatives of all three primary germ layers. We describe in this paper conditions to induce differentiation of embryonic stem cells reliably and at high efficiency into adipocytes. A prerequisite is to treat early developing embryonic stem cell-derived embryoid bodies with retinoic acid for a precise period of time. Retinoic acid could not be substituted by adipogenic hormones nor by potent activators of peroxisome proliferator-activated receptors. Treatment with retinoic acid resulted in the subsequent appearance of large clusters of mature adipocytes in embryoid body outgrowths. Lipogenic and lipolytic activities as well as high level expression of adipocyte specific genes could be detected in these cultures. Analysis of expression of potential adipogenic genes, such as peroxisome proliferator-activated receptors γ and δ and CCAAT/enhancer binding protein β, during differentiation of retinoic acidtreated embryoid bodies has been performed. The temporal pattern of expression of genes encoding these nuclear factors resembled that found during mouse embryogenesis. The differentiation of embryonic stem cells into adipocytes will provide an invaluable model for the characterisation of the role of genes expressed during the adipocyte development programme and for the identification of new adipogenic regulatory genes.
Immunohistochemical localization of advanced glycosylation end products in coronary atheroma and cardiac tissue in diabetes mellitus. (1993)

Advanced glycosylation end products (AGEs) accumulate on long-lived extracellular matrix proteins and have been implicated in the micro- and macrovascular complications of diabetes mellitus. Within the arterial wall, AGE-modified proteins increase vascular permeability, inactivate nitric oxide activity, and induce the release of growth-promoting cytokines. Recently developed anti-AGE antibodies were used in an immunohistochemical analysis of coronary arteries obtained from type II diabetic and nondiabetic patients. High levels of AGE reactivity were observed within the atherosclerotic plaque present in vessels from selected patients with diabetes. Considered together with the pathological effects of AGEs on vascular wall homeostasis, these data support the role of advanced glycosylation in the rapidly progressive atherosclerosis associated with diabetes mellitus.
Growth of inch-sized KCa0.8Sr0.2I3:Eu2+scintillating crystals and high performance for gamma-ray detection (2016)

A quaternary iodide KCa0.8Sr0.2I3:Eu2+ scintillator with 2.5% energy resolution at 662 keV in a 5 mm3 sample shows great potential for use in gamma-ray spectroscopy applications. In this work, we report the state-of-the-art growth of high quality 25, 38, and 50 mm diameter KCa0.8Sr0.2I3:Eu2+ single crystals by the vertical self-seeding Bridgman method. KCa0.8Sr0.2I3:Eu2+ with a size of ∅25 mm × 25 mm can achieve excellent energy resolutions of 3.15% at 662 keV and 6.8% at 122 keV irradiation, which are superior to that of a commercial NaI:Tl+ of the same size. The nonuniformity of light collection and production in ∅25 mm × 25 mm and ∅38 mm × 38 mm KCa0.8Sr0.2I3:Eu2+ crystals was evaluated by using a technique based on a collimated 137Cs source and coupling the crystal to a photomultiplier tube (PMT) in different directions. The performances of the packaged crystals for practical use were also measured.
Aggresomes and Autophagy Generate Sites for Virus Replication (2006)

The replication of many viruses is associated with specific intracellular compartments called virus factories or virioplasm. These are thought to provide a physical scaffold to concentrate viral components and thereby increase the efficiency of replication. The formation of virus replication sites often results in rearrangement of cellular membranes and reorganization of the cytoskeleton. Similar rearrangements are seen in cells in response to protein aggregation, where aggresomes and autophagosomes are produced to facilitate protein degradation. Here I review the evidence that some viruses induce aggresomes and autophagosomes to generate sites of replication.
Chemical investigation of ceylonese plants. Part VII. Extractives of Calophyllum thwaitesii Planch and Triana and Calophyllum walkeri Wight (Guttiferae) (1974)

The bark and timber extractives of C. thwaitesii Planch and Triana and C. walkeri Wight have been studied. The former contained taraxerol and friedelin in the bark whilst the latter had taraxerol and β-simiarenol. In addition a new di-isoprenylated xanthone, named thwaitesixanthone, has been isolated from the former and shown to be 13-hydroxy-3,3,10,10-tetramethyl-3H,10H-dipyrano[3,2-a:2′,3′-i]xanthen-14-one (IV) while calabaxanthone, 5-hydroxy-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-2H-pyrano[3,2-b]xanthen-6-one (I) was isolated from the latter. The timber extractives of both species gave 1,5-dihydroxyxanthone, 1,7-dihydroxyxanthone, jacareubin (IIa), and β-sitosterol. The latter species also contained guanandin (VIII), 1,3,5-trihydroxy-2-(3-methylbut-2-enyl)xanthone (X), and the new metabolite 1,5-dihydroxy-2,3-dimethoxyxanthone (IX).
Identification and Initial Characterization of Four Novel Members of the Interleukin-1 Family (2000)

Interleukin-1 (IL-1), fibroblast growth factors (FGFs), and their homologues are secreted factors that share a common beta-barrel structure and act on target cells by binding to cell surface receptors with immunoglobulin-like folds in their extracellular domain. While numerous members of the FGF family have been discovered, the IL-1 family has remained small and outnumbered by IL-1 receptor homologues. From expressed sequence tag data base searches, we have now identified four additional IL-1 homologues, IL-1H1, IL-1H2, IL-1H3, and IL-1H4. Like most other IL-1/FGFs, these proteins do not contain a hydrophobic leader sequence. IL-1H4 has a propeptide sequence, while IL-1H1, IL-1H2, and IL-1H3 encode only the mature protein. Circular dichroism spectra and thermal stability analysis suggest that IL-1H1 folds similarly to IL-1ra. The novel homologues are not widely expressed in mammals. IL-1H1 is constitutively expressed only in placenta and the squamous epithelium of the esophagus. However, IL-1H1 could be induced in vitro in keratinocytes by interferon-gamma and tumor necrosis factor-alpha and in vivo via a contact hypersensitivity reaction or herpes simplex virus infection. This suggests that IL-1H1 may be involved in pathogenesis of immune mediated disease processes. The addition of four novel IL-1 homologues suggests that the IL-1 family is significantly larger than previously thought.
Design-time simulation of a large-scale, distributed object system (1998)

We present a case study in using simulation at design time to predict the performance and scalability properties of a large-scale distributed object system. The system, called Consul, is a network management system designing to support hundreds of operators managing millions of network devices. It is essential that a system such as Consul be designed with performance and scalability in mind, but due to Consul's complexity and scale, it is hard to reason about performance and scalability using ad hoc techniques. We built a simulation of Consul's design to guide the design process by enabling performanace and scalability analysis of various design alternatives. A major challenge in doing design-time simulation is that many parameters for the simulation are based on estimates rather than measurements. We developed analysis methods that derive conclusions that are valid in the presence of estimation errors. In this article, we describe our scalability analysis method for design simulations of distributed object systems. The main idea is to use relative and comparative reasoning to analyze design alternatives and compare transaction behaviors. We demonstrate the analysis approach by describing its application to Consul.
Assessing the Influence of Different ROI Selection Strategies on Functional Connectivity Analyses of fMRI Data Acquired During Steady-State Conditions (2011)

In blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI), assessing functional connectivity between and within brain networks from datasets acquired during steady-state conditions has become increasingly common. However, in contrast to connectivity analyses based on task-evoked signal changes, selecting the optimal spatial location of the regions of interest (ROIs) whose timecourses will be extracted and used in subsequent analyses is not straightforward. Moreover, it is also unknown how different choices of the precise anatomical locations within given brain regions influence the estimates of functional connectivity under steady-state conditions. The objective of the present study was to assess the variability in estimates of functional connectivity induced by different anatomical choices of ROI locations for a given brain network. We here targeted the default mode network (DMN) sampled during both resting-state and a continuous verbal 2-back working memory task to compare four different methods to extract ROIs in terms of ROI features (spatial overlap, spatial functional heterogeneity), signal features (signal distribution, mean, variance, correlation) as well as strength of functional connectivity as a function of condition. We show that, while different ROI selection methods produced quantitatively different results, all tested ROI selection methods agreed on the final conclusion that functional connectivity within the DMN decreased during the continuous working memory task compared to rest.
Design considerations for a femtosecond pulse laser balancing self phase modulation, group velocity dispersion, saturable absorption, and saturable gain (1986)

This paper describes the design and operating characteristics of a femtosecond pulse ring dye laser that employs the combined effects of self phase modulation, group velocity dispersion, saturable absorption, and saturable gain to generate pulses as short as 27 fs.