gebhart/patrepeval huggingface dataset:
Issues in structural health monitoring employing smart sensors (2007)

Smart sensors densely distributed over structures can provide rich information for structural monitoring using their onboard wireless communication and computational capabilities. However, issues such as time synchronization error, data loss, and dealing with large amounts of harvested data have limited the implementation of full-fledged systems. Limited network resources (e.g. battery power, storage space, bandwidth, etc.) make these issues quite challenging. This paper first investigates the effects of time synchronization error and data loss, aiming to clarify requirements on synchronization accuracy and communication reliability in SHM applications. Coordinated computing is then examined as a way to manage large amounts of data.
PRINTS-S: the database formerly known as PRINTS (2000)

The PRINTS database houses a collection of protein family fingerprints. These are groups of motifs that together are diagnostically more potent than single motifs by virtue of the biological context afforded by matching motif neighbours. Around 1200 fingerprints have now been created and stored in the database. The September 1999 release (version 24.0) encodes approximately 7200 motifs, covering a range of globular and membrane proteins, modular polypeptides and so on. In addition to its continued steady growth, we report here several major changes to the resource, including the design of an automated strategy for database maintenance, and implementation of an object-relational schema for more efficient data management. The database is accessible for BLAST, fingerprint and text searches at http://www.bioinf.man.ac. uk/dbbrowser/PRINTS/
Protective immunity to Shiga-like toxin I following oral immunization with Shiga-like toxin I B-subunit-producing Vibrio cholerae CVD 103-HgR (1996)

This study addresses a mechanism for inducing systemic immunity to Shiga-like toxins by oral administration of a Shiga-like toxin I B-subunit-expressing Vibrio cholerae vaccine strain [CVD 103-HgR(pDA60)]. Two sets of three rabbits were given either CVD 103-HgR or CVD 103-HgR(pDA60) orally. All rabbits immunized with CVD 103-HgR(pDA60) developed neutralizing serum antibodies to Shiga-like toxin I. None of the controls developed such antibodies.
Introduction to Computer Graphics (1993)

From the Publisher:
This new introductory text to computer graphics is an adaptation of Computer Graphics: Principles and Practice, Second Edition, which remains the most comprehensive and authoritative work in the field. While retaining the currency and accuracy of the larger book, this abbreviated version focuses on topics essential for all beginners in computer graphics and provides expanded explanations for readers with little or no technical background. Worked examples have been added to illustrate important concepts and techniques, and program code has been written in the C language to enhance the book's usefulness. In addition, the book contains an extensive illustration program, with more than 50 full-color images.

Topic coverage includes basic graphics programming, hardware, and applications. Important algorithms are included to facilitate implementation of both 2D and 3D graphics. A separate chapter covers SPHIGSa simplified dialect of the PHIGS 3D standardand coincides with the availability of an updated version of the software. Chapter 9 and presents a concise overview of interaction issues and techniques. Advanced material from the larger book has been condensed, and the mathematics needed for it has been explained carefully . 

The result is an accessible introduction to computer graphics, crafted to provide a solid foundation for further work in this exciting field.
Features
Adaptation of the definitive computer graphics book in the fieldhalf the length.
Presents key concepts geared toward students with minimal technical background.
Provides worked examples in C.
Retains the highlevel of teaching standards of the parent graphics text.
Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation (2001)

The introduction of chemically unique groups into proteins by means of non-natural amino acids has numerous applications in protein engineering and functional studies. One method to achieve this involves the utilization of a non-natural amino acid by the cell's native translational apparatus. Here we demonstrate that a methionine surrogate, azidohomoalanine, is activated by the methionyl-tRNA synthetase of Escherichia coli and replaces methionine in proteins expressed in methionine-depleted bacterial cultures. We further show that proteins containing azidohomoalanine can be selectively modified in the presence of other cellular proteins by means of Staudinger ligation with triarylphosphine reagents. Incorporation of azide-functionalized amino acids into proteins in vivo provides opportunities for protein modification under native conditions and selective labeling of proteins in the intracellular environment.
Thymocyte responsiveness to endogenous glucocorticoids is required for immunological fitness (2012)

Generation of a self-tolerant but antigen-responsive T cell repertoire occurs in the thymus. Although glucocorticoids are usually considered immunosuppressive, there is also evidence that they play a positive role in thymocyte selection. To address the question of how endogenous glucocorticoids might influence the adaptive immune response, we generated GRlck-Cre mice, in which the glucocorticoid receptor gene (GR) is deleted in thymocytes prior to selection. These mice were immunocompromised, with reduced polyclonal T cell proliferative responses to alloantigen, defined peptide antigens, and viral infection. This was not due to an intrinsic proliferation defect, because GR-deficient T cells responded normally when the TCR was cross-linked with antibodies or when the T cell repertoire was "fixed" with αβ TCR transgenes. Varying the affinity of self ligands in αβ TCR transgenic mice showed that affinities that would normally lead to thymocyte-positive selection caused negative selection, and alterations in the TCR repertoire of polyclonal T cells were confirmed by analysis of TCR Vβ CDR3 regions. Thus, endogenous glucocorticoids are required for a robust adaptive immune response because of their promotion of the selection of T cells that have sufficient affinity for self, and the absence of thymocyte glucocorticoid signaling results in an immunocompromised state.
Effect of Dietary Calcium and Age on Jejunal Calcium Absorption in Humans Studied by Intestinal Perfusion (1973)

Jejunal calcium absorption was measured from test solutions containing 1.0, 2.5, 5, and 10 mM calcium (as calcium gluconate). Absorption rates increased progressively as luminal calcium concentration was increased, although there was a tendency toward saturation of the absorptive process at the higher concentrations. Calcium absorption was higher in normal young adults than in normal subjects over age 60. In both groups a 300 mg calcium diet for 4-8 wk enhanced calcium absorption relative to absorption rates after 4-8 wk on a 2,000 mg calcium diet. This adaptation was more definite and dramatic in the young than in the old subjects. Indirect estimates suggest that adaptation to a low calcium diet and the higher absorption in young than old normal subjects are mediated by an increased V(max) rather than a decreased K(m).
Cytokine and Growth Factor mRNA Expression Patterns Associated with the Hypercontracted, Hyperpigmented Healing Phenotype of Red Duroc Pigs: A Model of Abnormal Human Scar Development? (2005)

Background: Skin wounds in red Duroc pigs heal with the formation of hypercontractile, hyperpigmented scars, similar in some respects to human hypertrophic scars. ObjectiveThe goal of this study was to characterize the mRNA expression patterns for a subset of relevant cytokines, growth factors, receptors, and transcription factors involved in the red Duroc scarring phenotype. Methods: Full-thickness and deep dermal wounds were created on the backs of juvenile female red Duroc pigs. Samples were taken every two weeks postwounding and total RNA and DNA were extracted and quantified. RT-PCR was performed using porcine gene-specific primers for 15 relevant molecules. Results: The majority of molecules examined exhibited a biphasic pattern of expression, with peaks of expression at days 14 and 56 postinjury. Conclusions: The molecular expression pattern observed correlates well with the gross healing phenotype and matrix molecule expression patterns previously reported in red Duroc pigs. These findings enhance our understanding of the processes associated with fibroproliferative scar-formation.
Neutron diffraction studies of the 1:1 and 2:1 cocrystals of benzene-1,2,4,5-tetracarboxylic acid and 4,4′-bipyridine (2006)

The 1:1 and 2:1 cocrystals of benzene-1,2,4,5-tetra­carboxylic acid (BTA) and 4,4′-bipyridine (BPY) have been studied using neutron diffraction at 215 and 20 K, respectively. BTA and BPY crystallize in a 1:1 ratio with 1.8 mol­ecules of water, viz. 4,4′-bipyridinium 2,5-dicarboxy­benzene-1,4-dicarboxyl­ate 1.8-hydrate, C10H12N22+·C10H4O82−·1.8H2O, (I), in the space group P\overline{1}, with both BTA and BPY lying on inversion centres. BTA and BPY crystallize in a 2:1 ratio, viz. 4,4′-bipyridinium bis­(2,4,5-tricarboxy­benzoate), C10H12N22+·2C10H5O8−, (II), in the space group Cc. The crystal structure of the 1:1 cocrystal contains one short N—H⋯O hydrogen bond [N⋯O = 2.6047 (19) Å] and one intra­molecular O—H⋯O hydrogen bond [O⋯O = 2.423 (3) Å]. The crystal structure of the 2:1 cocrystal contains two N—H⋯O hydrogen bonds [N⋯O = 2.639 (3) and 2.674 (2) Å], and two intra­molecular [O⋯O = 2.404 (3) and 2.420 (3) Å] and four strong inter­molecular O—H⋯O hydrogen bonds [O⋯O = 2.613 (3), 2.718 (3), 2.628 (3) and 2.739 (3) Å].
ChemInform Abstract: Rearrangement of Ammonium Ylides Produced by Intramolecular Reaction of Catalytically Generated Metal Carbenoids. Part 1. Synthesis of Cyclic Amines. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Enhanced MAPK signaling drives ETS1-mediated induction of miR-29b leading to downregulation of TET1 and changes in epigenetic modifications in a subset of lung SCC (2016)

Non-small-cell lung cancer is the leading cause of cancer death worldwide and is comprised of several histological subtypes, the two most common being adenocarcinoma (AC) and squamous cell carcinoma (SCC). Targeted therapies have successfully improved response rates in patients with AC tumors. However, the majority of SCC tumors lack specific targetable mutations, making development of new treatment paradigms for this disease challenging. In the present study, we used iterative non-negative matrix factorization, an unbiased clustering method, on mRNA expression data from the cancer genome atlas (TCGA) and a panel of 24 SCC cell lines to classify three disease segments within SCC. Analysis of gene set enrichment and drug sensitivity identified an immune-evasion subtype that showed increased sensitivity to nuclear factor-κB and mitogen-activated protein kinase (MAPK) inhibition, a replication-stress associated subtype that showed increased sensitivity to ataxia telangiectasia inhibition, and a neuroendocrine-associated subtype that showed increased sensitivity to phosphoinositide 3-kinase and fibroblast growth factor receptor inhibition. Additionally, each of these subtypes exhibited a unique microRNA expression profile. Focusing on the immune-evasion subtype, bioinformatic analysis of microRNA promoters revealed enrichment for binding sites for the MAPK-driven ETS1 transcription factor. Indeed, we found that knockdown of ETS1 led to upregulation of eight microRNAs and downregulation of miR-29b in the immune-evasion subtype. Mechanistically, we found that miR-29b targets the DNA-demethylating enzyme, TET1, for downregulation resulting in decreased 5-hmC epigenetic modifications. Moreover, inhibition of MAPK signaling by gefitinib led to decreased ETS1 and miR-29b expression with a corresponding increase in TET1 expression and increase in 5-hmC. Collectively, our work identifies three subtypes of lung SCC that differ in drug sensitivity and shows a novel mechanism of miR-29b regulation by MAPK-driven ETS1 expression which leads to downstream changes in TET1-mediated epigenetic modifications.
Inducible Apoptosis as a Safety Switch for Adoptive Cell Therapy (2011)

The iCasp9 cell-suicide system may increase the safety of cellular therapies and expand their clinical applications. (Funded by the National Heart, Lung, and Blood Institute and the National Cancer Institute; ClinicalTrials.gov number, NCT00710892.).
Human Immunodeficiency Virus Replication in a Primary Effusion Lymphoma Cell Line Stimulates Lytic-Phase Replication of Kaposi’s Sarcoma-Associated Herpesvirus (1999)

Human immunodeficiency virus (HIV) and Kaposi's sarcoma-associated herpesvirus (KSHV) coinfect many individuals in North America and in parts of Africa. Infection with HIV is a leading risk factor for the development of Kaposi's sarcoma (KS). In this study, we tested the hypothesis that HIV infection of common or adjacent cells would stimulate replication and spread of KSHV. Infection of a primary effusion lymphoma cell line by vesicular stomatitis virus type G-pseudotyped HIV type 1 led to a rapid induction of lytic-phase KSHV replication. Induction of lytic KSHV replication by HIV required active replication of HIV. The addition of the nucleoside reverse transcriptase inhibitor azidothymidine or the protease inhibitor indinavir to the culture prevented HIV spread and inhibited the associated induction of KSHV lytic replication. Lytic replication occurred in both HIV-infected and HIV-uninfected cells within the culture, and could be induced in uninfected cells via a soluble factor released from the HIV-infected cells. Transmission of infectious KSHV to an uninfected target cell was enhanced by HIV replication and was inhibited by antiretroviral drugs. These results may have implications for the pathogenesis and treatment of KS in individuals coinfected with KSHV and HIV.
Enhancement of choleragen ADP-ribosyltransferase activities by guanyl nucleotides and a 19-kDa membrane protein. (1987)

Choleragen activates adenylate cyclase by catalyzing, in the presence of NAD, the ADP-ribosylation of Gs alpha, the stimulatory guanyl nucleotide-binding protein of the cyclase system. Kahn and Gilman [Kahn, R. A. & Gilman, A. G. (1986) J. Biol. Chem. 261, 7906-7911] identified another guanyl nucleotide-binding protein termed ADP-ribosylation factor (ARF) that stimulated this reaction. It was proposed that the toxin substrate is an ARF-Gs alpha complex and that ARF may have a physiological role in regulation of Gs alpha activity. We have found that purified ARF from bovine brain enhances not only the ADP-ribosylation of Gs alpha but also Gs alpha-independent choleragen-catalyzed reactions. These are (i) ADP-ribosylation of agmatine, a low molecular weight guanidino compound; (ii) ADP-ribosylation of several proteins unrelated to Gs alpha; and (iii) auto-ADP-ribosylation of the toxin A1 peptide. These reactions, as well as the ADP-ribosylation of ARF itself, were stimulated by GTP or stable GTP analogues such as guanyl-5'-yl imido-beta gamma-diphosphate and guanosine 5'-O-[gamma-thio]triphosphate; GDP and guanosine 5'-O-[beta-thio]diphosphate were inactive. These observations are consistent with the conclusion that ARF interacts directly with the A subunit of choleragen in a GTP-dependent fashion thereby enhancing catalytic activity manifest as transfer of ADP-ribose to Gs alpha and other proteins, to the toxin A1 peptide, or to agmatine. It is tempting to speculate that ARF may be involved in regulating one or another of the ADP-ribosyltransferases found in animal cells.
A Virulent Bioluminescent and Fluorescent Dual-Reporter Marek's Disease Virus Unveils an Alternative Spreading Pathway in Addition to Cell-to-Cell Contact (2014)

Marek's disease virus (MDV) is a growing threat for the poultry industry. Unfortunately, despite successful vaccination against the disease, MDV remains in circulation within vaccinated flocks, leading to the selection of increasingly virulent pathotypes. Detailed knowledge of the virus biology and the host-virus interaction is required to improve the vaccine efficiency. In the present study, I engineered an original, dual-reporter MDV to track and quantify virus replication in vitro and in vivo.
Characterization of A2B5+ glial precursor cells from cryopreserved human fetal brain progenitor cells (2002)

The identification and characterization of human neural precursor cells are critical in extending our understanding of central nervous system development from model animal systems to our own species. Moreover, availability of well-characterized populations of human cells is of potential value in endeavors ranging from cell transplantation to drug screening. We have isolated a population of continuously dividing glial-restricted precursor cells from commercially available cryopreserved 18-20 weeks old fetal brain neural progenitor cells. These human glial-restricted precursor cells are A2B5(+) and do not express polysialylated E-NCAM (PSA-NCAM). They can be grown as purified populations in serum-free medium supplemented with basic fibroblast growth factor (bFGF) and can be induced to generate cells with the antigenic characteristics of oligodendrocytes and distinct astrocytic populations.
Texture synthesis by non-parametric sampling (1999)

A non-parametric method for texture synthesis is proposed. The texture synthesis process grows a new image outward from an initial seed, one pixel at a time. A Markov random field model is assumed, and the conditional distribution of a pixel given all its neighbors synthesized so far is estimated by querying the sample image and finding all similar neighborhoods. The degree of randomness is controlled by a single perceptually intuitive parameter. The method aims at preserving as much local structure as possible and produces good results for a wide variety of synthetic and real-world textures.
Characterization of the CHD family of proteins (1997)

The murine gene CHD1 (MmCHD1) was previously isolated in a search for proteins that bound a DNA promoter element. The presence of chromo (chromatin organization modifier) domains and an SNF2-related helicase/ATPase domain led to speculation that this gene regulated chromatin structure or gene transcription. This study describes the cloning and characterization of three novel human genes related to MmCHD1. Examination of sequence databases produced several more related genes, most of which were not known to be similar to MmCHD1, yielding a total of 12 highly conserved CHD genes from organisms as diverse as yeast and mammals. The major region of sequence variation is in the C-terminal part of the protein, a region with DNA-binding activity in MmCHD1. Targeted deletion of ScCHD1, the sole Saccharomyces cerevesiae CHD gene, was performed with deletion strains being less sensitive than wild type to the cytotoxic effect of 6-azauracil. This finding suggested that enhanced transcriptional arrest at RNA polymerase II pause sites due to 6-azauracil-induced nucleotide pool depletion was reduced in the deletion strain and that ScCHD1 inhibited transcription. This observation, along with the known roles of other proteins with chromo or SNF2-related helicase/ATPase domains, suggests that alteration of gene expression by CHD genes might occur by modifications of chromatin structure, with altered access of the transcriptional apparatus to its chromosomal DNA template.
Characteristics of Coupled Microstriplines (1979)

Semiempirical design equations for the even- and odd-mode characteristics of coupled microstriplines are presented. The characteristics include capacitance, effective dielectric constant, impedance, and losses. The coupled line capacitances are obtained by suitably dividing the total capacitance into parallel plate and fringing capacitances. These capacitances are then used to determine other characteristics. The accuracy of characteristic impedances obtained from these capacitances is better than 3 percent. The sensitivity of the characteristics of coupled microstriplines to the tolerance in parameters is described. It is observed that the effect of tolerances on the coupling constant of a directional coupler increases with the increase in the value of coupling constant. The effects of dispersion and the finite thickness of metal strips have been included. It is noticed that the dispersion is more pronounced for even mode, whereas finite strip thickness affects odd mode to larger extent.
Soft and Wet Conducting Polymers for Artificial Muscles (1998)

Muscles convert chemical energy to mechanical energy plus heat at constant temperature. The search for artificial muscles that do the same is described, beginning with polymer gels—which were restricted to slow movements and had high energy consumption—and ending with the bilayer devices that have been constructed from conducting polymers more recently. The mechanism of operation of these devices is explained, showing how the electrochemically stimulated conformational movements of the conducting polymer chains are translated into macroscopic movements.
In Junk We Trust: Repetitive Dna, Epigenetics and Facioscapulohumeral Muscular Dystrophy (2010)

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant myopathy with a peculiar etiology. Unlike most genetic disorders, FSHD is not caused by mutations in a protein-coding gene. Instead, it is associated with contraction of the D4Z4 macrosatellite repeat array located at 4q35. Interestingly, D4Z4 deletion is not sufficient per se to cause FSHD. Moreover, the disease severity, its rate of progression and the distribution of muscle weakness display great variability even among close family relatives. Hence, additional genetic and epigenetic events appear to be required for FSHD pathogenesis. Indeed, recent findings suggest that virtually all levels of epigenetic regulation, from DNA methylation to higher order chromosomal architecture, exhibit alterations in the disease locus causing deregulation of 4q35 gene expression, ultimately leading to FSHD.
Studies on coagulation and the development of an automatic computerized bipolar coagulator (1991)

A new computerized bipolar coagulator is described in which tissue heating is switched off automatically when adequate vessel occlusion has been achieved, thus preventing overheating, undue tissue damage, cutting, and sticking of the forceps. Experiments with radiofrequency (rf) heating of albumin or arteries revealed an impedance minimum at the moment of coagulation. The attainment of this impedance minimum is transmitted electronically via a microprocessor to the coagulator, which automatically shuts off the rf energy supply. In experiments, adequate artery strength and avoidance of the drawbacks of conventional coagulation methods were achieved when rf heating was shut off soon after the impedance minimum was reached. Neither irrigation for cooling nor cleaning of the forceps tips was necessary. Electronic feedback through the same cables as used for coagulation enabled the use of conventional bipolar cables and forceps. The bipolar coagulator described can also be used for conventional bipolar coagulation under visual control. The microcomputer enables: 1) automatic coagulation cycles that start when tissue is picked up in the forceps and stop automatically on completion of the seal; 2) the change of power setting from a pedal and activation of automatic cycles by the pedal as described above or surgeon-controlled coagulation, which facilitates the use of alternative debridement with inactive forceps; 3) cable testing; and 4) negligible disturbance of the intraoperative monitoring equipment.