gebhart/patrepeval huggingface dataset:
A Developmentally Modulated Chromatin Structure at the Mouse Immunoglobulin κ 3′ Enhancer (1996)

Transcription of the mouse immunoglobulin kappa gene is controlled by two enhancers: the intronic enhancer (Ei) that occurs between the joining (J kappa) and constant (C kappa) exons and the 3' enhancer (E3') located 8.5 kb downstream of the gene. To understand the role of E3' in the activation of the mouse immunoglobulin kappa gene, we studied its chromatin structure in cultured B-cell lines arrested at various stages of differentiation. We found that 120 bp of the enhancer's transcriptional core becomes DNase I hypersensitive early in B-cell development. Genomic footprinting of pro-B and pre-B cells localized this chromatin alteration to B-cell-specific protections at the region including the direct repeat (DR) and the sequence downstream of the DR (DS), the PU.1-NFEM-5 site, and the core's E-box motif, identifying bound transcription factors prior to kappa gene rearrangement. Early footprints were, however, not detected at downstream sites proposed to play a negative role in transcription. The early chromatin structure persisted through the mature B-cell stage but underwent a dramatic shift in plasma cells, correlating with the loss of guanosine protection within the DR-DS junction and the appearance of novel footprints at a GC-rich motif upstream and the NF-E1 (YY1/delta)-binding site downstream. Gel shift analysis demonstrated that the DR-DS junction is bound by a factor with properties similar to those of BSAP (B-cell-specific activator protein). These results reveal developmental-stage-specific changes in the composition of nuclear factors bound to E3', clarify the role of factors that bind constitutively in vitro, and point to the differentiation of mature B cells to plasma cells as an important transitional point in the function of this enhancer. The observed changes in nuclear factor composition were accompanied by the rearrangement of positioned nucleosomes that flank the core region, suggesting a role for both nuclear factors and chromatin structure in modulating kappa E3' function during B-cell development. The functional implications of the observed chromatin alterations are discussed in the context of recent studies on kappa E3' and the factors that bind to it.
Movable-multimedia (2006)

IP-based Multimedia creation and consumption is becoming available on an increasing spectrum of devices ranging from low-powered portable devices like cell phones and PDA's to high powered static devices like desktops PCs and IPTVs. High-speed wireless and wire-line network access is becoming widespread. Multimedia services like IPTV, Video-on-demand and Video-conferencing are becoming main stream. These developments have paved the way for creating innovative concepts like session mobility for multimedia applications. Session mobility enables seamless transfer of an on-going multimedia session between different devices based on user preferences. We examine the motivations and use cases for session mobility. In this paper we evaluate architectural design constraints and propose architectural solutions for session mobility. We evaluate current session mobility mechanisms and propose requirements for new mechanisms.
Voice Activity Detection based on Generalized Gamma Distribution (2006)

We propose a voice activity detection (VAD) algorithm based on the generalized gamma distribution (G/spl Gamma/D). The distributions of noise spectra and noisy speech spectra, including speech-inactive intervals, are modeled by a set of G/spl Gamma/Ds and applied to the likelihood ratio test (LRT) for VAD. The parameters of G/spl Gamma/D are estimated through an on-line maximum likelihood (ML) estimation procedure where the global speech absence probability (GSAP) is incorporated under a forgetting scheme. Experimental results show that the proposed VAD algorithm, based on G/spl Gamma/D, outperformed the algorithms based on other statistical models.
Erratum to: Inducible expression of the GLT‐1 glutamate transporter in a CHO cell line selected for low endogenous glutamate uptake (FEBS 19804) (1998)

On page 339 the corresponding author should have been given as Dr. Line M. Levy (as shown above) and not Dr. David Attwell (as shown erroneously in the publication). Dr. Levy can be contacted at the Department of Anatomy, University of Oslo, P.O. Box 1105, Blindern, N-0317 Oslo, Norway. Fax: (47) 2285 1278; E-mail: [email protected] The publisher apologises to authors and readers for this error.
IgA Nephropathy (2013)

IgA nephropathy is a common glomerular disease that is an important cause of kidney failure. This review discusses advances in the therapy and understanding of the molecular basis of IgA nephropathy, a common glomerulopathy that not infrequently leads to kidney failure.
Synthetic Vaccines Consisting of Tumor‐Associated MUC1 Glycopeptide Antigens and Bovine Serum Albumin (2005)

Sweet medicine: The mucin MUC1 is highly overexpressed on epithelial tumor cells. Glycopeptides 1 (from the repeating unit of MUC1) carrying various important sialylated tumor-associated carbohydrate antigens R were synthesized and coupled to bovine serum albumin (to generate anticancer vaccines) and to microtiter plates (to test the selectivity of the immune response).
Towards the Semantic Web: Collaborative Tag Suggestions (2006)

Content organization over the Internet went through several interesting phases of evolution: from structured directories to unstructured Web search engines and more recently, to tagging as a way for aggregating information, a step towards the semantic web vision. Tagging allows ranking and data organization to directly utilize inputs from end users, enabling machine processing of Web content. Since tags are created by individual users in a free form, one important problem facing tagging is to identify most appropriate tags, while eliminating noise and spam. For this purpose, we define a set of general criteria for a good tagging system. These criteria include high coverage of multiple facets to ensure good recall, least effort to reduce the cost involved in browsing, and high popularity to ensure tag quality. We propose a collaborative tag suggestion algorithm using these criteria to spot high-quality tags. The proposed algorithm employs a goodness measure for tags derived from collective user authorities to combat spam. The goodness measure is iteratively adjusted by a reward-penalty algorithm, which also incorporates other sources of tags, e.g., content-based auto-generated tags. Our experiments based on My Web 2.0 show that the algorithm is effective.
Effect of Perforation on the Sensing Properties of Monolayer-Capped Metallic Nanoparticle Films (2012)

We report on the effect of perforation within a monolayer-capped metallic nanoparticle (MCNP) film on sensing of volatile organic compounds (VOCs) and water molecules. Our results show that continuous MCNP film exhibits positive responses on exposure to VOCs and to water, consistent with the swelling and dielectric sensing mechanisms. In contrast, perforated films exhibit positive responses on exposure to VOCs but a high-magnitude negative response on exposure to high levels of water. The negative responses were higher by at least 1 order of magnitude compared with the positive responses. The results are explained in terms of ionization of condensed water and/or SiO2 sites in MCNP-free domains under applied voltage, side-by-side with the tunneling mechanism within the MCNP domains. The controlled morphology afforded by MCNP assemblies, combined with the existence of multiple sensing mechanisms under real-world humidity conditions, would enable a host of new fundamental and applied opportunities.
WOOD-BASED FILTER FOR NITRATE REMOVAL IN SEPTIC SYSTEMS (2005)

The recognition that septic systems can generate groundwater plumes with nitrate concentrations exceeding thedrinking water limit has led to a need for improved nitrogen removal in septic systems. Long-term (3 to 5 year) monitoringresults are presented for four full-scale, on-site wastewater treatment systems using a novel porous media filter (Nitrex filter)for enhanced nitrogen removal. The filter removes nitrogen by denitrification of pretreated, nitrified, septic tank effluent usinga slowly soluble carbon source (wood byproduct material) incorporated into the filter. Results are presented for a house (sewageflow ~1 m3 d-1), a trailer park (7 m3 d-1), a communal residence (18 m3 d-1), and an inn (73 m3 d-1). In each case, theseptic tank effluent was pretreated using a sand filter, then flowed passively through the denitrification filter, and finally wasdispersed in a conventional tile bed. Influent (sand filter) NO3-N concentrations, averaging 14.2 to 37.7 mg L-1, weresignificantly attenuated in the denitrification filters at each site (p < 0.05) by amounts ranging between 87% and 98%.Reaction rates were temperature dependent, ranging from 7 to >10 mg N L-1 d-1, and showed no sign of deteriorating withsystem age at any of the sites. Results support previous mass balance calculations and pilot-scale field trials, suggesting thatsuch filters have the potential to operate for years without the need for media replenishment. These filters offer a practicalsolution to nitrate control in small to medium sized on-site wastewater treatment systems where simplicity of operation andlow maintenance are desirable.
Markers of DNA Repair and Susceptibility to Cancer in Humans: an Epidemiologic Review (2000)

DNA repair is a system of defenses designed to protect the integrity of the genome. Deficiencies in this system likely lead to the development of cancer. The epidemiology of DNA repair capacity and of its effect on cancer susceptibility in humans is, therefore, an important area of investigation. We have summarized all of the published epidemiologic studies on DNA repair in human cancer through 1998 (n = 64) that addressed the association of cancer susceptibility with a putative defect in DNA repair capacity. We have considered study design, subject characteristics, potential biases, confounding variables, and sources of technical variability. Assays of DNA repair capacity used, to date, can be broadly grouped into five categories: 1) tests based on DNA damage induced with chemicals or physical agents, such as the mutagen sensitivity assay, the G(2)-radiation assay, induced micronuclei, and the Comet assay; 2) indirect tests of DNA repair, such as unscheduled DNA synthesis; 3) tests based on more direct measures of repair kinetics, such as the host cell reactivation assay; 4) measures of genetic variation associated with DNA repair; and 5) combinations of more than one category of assay. The use of such tests in human populations yielded positive and consistent associations between DNA repair capacity and cancer occurrence (with odds ratios in the range of 1. 4-75.3, with the majority of values between 2 and 10). However, the studies that we have reviewed have limitations, including small sample size, "convenience" controls, the use of cells different from the target organ, and the use of mutagens that do not occur in the natural environment. The evolving ability to study polymorphisms in DNA repair genes may contribute to new understandings about the mechanisms of DNA repair and the way in which DNA repair capacity affects the development of cancer.
Radiation Pneumonitis and Fibrosis in Mouse Lung Assayed by Respiratory Frequency and Histology (1980)

E. L. Travis, J. D. Down, S. J. Holmes, B. Hobson, Radiation Pneumonitis and Fibrosis in Mouse Lung Assayed by Respiratory Frequency and Histology, Radiation Research, Vol. 84, No. 1 (Oct., 1980), pp. 133-143
Interaction of an immunodominant epitope with Ia molecules in T-cell activation. (1988)

The amino acid sequence corresponding to residues 107-116 of hen egg-white lysozyme (HEL) has been identified as containing an immunodominant T-cell epitope recognized in association with the I-Ed molecule. The immunodominance of this epitope in HEL-primed H-2d mice was demonstrated by analysis of the T-cell proliferative response induced by synthetic peptides covering almost the entire HEL sequence. All the T-cell hybridomas from H-2d mice analyzed recognize the HEL sequence 107-116 in association with the I-Ed molecule. Correlating with the restriction of T-cell recognition, HEL-(105-120)-peptide binds to I-Ed but not to I-Ad molecules. Conservative or semiconservative substitutions at positions 113 (Asn----Lys), 114 (Arg----His), or 115 (Cys----Ala) abrogate the ability of HEL-(105-120) to activate T cells. Substitutions at residues 113 and 115 affect T-cell recognition but not the binding to I-Ed molecules, whereas, as shown by binding data and competition experiments, an Arg----His substitution at position 114 profoundly impairs the capacity of the peptide to interact with I-Ed molecules. In agreement with these results, [Lys113]HEL-(105-120)-peptide but not [His114]HEL-(105-120)-peptide was found to be immunogenic in H-2d mice. Thus, a single semiconservative substitution drastically reduces binding capacity and abolishes immunogenicity, suggesting that a strict correlation exists between binding of a peptide to Ia molecules and its immunogenicity.
Direct least-squares estimation of spatiotemporal distributions from dynamic SPECT projections using a spatial segmentation and temporal B-splines (2000)

Artifacts can result when reconstructing a dynamic image sequence from inconsistent, as well as insufficient and truncated, cone beam single photon emission computed tomography (SPECT) projection data acquired by a slowly rotating gantry. The artifacts can lead to biases in kinetic model parameters estimated from time-activity curves generated by overlaying volumes of interest on the images. However, the biases in time-activity curve estimates and subsequent kinetic parameter estimates can be reduced significantly by first modeling the spatial and temporal distribution of the radiopharmaceutical throughout the projected field of view, and then estimating the time-activity curves directly from the projections. This approach is potentially useful for clinical SPECT studies involving slowly rotating gantries, particularly those using a single-detector system or body contouring orbits with a multidetector system. We have implemented computationally efficient methods for fully four-dimensional (4-D) direct estimation of spatiotemporal distributions from dynamic SPECT projection data. Temporal B-splines providing various orders of temporal continuity, as well as various time samplings, were used to model the time-activity curves for segmented blood pool and tissue volumes in simulated cone beam and parallel beam cardiac data acquisitions. Least-squares estimates of time-activity curves were obtained quickly using a workstation. Given faithful spatial modeling, accurate curve estimates were obtained using cubic, quadratic, or linear B-splines and a relatively rapid time sampling during initial tracer uptake. From these curves, kinetic parameters were estimated accurately for noiseless data and with some bias for noisy data. A preliminary study of spatial segmentation errors showed that spatial model mismatch adversely affected quantitative accuracy, but also resulted in structured errors (projected model versus raw data) that were easily detected in our simulations. This suggests iterative refinement of the spatial model to reduce structured errors as an area of future research.
Molecular biology of human papillomavirus infection and cervical cancer (2006)

HPVs (human papillomaviruses) infect epithelial cells and cause a variety of lesions ranging from common warts/verrucas to cervical neoplasia and cancer. Over 100 different HPV types have been identified so far, with a subset of these being classified as high risk. High-risk HPV DNA is found in almost all cervical cancers (>99.7%), with HPV16 being the most prevalent type in both low-grade disease and cervical neoplasia. Productive infection by high-risk HPV types is manifest as cervical flat warts or condyloma that shed infectious virions from their surface. Viral genomes are maintained as episomes in the basal layer, with viral gene expression being tightly controlled as the infected cells move towards the epithelial surface. The pattern of viral gene expression in low-grade cervical lesions resembles that seen in productive warts caused by other HPV types. High-grade neoplasia represents an abortive infection in which viral gene expression becomes deregulated, and the normal life cycle of the virus cannot be completed. Most cervical cancers arise within the cervical transformation zone at the squamous/columnar junction, and it has been suggested that this is a site where productive infection may be inefficiently supported. The high-risk E6 and E7 proteins drive cell proliferation through their association with PDZ domain proteins and Rb (retinoblastoma), and contribute to neoplastic progression, whereas E6-mediated p53 degradation prevents the normal repair of chance mutations in the cellular genome. Cancers usually arise in individuals who fail to resolve their infection and who retain oncogene expression for years or decades. In most individuals, immune regression eventually leads to clearance of the virus, or to its maintenance in a latent or asymptomatic state in the basal cells.
NKp46 O-Glycan Sequences That Are Involved in the Interaction with Hemagglutinin Type 1 of Influenza Virus (2010)

Natural killer (NK) cells serve as a crucial first-line defense against tumors and virus-infected cells. We previously showed that lysis of influenza virus (IV)-infected cells is mediated by the interaction between the NK receptor, NKp46, and the IV hemagglutinin (HA) type 1 expressed by the infected cells. This interaction requires the presence of sialyl groups on the NKp46-T225 O-glycoforms. In the current study, we analyzed the O-glycan sequences that are imperative for the interaction between recombinant NKp46 (rNKp46) and IV H1N1 strains. We first showed that rNKp46 binding to IV H1N1 is not mediated by a glycoform unique to the Thr225 site. We then characterized the O-glycan sequences that mediate the interaction of rNKp46 and IV H1N1; we employed rNKp46s with dissimilar glycosylation patterns and IV H1N1 strains with different sialic acid alpha2,3 and alpha2,6 linkage preferences. The branched alpha2,3-sialylated O-glycoform Neu5NAcalpha2,3-Galbeta1,4-GlcNAcbeta1,6[Neu5NAcalpha2,3-Galbeta1,3]GalNAc competently mediated the interaction of rNKp46 with IV H1N1, manifesting a preference for alpha2,3 linkage. In contrast, the linear alpha2,3-sialylated O-glycoform Neu5NAcalpha2,3-Galbeta1,3-GalNAc was not correlated with enhanced interaction between rNKp46 and IV H1N1 or a preference for alpha2,3 linkage. The branched alpha2,3- and alpha2,6-sialylated O-glycoform Neu5NAcalpha2,3-Galbeta1,3[Neu5NAcalpha2,6]GalNAc competently mediated the interaction of rNKp46 with IV H1N1, manifesting a preference for alpha2,6 linkage. Previous viral HA-binding-specificity studies were performed with glycopolymer conjugates, free synthetic sialyl oligosaccharides, and sialidase-treated cells. This study shed light on the O-glycan sequences involved in the interaction of glycoprotein and viral hemagglutinins and may help in the design of agents inhibitory to hemagglutinin for influenza treatment.
Root resorption before and after orthodontic treatment: a clinical study of contributory factors (2010)

This clinical study evaluated factors related to root resorption before (T1) and after (T2) orthodontic treatment. Ninety-six subjects between 9 and 34 years (34 males and 62 females) who had been treated using fixed appliances for at least 1 year and who had panoramic radiographs at T1 and T2 were selected. The relationship between root resorption at T1 and T2, with regard to gender, age, extraction versus non-extraction patterns, specific teeth and treatment duration was investigated. No statistically significant differences in root resorption were found in relation to gender. Significant differences in root resorption (P = 0.000, P < 0.01) and also in treatment duration (P = 0.036, P < 0.05) were noted between the extraction and non-extraction groups; extraction and treatment duration correlated with T2 mean root resorption. Patient age correlated with root resorption of the upper incisors at T1 and T2. Using multiple regression analysis, age and duration of treatment were found to be more associated with root resorption than with extractions; the presence of root resorption at T1 was associated with T2 root resorption, especially of the anterior teeth.
Dominant genetic alterations in immortalization: Role for 20q gain (1999)

Gain of 20q has been observed in many cancer types, including bladder cancers. However, the biological significance of low-copy-number 20q gain in human cancer pathogenesis has not yet been defined. We reported that immortalization of human uroepithelial cells (HUC) transformed with human papillomavirus 16 (HPV 16) E7 is associated with single-copy 20q gain (P = 2 × 10-7). We also observed 20q13.2 amplification in some cell lines, but only after 20 passages. Thus, we hypothesized that low-copy gain of 20q gene(s) contributes in a dominant way to bypassing HUC senescence. To test this hypothesis, we fused precrisis E7-transformed HUCs (pcE7s) with three independent immortal E7-HUCs that acquired a single-copy 20q gain at immortalization. In one of these lines, a single-copy gain of 20q and a 10p12.1–pter loss were the only cytogenetic alterations. Immortal cell hybrids were obtained with all three crosses. Southern analysis for unique HPV16 insertion sites, as well as fluorescence in situ hybridization (FISH) with whole chromosome 20 painting probes (WCP20) for marker chromosomes in the immortal clones, confirmed the hybrid and independent nature of representative immortal clones. In contrast, when we used the same protocol, no immortal somatic cell hybrids were obtained when HPV16 E6 immortal HUC (E6-HUC) that showed 3p and 9p losses, but no 20q gain, were fused with precrisis E6-transformed HUC (pcE6s). This latter observation is consistent with many results demonstrating that recessive changes are required for cell immortalization. Therefore, the new results reported herein for the first time demonstrate that dominant changes can contribute to bypassing senescence, and that such genes may be located on 20q. Genes Chromosomes Cancer 26:304–311, 1999. © 1999 Wiley-Liss, Inc.
Green Phosphorescent Dendrimer for Light-Emitting Diodes (2002)

Highly efficient organic LEDs made by solution processing are reported. It is shown that the dendritic architecture (see Figure) can be used to solubilize luminescent chromophores and form uniform films of blends. The simple device structures containing a light-emitting chromophore are amongst the most efficient solution-processed devices reported. Thanks to this technique, the inkjet printing of phosphorescent materials becomes feasible.