gebhart/patrepeval huggingface dataset:
Characterization of the murine antibody response to peptides representing the variable domains of the major outer membrane protein of Chlamydia pneumoniae (1996)

In an attempt to gain more knowledge about the immunogenicity of the variable domains (VDs) of the major outer membrane protein (MOMP) of Chlamydia pneumoniae, peptides representing these areas were used to immunize BALB/c and C57BL/6 mice. Antisera to the peptides and to peptides conjugated to keyhole limpet hemocyanin (KLH) were characterized by their ability to recognize the immunizing peptide and elementary bodies (EBs) of C. pneumoniae by enzyme-linked immunosorbent assay (ELISA) and Western blot (immunoblot). In addition, antiserum was analyzed for its molecular specificity by a pepscan as well as its in vitro neutralizing ability. In general, results obtained with antisera to the peptides paralleled the results obtained with the antisera to the KLH-conjugated peptides except that the titers or strength of reaction in the assays was less. Antisera to the VDs in both strains of mice gave ELISA titers to the homologous VD peptide ranging from 1,000 to >64,000. The strength of reactivity with the reduced MOMP as judged by Western blot, in most cases, paralleled the ELISA titer to the peptide. However, only antisera raised in both strains of mice to the VD1 and VD4 peptides reacted strongly with the EBs, suggesting surface exposure of these VDs. In addition, antisera to VD3 from C57BL/6 mice gave strong reactivity to EBs. By pepscan analysis antisera from both strains of mice reacted with several VD1 and VD3 octameric peptides, with weaker reactivity being seen with the octameric peptides in the other two VDs. This was in contrast to antisera raised to EBs of C. pneumoniae TW-183, which identified two immunogenic regions, one in VD1 and the other mapped to VD4. While antisera raised to EBs strongly neutralized the infectivity of C. pneumoniae, none of the peptide antisera was able to neutralize. In addition, peptides to the VDs were not able to block the neutralizing ability of the antisera to EBs of C. pneumoniae. Therefore, these results suggest that the VDs of the MOMP of C. pneumoniae are surface exposed but do not elicit neutralizing antibodies when linear peptides representing them are used as the immunogen.
Specific chromosomal abnormalities in malignant human gliomas. (1988)

Karyotypic analysis of 54 malignant human gliomas (5 anaplastic astrocytomas, 43 glioblastoma multiformes, 3 gliosarcomas, 2 giant cell glioblastomas, 1 anaplastic mixed glioma) has demonstrated that 12 tumors contained normal stemlines or only lacked one sex chromosome. The 42 tumors with abnormal karyotypes included 38 tumors which could be completely analyzed. Six of these 38 cases had near-triploid or near-tetraploid stemlines and 32 had near-diploid stemlines. Statistically significant numerical deviations in the near-diploid group were gains of chromosome 7 (26 of 32; P less than 0.001), and losses of chromosome 10 (19 of 32; P less than 0.001). Double minutes occurred in 18 of 32 near diploid tumors. The distribution of structural abnormalities was analyzed statistically by comparing the incidence of breakpoint in each chromosomal arm to the expected value based on chromosomal arm length. This analysis demonstrated that structural abnormalities of 9p and 19q were significant statistically (P less than 0.005 and P = 0.02, respectively). Although chromosome 1, 6p, the centromeric region of chromosome 11, 13q, and 15q were also frequently involved in structural abnormalities, the incidence of these breaks did not reach statistical significance. This demonstration of specific chromosomal abnormalities in near-diploid gliomas provides the basis for the investigation of genes which may be quantitatively or qualitatively altered in these neoplasms.
Development of fetal hearing (1994)

Previous research has revealed that the human fetus responds to sound, but to date there has been little systematic investigation of the development of fetal hearing. The development of fetal behavioural responsiveness to pure tone auditory stimuli (100 Hz, 250 Hz, 500 Hz, 1000 Hz, and 3000 Hz) was examined from 19 to 35 weeks of gestational age. Stimuli were presented by a loudspeaker placed on the maternal abdomen and the fetus's response, a movement, recorded by ultrasound. The fetus responded first to the 500 Hz tone, where the first response was observed at 19 weeks of gestational age. The range of frequencies responded to expanded first downwards to lower frequencies, 100 Hz and 250 Hz, and then upwards to higher frequencies, 1000 Hz and 3000 Hz. At 27 weeks of gestational age, 96% of fetuses responded to the 250 Hz and 500 Hz tones but none responded to the 1000 Hz and 3000 Hz tones. Responsiveness to 1000 Hz and 3000 Hz tones was observed in all fetuses at 33 and 35 weeks of gestational age, respectively. For all frequencies there was a large decrease (20-30 dB) in the intensity level required to elicit a response as the fetus matured. The observed pattern of behavioural responsiveness reflects underlying maturation of the auditory system. The sensitivity of the fetus to sounds in the low frequency range may promote language acquisition and result in increased susceptibility to auditory system damage arising from exposure to intense low frequency sounds.
Cooperative Interactions between Activating Transcription Factor 4 and Runx2/Cbfa1 Stimulate Osteoblast-specific Osteocalcin Gene Expression (2005)

The role of ATF4 (activating transcription factor 4) in osteoblast differentiation and bone formation was recently described using ATF4-deficient mice (Yang, X., Matsuda, K., Bialek, P., Jacquot, S., Masuoka, H. C., Schinke, T., Li, L., Brancorsini, S., Sassone-Corsi, P., Townes, T. M., Hanauer, A., and Karsenty, G. (2004) Cell 117, 387-398). However, the mechanisms of ATF4 in bone cells are still not clear. In this study, we determined the molecular mechanisms through which ATF4 activates the mouse osteocalcin (Ocn) gene 2 (mOG2) expression and mOG2 promoter activity. ATF4 increased the levels of Ocn mRNA and mOG2 promoter activity in Runx2-containing osteoblasts but not in non-osteoblastic cells that lack detectable Runx2 protein. However, ATF4 increased Ocn mRNA and mOG2 promoter activity in non-osteoblastic cells when Runx2 was co-expressed. Mutational analysis of the OSE1 (ATF4-binding site) and the two OSE2s (Runx2-binding sites) in the 657-bp mOG2 promoter demonstrated that ATF4 and Runx2 activate Ocn via cooperative interactions with these sites. Pull-down assays using nuclear extracts from osteoblasts or COS-7 cells overexpressing ATF4 and Runx2 showed that both factors are present in either anti-ATF4 and anti-Runx2 immunoprecipitates. In contrast, pull-down assays using purified glutathione S-transferase fusion proteins were unable to demonstrate a direct physical interaction between ATF4 and Runx2. Thus, accessory factors are likely involved in stabilizing interactions between these two molecules. Regions within Runx2 required for ATF4 complex formation and activation were identified. Deletion analysis showed that the leucine zipper domain of ATF4 is critical for Runx2 activation. This study is the first demonstration that cooperative interactions between ATF4 and Runx2/Cbfa1 stimulate osteoblast-specific Ocn expression and suggests that this regulation may represent a novel intramolecular mechanism regulating Runx2 activity and, thereby, osteoblast differentiation and bone formation.
Regional Interactive Image Segmentation Networks (2017)

The interactive image segmentation model allows users to iteratively add new inputs for refinement until a satisfactory result is finally obtained. Therefore, an ideal interactive segmentation model should learn to capture the user's intention with minimal interaction. However, existing models fail to fully utilize the valuable user input information in the segmentation refinement process and thus offer an unsatisfactory user experience. In order to fully exploit the user-provided information, we propose a new deep framework, called Regional Interactive Segmentation Network (RIS-Net), to expand the field-of-view of the given inputs to capture the local regional information surrounding them for local refinement. Additionally, RIS-Net adopts multiscale global contextual information to augment each local region for improving feature representation. We also introduce click discount factors to develop a novel optimization strategy for more effective end-to-end training. Comprehensive evaluations on four challenging datasets well demonstrate the superiority of the proposed RIS-Net over other state-of-the-art approaches.
Effects processing on audio subband data (1996)

This paper will show that computing standard audio effects algorithms such as reverberation, echo, chorus and flange will use less memory and computations when performing the operations on the critically sampled subband data than on the fullrate time domain signal. Not only can effects in the subband domain be obtained to sound close to the effects in the time domain, but new types of effects are now possible because different effects can be placed in separate subbands. The MPEG Audio filter bank, which also splits the audio into subbands, is used in this discussion to show that standard MPEG audio decoders could easily be augmented to include effects processors as well. 1 Introduction Since the MPEG Audio (layers I,II) standard has become a prominent data compression algorithm in the consumer multimedia market, it exists on many platforms ranging from personal computers to workstations to video games. For most of these applications, some sort of audio post-processing is desired by th...
Multifocusing 3D diffraction imaging for detection of fractured zones in mudstone reservoirs: Case history (2014)

Abstract Diffracted waves are generated by a wave incident on a subsurface obstruction (of a size less than a seismic wavelength) that acts as a point source, scattering the wave in all directions. In the most general terms, diffractors are points and edges and they typically appear in the subsurface as faults, steep reef edges, karsts, or extensive systems of well-developed fractures. Diffracted waves are rarely imaged in sufficient detail for interpretation because they have low amplitudes compared to the reflectivity data, and standard processing flows are not optimized for them. Diffraction imaging, in the form of diffraction multifocusing, is a seismic processing technique that separates the recorded diffractions from the specular reflections (waves reflected from a smooth surface that obey Snell’s law). A 3D volume of the semblance of the diffracted energy can be created and interpreted to indicate the presence of the diffractors. We applied diffraction imaging to seismic data acquired above a fractured mudstone oil reservoir. In an unconventional reservoir, there may be additional hydrocarbon storage or permeability in the fractures that could affect drilling, completions, and production. We mapped the diffraction energy at the reservoir level and correlated it with rates of initial production of the wells. In addition, the diffraction imaging amplitudes were qualitatively related to gas shows encountered during drilling and may be used to predict the relative increase or decrease in gas shows in this reservoir. The ability to predict the presence of natural fractures allowed us to spatially locate well trajectories and may impact decisions regarding well operations and completions.
Immune responses and outcome after vaccination with glioma-associated antigen peptides and poly-ICLC in a pilot study for pediatric recurrent low-grade gliomas (2016)

GAA peptide vaccination in children with recurrent LGGs is generally well tolerated, with preliminary evidence of immunological and clinical activity.
Interaction of ribonuclease A with aqueous 2-methyl-2,4-pentanediol at pH 5.8 (1978)

The interactions between ribonuclease A and solvent components in aqueous 2-methyl-2,4-pentanediol (MPD) have been investigated by differential refractometry and light scattering at pH 5.8, i.e., conditions similar to those used to crystallize the protein from this solvent system. Application of multicomponent thermodynamic theory shows that, at all solvent compositions up to 50% (v/v) MPD, the protein is preferentially hydrated; i.e., addition of ribonuclease to the mixed solvent leads to an increase in the chemical potential of MPD. This unfavorable thermodynamic interaction leads to phase separation, probably caused by local salting out of the MPD by the charges on the surface of the protein molecule. A parallel examination by circular dichroism (CD) has shown that the CD spectrum of ribonuclease in 50% MPD is indistinguishable from that in dilute buffer.
Mitochondrial Evolution (1999)

The serial endosymbiosis theory is a favored model for explaining the origin of mitochondria, a defining event in the evolution of eukaryotic cells. As usually described, this theory posits that mitochondria are the direct descendants of a bacterial endosymbiont that became established at an early stage in a nucleus-containing (but amitochondriate) host cell. Gene sequence data strongly support a monophyletic origin of the mitochondrion from a eubacterial ancestor shared with a subgroup of the alpha-Proteobacteria. However, recent studies of unicellular eukaryotes (protists), some of them little known, have provided insights that challenge the traditional serial endosymbiosis-based view of how the eukaryotic cell and its mitochondrion came to be. These data indicate that the mitochondrion arose in a common ancestor of all extant eukaryotes and raise the possibility that this organelle originated at essentially the same time as the nuclear component of the eukaryotic cell rather than in a separate, subsequent event.
Peer Reviewed: Detection of Explosives by Electronic Noses (2003)

ADVERTISEMENT RETURN TO ISSUEPREVFeaturesNEXTPeer Reviewed: Detection of Explosives by Electronic NosesHandheld chemical-sensing systems come in several varieties and offer advantages over the traditional bomb-sniffing dog.Jehuda YinonCite this: Anal. Chem. 2003, 75, 5, 98 A–105 APublication Date (Web):March 1, 2003Publication History Published online1 March 2003Published inissue 1 March 2003https://pubs.acs.org/doi/10.1021/ac0312460https://doi.org/10.1021/ac0312460newsACS Publications. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views5264Altmetric-Citations192LEARN 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 PDF (409 KB) Get e-Alertsclose SUBJECTS:Explosives Get e-Alerts
Growth of Self-Organized GaN Nanostructures on Al2O3(0001) by RF-Radical Source Molecular Beam Epitaxy (1997)

Columnar GaN nanostructures (GaN nanocolumns) were grown on Al 2 O 3 (0001) by RF-radical source molecular beam epitaxy (RF-MBE) through a self-organization process. The nanocolumns were grown at high density, with the c -axis maintained perpendicular to the substrate surface. The dependence of column diameter and density on growth conditions was systematically investigated. The average diameter was minimized to 53 nm and the density of the GaN nanocolumns was 130×10 12 columns per square meter.
Repulsive Guidance Molecule Plays Multiple Roles in Neuronal Differentiation and Axon Guidance (2006)

Repulsive guidance molecule (RGM) is a membrane-bound protein originally isolated as a guidance molecule for retinal axons. Three RGM isoforms (RGMa-RGMc) exist in vertebrates. We showed previously that RGMa is a cell-survival factor in the neuroepithelium of chick embryos that suppresses the proapoptotic activity of its receptor neogenin. In the present study, we performed gain- and loss-of-function analysis of RGMa in chick embryos to further investigate RGMa function. We found that RGMa overexpression promotes neuronal differentiation, whereas RGMa small interference RNA represses it. Similar experiments conducted at later developmental stages using retroviral vectors reveal that perturbation of RGMa expression disturbs the retinotectal projection. Our work provides the first evidence for a role for RGMs in axon guidance in vivo. In addition, these results suggest that RGMa exerts multiple functions during neural development.
Inhibition of T cell activation and autoimmune diabetes using a B cell surface-linked CTLA-4 agonist (2006)

CTL-associated antigen 4 (CTLA-4) engagement negatively regulates T cell activation and function and promotes immune tolerance. However, it has been difficult to explore the biology of selective engagement of CTLA-4 in vivo because CTLA-4 shares its ligands, B7-1 and B7-2, with CD28. To address this issue, we developed a Tg mouse expressing a single-chain, membrane-bound anti-CTLA-4 Ab (scFv) on B cells. B and T cells developed normally and exhibited normal phenotype in the steady state and after activation in these mice. However, B cells from scFv Tg+ mice (scalphaCTLA4+) prevented T cell proliferation and cytokine production in mixed lymphocyte reactions. Additionally, mice treated with scalphaCTLA4+ B cells had decreased T cell-dependent B cell Ab production and class switching in vivo after antigen challenge. Furthermore, expression of this CTLA-4 agonist protected NOD mice from spontaneous autoimmune diabetes. Finally, this disease prevention occurred in Treg-deficient NOD.B7-1/B7-2 double-knockout mice, suggesting that the effect of the CTLA-4 agonist directly attenuates autoreactive T cell activation, not Treg activation. Together, results from this study demonstrate that selective ligation of CTLA-4 attenuates in vivo T cell responses, prevents development of autoimmunity, and represents a novel immunotherapeutic approach for the induction and maintenance of peripheral tolerance.
The endogenous cannabinoid anandamide inhibits human breast cancer cell proliferation (1998)

Anandamide was the first brain metabolite shown to act as a ligand of "central" CB1 cannabinoid receptors. Here we report that the endogenous cannabinoid potently and selectively inhibits the proliferation of human breast cancer cells in vitro. Anandamide dose-dependently inhibited the proliferation of MCF-7 and EFM-19 cells with IC50 values between 0.5 and 1.5 microM and 83-92% maximal inhibition at 5-10 microM. The proliferation of several other nonmammary tumoral cell lines was not affected by 10 microM anandamide. The anti-proliferative effect of anandamide was not due to toxicity or to apoptosis of cells but was accompanied by a reduction of cells in the S phase of the cell cycle. A stable analogue of anandamide (R)-methanandamide, another endogenous cannabinoid, 2-arachidonoylglycerol, and the synthetic cannabinoid HU-210 also inhibited EFM-19 cell proliferation, whereas arachidonic acid was much less effective. These cannabimimetic substances displaced the binding of the selective cannabinoid agonist [3H]CP 55, 940 to EFM-19 membranes with an order of potency identical to that observed for the inhibition of EFM-19 cell proliferation. Moreover, anandamide cytostatic effect was inhibited by the selective CB1 receptor antagonist SR 141716A. Cell proliferation was arrested by a prolactin mAb and enhanced by exogenous human prolactin, whose mitogenic action was reverted by very low (0.1-0.5 microM) doses of anandamide. Anandamide suppressed the levels of the long form of the prolactin receptor in both EFM-19 and MCF-7 cells, as well as a typical prolactin-induced response, i.e., the expression of the breast cancer cell susceptibility gene brca1. These data suggest that anandamide blocks human breast cancer cell proliferation through CB1-like receptor-mediated inhibition of endogenous prolactin action at the level of prolactin receptor.
Tolerance and autoimmunity in TCR transgenic mice specific for myelin basic protein (1999)

T-cell receptor (TCR) transgenic mice provide the ability to follow the maturation and fate of T cells specific for self-antigens in vivo. This technology represents a major breakthrough in the study of autoimmune diseases in which specific antigens have been implicated. Proteins expressed within the central nervous system are believed to be important autoantigens in multiple sclerosis. TCR transgenic models specific for myelin basic protein (MBP) allowed us to assess the role of tolerance in providing protection from T cells with this specificity. Our studies demonstrate that T cells specific for the immunodominant epitope of MBP do not undergo tolerance in vivo and that TCR transgenic mice are susceptible to spontaneous autoimmune disease. The susceptibility to spontaneous disease is dependent on exposure to microbial antigens. MBP TCR transgenic models expressing TCRs specific for the same epitope of MBP but utilizing different V alpha genes exhibit differing susceptibilities to spontaneous disease. These data support the idea that genetic and environmental differences play a role in susceptibility to autoimmunity. MBP TCR transgenic models are playing an important role in defining mechanisms by which infectious agents trigger autoimmune disease as well as defining mechanisms by which tolerance is induced to distinct epitopes within self-antigens.
U.S. Food and Drug Administration Approves Paclitaxel Protein-Bound Particles (Abraxane®) in Combination with Gemcitabine as First-Line Treatment of Patients with Metastatic Pancreatic Cancer (2013)

No abstract available
A RET double mutation in the germline of a kindred with FMTC (2000)

Activating germline mutations of the RET proto-oncogene are found in more than 90% of families with multiple endocrine neoplasia type 2a (MEN 2a) and familial medullary thyroid carcinoma (FMTC). The majority of patients with these hereditary tumors carry germline mutations that result in the substitution of one of five cysteine residues in exon 10 and 11. Different mutations in exons 13, 14 and 15 affecting non-cysteine residues have also been described but are considered to be rare. We now for the first time report a double mutation of the RET proto-oncogene occurring in the germline of a kindred with FMTC. Both mutations occur within the tyrosine kinase domain in exon 14 and lead to the substitution of valine 804 by methionine and arginine 844 by leucine. Since the double mutated allele cosegregated with the disease and was not identified in 200 unrelated normal probands, we conclude that they represent mutations that predispose the individual to the development of FMTC with a mild phenotype.