gebhart/patrepeval huggingface dataset:
HLA-A*0201-restricted CEA-derived Peptide CAP1 Is Not a Suitable Target for T-cell-based Immunotherapy (2010)

Carcinoembryonic antigen (CEA) is a potential target for antigen-specific immunotherapy, as it is frequently overexpressed in human carcinomas. Moreover, an epitope derived from CEA, designated CAP1 (YLSGANLNL), has been proposed as naturally processed and presented by tumors in the human leukocyte antigen (HLA)-A*0201 context. Our aim was to fully characterize and assess the clinical relevance of the HLA-A*0201-restricted cytotoxic T lymphocyte (CTL) response against CEA. Stable and potent artificial antigen presenting cells (AAPCs) were used to evaluate T-cell response against CEA. These cells efficiently activate CTLs against tumor-derived epitopes after transduction with the antigenic peptides or full-length proteins. We found that AAPCs genetically modified to express CAP1, the agonist peptide CAP1-6D, or the whole CEA protein were not able to activate CAP1-specific CTLs from HLA-A*0201+ healthy donors or patients with colorectal carcinoma, even after multiple stimulations. In addition, we showed that a CAP1-specific T-cell clone, obtained after multiple stimulations of T cells of a HLA-A*0201+ healthy donor in vitro with autologous antigen presenting cells, recognized CEA(-) HLA-A*0201+ tumors transduced with a minigene encoding CAP1 but failed to react against HLA-A*0201+ tumor cells expressing CEA. Finally, AAPCs expressing the whole CEA protein did not induce any specific CTL response against CEA+ HLA-A*0201+ tumor cells highlighting the potential difficulty of mounting an efficacious T-cell response against this autoantigen. Altogether, our data indicate that CAP1 is not efficiently processed and presented by CEA+ tumor cells, and therefore, is not an appropriate target for T-cell-based immunotherapy.
A major isoform of the maize plasma membrane H(+)-ATPase: characterization and induction by auxin in coleoptiles. (1996)

The plasma membrane (PM) H(+)-ATPase has been proposed to play important transport and regulatory roles in plant physiology, including its participation in auxin-induced acidification in coleoptile segments. This enzyme is encoded by a family of genes differing in tissue distribution, regulation, and expression level. A major expressed isoform of the maize PM H(+)-ATPase (MHA2) has been characterized. RNA gel blot analysis indicated that MHA2 is expressed in all maize organs, with highest levels being in the roots. In situ hybridization of sections from maize seedlings indicated enriched expression of MHA2 in stomatal guard cells, phloem cells, and root epidermal cells. MHA2 mRNA was induced threefold when nonvascular parts of the coleoptile segments were treated with auxin. This induction correlates with auxin-triggered proton extrusion by the same part of the segments. The PM H(+)-ATPase in the vascular bundies does not contribute significantly to auxin-induced acidification, is not regulated by auxin, and masks the auxin effect in extracts of whole coleoptile segments. We conclude that auxin-induced acidification in coleoptile segments most often occurs in the nonvascular tissue and is mediated, at least in part, by increased levels of MHA2.
Truncated Dipeptidyl Peptidase IV Is a Potent Anti-Adhesion and Anti-Metastasis Peptide for Rat Breast Cancer Cells (1998)

A novel adhesion receptor/ligand pair was shown recently to mediate lung vascular arrest and metastasis of rat breast cancer cells. The interacting adhesion molecules are endothelial dipeptidyl peptidase IV (DPP IV) and tumor cell surface-associated, polymeric fibronectin (FN). A truncated DPP IV (DPP IV(31-767): amino acids 31-767) in which the FN-binding site is preserved is shown here to mask the breast cancer cell surface-associated FN complexes, causing a dose-dependent inhibition of adhesion to endothelial DPP IV and impeding lung colony formation by approximately 80%. Since surface accumulation of FN is chiefly occurring during dissemination in the blood and since many cancer cell types have surface receptors by which they may initiate FN accumulation on their surfaces, the present anti-metastatic treatment modality may extend its efficacy farther than appreciated by this study.
Effect of tumor removal on mucosal protein synthesis in patients with colorectal cancer (2003)

It is currently controversial whether mucosal hyperproliferation is involved in colorectal cancerogenesis. The purpose of the present study was to examine protein synthetic rate as an indicator of potential tissue proliferation in grossly normal rectal mucosa from cancer-bearing subjects and to compare this rate with that in mucosa from subjects posttumor removal. Six postabsorptive patients with localized rectal cancer and five postsurgical control subjects received a primed constant infusion of [1-(13)C]leucine (0.16 micromol/kg min, 9.6 micromol/kg prime). Forceps biopsies from the mucosa were taken after 3 and 6 h. Protein synthesis was calculated from protein-bound leucine enrichment (determined by capillary GC-combustion IRMS) and from the enrichment of free intracellular leucine (determined by GC-quadrupole MS). In cancer-bearing subjects, mucosal protein synthesis amounted to 1.28 +/- 0.24%/h. This rate was significantly higher (P < 0.05) than the corresponding rate of mucosa from patients after cancer removal (0.69 +/- 0.09%/h). These findings do not support the concept that colorectal cancer originates from a proliferative disease of the whole colon. Increased mucosal protein synthesis appears to depend on the presence of the tumor itself and should therefore be considered a secondary phenomenon.
Novel putative SREBP and LXR target genes identified by microarray analysis in liver of cholesterol-fed mice (2003)

High-cholesterol diets elicit changes in gene expression via such transcription factors as sterol-regulatory element binding proteins (SREBPs) and liver X receptors (LXRs). We used Affymetrix microarrays to identify genes in mouse liver regulated by dietary cholesterol (0.0% vs. 0.5% cholesterol wt/wt). Three independent experiments were performed, and data were analyzed with Affymetrix Microarray Suite and ANOVA statistical software. There were 69 unique Unigene clusters consistently regulated by dietary cholesterol (37 downregulated and 32 upregulated). The array results were confirmed by quantitative RT-PCR (Q-PCR) for seven of nine downregulated genes and five of six upregulated genes. A time course of dietary cholesterol feeding over 1 week revealed different temporal patterns of gene regulation for these confirmed genes. Six downregulated genes were examined in transgenic mice overexpressing truncated nuclear forms of SREBP-1a and SREBP-2, and all were induced in these mice. A second microarray analysis of mice treated with the LXR agonist TO901317 confirmed that 13 of the 32 cholesterol upregulated genes were also LXR-activated. This array result was confirmed by Q-PCR for three of three genes. In summary, these studies identified and confirmed six novel dietary cholesterol-regulated genes, three putative SREBP target genes (calcium/calmodulin-dependent protein kinase 1D, fatty acid binding protein 5, and proprotein convertase subtilisin/kexin 9), and three putative LXR target genes (a disintegrin and metalloprotease domain 11, apoptosis-inhibitory 6, and F-box-only protein 3).
Purification and partial characterization of a cholinergic neuronal differentiation factor. (1985)

The choice of transmitter made by postmitotic rat sympathetic neurons in cell culture can be controlled by the environment in which they develop. One of the differentiation signals is a protein secreted by heart cells that can induce previously noradrenergic neurons to synthesize acetylcholine and form cholinergic synapses. This change in phenotype occurs without alteration in neuronal survival or growth. The differentiation factor has now been purified at least 100,000-fold, and it is homogeneous by several criteria. (i) The cholinergic activity comigrates with a single 125I-labeled protein band of 45 kDa in one-dimensional NaDodSO4/PAGE. (ii) The biological activity comigrates precisely with a series of five 125I-labeled protein spots of 45 kDa in two-dimensional gel electrophoresis. (iii) Treatment of the 45-kDa band with endo-beta-N-acetylglucosaminidase F reduces the apparent molecular size of both the labeled protein and the biological activity to a band of 22 kDa. The data suggest that the differentiation factor is a slightly basic glycoprotein with at least six glycosylation sites.
Endogenous retinoids in the zebrafish embryo and adult (1996)

Retinoic acid and its isoforms are considered to be endogenous compounds which regulate embryonic development. In the work reported here we have determined which retinoids are present in zebrafish embryos and how their levels change throughout development and into adulthood. All-trans-RA is present and its level does not change significantly during embryogenesis. We failed to detect other retinoic acid isomers such as 9-cis-RA and 4-oxo-RA, but we did observe a rapid rise in the level of didehydroretinol after gastrulation. The most striking result is that the zebrafish embryo, like Xenopus and tunicates, contains a vast excess of t-retinal whereas the embryos of higher vertebrates have an excess of t-retinol. However, as the zebrafish grows, the levels of t-retinol rise so that by adulthood t-retinol and t-retinal concentrations are more equivalent, indicating a changing pattern of retinoid metabolism with growth. To examine the significance of the use of t-retinal as a precursor of t-RA we treated embryos with disulphiram, an inhibitor of retinaldehyde dehydrogenase. This resulted in embryos with an undulating notochord and correspondingly abnormal somites and ventral floor plate. In contrast to this effect, 4-methylpyrazole, which inhibits alcohol dehydrogenases, had no effect on development. This effect of disulphiram suggests that t-RA may be involved in the establishment of the anteroposterior axis of the embryo.
Antisense oligonucleotide induced exon skipping and the dystrophin gene transcript: cocktails and chemistries (2007)

The combination of 2 AOs, directed at appropriate motifs in target exons was found to induce very efficient targeted exon skipping during processing of the dystrophin pre-mRNA. This combinatorial effect is clearly synergistic and is not influenced by the chemistry of the AOs used to induce exon excision. A hierarchy in exon skipping efficiency, observed with overlapping AOs composed of 2'-O-methyl modified bases, was also observed when these same sequences were evaluated as phosphorodiamidate morpholino oligomers, indicating design parameters established with one chemistry may be applied to the other.
Liporecycling: A Technique for Facial Rejuvenation and Body Contouring (2000)

Background. Soft tissue augmentation using autologous fat is a standard method in facial rejuvenation and in refinement of body contouring. Different procedures by different authors have been described, each with its specific advantages and disadvantages. Objective. The purpose of this article is to describe a method of harvesting, processing, and reinjection of fat that provides new aspects and advantages compared to previously described procedures. Methods. We report about a new method of autologous fat grafting. Fat is harvested during machine-assisted liposuction in tumescent local anesthesia with microcannulas, processed in a special open manner, and reinjected through a 24-gauge needle for intra- and subdermal augmentation. Results. Short- and long-term results are equivalent to other methods of fat cell grafting. Conclusion. Advantages of the described method include easy harvesting during conventional machine-assisted liposuction, the possibility of removing undesired bands of fibrous tissue from the graft, and easy passage through a 24-gauge needle. Thus sub- and intradermal augmentation is possible with the same material and syringe.
Structure, Replication, and Recombination of Retrovirus Genomes: Some Unifying Hypotheses (1979)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Atmosphere Controlled Processing of Ga-Substituted Garnets for High Li-Ion Conductivity Ceramics (2014)

Ga-substituted La3Zr2Li7O12 garnet is shown to be a promising Li-ion conducting electrolyte material. The strategy adopted in this study is the substitution of Li by Ga, thereby creating Li vacancies and enhancing the Li conductivity. Solid State Magic Angle Spinning Nuclear Magnetic Resonance (MAS NMR) measurements have been used to identify the location of the substituted Ga in the structure and its effect on the Li distribution and mobility. In addition MAS NMR was used to follow the effect of protonation due to atmospheric moisture on the sintering behavior of these materials. In particular, it is shown that the Ga atoms are located in tetrahedral positions promoting the random distribution of lithium over the available sites, hence promoting an increase in the conductivity. Control of the sintering conditions by using a dry O2 atmosphere leads to the formation of dense ceramic materials and avoids the degradation process due to the exchange of Li+ by H+ from atmospheric moisture. Electrochemical Impedance Spectroscopy data show total conductivities as high as 1.3 and 2.2 mS cm–1 at 24 and 42 °C, respectively, which are among the highest Li ion conductivities reported for garnet-structured materials to date.
Unsupervised learning of image manifolds by semide .nite programming (2004)

Can we detect low dimensional structure in high dimensional data sets of images and video? The problem of dimensionality reduction arises often in computer vision and pattern recognition. In this paper, we propose a new solution to this problem based on semidefinite programming. Our algorithm can be used to analyze high dimensional data that lies on or near a low dimensional manifold. It overcomes certain limitations of previous work in manifold learning, such as Isomap and locally linear embedding. We illustrate the algorithm on easily visualized examples of curves and surfaces, as well as on actual images of faces, handwritten digits, and solid objects.
Analysis of the heavy chain repertoire of human peripheral B cells using single-cell polymerase chain reaction (1995)

The VH gene repertoire of human peripheral B cells was analyzed using PCR analysis of individual blood B cells. Because genomic DNA of single B cells was analyzed, data from both productive and nonproductive VDJ rearrangements were obtained. Nine out of 75 B cells contained both functional and nonfunctional rearrangement products, whereas 62/75 had a single productive VDJ rearrangement. The distribution of VH families was ordered in accordance with the germline complexity, although a bias toward VH3 and some of its members was found. This bias was noted in both the productively and nonproductively rearranged repertoires, indicating that it resulted from molecular and not selective processes. Evidence for negative selection of certain VH3 and VH4 family members was noted in that they were found less often as productive than nonproductive VDJ rearrangements. In addition, evidence for positive selection based on CDR3 was obtained, in that JH6 and DXP'1 were found at a higher frequency in the productively compared with the nonproductively rearranged repertoire. The CDR3 segments were markedly heterogenous, with a much greater degree of variability noted in the nonproductive VDJ rearrangements. Finally, a much greater frequency of mutations was noted in the nonproductively rearranged VH genes within individual B cells. These results have begun to delineate the human peripheral B cell repertoire and identify processes that shape it both positively and negatively.
Granulocyte/macrophage-colony stimulating factor produced by recombinant avian poxviruses enriches the regional lymph nodes with antigen-presenting cells and acts as an immunoadjuvant. (2001)

Recombinant avian poxviruses [fowlpox and canarypox (ALVAC)], restricted for replication in nonavian cell substrates and expressing granulocyte/macrophage-colony stimulating factor (avipox-GM-CSF), were evaluated for their ability to enrich an immunization site with antigen-presenting cells (APCs) and, in turn, function as biological vaccine adjuvants. Avipox-GM-CSF administered as a single s.c. injection significantly enhanced the percentage and absolute number of APCs in the regional lymph nodes that drain the injection site. Both the magnitude and duration of the cellular and phenotypic increases within the lymph nodes induced by the avipox-GM-CSF viruses were significantly (P < 0.05) greater than those measured in mice treated with four daily injections of recombinant GM-CSF protein. Temporal studies revealed that the APC enrichment of regional lymph nodes was sustained for 21-28 days after injection of the recombinant avipox virus expressing GM-CSF and, moreover, three injections of the recombinant virus could be given without any appreciable loss of in vivo bioactivity. Mice expressing human carcinoembryonic antigen (CEA) as a transgene (CEA.Tg) developed CEA-specific humoral and cell-mediated immunity after being immunized with avipox-CEA. The coadministration of recombinant avipox viruses expressing CEA and GM-CSF significantly enhanced CEA-specific host immunity with an accompanying immunotherapeutic response in tumor-bearing CEA.Tg mice. The optimal use of avipox-GM-CSF, in terms of dose and dose schedule, especially when used with different immunogens, remains to be determined. Nonetheless, the present findings demonstrate: (a) the effective delivery of GM-CSF to an immunization site using a recombinant avian poxvirus; (b) the compatibility of delivering an antigen and GM-CSF in replication-defective viruses to enhance antigen-specific immunity; and (c) the combined use of recombinant avipox viruses expressing CEA and GM-CSF to generate antitumor immunity directed at a self tumor antigen.
Marching velocity of capillary meniscuses in microchannels (2003)

This paper describes a new method and an analytical model for characterizing the surface energy inside a microchannel using the measurement of the marching velocity of a capillary meniscus. This method is based on the fact that surface tension of a liquid meniscus in a hydrophilic case produces pressure to pull liquid into the channel and the velocity of the meniscus is related to the surface energy. Both Parylene and silicon nitride microchannels with different surface conditions were fabricated to perform the liquid-filling experiments. It is shown that our model agrees well with the data and this is a valid method.
The Design and Implementation of AQuA: An Adaptive Quality of Service Aware Object-Based Storage Device (2006)

As storage systems are becoming larger and more complicated, they must handle an increasing variety of data storage needs. Storage system Quality of Service (QoS) has therefore become an important issue. Storage systems must be able to deliver satisfactory performance under both expected and unexpected workloads and, increasingly, must handle data (such as multimedia data) with real timeliness requirements. We are developing a petascale high-performance distributed object-based storage system called Ceph. Ceph’s object storage architecture and other unique features have given rise to new QoS issues that require new solutions. In this paper, we first discuss the issues involved with the design of the overall QoS framework, we then present the design and implementation of AQuA, an adaptive QoS-aware object-based storage device (OSD) suitable for use as the fundamental building block in an overall QoS-capable object-based storage system.
Block-Matching Convolutional Neural Network for Image Denoising (2017)

There are two main streams in up-to-date image denoising algorithms: non-local self similarity (NSS) prior based methods and convolutional neural network (CNN) based methods. The NSS based methods are favorable on images with regular and repetitive patterns while the CNN based methods perform better on irregular structures. In this paper, we propose a block-matching convolutional neural network (BMCNN) method that combines NSS prior and CNN. Initially, similar local patches in the input image are integrated into a 3D block. In order to prevent the noise from messing up the block matching, we first apply an existing denoising algorithm on the noisy image. The denoised image is employed as a pilot signal for the block matching, and then denoising function for the block is learned by a CNN structure. Experimental results show that the proposed BMCNN algorithm achieves state-of-the-art performance. In detail, BMCNN can restore both repetitive and irregular structures.
Subpicosecond ultraviolet laser ablation of diamond: Nonlinear properties at 248 nm and time-resolved characterization of ablation dynamics (1995)

Ablation of diamond by short UV pulses is reported. The ablation threshold for 500 fs pulses at 248 nm was found to be 0.6 J/cm2 (equal to a peak intensity of 1.1 TW/cm2). Intensity-dependent transmission measurements from low intensities to 100 GW/cm2 showed that two-photon absorption is the dominant nonlinearity in this range and the two-photon absorption coefficient was measured to be (1.6±0.3) cm/GW. In the intensity regime above threshold (≳1 TW/cm2), however, low ablation rates indicate strong absorption by laser induced free carriers. The dynamics of diamond ablation was investigated time-resolved using pump probe transmission and pulse pair ablation measurements. Ablation with short pulses at 248 nm is also compared to ablation with 15 ns pulses at 193 nm.
Risperidone and megacolon. (2002)

Risperidone is an atypical anti-psychotic medication with both 5HT2 receptor and D2 dopamine receptor antagonism. Its use has been reported to be generally safe with very few gastro-intestinal (GI) adverse or side effects. In this paper, we describe a case of megacolon associated with the use of risperidone. A 44-year-old man suffering from schizophrenia was treated with risperidone and developed gross abdominal distension after twenty-five days. Abdominal X-ray and colonoscopy showed megacolon. He improved following a surgical decompression and a reduction of risperidone dosage. We discuss the neuro-electro-physiological mechanisms of gastro-intestinal motility and conclude that the risperidone-associated megacolon may be dose-related and that there should be a heightened awareness of such possible GI complication when using risperidone.
Human antibody RNase fusion protein targeting CD30+ lymphomas (2008)

Targeted RNases (TRs) are immunoenzymes with ribonucleases as cytotoxic effector domains, which are less immunogenic as plant or bacterial toxin components of classical immunotoxins. In this study, we show the generation and production of the first entirely human TR (huTR) directed against CD30+ lymphomas. The scFv-Fc-RNase construct was produced in human embryonic kidney (HEK) 293T cells, yielding up to 4 mg/L soluble protein after purification by protein A affinity chromatography. Size exclusion chromatography revealed a homodimer of the predicted molecular mass. Surface plasmon resonance analysis revealed an affinity to CD30 of KD of less than 1 nM for both the scFv-Fc and the scFv-Fc-RNase proteins. Internalization of the scFv-Fc-RNase protein by CD30+ Karpas-299 cells was demonstrated by confocal microscopy. Proliferation of the CD30+ lymphoma cell line Karpas-299 was strongly inhibited by CD30-specific huTR protein (IC50=3.3 nM). The huTR is a promising candidate for the immunotherapy of CD30+ lymphomas because of its expected low immunogenicity, good production yields, and potent effector function upon target cell binding and internalization. Its modular design is set to target other internalizing tumor antigens using different antibody domains.