gebhart/patrepeval huggingface dataset:
Intratumor Heterogeneity of Cancer/Testis Antigens Expression in Human Cutaneous Melanoma Is Methylation-Regulated and Functionally Reverted by 5-Aza-2′-deoxycytidine (2004)

Cancer/testis antigens (CTA) are suitable targets for immunotherapy of human malignancies, and clinical trials are mainly focusing on MAGE-A3. However, the heterogeneous intratumor expression of CTA may hamper the effectiveness of CTA-directed vaccination through the emergence of CTA-negative neoplastic clones. We investigated the intratumor heterogeneity of CTA in human melanoma and the underlying molecular mechanism(s) at clonal level using 14 single cell clones generated from the melanoma lesion Mel 313. Reverse transcription-PCR revealed a highly heterogeneous expression of MAGE-A1, -A2, -A3, -A4, -A6, GAGE 1-6, SSX 1-5, and PRAME among melanoma clones. Only nine clones expressed MAGE-A3 and competitive reverse transcription-PCR identified relative differences in the number of mRNA molecules of up to 130-fold between clones 5 and 14. This clonal heterogeneity of MAGE-A3 expression correlated with the methylation status of specific CpG dinucleotides in MAGE-A3 promoter: i.e., hypomethylated CpG dinucleotides at positions -321, -151, -19, -16, -5, -2, +21, and +42 were found in clones expressing high but not low levels of MAGE-A3. Supporting the role of DNA methylation in generating the intratumor heterogeneity of CTA, the DNA hypomethylating agent 5-aza-2'-deoxycytidine (5-AZA-dCyd) invariably induced their expression in all CTA-negative clones. Furthermore, 5-AZA-dCyd-treatment reduced to 6 folds the differential expression of MAGE-A3 between clones 5 and 14, which became recognized to a similar extent by T cells specific for a MAGE-A-encoded peptide. These findings identify promoter methylation as directly responsible for the intratumoral heterogeneity of therapeutic CTA in melanoma and foresee the use of 5-AZA-dCyd to overcome the limitations set by their intratumor heterogeneous expression to CTA-based vaccine therapy.
Identification and sequence analysis of a gene encoding gp67, an abundant envelope glycoprotein of the baculovirus Autographa californica nuclear polyhedrosis virus (1989)

Monoclonal antibodies with specificity for the abundant envelope surface glycoprotein (gp67) of Autographa californica nuclear polyhedrosis virus (AcMNPV) were used to screen a lambda gt11 expression library of AcMNPV DNA fragments. The gp67 gene was mapped to the left end of the EcoRI H fragment in a right-to-left orientation on the consensus map of AcMNPV. A 2.1-kilobase transcript which hybridized to the region was first detected in cell extracts at 2 h postinfection; it peaked in abundance at 18 h postinfection and thereafter was present at lower levels. The nucleotide sequence of the region was determined, and a 1,590-nucleotide open reading frame flanked by an AT-rich sequence was identified that could encode a polypeptide with 529 amino acid residues (molecular mass of 60,167 daltons). Computer analysis indicated that the peptide possesses two hydrophobic regions near the N and C termini as well as six potential N-linked glycosylation sites. We suggest that following cleavage of a signal peptide, the polypeptide undergoes further processing and becomes anchored at its C terminus in the virus envelope. The final seven amino acid residues at the C terminus contain basic amino acids and may have a role in virion assembly.
Cu Salt Ink Formulation for Printed Electronics using Photonic Sintering (2013)

We formulate copper salt (copper formate/acetate/oleate) precursor inks for photonic sintering using high-intensity pulsed light (HIPL) based on the ink's light absorption ability. The inks can be developed through controllable crystal field splitting states (i.e., the ligand weights and their coordination around the metal centers). The inks' light absorption properties are extremely sensitive to the carbon chain lengths of the ligands, and the ink colors can drastically change. From the relationship between the ratios of C/Cu and the required sintering energies, it is possible to ascertain that the integral absorbance coefficients are strongly correlated with the photonic sintering behavior. These results suggest that the ink absorbance properties are the most important factors in photosintering. The wires formed by sintered copper formate complex ink via the HIPL method showed good electronic conduction, achieving a low resistivity of 5.6 × 10(-5) Ω cm. However, the resistivity of the wires increased with increasing contains carbon chain length of the inks, suggesting that large amounts of residual carbon have negative effects on both the wire's surface morphology and the electrical conductivity. We find in this study that high light absorptivity and low carbon inks would lead to a lower environmental load in future by reducing both energy usage and carbon oxide gas emissions.
ChemInform Abstract: Practical, Asymmetric Synthesis of Aromatic‐Substituted Bulky and Hydrophobic Tryptophan Derivatives. (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.
Histone Methyltransferase NSD2/MMSET Mediates Constitutive NF-κB Signaling for Cancer Cell Proliferation, Survival, and Tumor Growth via a Feed-Forward Loop (2012)

Constitutive NF-κB activation by proinflammatory cytokines plays a major role in cancer progression. However, the underlying mechanism is still unclear. We report here that histone methyltransferase NSD2 (also known as MMSET or WHSC1), a target of bromodomain protein ANCCA/ATAD2, acts as a strong coactivator of NF-κB by directly interacting with NF-κB for activation of target genes, including those for interleukin-6 (IL-6), IL-8, vascular endothelial growth factor A (VEGFA), cyclin D, Bcl-2, and survivin, in castration-resistant prostate cancer (CRPC) cells. NSD2 is recruited to the target gene promoters upon induction and mediates NF-κB activation-associated elevation of histone H3K36me2 and H3K36me3 marks at the promoter, which involves its methylase activity. Interestingly, we found that NSD2 is also critical for cytokine-induced recruitment of NF-κB and acetyltransferase p300 and histone hyperacetylation. Importantly, NSD2 is overexpressed in prostate cancer tumors, and its overexpression correlates with NF-κB activation. Furthermore, NSD2 expression is strongly induced by tumor necrosis factor alpha (TNF-α) and IL-6 via NF-κB and plays a crucial role in tumor growth. These results identify NSD2 to be a key chromatin regulator of NF-κB and mediator of the cytokine autocrine loop for constitutive NF-κB activation and emphasize the important roles played by NSD2 in cancer cell proliferation and survival and tumor growth.
Survival of Effector CD8+ T Cells during Influenza Infection Is Dependent on Autophagy (2015)

The activation and expansion of effector CD8(+) T cells are essential for controlling viral infections and tumor surveillance. During an immune response, T cells encounter extrinsic and intrinsic factors, including oxidative stress, nutrient availability, and inflammation, that can modulate their capacity to activate, proliferate, and survive. The dependency of T cells on autophagy for in vitro and in vivo activation, expansion, and memory remains unclear. Moreover, the specific signals and mechanisms that activate autophagy in T effector cells and their survival are not known. In this study, we generated a novel inducible autophagy knockout mouse to study T cell effector responses during the course of a virus infection. In response to influenza infection, Atg5(-/-) CD8(+) T cells had a decreased capacity to reach the peak effector response and were unable to maintain cell viability during the effector phase. As a consequence of Atg5 deletion and the impairment in effector-to-memory cell survival, mice fail to mount a memory response following a secondary challenge. We found that Atg5(-/-) effector CD8(+) T cells upregulated p53, a transcriptional state that was concomitant with widespread hypoxia in lymphoid tissues of infected mice. The onset of p53 activation was concurrent with higher levels of reactive oxygen species (ROS) that resulted in ROS-dependent apoptotic cell death, a fate that could be rescued by treating with the ROS scavenger N-acetylcysteine. Collectively, these results demonstrate that effector CD8(+) T cells require autophagy to suppress cell death and maintain survival in response to a viral infection.
A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison (1991)

This article describes the latest version of an RNA folding algorithm that predicts both optimal and suboptimal solutions based on free energy minimization. A number of RNA's with known structures deduced from comparative sequence analysis are folded to test program performance. The group of solutions obtained for each molecule is analysed to determine how many of the known helixes occur in the optimal solution and in the best suboptimal solution. In most cases, a structure about 80% correct is found with a free energy within 2% of the predicted lowest free energy structure.
Histopathologic study of the mode of inhibition of cellular proliferation by urethane; effect of urethane on Walker rat carcinoma 256. (1949)

The effect of urethane on cellular proliferation in the Walker rat carcinoma 256 was studied in an attempt to determine the mode of action of this drug. By using easily manipulated synthetic diets it was possible to show that urethane inhibits cellular proliferation in part by nutritional debilitation of the animal. This indirect effect did not account for the total inhibition of the growth of the tumor. By means of histologic and cytologic techniques, urethane was found not to have an effect like colchicine but to cause an increase in the number of probably fatal abnormal mitoses in the malignant cells. The possible explanation was advanced that the inhibition of tumors by urethane beyond that due to altered metabolism was the result of the production of non-proliferating daughter cells by these mitotic abnormalities.
Lignins and Ferulate−Coniferyl Alcohol Cross-Coupling Products in Cereal Grains (2004)

Plant cell walls containing suberin or lignin in the human diet are conjectured to protect against colon cancer. To confirm the existence of authentic lignin in cereal grain dietary fibers, the DFRC (derivatization followed by reductive cleavage) method was applied to different cereal grain dietary fibers. By cleavage of diagnostic arylglycerol-beta-aryl (beta-O-4) ether linkages and identification of the liberated monolignols, it was ascertained that lignins are truly present in cereal grains. From the ratios of the liberated monolignols coniferyl alcohol and sinapyl alcohol, it is suggested that lignin compositions vary among cereals. Furthermore, dimeric cross-coupling products, comprising ferulate and coniferyl alcohol, were identified in most cereal fibers investigated. These ferulate 4-O-beta- and 8-beta-coniferyl alcohol cross-coupled structures indicate radical cross-coupling of polysaccharides to lignin precursors via ferulate.
Synthesis of .beta.-D-mannopyranosides and .beta.-L-rhamnopyranosides by glycosidation at C-1 (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of .beta.-D-mannopyranosides and .beta.-L-rhamnopyranosides by glycosidation at C-1Vinai K. Srivastava and Conrad SchuerchCite this: J. Org. Chem. 1981, 46, 6, 1121–1126Publication Date (Print):March 1, 1981Publication History Published online1 May 2002Published inissue 1 March 1981https://pubs.acs.org/doi/10.1021/jo00319a016https://doi.org/10.1021/jo00319a016research-articleACS PublicationsRequest reuse permissionsArticle Views574Altmetric-Citations101LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Bone stem cells (1998)

Osteoblasts are the skeletal cells responsible for synthesis, deposition, and mineralization of the extracellular matrix of bone. By mechanisms that are only beginning to be understood, stem and primitive osteoprogenitors and related mesenchymal precursors arise in the embryo and at least some appear to persist in the adult organism, where they contribute to replacement of osteoblasts in bone turnover and in fracture healing. In this paper, the nature of these cells, whether they constitute a stem cell pool or a committed progenitor pool, and aspects of their apparent plasticity are discussed. Current understanding of differential expression of osteoblast-associated genes during osteoprogenitor proliferation and differentiation to mature matrix synthesizing osteoblasts is summarized. Finally, evidence is discussed that supports the hypothesis that the mature osteoblast phenotype is heterogeneous with subpopulations of osteoblasts expressing only subsets of the known osteoblast markers, raising also the possibility of multiple parallel differentiation pathways and perhaps even different progenitor pools. J. Cell. Biochem. Suppls. 30/31:73-82, 1998. © 1998 Wiley-Liss, Inc.
Radiation Exposure of Distributed-Feedback Lasers for Use in Atom Trapping and Atom Interferometry (2011)

Semiconductor DFB lasers are compact, efficient, robust light sources suitable for use in laser trapping and cooling and for atom interferometry using alkali atoms. Two commercially available DFB lasers (LD-0852-0150-DFB, Eagleyard Photonics) emitting at 852 nm were subjected to gamma and flash x-ray (FXR) radiation, to a total dose of 200 krad (in two exposures) and a prompt dose of 1.2 krad per shot, respectively. We measured frequency shifts and output power before, during and after exposures with the lasers tuned to the Cs D2 resonance. Radiation induced frequency excursions were smaller than the Doppler broadened linewidth. Radiation induced output power losses were negligible in flash x-ray and 1.8 dB after each of the two 100 krad gamma exposures. These results demonstrate that spectroscopy-grade DFB lasers can survive and function in very adverse radiation environments, making possible the radiation-hard implementation of cold atom based clocks and atom interferometer inertial sensors.
Alterations of the Immunoglobulin Heavy Chain Locus in Progressive B-cell Lymphomas (1998)

Twenty-two patients with relapsed or progressive B-cell lymphomas (BCL) were analysed for alterations in the rearrangement status in the immunoglobulin heavy (IgH) chain gene in samples obtained on different occasions during the course of the disease. The analysis was performed using Southern blot hybridization of the IgH gene and polymerase chain reaction (PCR) amplification of the VH gene families combined with single-strand conformation polymorphism (SSCP) analysis. Using Southern blot analysis, we found that all 22 lymphomas displayed clonal IgH rearrangements, and changes during tumour progression occurred in 8 cases. These alterations were mainly observed in cases with follicular or transformed lymphomas. More than one malignant (sub)clone, indicated by more than two rearranged bands, was detected in one case at diagnosis and in three cases at relapse. Outgrowth of subclones with divergent rearrangement patterns in different compartments was also observed in 2 out of 8 cases. PCR-SSCP analysis indicated that all 15 cases studied displayed clonal rearrangements and in 6 cases altered rearrangement patterns were detected in later samples. Southern blotting and PCR-SCCP analysis gave equivalent results. No association was found between time to relapse or survival time and alterations in rearrangement pattern. The present study illustrates that the neoplastic cell clones in BCL often display alterations in their IgH locus, but the significance of this feature remains to be clarified.
Effects of Citicoline Combined With Thrombolytic Therapy in a Rat Embolic Stroke Model (1999)

These results demonstrate that the combination of low-dose citicoline and rtPA significantly reduced infarct size in this focal ischemia model.
Phase III Trial of Bevacizumab Plus Interferon Alfa-2a in Patients With Metastatic Renal Cell Carcinoma (AVOREN): Final Analysis of Overall Survival (2010)

Bevacizumab plus IFN is active as first-line treatment in patients with mRCC. Most patients with mRCC receive multiple lines of therapy, so considering the overall sequence of therapy when selecting first-line therapy may optimize patient benefit.
Effects of Angiogenesis Inhibitors on Multistage Carcinogenesis in Mice (1999)

Solid tumors depend on angiogenesis for their growth. In a transgenic mouse model of pancreatic islet cell carcinogenesis (RIP1-Tag2), an angiogenic switch occurs in premalignant lesions, and angiogenesis persists during progression to expansive solid tumors and invasive carcinomas. RIP1-Tag2 mice were treated so as to compare the effects of four angiogenesis inhibitors at three distinct stages of disease progression. AGM-1470, angiostatin, BB-94, and endostatin each produced distinct efficacy profiles in trials aimed at preventing the angiogenic switch in premalignant lesions, intervening in the rapid expansion of small tumors, or inducing the regression of large end-stage cancers. Thus, anti-angiogenic drugs may prove most efficacious when they are targeted to specific stages of cancer.
How to Interpret LC3 Immunoblotting (2007)

Microtubule-associated protein light chain 3 (LC3) is now widely used to monitor autophagy. One approach is to detect LC3 conversion (LC3-I to LC3-II) by immunoblot analysis because the amount of LC3-II is clearly correlated with the number of autophagosomes. However, LC3-II itself is degraded by autophagy, making interpretation of the results of LC3 immunoblotting problematic. Furthermore, the amount of LC3 at a certain time point does not indicate autophagic flux, and therefore, it is important to measure the amount of LC3-II delivered to lysosomes by comparing LC3-II levels in the presence and absence of lysosomal protease inhibitors. Another problem with this method is that LC3-II tends to be much more sensitive to be detected by immunoblotting than LC3-I. Accordingly, simple comparison of LC3-I and LC3-II, or summation of LC3-I and LC3-II for ratio determinations, may not be appropriate, and rather, the amount of LC3-II can be compared between samples.
Hierarchical Incremental Path Planning and Situation-Dependent Optimized Dynamic Motion Planning Considering Accelerations (2007)

This paper studies a hierarchical approach for incrementally driving a nonholonomic mobile robot to its destination in unknown environments. The A* algorithm is modified to handle a map containing unknown information. Based on it, optimal (discrete) paths are incrementally generated with a periodically updated map. Next, accelerations in varying velocities are taken into account in predicting the robot pose and the robot trajectory resulting from a motion command. Obstacle constraints are transformed to suitable velocity limits so that the robot can move as fast as possible while avoiding collisions when needed. Then, to trace the discrete path, the system searches for a waypoint-directed optimized motion in a reduced 1-D translation or rotation velocity space. Various situations of navigation are dealt with by using different strategies rather than a single objective function. Extensive simulations and experiments verified the efficacy of the proposed approach.
Multiple Distinct Splicing Enhancers in the Protein-Coding Sequences of a Constitutively Spliced Pre-mRNA (1999)

We have identified multiple distinct splicing enhancer elements within protein-coding sequences of the constitutively spliced human beta-globin pre-mRNA. Each of these highly conserved sequences is sufficient to activate the splicing of a heterologous enhancer-dependent pre-mRNA. One of these enhancers is activated by and binds to the SR protein SC35, whereas at least two others are activated by the SR protein SF2/ASF. A single base mutation within another enhancer element inactivates the enhancer but does not change the encoded amino acid. Thus, overlapping protein coding and RNA recognition elements may be coselected during evolution. These studies provide the first direct evidence that SR protein-specific splicing enhancers are located within the coding regions of constitutively spliced pre-mRNAs. We propose that these enhancers function as multisite splicing enhancers to specify 3' splice-site selection.
RNA Silencing in Productive Virus Infections (2005)

RNA silencing can reduce the expression of specific genes through posttranscriptional gene silencing, the microRNA pathway, and also through transcriptional gene silencing. Posttranscriptional gene silencing also acts as an antivirus mechanism. By suppressing this antivirus defense mechanism, viruses affect all three silencing pathways in addition to the intercellular signaling mechanism that transmits RNA-based messages throughout the plant. Productive virus infection may therefore disrupt the normal gene expression patterns in plants, resulting, at least in part, in a symptomatic phenotype. This review examines the cellular world that viruses exploit to provide some insight into the molecular interactions that occur during the virus infection cycle and how these produce the symptoms on infected plants.
Cytological and biochemical characterization of the FtsA cell division protein of Bacillus subtilis (2001)

The actin-like protein FtsA is present in many eubacteria, and genetic experiments have shown that it plays an important, sometimes essential, role in cell division. Here, we show that Bacillus subtilis FtsA is targeted to division sites in both vegetative and sporulating cells. As in other organisms FtsA is probably recruited immediately after FtsZ. In sporulating cells of B. subtilis FtsZ is recruited to potential division sites at both poles of the cell, but asymmetric division occurs at only one pole. We have now found that FtsA is recruited to only one cell pole, suggesting that it may play an important role in the generation of asymmetry in this system. FtsA is present in much higher quantities in B. subtilis than in Escherichia coli, with approximately one molecule of FtsA for five of FtsZ. This means that there is sufficient FtsA to form a complete circumferential ring at the division site. Therefore, FtsA may have a direct structural role in cell division. We have purified FtsA and shown that it behaves as a dimer and that it has both ATP-binding and ATP-hydrolysis activities. This suggests that ATP hydrolysis by FtsA is required, together with GTP hydrolysis by FtsZ, for cell division in B. subtilis (and possibly in most eubacteria).