gebhart/patrepeval huggingface dataset:
Expression profile analysis of head and neck squamous cell carcinomas using data from The Cancer Genome Atlas (2016)

Head and neck squamous cell carcinoma (HNSCC) is the major histological type of head and neck cancer and no curative treatments are currently available. Using advanced sequencing technologies, The Cancer Genome Atlas (TCGA) has produced large‑scale sequencing data, which provide unprecedented opportunities to reveal molecular mechanisms of cancer. The present study analyzed the mRNA and micro (mi)RNA expression data of HNSCC and normal control tissues released by the TCGA database using a bioinformatics approach to explore underlying molecular mechanisms. The mRNA and miRNA expression data were downloaded from the TCGA database and differentially expressed genes (DEGs) and miRNAs (DEMs) between HNSCC and normal head and neck tissues were identified using TwoClassDif. Subsequently, the gene functions and pathways which are significantly altered in HNSCC were identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Regulatory networks among DEGs and DEMs were then constructed, and transcription factors (TFs) potentially regulating the DEGs and DEMs were determined and a TF ‑ miRNA ‑ gene network was established. A total of 2,594 significant DEGs (1,087 upregulated and 1,507 downregulated), and 25 DEMs (8 upregulated and 17 downregulated) were identified in HNSCC compared with normal control samples. These DEGs were significantly enriched in GOs and KEGG pathways such as mitosis, cell cycle, Wnt, JAK/STAT and TLR signaling pathway. CPBP, NF‑AT1 and miR‑1 were situated in the central hub of the TF ‑ miRNA ‑ gene network, underlining their central roles in regulatory processes specific for HNSCC. The present study enhanced the current understanding of the molecular mechanisms underlying HNSCC and may offer novel strategies for its prevention, diagnosis and treatment.
Sigma receptors are associated with cortical limbic areas in the primate brain (1992)

Putative sigma receptors are a current target for antipsychotic drug development. Novel antipsychotic agents which possess selective and high affinity for sigma binding sites may serve as an alternative to the principal neuroleptic drugs currently in clinical use which mediate extrapyramidal side effects and dyskinesias through their blockade of dopamine receptors. We have used in vitro autoradiography to localize putative sigma receptors labelled with (+)-[3H]-3-(3-hydroxyphenyl)-N-(1-propyl)piperidine [(+)-[3H]-3-PPP] in the brain of the rhesus macaque. The binding characteristics of (+)-[3H]-3-PPP in the primate brain were comparable to those previously described in the rodent. Saturation analysis demonstrated a single class of sites in cerebellar and hippocampal membranes with a Kd value of 28 nM. Sigma receptors labeled with (+)-[3H]-3-PPP in the primate brain displayed the appropriate rank order of potency and stereoselectivity in competition binding assays. Haloperidol displaced (+)-[3H]-3-PPP binding in the low nanomolar range, and the (+) isomer of pentazocine was 50-fold more potent than (-) pentazocine. Computerized densitometric analysis of the autoradiograms demonstrated a striking enrichment of sigma binding sites over the paralimbic belt cortices, including the orbitofrontal, cingulate, insular, parahippocampal, and temporopolar gyri. Peak densities of sigma receptors were seen over the medial and central nuclei of the amygdala and were widely distributed within the hippocampal formation. Sigma binding sites densities were elevated over the suprachiasmatic and supraoptic nuclei of the hypothalamus. Moderate sigma receptor densities were observed over the ventromedial sectors of the caudate and the putamen. Sigma receptors were also elevated over autonomic relay nuclei of the brainstem, including the nucleus of the solitary tract and the dorsal motor nucleus of the vagus. The distribution of sigma receptors in the primate brain suggests that the paralimbic belt cortices, amygdala, hippocampus, hypothalamus, and autonomic relay nuclei of the brainstem may be interrelated by a topographic chemical linkage. The autoradiographic visualization of sigma receptor distributions in the primate brain provides further support for a role of sigma receptor mechanisms in the functions of the limbic system.
Si/SiGe p-Channel MOSFETs (1991)

High quality Si1~xGex p-channel MOSFETs have been fabricated in an integrable process using both thermal or PECVD gate oxides and selective UHV CVD for the Si/Si1 - x Gex channels. We show that optimally designed Si/Si1-xGex MOSFETs exhibit up to 7-% higher transconductance at 300K than control Si p-channel devices. Si/SiGe p-channel devices with thermal and PECVD gate oxides show comparable device characteristics.
Choline oxidase, a catabolic enzyme in Arthrobacter pascens, facilitates adaptation to osmotic stress in Escherichia coli (1991)

Choline oxidase (EC 1.1.3.17) is a bifunctional enzyme that is capable of catalyzing glycine betaine biosynthesis from choline via betaine aldehyde. A gene (cox) encoding this enzyme in the gram-positive soil bacterium Arthrobacter pascens was isolated and characterized. This gene is contained within a 1.9-kb fragment that encodes a polypeptide of approximately 66 kDa. Transfer of this gene to an Escherichia coli mutant that is defective in betaine biosynthesis resulted in an osmotolerant phenotype. This phenotype was associated with the ability of the host to synthesize and assemble an enzymatically active choline oxidase that could catalyze biosynthesis of glycine betaine from an exogenous supply of choline. Although glycine betaine functions as an osmolyte in several different organisms, it was not found to have this role in A. pascens. Instead, both choline and glycine betaine were utilized as carbon sources. In A. pascens synthesis and activity of choline oxidase were modulated by carbon sources and were susceptible to catabolite repression. Thus, cox, a gene concerned with carbon utilization in A. pascens, was found to play a role in adaptation to an environmental stress in a heterologous organism. In addition to providing a possible means of manipulating osmotolerance in other organisms, the cox gene offers a model system for the study of choline oxidation, an important metabolic process in both procaryotes and eucaryotes.
A Maximum-Likelihood Synchronization Scheme for GPS Positioning in Multipath, Interference, and Weak Signal Environments (2006)

In this paper, a novel multipath parameters estimation approach for GPS receivers using the maximum likelihood (ML) principle is proposed. Exploiting the replication property of the GPS C/A code within each symbol, we develop a coherent preprocessing approach based on a sample mean model. This model employs long integration time that improves the SNR and enhances receiver robustness against interference and weak signal effects. It also allows a simplified expression for the likelihood function which facilitates the use of computationally efficient iterative techniques for solving the complex ML optimization problem. In the proposed approach, the ML estimator is iteratively computed using the fast and low-complexity SAGE (Space-Alternating Generalized Expectation Maximization) algorithm. The proposed scheme is a candidate for indoor GPS navigation, as demonstrated by computer simulations.
Genomic profile of a secretory breast cancer with an ETV6–NTRK3 duplication (2009)

To the best of our knowledge, this is the first time a carcinoma has been shown to harbour a duplication of the ETV6-NTRK3 translocation. The presence of an additional copy of the derivative chromosome der(15)t(12;15) coupled with deletion of the other derivative der(12)t(12;15) in the modal population of cancer cells suggests that this was either an early phenomenon or conferred additional growth advantage on neoplastic cells.
Enhancement of carcinogenesis by the natural anticarcinogen indole-3-carbinol. (1987)

Indole-3-carbinol (I3C), a natural constituent of cruciferous vegetables, is an inhibitor in several experimental animal models of carcinogenesis by polynuclear aromatic hydrocarbons or aflatoxin B1 (AFB1) when administered prior to or during carcinogen exposure. For assessment of the postinitiation effects of I3C, rainbow trout were exposed to dietary I3C in two different protocols--before and during AFB1 exposure or after AFB1 exposure only. Preinitiation exposure to I3C reduced AFB1-initiated hepatocellular carcinomas in trout as previously reported, but post-initiation I3C exposure strongly enhanced the tumor incidence above the positive AFB1 control. These results reveal the need for additional research to elucidate the overall effect of I3C on chemical carcinogenesis.
Structural diversity of supercoiled DNA (2015)

By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.
Lymphokine-like activity of 8-mercaptoguanosine: induction of T and B cell differentiation. (1985)

Lymphocyte proliferation and differentiation result from ordered cellular interactions governed by soluble products (lymphokines). Dissecting the individual steps in these processes has been difficult, due to a paucity of pure lymphokines. Recently, it was reported that the derivatized ribonucleoside 8-mercaptoguanosine (8MGuo) has both mitogenic and differentiative effects on murine B cells. In the present studies, we tested 8MGuo for its ability to stimulate both B and T cell responses. In contrast to the murine studies, 8MGuo does not stimulate rat B cells to proliferate and, when tested for B cell growth factor-like activity, no stimulation was observed. The addition of 8MGuo (0.5 to 1 mM final concentration) to mitogen-stimulated B cells led to a marked increase in IgM and a modest increase in IgG secretion. When mixed with conditioned medium, 8MGuo acted synergistically in stimulating secretion of both isotypes, arguing that 8MGuo has both B cell-differentiating factor-mu (BCDF-mu) and BCDF-gamma activity. 8MGuo had no IL 2-like activity when tested on a mouse IL 2-dependent cell line, and no IL 1-like activity on addition to mouse thymocytes with or without submitogenic doses of lectin. However, when added to cultures of murine allogeneic cells in which the stimulating cell populations had been heat-inactivated, 8MGuo induced the generation of specific allogeneic cytotoxic T lymphocytes. Together, these results suggest that a simple derivatized nucleoside can induce both T and B cell differentiation without concomitant proliferation, and thus represent a unique probe for studying events in lymphocyte differentiation.
Pulsed Ultrafiltration Mass Spectrometry:  A New Method for Screening Combinatorial Libraries (1997)

In response to the need for rapid screening of combinatorial libraries to identify new lead compounds during drug discovery, we have developed an on-line combination of ultrafiltration and electrospray mass spectrometry, called pulsed ultrafiltration mass spectrometry, which facilitates the identification of solution-phase ligands in library mixtures that bind to solution-phase receptors. After ligands contained in a library mixture were bound to a macromolecular receptor, e.g., human serum albumin or calf intestine adenosine deaminase, the ligand-receptor complexes were purified by ultrafiltration and then dissociated using methanol to elute the ligands into the electrospray mass spectrometer for detection. Ligands with dissociation constants in the micromolar to nanomolar range were successfully bound, released, and detected using this method, including warfarin, salicylate, furosemide, and thyroxine binding to human serum albumin, and erythro-9-(2-hydroxy-3-nonyl)adenine binding to calf intestine adenosine deaminase. Repetitive bind- and-release experiments demonstrated that the receptor could be reused. Thus, pulsed ultrafiltration mass spectrometry was shown to provide a simple and powerful new method for the screening of combinatorial libraries in support of new drug discovery.
Extracellular matrix provides an optimal niche for the maintenance and propagation of mesenchymal stem cells (2010)

Relatively little is known about the cellular and molecular mechanisms underlying the control of mesenchymal stem cell (MSC) proliferation, differentiation, and survival. This presents difficulties in following and characterizing cells along the lineage because of our inability to isolate and obtain a sufficient number of homogeneous MSCs using current culture systems for in vitro expansion. Adjusting the cellular machinery to allow greater proliferation can lead to other unwanted outcomes, such as unmanageable precancerous changes, or differentiation down an undesired pathway. Recently, it has become increasingly evident that the extracellular matrix (ECM) is an important component of the cellular niche in a tissue, supplying critical biochemical and physical signals to initiate and sustain cellular functions. Indeed, it is very doubtful that the intricate and highly ordered nature of the ECM could be reproduced with synthetic or purified components. This review cites evidence that supports an alternative approach for maintenance of MSCs by simulating in vitro the bone marrow ECM, where MSCs reside in vivo, and discusses the potential mechanisms whereby the ECM regulates the exposure of cells to growth factors that subsequently control MSC replication and differentiation, and also how the ECM provides unique cues that govern the lineage specification and differentiation of MSCs.
A photobioreactor system for precision cultivation of photoautotrophic microorganisms and for high‐content analysis of suspension dynamics (2008)

Small-scale photobioreactors for cultivation of photoautotrophic microbes are required for precise characterization of the growth parameters of wild-type and engineered strains of these organisms, for their screening, and for optimization of culture conditions. Here, we describe the design and use of a flat-cuvette photobioreactor that allows accurate control of culture irradiance, temperature, pH, and gas composition combined with real-time monitoring by a built-in fluorometer and densitometer. The high-power LED light source generates precise irradiance levels that are programmed by user-designed protocols. The irradiance, temperature, and gas composition may be static or dynamically modulated, while optical density and pH may be stabilized in turbidostat and pH-stat modes, respectively. We demonstrate that the instrument is able to detect minute variations of growth caused, for example, by sudden dilution or by circadian rhythms. The sensitivity of the instrument is sufficient to monitor suspension optical density as low as 10(-2). This newly designed photobioreactor can significantly contribute to the study and use of photoautotrophic microbes in systems biology and biotechnology.
Mapping of Disulfide Bridges in Antifreeze Proteins from Overwintering Larvae of the Beetle Dendroides canadensis (1998)

Antifreeze proteins (AFPs) have been identified in certain high-latitude marine fish, insects and other terrestrial arthropods, and plants. Despite considerable structural variation, the mechanisms of their noncolligative antifreeze activity are probably quite similar. AFPs hydrogen bond onto the surface of potential seed ice crystals at preferred growth sites, thereby preventing growth of the crystals. AFPs from overwintering larvae of the beetle Dendroidescanadensis are among the most active AFPs. These 8.7-kDa proteins consist of seven 12- or 13-mer repeating units. Their most striking feature is the location of cysteines every six residues throughout their length. Consequently, identification of the disulfide linkages of these cysteines is essential to understanding the structure of these AFPs. This study demonstrated that all of the 16 Cys residues in the Dendroides AFPs are disulfide bridged. All of the seven 12- or 13-mer repeats have internal disulfide bridges, and in all but the first repeat the Cys residues at positions 1 and 7 of the repeats are linked. In repeat 1 the Cys at position 1 is linked to the Cys at position 10, rather than the Cys at position 7 as in the other repeats, and the Cys at position 7 of the first repeat is linked to a Cys at position 4 of the second repeat. The disulfide bridges probably function to position the hydrophilic side chains of serine and threonine residues so that they hydrogen bond with ice.
Impact of metal contact misalignment in silicon ink selective emitter solar cells (2010)

A selective emitter is a front-contact solar cell configuration in which surface regions under the front contacts are heavily doped to improve ohmic contact, while remaining emitter surface regions are lightly doped to minimize charge carrier recombination and improve blue spectrum response. Since the highly doped regions are relatively narrow, front contact misalignment will tend to have a detrimental impact on cell performance. In this report we quantify the impact of misalignment for solar cells manufactured with Innovalight Cougar™ Platform and Innovalight Silicon Ink. The Innovalight Cougar™ Platform is a portfolio of simple to implement technologies that, when combined with Innovalight Silicon Ink, enables the manufacture of a selective emitter (SE) solar cell with a non-masking single-step diffusion. Innovalight Silicon Ink, used to create the heavily doped regions, is a highly engineered silicon nanoparticle colloidal dispersion, implemented for both high volume inkjet and screen deposition, and further optimized to be produced and delivered in commercial volumes. Test cells were fabricated with a set of varying offsets between the highly doped regions and front silver features, thus controlling the amount of translation misalignment. We characterized the alignment accuracy by an automated vision system and report center-to-center offset values of less than ±10 μm for cells with designed offset of zero (see also). We demonstrate the cell performance remains unchanged, as long as the silver print does not extend past the highly doped regions (as defined by the deposited Innovalight Silicon Ink). For increasing misalignment offset, the major impact is an increase in series resistance resulting in a 26 % reduction in fill factor. Additionally, the open circuit voltage and short circuit current of the Cougar cells are reduced by 1-2 % due to increased recombination in the emitter. Taking tolerances of an industrial-scale production process into account, the processing window to ensure optimal cell performance without degradation due to misalignment of metal and SE pattern is specified.
Total Synthesis of Pamamycin-607 (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTTotal Synthesis of Pamamycin-607Eun Lee, Jeong, Eun Joo Kang, Lee Taek Sung, and Sung Kil HongView Author Information School of Chemistry and Molecular Engineering Seoul National University, Seoul 151-747, Korea Cite this: J. Am. Chem. Soc. 2001, 123, 41, 10131–10132Publication Date (Web):September 20, 2001Publication History Received24 May 2001Published online20 September 2001Published inissue 1 October 2001https://pubs.acs.org/doi/10.1021/ja016272zhttps://doi.org/10.1021/ja016272zrapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1473Altmetric-Citations48LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Anions,Cyclization,Ketones,Organic compounds,Organic reactions Get e-Alerts
Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins (2015)

Antibodies are powerful tools in life sciences research, as well as in diagnostic and therapeutic applications, because of their ability to bind given molecules with high affinity and specificity. Using current methods, however, it is laborious and sometimes difficult to generate antibodies to target specific epitopes within a protein, in particular if these epitopes are not effective antigens. Here we present a method to rationally design antibodies to enable them to bind virtually any chosen disordered epitope in a protein. The procedure consists in the sequence-based design of one or more complementary peptides targeting a selected disordered epitope and the subsequent grafting of such peptides on an antibody scaffold. We illustrate the method by designing six single-domain antibodies to bind different epitopes within three disease-related intrinsically disordered proteins and peptides (α-synuclein, Aβ42, and IAPP). Our results show that all these designed antibodies bind their targets with good affinity and specificity. As an example of an application, we show that one of these antibodies inhibits the aggregation of α-synuclein at substoichiometric concentrations and that binding occurs at the selected epitope. Taken together, these results indicate that the design strategy that we propose makes it possible to obtain antibodies targeting given epitopes in disordered proteins or protein regions.