gebhart/patrepeval huggingface dataset:
Histone H3 variants and their potential role in indexing mammalian genomes: The “H3 barcode hypothesis” (2006)

In the history of science, provocative but, at times, controversial ideas have been put forward to explain basic problems that confront and intrigue the scientific community. These hypotheses, although often not correct in every detail, lead to increased discussion that ultimately guides experimental tests of the principal concepts and produce valuable insights into long-standing questions. Here, we present a hypothesis, the "H3 barcode hypothesis." Hopefully, our ideas will evoke critical discussion and new experimental approaches that bear on general topics, such as nuclear architecture, epigenetic memory, and cell-fate choice. Our hypothesis rests on the central concept that mammalian histone H3 variants (H3.1, H3.2, and H3.3), although remarkably similar in amino acid sequence, exhibit distinct posttranslational "signatures" that create different chromosomal domains or territories, which, in turn, influence epigenetic states during cellular differentiation and development. Although we restrict our comments to H3 variants in mammals, we expect that the more general concepts presented here will apply to other histone variant families in organisms that employ them.
Flexible Circuits and Architectures for Ultralow Power (2010)

Subthreshold digital circuits minimize energy per operation and are thus ideal for ultralow-power (ULP) applications with low performance requirements. However, a large range of ULP applications continue to face performance constraints at certain times that exceed the capabilities of subthreshold operation. In this paper, we give two different examples to show that designing flexibility into ULP systems across the architecture and circuit levels can meet both the ULP requirements and the performance demands. Specifically, we first present a method that expands on ultradynamic voltage scaling (UDVS) to combine multiple supply voltages with component level power switches to provide more efficient operation at any energy-delay point and low overhead switching between points. This system supports operation across the space from maximum performance, when necessary, to minimum energy, when possible. It thus combines the benefits of single- <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</sub> , multi- <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</sub> , and dynamic voltage scaling (DVS) while improving on them all. Second, we propose that reconfigurable subthreshold circuits can increase applicability for ULP embedded systems. Since ULP devices conventionally require custom circuit design but the manufacturing volume for many ULP applications is low, a subthreshold field programmable gate array (FPGA) offers a cost-effective custom solution with hardware flexibility that makes it applicable across a wide range of applications. We describe the design of a subthreshold FPGA to support ULP operation and identify key challenges to this effort.
Docking of Cationic Antibiotics to Negatively Charged Pockets in RNA Folds (1999)

The binding of aminoglycosides to RNA provides a paradigm system for the analysis of RNA-drug interactions. The electrostatic field around three-dimensional RNA folds creates localized and defined negatively charged regions which are potential docking sites for the cationic ammonium groups of aminoglycosides. To explore in RNA folds the electronegative pockets suitable for aminoglycoside binding, we used calculations of the electrostatic field and Brownian dynamics simulations of cation diffusion. We applied the technique on those RNA molecules experimentally known to bind aminoglycosides, namely, two tobramycin aptamers (Wang, Y.; Rando, R. R. Chem. Biol. 1995, 2, 281-290): the aminoglycoside-binding region in 16S ribosomal RNA (Moazed, S.; Noller, H. F. Nature 1987, 327, 389-394) and the TAR RNA from human immunodeficiency virus (Mei, H.-Y.; et al. Bioorg. Med. Chem. Lett. 1995, 5, 2755-2760). For the aptamers and ribosomal RNA, for which the binding sites of the aminoglycosides are known, a good agreement between negatively charged pockets and the binding positions of the drugs was found. On the basis of variations between neomycin-like and kanamycin-like aminoglycosides in the interaction with the electrostatic field of ribosomal RNA, we propose a model for the different binding specificities of these two classes of drugs. The spatial congruence between the electronegative pockets in RNA folds and binding positions of aminoglycosides was used to dock aminoglycosides to ribosomal and TAR RNAs. Molecular dynamics simulations were used to analyze possible RNA-drug interactions. Aminoglycosides inhibit the binding of the viral Tat protein to TAR RNA; however, the drug-binding sites are still unknown. Thus, our docking approach provides first structural models for TAR-aminoglycoside complexes. The RNA-drug interactions observed in the modeled complexes support the view that the antibiotics might lock TAR in a conformation with low affinity for the Tat protein, explaining the experimentally found aminoglycoside inhibition of the Tat-TAR interaction (Mei, H.-Y.; et al. Bioorg. Med. Chem. Lett. 1995, 5, 2755-2760).
Rearrangement and transcription of a T-cell receptor beta-chain gene in different T-cell subsets. (1985)

The functionally defined sets of T lymphocytes--helper T cells, cytotoxic T cells, and suppressor T cells--were examined for the possible involvement of a recently identified T-cell receptor beta gene locus in receptor formation. Since gene rearrangements are required for functional gene expression, cloned T-cell lines from each of the groups were surveyed for the expression of unique gene rearrangements. In addition, cell lines that showed gene rearrangements were further tested for the expression of the mature 1.2- to 1.3-kilobase mRNA transcribed from a productive gene rearrangement. The results of such experiments show that helper and cytotoxic T cells may use a common beta chain of the receptor, whereas suppressor cells do so rarely, if at all.
Convenient preparation of solutions of superoxide anion and the reaction of superoxide anion with a copper(II) complex (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConvenient preparation of solutions of superoxide anion and the reaction of superoxide anion with a copper(II) complexJoan S. Valentine and Anne B. CurtisCite this: J. Am. Chem. Soc. 1975, 97, 1, 224–226Publication Date (Print):January 1, 1975Publication History Published online1 May 2002Published inissue 1 January 1975https://pubs.acs.org/doi/10.1021/ja00834a058https://doi.org/10.1021/ja00834a058research-articleACS PublicationsRequest reuse permissionsArticle Views1171Altmetric-Citations183LEARN 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
Wave-front correction and production of Zernike modes with a liquid-crystal spatial light modulator (1997)

I describe a nematic liquid-crystal spatial light modulator that can be used as a high-precision wave-front control device. I present results showing the open-loop correction of wave-front aberrations and demonstrate wave-front shaping by the production and quantification of the first 15 significant Zernike terms.
Transformation of group A streptococci by electroporation (1988)

The introduction, via electroporation, of free plasmid DNA into three strains of Streptococcus pyogenes is described. The method is very simple and rapid and efficiencies vary from 1 × 103 to 4 × 104 per µg of DNA. The method was also used to introduce an integrative plasmid and transformants were obtained, albeit at a somewhat lower frequency (2 × 102). Some of the plasmids used in this study are derivatives of the Lactococcus lactis subsp. cremoris Wg2 plasmid pWV01. These broad host range vectors replicate in Gram-positives as well as Gram-negatives (viz. Escherichia coli). Here we show that they also replicate in S. pyogenes and S. sanguis.
Arthritis Provoked by Linked T and B Cell Recognition of a Glycolytic Enzyme (1999)

The hallmark of rheumatoid arthritis (RA) is specific destruction of the synovial joints. In a mouse line that spontaneously develops a disorder with many of the features of human RA, disease is initiated by T cell recognition of a ubiquitously expressed self-antigen; once initiated, pathology is driven almost entirely by immunoglobulins. In this study, the target of both the initiating T cells and pathogenic immunoglobulins was identified as glucose-6-phosphate isomerase, a glycolytic enzyme. Thus, some forms of RA or related arthritides may develop by a mechanism fundamentally different from the currently popular paradigm of a joint-specific T cell response.
Complete nucleotide sequence of a functional HLA-DPβ gene and the region between the DPβ1 and DPα1 genes: comparison of the 5′ ends of HLA class II genes (1985)

The complete nucleotide sequence of an HLA-DP beta 1 gene and part of the adjacent DP alpha 1 gene, up to and including the signal sequence exon, were determined. The sequence of the DP beta 1 gene identified it as the DPw4 allele. The six exons of the DP beta 1 gene spanned over 11,000 bp of sequence. The arrangement of the gene was broadly analogous to genes of other class II beta chains. The beta 1 exon was flanked by introns of over 4 kb. Comparisons with published sequences of cDNA clones indicated that an alternative splice junction, at the 3' end of the gene, is used in at least one allele. Variation in choice of splice junction indicates an additional mechanism for allelic variation in class II genes. The sequence also indicated that the DP beta 1 and DP alpha 1 genes are separated by only 2 kb at their 5' ends. Comparison of the 5' ends of the DP alpha 1 and beta 1 genes with other class II sequences, including the DZ alpha gene, showed conservation of several blocks of sequences thought to be involved in control of expression. Some areas of the introns were partially conserved in the DQ beta gene, and several other intron sequences were homologous to sequences found in other unrelated genes.
cDNA Cloning and mRNA Expression of a Serine Proteinase Inhibitor Secreted by Cancer Cells: Identification as Placental Protein 5 and Tissue Factor Pathway Inhibitor-2 (1994)

A serine proteinase inhibitor was purified from conditioned medium of the human glioblastoma cell line T98G. Analysis of its partial amino acid sequences indicated that this protein was identical to placental protein 5 (PP5), a placenta-derived glycoprotein with serine proteinase inhibitor activity, the amino acid sequence of which had been partially determined. cDNA cloning of PP5 demonstrated that it belonged to the Kunitz-type serine proteinase inhibitor family, having three putative Kunitz-type inhibitor domains, and that it was identical to a recently reported inhibitor, tissue factor pathway inhibitor-2 (TFPI-2) [Sprecher et al. (1994) Proc. Natl. Acad. Sci. USA 91, 3353-3357]. PP5/TFPI-2 transcripts were highly abundant in the full-term placenta and widely expressed in various adult human tissues, such as the liver, skeletal muscle, heart, kidney, and pancreas. Several ovarian carcinoma cells as well as T98G also contained significant amounts of the transcripts.
Recognition of a Ubiquitous Self Antigen by Prostate Cancer-Infiltrating CD8 + T Lymphocytes (2008)

Substantial evidence exists that many tumors can be specifically recognized by CD8+ T lymphocytes. The definition of antigens targeted by these cells is paramount for the development of effective immunotherapeutic strategies for treating human cancers. In a screen for endogenous tumor-associated T cell responses in a primary mouse model of prostatic adenocarcinoma, we identified a naturally arising CD8+ T cell response that is reactive to a peptide derived from histone H4. Despite the ubiquitous nature of histones, T cell recognition of histone H4 peptide was specifically associated with the presence of prostate cancer in these mice. Thus, the repertoire of antigens recognized by tumor-infiltrating T cells is broader than previously thought and includes peptides derived from ubiquitous self antigens that are normally sequestered from immune detection.
Molecular imaging of proteins in tissues by mass spectrometry (2008)

Imaging MS (IMS) is an emerging technology that permits the direct analysis and determination of the distribution of molecules in tissue sections. Biological molecules such as proteins, peptides, lipids, xenobiotics, and metabolites can be analyzed in a high-throughput manner with molecular specificity not readily achievable through other means. Tissues are analyzed intact and thus spatial localization of molecules within a tissue is preserved. Several studies are presented that focus on the unique types of information obtainable by IMS, such as Abeta isoform distributions in Alzheimer's plaques, protein maps in mouse brain, and spatial protein distributions in human breast carcinoma. The analysis of a biopsy taken 100 years ago from a patient with amyloidosis illustrates the use of IMS with formalin-fixed tissues. Finally, the registration and correlation of IMS with MRI is presented.
Decreased expression of TGF- type II receptor in bronchial glands of smokers with COPD (2005)

In the bronchial glands of smokers with COPD there is decreased expression of TGF-beta RII which is associated with bronchial gland enlargement. These findings support the view that the absence of TGF-beta signalling may induce structural changes in the bronchial glands which, in turn, may promote mucus hypersecretion.
Taste-active Components in Foods, with Concentration on Umami Compounds (2009)

A century ago, an amino acid, L-glutamate (Glu), was found to be the important substance for umami (savory) taste of a Japanese soup stock cooked with sea tangle. Since that time, umami seasoning has been used to make foods palatable all over the world. Chemical analysis proved that Glu had been used for savory seasonings around the world, though its taste had been hidden behind the flavors of fat or herbs. Recently, research has shown that Glu affects the chemical senses not only in the oral cavity but also in the gastrointestinal tract, and it modulates the ingestion, digestion and metabolism of proteins. Umami taste, one of the five basic tastes along with sweet, salty, sour and bitter tastes, derived from Japanese cuisine, might be applicable for the nutritional care of elderly people, who are at risk for protein malnutrition even in developed countries.
Increasing the energy density of vegetative tissues by diverting carbon from starch to oil biosynthesis in transgenic Arabidopsis (2011)

Increasing the energy density of biomass by engineering the accumulation of triacylglycerols (TAGs) in vegetative tissues is synergistic with efforts to produce biofuels by conversion of lignocellulosic biomass. Typically, TAG accumulates in developing seeds, and little is known about the regulatory mechanisms and control factors preventing oil biosynthesis in vegetative tissues in most plants. Here, we engineered Arabidopsis thaliana to ectopically overproduce the transcription factor WRINKLED1 (WRI1) involved in the regulation of seed oil biosynthesis. Furthermore, we reduced the expression of APS1 encoding a major catalytic isoform of the small subunit of ADP-glucose pyrophosphorylase involved in starch biosynthesis using an RNAi approach. The resulting AGPRNAi-WRI1 lines accumulated less starch and more hexoses. In addition, these lines produced 5.8-fold more oil in vegetative tissues than plants with WRI1 or AGPRNAi alone. Abundant oil droplets were visible in vegetative tissues. TAG molecular species contained long-chain fatty acids, similar to those found in seed oils. In AGPRNAi-WRI1 lines, the relative expression level of sucrose synthase 2 was considerably elevated and correlated with the level of sugars. The relative expression of the genes encoding plastidic proteins involved in de novo fatty acid synthesis, biotin carboxyl carrier protein isoform 2 and acyl carrier protein 1, was also elevated. The relative contribution of TAG compared to starch to the overall energy density increased 9.5-fold in one AGPRNAi-WRI1 transgenic line consistent with altered carbon partitioning from starch to oil.
Polyunsaturated membranes are required for photosynthetic competence in a mutant ofArabidopsis (1998)

High levels of polyunsaturation are characteristic of all the membranes of plant and animal cells. For example, the chloroplasts of leaf cells contain about 75-80% polyunsaturated fatty acids. For the extra-chloroplast membranes in leaf cells and the membranes of non-photosynthetic tissues, values of 60-65% are typical. We report here the production of Arabidopsis double mutants that contain negligible levels of polyunsaturated fatty acids. The mutants were not capable of autotrophic growth and produced extremely chlorotic cotyledons and leaves. However, on sucrose media, the double mutants were robust plants showing strong leaf and root development. These observations indicate that the vast majority of receptor-mediated and transport-related membrane functions required to sustain the organism and induce proper development are adequately supported in the absence of polyunsaturated lipids. By contrast, photosynthesis is one process that does require high levels of membrane polyunsaturation.
Ultrafast differential sample and hold using low temperature grown GaAs MSM for photonic A/D conversion (2000)

Summary form only given.Many proposed photonic ADC systems consist of an input electrical signal biasing an optical modulator whose output is optically demultiplexed to an array of electrical ADCs. However, the speed and linearity of the optical modulator limit the performance of these systems. To circumvent this problem, we propose a sample and hold scheme utilizing LT grown GaAs MSM switches. The short recombination lifetime and high mobility of LT grown GaAs allow high-speed operation with good sensitivity. Optically triggered by a short pulse laser, the switches would be attached to a transmission line and would sample the input electrical signal onto a hold capacitor.
Binary Mutual Diffusion Coefficients of Aqueous Solutions of Sucrose, Lactose, Glucose, and Fructose in the Temperature Range from (298.15 to 328.15) K (2006)

Binary mutual diffusion coefficients measured by the Taylor dispersion method in two different laboratories (University of Naples, Federico II, Italy, and University of Coimbra, Portugal) are reported for aqueous solutions of lactose, sucrose, glucose, and fructose at various concentrations (0.001 to 0.1) mol·dm-3 and temperatures (298.15 to 328.15) K. The hydrodynamic radius and activation energy for the diffusion of aqueous sugars are calculated from those results. In addition, the measured diffusion coefficients are used with the Hartley equation to estimate activity coefficients for aqueous lactose, sucrose, glucose, and fructose.
High transconductance and velocity overshoot in NMOS devices at the 0.1- mu m gate-length level (1988)

Transport properties are investigated in self-aligned NMOS devices with gate lengths down to 0.07 mu m. Velocity overshoot was observed in the form of the highest transconductances measured to date in Si FETs, as well as in the trend of the transconductance with gate length. The measured transconductance reached 910 mu S/ mu m at liquid-nitrogen temperature and 590 mu S/ mu m at room temperature. Velocity overshoot, by making such transconductances possible, should extend the value of miniaturization to dimensions that are smaller than what was commonly assumed to be worthwhile to pursue.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Real-time three-dimensional Fourier-domain optical coherence tomography video image guided microsurgeries (2012)

The authors describe the development of an ultrafast three-dimensional (3D) optical coherence tomography (OCT) imaging system that provides real-time intraoperative video images of the surgical site to assist surgeons during microsurgical procedures. This system is based on a full-range complex conjugate free Fourier-domain OCT (FD-OCT). The system was built in a CPU-GPU heterogeneous computing architecture capable of video OCT image processing. The system displays at a maximum speed of 10 volume/s for an image volume size of 160 × 80 × 1024(X × Y × Z) pixels. We have used this system to visualize and guide two prototypical microsurgical maneuvers: microvascular anastomosis of the rat femoral artery and ultramicrovascular isolation of the retinal arterioles of the bovine retina. Our preliminary experiments using 3D-OCT-guided microvascular anastomosis showed optimal visualization of the rat femoral artery (diameter<0.8 mm), instruments, and suture material. Real-time intraoperative guidance helped facilitate precise suture placement due to optimized views of the vessel wall during anastomosis. Using the bovine retina as a model system, we have performed "ultra microvascular" feasibility studies by guiding handheld surgical micro-instruments to isolate retinal arterioles (diameter ~0.1 mm). Isolation of the microvessels was confirmed by successfully passing a suture beneath the vessel in the 3D imaging environment.
Cyclin G1 Is a Target of miR-122a, a MicroRNA Frequently Down-regulated in Human Hepatocellular Carcinoma (2007)

We investigated the role of microRNAs (miRNAs) in the pathogenesis of human hepatocellular carcinoma (HCC). A genome-wide miRNA microarray was used to identify differentially expressed miRNAs in HCCs arisen on cirrhotic livers. Thirty-five miRNAs were identified. Several of these miRNAs were previously found deregulated in other human cancers, such as members of the let-7 family, mir-221, and mir-145. In addition, the hepato-specific miR-122a was found down-regulated in approximately 70% of HCCs and in all HCC-derived cell lines. Microarray data for let-7a, mir-221, and mir-122a were validated by Northern blot and real-time PCR analysis. Understanding the contribution of deregulated miRNAs to cancer requires the identification of gene targets. Here, we show that miR-122a can modulate cyclin G1 expression in HCC-derived cell lines and an inverse correlation between miR-122a and cyclin G1 expression exists in primary liver carcinomas. These results indicate that cyclin G1 is a target of miR-122a and expand our knowledge of the molecular alterations involved in HCC pathogenesis and of the role of miRNAs in human cancer.