gebhart/patrepeval huggingface dataset:
Unstabilized DNA Breaks in Lymphocytes of Patients with Different Subsets of Systemic Sclerosis (2007)

The clastogenic effects on DNA, proven by the presence of micronuclei (MN) and the protective cellular mechanisms normally used to stabilize DNA breaks were investigated in three subsets of patients with systemic sclerosis (SSc). The frequency of MN found in cultures of peripheral lymphocytes in patients with anticentromere and antitopoisomerase I antibodies was significantly higher than that in the control group. The group with anticentromere antibody showed a significantly higher frequency of MN than did the subjects with antitopoisomerase antibody (4.22% versus 2.34%, P < 0.001). Patients with anti-RNA polymerase III, instead, had a low prevalence of typical micronucleated cells (0.98%), not significantly different from that of the healthy controls (0.82%). Moreover, when MN was characterized for the presence or absence of DNA fragments with free 3'-OH ends by digoxigenin-dUTP (DIG-dUTP) using terminal deoxynucleotidil transferase, its frequency was found to be increased in the groups with anticentromere and antitopoisomerase I antibodies with respect to that in the controls. The increase was significantly higher in the lymphocytes of the patients with anticentromere than in those with antitopoisomerase I antibody (35% versus 20.08%, P < 0.001). Nonetheless, the prevalence of unstable DNA fragments in patients with anti-RNA polymerase III antibody was low (2.05%) and not significantly different from that of the control group (1.18%). Our results indicate that there is a clastogenic effect on DNA and an interference in the protective cellular mechanisms normally stabilizing DNA breaks only in some subsets of SSc patients.
PU.1 and ICSBP control constitutive and IFN-γ-regulated<i>Tlr9</i>gene expression in mouse macrophages (2007)

Macrophages are activated by unmethylated CpG-containing DNA (CpG DNA) via TLR9. IFN-gamma and LPS can synergize with CpG DNA to enhance proinflammatory responses in murine macrophages. Here, we show that LPS and IFN-gamma up-regulated Tlr9 mRNA in murine bone marrow-derived macrophages (BMM). The ability of LPS and IFN-gamma to induce Tlr9 mRNA expression in BMM was dependent on the presence of the growth factor, CSF-1, which is constitutively present in vivo. However, there were clear differences in mechanisms of Tlr9 mRNA induction. LPS stimulation rapidly removed the CSF-1 receptor (CSF-1R) from the cell surface, thereby blocking CSF-1-mediated transcriptional repression and indirectly inducing Tlr9 mRNA expression. By contrast, IFN-gamma activated the Tlr9 promoter directly and only marginally affected cell surface CSF-1R expression. An approximately 100-bp proximal promoter of the murine Tlr9 gene was sufficient to confer basal and IFN-gamma-inducible expression in RAW264.7 cells. A composite IFN regulatory factor (IRF)/PU.1 site upon the major transcription start site was identified. Mutation of the binding sites for PU.1 or IRF impaired basal promoter activity, but only the IRF-binding site was required for IFN-gamma induction. The mRNA expression of the IRF family member IFN consensus-binding protein [(ICSBP)/IRF8] was coregulated with Tlr9 in macrophages, and constitutive and IFN-gamma-inducible Tlr9 mRNA expression was reduced in ICSBP-deficient BMM. This study therefore characterizes the regulation of mouse Tlr9 expression and defines a molecular mechanism by which IFN-gamma amplifies mouse macrophage responses to CpG DNA.
Human single-chain Fv fragments from a combinatorial library using the loxP-Cre recombination system (1999)

A human scFv display library has been constructed from peripheral blood lymphocytes of a patient suffering from Hashimoto's thyroiditis. Upon induction of Cre recombinase, the amplified VH and VL genes were recombined via two loxP sites inserted in amplification primers to construct in vitro scFv genes. Either soluble scFvs or scFvs displayed on phage were screened for binding to human thyroglobulin after two pannings with this antigen. Three scFvs were obtained which showed very similar nucleotidic sequences. The VH genes expressed display 96.4% nucleotide sequence homology with the germline VH251 gene, one of the two functional members of the small VH5 family and are mutated in sites already described as "selectively neutral" mutations and the VL genes are close to the germline DPL8 gene. These scFvs bind not only to human thyroglobulin but also to other self and exogenous antigens.
Performance Mapping of Multijunction Solar Cells Based on Electroluminescence (2009)

Electroluminescence intensity maps of all three subcells of space grade III-V multijunction cells were obtained with the help of dedicated imaging sensors at a range of different injection currents. Solely based on these data, making use of the homogeneity of one subcell, the local diode properties of an equivalent single junction cell were obtained and converted into spatial distributions of open circuit voltage ( <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">oc</sub> ) and current at a fixed operating voltage ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">op</sub> ). On a sample basis of more than 200 cells, <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">oc</sub> and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">op</sub> characterizing the entire cell were determined with an accuracy of plusmn3 mV and plusmn5 mA, respectively.
From Perception to Activation: The Molecular-Genetic and Biochemical Landscape of Disease Resistance Signaling in Plants (2010)

More than 60 years ago, H.H. Flor proposed the "Gene-for-Gene" hypothesis, which described the genetic relationship between host plants and pathogens. In the decades that followed Flor's seminal work, our understanding of the plant-pathogen interaction has evolved into a sophisticated model, detailing the molecular genetic and biochemical processes that control host-range, disease resistance signaling and susceptibility. The interaction between plants and microbes is an intimate exchange of signals that has evolved for millennia, resulting in the modification and adaptation of pathogen virulence strategies and host recognition elements. In total, plants have evolved mechanisms to combat the ever-changing landscape of biotic interactions bombarding their environment, while in parallel, plant pathogens have co-evolved mechanisms to sense and adapt to these changes. On average, the typical plant is susceptible to attack by dozens of microbial pathogens, yet in most cases, remains resistant to many of these challenges. The sum of research in our field has revealed that these interactions are regulated by multiple layers of intimately linked signaling networks. As an evolved model of Flor's initial observations, the current paradigm in host-pathogen interactions is that pathogen effector molecules, in large part, drive the recognition, activation and subsequent physiological responses in plants that give rise to resistance and susceptibility. In this Chapter, we will discuss our current understanding of the association between plants and microbial pathogens, detailing the pressures placed on both host and microbe to either maintain disease resistance, or induce susceptibility and disease. From recognition to transcriptional reprogramming, we will review current data and literature that has advanced the classical model of the Gene-for-Gene hypothesis to our current understanding of basal and effector triggered immunity.
Genome-Wide DNA Methylation Analysis of Hypothalamus During the Onset of Puberty in Gilts (2019)

Although selection of the early age at puberty in gilts will make for a favorable effect on the reproductivity of sow, a large proportion of phenotypic variation in age at puberty of gilts cannot be explained by genetics. Previous studies have implicated hypothalamic DNA methylation in the onset of puberty in mammals. However, the underlying molecular mechanism regarding the regulation of the onset of puberty has remained largely unexplored in gilts. Herein, the genome-scale DNA methylation of hypothalamus was acquired, using the reduced representation bisulfite sequencing, to compare and describe the changes of DNA methylation across Pre-, In- and Post-pubertal gilts. In this study, the average methylation levels of CpGs and CpHs (where H = C, T, or A) in CpG islands- and gene-related regions were gradually decreased in hypothalamic methylomes during the pubertal transition. Comparisons of Pre- vs. In-, In- vs. Post-, and Pre- vs. Post-pubertal stage revealed that there were 85726, 92914, and 100421 differentially methylated CpGs and 5940, 14804, and 16893 differentially methylated CpHs (where H = C, T, or A) in the hypothalamic methylomes. The methylation changes of CpHs were more dynamic than that of CpGs, and methylation changes of CpGs and CpHs were likely to be, respectively, involved in the developmental processes of reproduction and the molecular processes of cellular communications in the hypothalamus. Moreover, methylation changes of CpHs were observed to overrepresent in the quantitative trait loci of age at puberty, and the biological function of these CpH methylation changes was enriched in the pancreas development in gilts. Furthermore, the mRNA levels of several differentially CpG or CpH methylated genes related to the transcription of RNA II polymerase, GnRH signaling pathway, Estrogen signaling pathway, PI3K-AKt signaling pathway, and Insulin signaling pathway, including <i>MAX</i>, <i>MMP2</i>, <i>FGF11</i>, <i>IGF1R</i>, <i>FGF21</i>, and <i>GSK3B</i>, were significantly changed across these pubertal stages in the hypothalamus. These results will help our understanding of how DNA methylation contributes to phenotypic variation of age at puberty.
TREND OF AMINO ACID COMPOSITION OF PROTEINS OF DIFFERENT TAXA (2006)

Archaea, bacteria and eukaryotes represent the main kingdoms of life. Is there any trend for amino acid compositions of proteins found in full genomes of species of different kingdoms? What is the percentage of totally unstructured proteins in various proteomes? We obtained amino acid frequencies for different taxa using 195 known proteomes and all annotated sequences from the Swiss-Prot data base. Investigation of the two data bases (proteomes and Swiss-Prot) shows that the amino acid compositions of proteins differ substantially for different kingdoms of life, and this difference is larger between different proteomes than between different kingdoms of life. Our data demonstrate that there is a surprisingly small selection for the amino acid composition of proteins for higher organisms (eukaryotes) and their viruses in comparison with the "random" frequency following from a uniform usage of codons of the universal genetic code. On the contrary, lower organisms (bacteria and especially archaea) demonstrate an enhanced selection of amino acids. Moreover, according to our estimates, 12%, 3% and 2% of the proteins in eukaryotic, bacterial and archaean proteomes are totally disordered, and long (> 41 residues) disordered segments are found to occur in 16% of arhaean, 20% of eubacterial and 43% of eukaryotic proteins for 19 archaean, 159 bacterial and 17 eukaryotic proteomes, respectively. A correlation between amino acid compositions of proteins of various taxa, show that the highest correlation is observed between eukaryotes and their viruses (the correlation coefficient is 0.98), and bacteria and their viruses (the correlation coefficient is 0.96), while correlation between eukaryotes and archaea is 0.85 only.
Lung Vessel Morphological Structure (2023)

In conclusion, we can say that during the transition of the muscular-elastic arteries to the muscular arteries on the side of the adventitia, an additional muscle layer is formed, which surrounds the vessel wall in the form of a spiral. As a result, the size of the middle layer of the artery increases. This leads to a change in the Kernogh index
Fluticasone propionate liposomes for pulmonary delivery (2009)

The objective of the present study was to entrap fluticasone propionate in liposomes and study in vitro lung deposition of both liposomal dispersion and dry powder inhalation using twin stage impinger and Anderson cascade impactor. Liposomes were prepared by lipid film hydration method and characterized for size, shape, morphology, entrapment efficiency and in vitro lung deposition. The spray dried liposomes were further characterized for various physicochemical properties such as physical appearance, density, flow properties, drug content and in vitro pulmonary deposition. Fine particle fraction was also determined. Liposomal dispersion of fluticasone propionate was successfully prepared with more than 90% entrapment. Spray dried liposomes had mean size of 3-4 μ and a fine powder fraction of 9-10 %. Inclusion of antistatic agents such as leucine and magnesium stearate did not improve the aerosolisation behaviour of dry inhalation powder in this study.
High Efficiency 3D Video Coding Using New Tools Based on View Synthesis (2013)

We propose a new coding technology for 3D video represented by multiple views and the respective depth maps. The proposed technology is demonstrated as an extension of the recently developed high efficiency video coding (HEVC). One base views are compressed into a standard bitstream (like in HEVC). The remaining views and the depth maps are compressed using new coding tools that mostly rely on view synthesis. In the decoder, those views and the depth maps are derived via synthesis in the 3D space from the decoded baseview and from data corresponding to small disoccluded regions. The shapes and locations of those disoccluded regions can be derived by the decoder without any side information transmitted. To achieve high compression efficiency, we propose several new tools such as depth-based motion prediction, joint high frequency layer coding, consistent depth representation, and nonlinear depth representation. The experiments show high compression efficiency of the proposed technology. The bitrate needed for transmission of two side views with depth maps is mostly less than 50% than that of the bitrate for a single-view video.
The real structure of Na<sub>3</sub>BiO<sub>4</sub> by electron microscopy, HR-XRD and PDF analysis (2005)

Abstract The real stucture of a new crystalline high temperature phase, metastable at room temperature, in the system sodium – bismuth – oxygen, β -Na 3 BiO 4 , was determinated using high resolution X-ray powder diffraction, pair distribution function analysis, and high resolution transmission electron microscopy. β -Na 3 BiO 4 was synthesized by anodic oxidation of bismuth(III)-oxide in a sodium hydroxide – lithium hydroxide melt. The average crystal structure of β -Na 3 BiO 4 at ambient conditions ( R 3 m, a = 3.32141(9) Å, c = 16.4852(5) Å) is structurally related to α -NaFeO 2 with metal layers almost statistically occupied in a Na:Bi ratio of 3:1. Analysis of the long-range order on the bulk material by Rietveld refinement led to approximately Na:Bi ratios of 2:1 and 4:1, in consecutive metal layers, while a detailed analysis of the local order by means of the pair distribution function revealed the existence of almost pure sodium layers and mixed 1:1 – sodium:bismuth layers. Complementary studies on single crystallites using high resolution transmission electron miscroscopy exhibited a complex domain structure with short-range ordered, partially ordered, and long-range ordered domains.
Synthesis of d-biotin from L-cystine via intramolecular [3+2]cycloaddition (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of d-biotin from L-cystine via intramolecular [3+2]cycloadditionEnrico G. Baggiolini, Hsi Lin Lee, Giacomo Pizzolato, and Milan R. UskokovicCite this: J. Am. Chem. Soc. 1982, 104, 23, 6460–6462Publication Date (Print):November 1, 1982Publication History Published online1 May 2002Published inissue 1 November 1982https://pubs.acs.org/doi/10.1021/ja00387a057https://doi.org/10.1021/ja00387a057research-articleACS PublicationsRequest reuse permissionsArticle Views1528Altmetric-Citations55LEARN 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
XDBus: a high-performance, consistent, packet-switched VLSI bus (2002)

The XDBus is a low-cost, synchronous, packet-switched VLSI bus designed for use in high-performance multiprocessors. The bus provides an efficient coherency protocol which guarantees processors a consistent view of memory in the presence of caches and IO. Low-voltage swing (GTL) CMOS drivers connected to balanced transmission line traces ensure low power as well as high speed for chip, board, and as backplane applications. The signaling scheme and coherency protocol work together to promote a high level of system integration, while permitting a wide variety of configurations to be realized. These configurations include small single board systems, multiple bus systems, multiboard backplane systems, and multilevel cache systems. The bus is used in several commercial systems including Sun Microsystem's new SPARCcenter 2000 series.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Regulation of homocysteine metabolism by Mycobacterium tuberculosis S-adenosylhomocysteine hydrolase (2013)

Mycobacterium tuberculosis modulates expression of various metabolism-related genes to adapt in the adverse host environment. The gene coding for M. tuberculosis S-adenosylhomocysteine hydrolase (Mtb-SahH) is essential for optimal growth and the protein product is involved in intermediary metabolism. However, the relevance of SahH in mycobacterial physiology is unknown. In this study, we analyze the role of Mtb-SahH in regulating homocysteine concentration in surrogate host Mycobacterium smegmatis. Mtb-SahH catalyzes reversible hydrolysis of S-adenosylhomocysteine to homocysteine and adenosine and we demonstrate that the conserved His363 residue is critical for bi-directional catalysis. Mtb-SahH is regulated by serine/threonine phosphorylation of multiple residues by M. tuberculosis PknB. Major phosphorylation events occur at contiguous residues Thr219, Thr220 and Thr221, which make pivotal contacts with cofactor NAD⁺. Consequently, phosphorylation negatively modulates affinity of enzyme towards NAD⁺ as well as SAH-synthesis. Thr219, Thr220 and Thr221 are essential for enzyme activity, and therefore, responsible for SahH-mediated regulation of homocysteine.
Role of Polyunsaturated Fatty Acids in Cancer and Their Use in Cancer Treatment (2019)

Cancer is defined as uncontrolled cell division, which could spread or invade various tissues. There are more than 200 types of cancer, including breast, skin, lung, colon, and prostate cancer, and lymphoma, the symptoms and indications of which vary depending on the type of tissues. Cancer has several treatments with different applications. For instance, chemotherapy, radiation therapy, surgery or their combination are common treatment modalities for cancer. However, a complete cure for cancer has not been achieved yet. On the other hand, novel drugs for cancer treatment are not efficient due to the ability of cancer cells to develop resistance against chemotherapeutic agents. Recently, natural compounds have been reported to improve the efficiency of cancer treatment. Polyunsaturated fatty acids (PUFAs) are natural compounds that could be used as dietary supplements in cancer patients. PUFAs are classified into two main categories, including n-3 and n-6 PUFAs. According to the literature, n-3 PUFAs exert protective effects against cancer through the induction of apoptotic pathways and suppressing cell proliferation, while n-6 PUFAs cause tumor formation by inducing cell growth and proliferation. Using PUFAs in combination with chemotherapeutic agents is considered to be an effective approach to the treatment of cancer patients through increasing cancer cell death. This review aimed to discuss the interactive effects of the structure and function of PUFAs on cancer and cell processes through various signaling pathways.
Increased Brain-Specific MiR-9 and MiR-124 in the Serum Exosomes of Acute Ischemic Stroke Patients (2016)

The aims of this study were to examine the alternation in serum exosome concentrations and the levels of serum exosomal miR-9 and miR-124, two brain-specific miRNAs, in acute ischemic stroke (AIS) patients and to explore the predictive values of these miRNAs for AIS diagnosis and damage evaluation. Sixty-five patients with AIS at the acute stage were enrolled and 66 non-stroke volunteers served as controls. Serum exosomes isolated by ExoQuick precipitations were characterized by transmission electron microscopy, nanoparticle-tracking analysis and western blotting. The levels of exosomal miR-9 and miR-124 were determined by real-time quantitative PCR. Compared with controls, the concentration of serum exosomes and the median levels of serum exosomal miR-9 and miR-124 were significantly higher in AIS patients (p<0.01). The levels of both miR-9 and miR-124 were positively correlated with National Institutes of Health Stroke Scale (NIHSS) scores, infarct volumes and serum concentrations of IL-6. The areas under the curve for exosomal miR-9 and miR-124 were 0.8026 and 0.6976, respectively. This proof of concept study suggests that serum exosomal miR-9 and miR-124 are promising biomarkers for diagnosing AIS and evaluating the degree of damage caused by ischemic injury. However, further studies are needed to explore the potential roles of the exosomes released from brain tissues in post stroke complications.
Dynamics of a Tunable Superfluid Junction (2011)

We study the population dynamics of a Bose-Einstein condensate in a double-well potential throughout the crossover from Josephson dynamics to hydrodynamics. At barriers higher than the chemical potential, we observe slow oscillations well described by a Josephson model. In the limit of low barriers, the fundamental frequency agrees with a simple hydrodynamic model, but we also observe a second, higher frequency. A full numerical simulation of the Gross-Pitaevskii equation giving the frequencies and amplitudes of the observed modes between these two limits is compared to the data and is used to understand the origin of the higher mode. Implications for trapped matter-wave interferometers are discussed.