gebhart/patrepeval huggingface dataset:
Transcriptome Complexity in a Genome-Reduced Bacterium (2009)

To study basic principles of transcriptome organization in bacteria, we analyzed one of the smallest self-replicating organisms, Mycoplasma pneumoniae. We combined strand-specific tiling arrays, complemented by transcriptome sequencing, with more than 252 spotted arrays. We detected 117 previously undescribed, mostly noncoding transcripts, 89 of them in antisense configuration to known genes. We identified 341 operons, of which 139 are polycistronic; almost half of the latter show decaying expression in a staircase-like manner. Under various conditions, operons could be divided into 447 smaller transcriptional units, resulting in many alternative transcripts. Frequent antisense transcripts, alternative transcripts, and multiple regulators per gene imply a highly dynamic transcriptome, more similar to that of eukaryotes than previously thought.
The specificity of human anti-cytochrome c autoantibodies that arise in autoimmune disease. (1990)

Cytochromes c (cyt c) are among the best characterized model Ag because their amino acid sequences and tertiary structures are well defined. One unique aspect of cyt c as an immunogen is its ability to induce autoantibody responses in animal models, although no pathology resulting from these responses has been reported. In this study, the presence and specificity of autoantibodies to cyt c were investigated in patients with SLE and related connective tissue diseases. Anti-cyt c antibodies were found in approximately 7% of patient sera and were statistically associated with the expression of antimitochondrial antibodies but were not statistically associated with any disease subset among those represented. Anti-cyt c was not associated with the presence of autoantibodies to DNA, histones, Ro, La, or Sm autoantigens. Most of the autoantibodies were specific for native or native-like forms of cyt c but antibodies to denatured forms were also apparent. Autoantibody binding was shown to be directed predominantly at selected sites of evolutionary variability within cyt c. The specificity of the human anti-cyt c autoantibodies appear to be similar to that of mouse anti-human cyt c antibodies and to autoantibodies elicited in mice against rat (mouse) cyt c.
Status of transgenic chicken models for developmental biology (2004)

The chick embryo is a classic model that has been used to gain insight into developmental processes and cell fate within the embryo for over a century. For the most part, investigators have implanted quail cells into a chicken embryo. A more powerful tool for developmental biology research than the quail:chick chimera system would be to have lines of transgenic chickens expressing reporter genes that are readily available to the research community. However, avian transgenic technology has been fraught with technical difficulties, and transgenic chickens expressing reporter genes have only recently been developed. The goal of this review is to report the technologies that have been used to generate transgenic chickens and to discuss the challenges in generating avian transgenics for developmental biology research.
Luminescence Quenching Behavior of an Oxygen Sensor Based on a Ru(II) Complex Dissolved in Polystyrene (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLuminescence Quenching Behavior of an Oxygen Sensor Based on a Ru(II) Complex Dissolved in PolystyrenePaul. Hartmann, Marc J. P. Leiner, and Max E. LippitschCite this: Anal. Chem. 1995, 67, 1, 88–93Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://pubs.acs.org/doi/10.1021/ac00097a015https://doi.org/10.1021/ac00097a015research-articleACS PublicationsRequest reuse permissionsArticle Views1118Altmetric-Citations143LEARN 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
Heparin‐induced thrombocytopenia: further studies of the effects of heparin‐dependent antibodies on platelets (1986)

Studies were performed with the sera of five patients with heparin-induced thrombocytopenia. Each patient serum was found to cause heparin-dependent aggregation of normal and Bernard-Soulier syndrome platelets but not Glanzmann's thrombasthenia or fixed normal platelets. This antibody effect was blocked by inhibition of both aerobic and anaerobic metabolism and an increase in intraplatelet c-AMP with prostaglandin E1. These findings suggest that the antibody-induced platelet aggregation was not a passive agglutination of cells but an active process requiring metabolic energy and membrane glycoproteins IIb/IIIa but not glycoprotein Ib. In addition, platelet aggregation by four patient sera was inhibited by aspirin or apyrase indicating a prostaglandin synthesis and ADP-dependent mechanism and the reaction could be suppressed by dipyridamole alone. However, platelet aggregation induced by the serum of one patient was only inhibited partially by the combination of aspirin and apyrase suggesting mediation of the antibody effect in part by a pathway independent of extracellular ADP and prostaglandin synthesis and this antibody reaction could only be completely suppressed by a combination of aspirin and dipyridamole. Heterogeneity exhibited by these antibodies may influence the choice and effectiveness of antiplatelet therapy in heparin-induced thrombocytopenia.
Imaging the Ocular Anterior Segment With Real-Time, Full-Range Fourier-Domain Optical Coherence Tomography (2008)

We have demonstrated a novel Fourier-domain optical coherence tomography system and signal-processing algorithm for full-range, real-time, artifact-free quantitative imaging of the anterior chamber. Cross-sectional full-range images comprising 1024 x 800 pixels (axial x lateral) were acquired and displayed at 6.7 images/s. Volumetric data comprising 1024 x 400 x 60 pixels (axial x lateral x elevation) were acquired in 4.5 seconds with real-time visualization of individual slices and 3-dimensional reconstruction performed in postprocessing. Details of the cornea, limbus, iris, anterior lens capsule, trabecular meshwork, and Schlemm's canal were visualized. Quantitative surface height maps of the corneal epithelium and endothelium were obtained from the volumetric data and used to generate corneal thickness maps.
Metal pumps liquid uphill (2009)

The behavior of liquids on a solid surface is determined by the surface wettability. In this work, by structuring metal surfaces with high-intensity femtosecond laser pulses, we engineer a unique surface pattern that dramatically modifies surface wetting properties. In a gravity-defying way, the treated metal surfaces make liquids sprint vertically uphill at an unprecedented speed of 1 cm/s. Furthermore, the surface structures we create here rapidly transport a significant amount of liquid against gravitation to an elevated point above the reservoir level, thus bringing this effect to potential real-life applications.
The Therapeutic Potential of Interleukin-1 and Tumor Necrosis Factor on Hematopoietic Stem Cells (1992)

Dose intensity is emerging as a crucial determinant of success in cytotoxic cancer therapy; however, myelosuppression presents as one of the major complications encountered with increased dose intensity. Therefore, investigators are looking at the use of cytokine administration in combination with cytotoxic therapy to overcome this problem. Interleukin-1 (IL-1) and tumor necrosis factor alpha (TNF-α) have been shown to be beneficial in protecting the hematopoietic system from radiation and chemotherapy. In this report, we give an overview of studies using IL-1 and TNF-α as protective agents and discuss possible mechanisms involved in their protective action. Mice pretreated with IL-1 and/or TNF-α were shown to be protected from the lethal effects of radiation and it has been suggested that the mechanism for this protection may be through the production of the antioxidant enzyme manganese superoxide dismutase. Similarly, aldehyde dehydrogenase, an enzyme important in the metabolic pathway of cyclophosphamide compounds, has been implicated as being important in the protection of hematopoietic cells from 4-hydroperoxycyclophosphamide. While IL-1 and TNF-α stimulate both of these enzymes, other mechanisms are probably also operative for other forms of chemotherapy, i.e. IL-1 and TNF-α were shown to protect hematopoietic progenitors from phenylketophosphamide, a cyclophosphamide derivative that is not metabolized by the enzyme aldehyde dehydrogenase. Furthermore, malignant as well as normal cells may possess receptors for these cytokines; therefore, IL-1 and TNF-α will have to be selective in their protection. They must be capable of protecting normal hematopoietic cells while rendering malignant cells susceptible to the toxic actions of the chemotherapy. Although this remains an open question, in the case of 4-HC toxicity, IL-1 and TNF-α appear to be selective since acute myelogenous leukemic cells are not protected from 4-HC administration. On the other hand, IL-1 and TNF-α were observed to protect A375 human melanoma cells from lethal irradiation. Thus, more studies will be necessary to determine the selective beneficial protective effects of IL-1 and TNF-α.
Modern approaches to new vaccines including prevention of AIDS (1989)

Well over half of the 58 papers from the September 1993 annual conference on new vaccines (presumably at Cold Springs Harbor) discuss AIDS; the rest cover immunology, gene vaccination, and bacteriology. Among the specific topics are recombinant viral vaccines expressing cytokine genes, polynucleotid
Enantioselective Total Synthesis of the Cyclotryptamine Alkaloid Idiospermuline (2003)

Stereogenic quaternary carbons present the primary challenge in the syntheses of trispyrrolidinoindoline alkaloids such as idiospermuline. In its synthesis the two contiguous quaternary centers are expediently addressed by combining the lithium dienolate of a differentially protected dihydroisoindigo with a tartrate-derived electrophile. The third quaternary stereocenter is introduced by a catalytic asymmetric Heck reaction.
Effects of Helicobacter pylori infection on mucin expression in gastric carcinoma and pericancerous tissues (2005)

The results indicate that H. pylori infection can alter the expression of some mucin genes in pericancerous mucosa and cancerous tissues of gastric carcinoma, then destroy the gastric mucosa barrier.
Homocysteine and its Derivatives as Possible Modulators of Neuronal and Non-Neuronal Cell Glutamate Receptors in Alzheimer's Disease (2007)

Homocysteine (HC) and its derivatives may be involved in the etiology of Alzheimer's Disease (AD), although the precise mechanisms by which these compounds could cause cellular pathology are still unclear. Because interactions of HC with glutamate receptors have been implicated in AD, receptor-mediated effects of HC and homocysteic acid (HCA) on neurons and lymphocytes have been analyzed. Activation of glutamate receptors by these compounds has been shown to increase intracellular calcium and free radical levels in both types of cells, which may serve as a signal for development of apoptosis. Activation of group III metabotropic glutamate receptors stimulates, whereas activation of group I and group II metabotropic glutamate receptors prevent, the excitotoxic action of HC and HCA. These effects may contribute to the neuronal pathology and immunosenescence that occur in AD. It is proposed that selective agonists of metabotropic glutamate receptors that counter the effects of HC and its derivatives may be used for correction of neuronal and immune cell metabolism in vivo under the conditions of hyperhomocysteinemia, which can occur in AD.
Cellular Proteins Bound to Immunodeficiency Viruses: Implications for Pathogenesis and Vaccines (1992)

Cellular proteins associated with immunodeficiency viruses were identified by determination of the amino acid sequence of the proteins and peptides present in sucrose density gradient-purified human immunodeficiency virus (HIV)-1, HIV-2, and simian immunodeficiency virus (SIV). beta 2 microglobulin (beta 2m) and the alpha and beta chains of human lymphocyte antigen (HLA) DR were present in virus preparations at one-fifth the concentration of Gag on a molar basis. Antisera to HLA DR, beta 2 m, as well as HLA class I precipitated intact viral particles, suggesting that these cellular proteins were physically associated with the surface of the virus. Antisera to class I, beta 2m, and HLA DR also inhibited infection of cultured cells by both HIV-1 and SIV. The specific, selective association of these cellular proteins in a physiologically relevant manner has major implications for our understanding of the infection process and the pathogenesis of immunodeficiency viruses and should be considered in the design of vaccines.
Selective killing of transformed cells by cyclin/cyclin-dependent kinase 2 antagonists (1999)

Recent studies identified a short peptide motif that serves as a docking site for cyclin/cyclin-dependent kinase (cdk) 2 complexes. Peptides containing this motif block the phosphorylation of substrates by cyclin A/cdk2 or cyclin E/cdk2. Here we report that cell membrane-permeable forms of such peptides preferentially induced transformed cells to undergo apoptosis relative to nontransformed cells. Deregulation of E2F family transcription factors is a common event during transformation and was sufficient to sensitize cells to the cyclin/cdk2 inhibitory peptides. These results suggest that deregulation of E2F and inhibition of cdk2 are synthetically lethal and provide a rationale for the development of cdk2 antagonists as antineoplastic agents.
STING Pathway Activation Stimulates Potent Immunity against Acute Myeloid Leukemia (2016)

Type I interferon (IFN), essential for spontaneous T cell priming against solid tumors, is generated through recognition of tumor DNA by STING. Interestingly, we observe that type I IFN is not elicited in animals with disseminated acute myeloid leukemia (AML). Further, survival of leukemia-bearing animals is not diminished in the absence of type I IFN signaling, suggesting that STING may not be triggered by AML. However, the STING agonist, DMXAA, induces expression of IFN-β and other inflammatory cytokines, promotes dendritic cell (DC) maturation, and results in the striking expansion of leukemia-specific T cells. Systemic DMXAA administration significantly extends survival in two AML models. The therapeutic effect of DMXAA is only partially dependent on host type I IFN signaling, suggesting that other cytokines are important. A synthetic cyclic dinucleotide that also activates human STING provided a similar anti-leukemic effect. These data demonstrate that STING is a promising immunotherapeutic target in AML.
A new method to determine MOSFET channel length (1980)

A new method is proposed to electrically determine MOS transistor channel length with both accuracy and convenience. Based on the linear region relationship between effective channel length L <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</inf> and channel resistance R <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">chan</inf> of an MOS transistor, this method determines L <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</inf> by applying relatively large but constant gate voltage to eliminate threshold voltage determination and takes into account external resistance. Comparison of this method with SEM measurement shows very good agreement (within ±0.1 µm resolution limit of our SEM technique).
Cyanobacterial-Type, Heteropentameric, NAD + -Reducing NiFe Hydrogenase in the Purple Sulfur Photosynthetic Bacterium Thiocapsa roseopersicina (2004)

Structural genes coding for two membrane-associated NiFe hydrogenases in the phototrophic purple sulfur bacterium Thiocapsa roseopersicina (hupSL and hynSL) have recently been isolated and characterized. Deletion of both hydrogenase structural genes did not eliminate hydrogenase activity in the cells, and considerable hydrogenase activity was detected in the soluble fraction. The enzyme responsible for this activity was partially purified, and the gene cluster coding for a cytoplasmic, NAD+-reducing NiFe hydrogenase was identified and sequenced. The deduced gene products exhibited the highest similarity to the corresponding subunits of the cyanobacterial bidirectional soluble hydrogenases (HoxEFUYH). The five genes were localized on a single transcript according to reverse transcription-PCR experiments. A sigma54-type promoter preceded the gene cluster, suggesting that there was inducible expression of the operon. The Hox hydrogenase was proven to function as a truly bidirectional hydrogenase; it produced H2 under nitrogenase-repressed conditions, and it recycled the hydrogen produced by the nitrogenase in cells fixing N2. In-frame deletion of the hoxE gene eliminated hydrogen evolution derived from the Hox enzyme in vivo, although it had no effect on the hydrogenase activity in vitro. This suggests that HoxE has a hydrogenase-related role; it likely participates in the electron transfer processes. This is the first example of the presence of a cyanobacterial-type, NAD+-reducing hydrogenase in a phototrophic bacterium that is not a cyanobacterium. The potential physiological implications are discussed.
Developmental toxicity of arecoline, the major alkaloid in betel nuts, in zebrafish embryos (2004)

Arecoline-treated embryos exhibited general developmental retardation in a dose-dependent manner. Our results from RT-PCR, in situ hybridization, and antioxidant-protection experiments indicate that the mechanism underlying growth retardation by arecoline in embryos is predominantly due to a general cytotoxic effect induced by depletion of intracellular thiols.
Differential Roles for Bone Morphogenetic Protein (BMP) Receptor Type IB and IA in Differentiation and Specification of Mesenchymal Precursor Cells to Osteoblast and Adipocyte Lineages (1998)

Cumulative evidence indicates that osteoblasts and adipocytes share a common mesenchymal precursor and that bone morphogenetic proteins (BMPs) can induce both osteoblast and adipocyte differentiation of this precursor. In the present study, we investigated the roles of BMP receptors in differentiation along these separate lineages using a well-characterized clonal cell line, 2T3, derived from the mouse calvariae. BMP-2 induced 2T3 cells to differentiate into mature osteoblasts or adipocytes depending upon culture conditions. To test the specific roles of the type IA and IB BMP receptor components, truncated and constitutively active type IA and IB BMP receptor cDNAs were stably expressed in these cells. Overexpression of truncated type IB BMP receptor (trBMPR-IB) in 2T3 cells completely blocked BMP-2-induced osteoblast differentiation and mineralized bone matrix formation. Expression of trBMPR-IB also blocked mRNA expression of the osteoblast specific transcription factor, Osf2/ Cbfa1, and the osteoblast differentiation-related genes, alkaline phosphatase (ALP) and osteocalcin (OC). BMP-2-induced ALP activity could be rescued by transfection of wild-type (wt) BMPR-IB into 2T3 clones containing trBMPR-IB. Expression of a constitutively active BMPR-IB (caBMPR-IB) induced formation of mineralized bone matrix by 2T3 cells without addition of BMP-2. In contrast, overexpression of trBMPR-IA blocked adipocyte differentiation and expression of caBMPR-IA induced adipocyte formation in 2T3 cells. Expression of the adipocyte differentiation-related genes, adipsin and PPARgamma, correlated with the distinct phenotypic changes found after overexpression of the appropriate mutant receptors. These results demonstrate that type IB and IA BMP receptors transmit different signals to bone-derived mesenchymal progenitors and play critical roles in both the specification and differentiation of osteoblasts and adipocytes.
fw2.2 : A Quantitative Trait Locus Key to the Evolution of Tomato Fruit Size (2000)

Domestication of many plants has correlated with dramatic increases in fruit size. In tomato, one quantitative trait locus (QTL), fw2.2, was responsible for a large step in this process. When transformed into large-fruited cultivars, a cosmid derived from the fw2.2 region of a small-fruited wild species reduced fruit size by the predicted amount and had the gene action expected for fw2.2. The cause of the QTL effect is a single gene, ORFX, that is expressed early in floral development, controls carpel cell number, and has a sequence suggesting structural similarity to the human oncogene c-H-ras p21. Alterations in fruit size, imparted by fw2.2 alleles, are most likely due to changes in regulation rather than in the sequence and structure of the encoded protein.
Total synthesis of (.+-.)-amarolide, a quassinoid bitter principle (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of (.+-.)-amarolide, a quassinoid bitter principleHiroshi Hirota, Akihisa Yokoyama, Katsuaki Miyaji, Toshio Nakamura, Michito Igarashi, and Takeyoshi TakahashiCite this: J. Org. Chem. 1991, 56, 3, 1119–1127Publication Date (Print):February 1, 1991Publication History Published online1 May 2002Published inissue 1 February 1991https://pubs.acs.org/doi/10.1021/jo00003a039https://doi.org/10.1021/jo00003a039research-articleACS PublicationsRequest reuse permissionsArticle Views360Altmetric-Citations10LEARN 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 Get e-Alerts