gebhart/patrepeval huggingface dataset:
Molecular cloning of developmentally regulated, low-abundance mRNA sequences from embryonic muscle. (1980)

To study the role of low-abundance, embryonic muscle-specific gene transcripts, we have developed a method to screen cDNA clones from embryonic muscle for such sequences. The protocol involves two stages: first, partial enrichment for cDNA clones carrying possible embryo-specific sequences by selecting clones of low-abundance sequences; and second, determination, by hybridization to RNA attached to diazobenzyloxymethyl-paper, which sequences from this category are regulated in an embryonic muscle-specific manner during development. At least three different clones were obtained which hybridized to sequences present in early muscle development but absent, or present at relatively low levels, at late embryonic and adult muscle stages. Two of these clones were not muscle-specific because they hybridized to poly(A)+RNA from liver or brain or both. The third clone, 106A4, did not detectably hybridize to total poly(A)+RNA at any stage of brain or liver development tested. This sequence also was not detectable in poly(A)+RNA from embryonic muscle progenitor cells. Thus, the 106A4 sequence is a likely candidate for an embryonic muscle-specific sequence. We have demonstrated that the 106A4 sequence is a mRNA, although the specific identity and function of the translated product is unknown. The method used to identify embryonic muscle-specific cDNA clones should be generally applicable for obtaining clones for low abundance transcripts regulated in a tissue-specific or developmental stage-specific manner.
Analysis of loss values for Australian rural catchments to underpin ARR guidance (2015)

As part of ARR Project 6, loss values were derived for a range of events on 38 rural catchments from across Australia. Based upon an earlier pilot study, the IL/CL and SWMOD loss models were selected for analysis. Loss values were estimated for each loss model for more than 1,000 events. The loss values are presented as both median values for each catchment and also as empirical distributions. The large data set allowed an investigation of how loss varies with rainfall characteristics including, event severity and antecedent rainfall. A range of catchment characteristics was also explored to see whether they could explain the variability in the derived loss values. Where possible, regional prediction equations were developed to estimate loss values for ungauged catchments. This analysis was used as the basis of developing recommendations for guidance in ARR for selection of loss values for design flood estimation.
Inhibition of poly(ADP)-ribose polymerase as a therapeutic strategy for breast cancer. (2010)

As knowledge increases about the processes underlying cancer, it is becoming feasible to design "targeted therapies" directed toward specific pathways that are critical to the genesis or maintenance of the malignant phenotype. Poly(ADP-ribose) polymerase (PARP) inhibitors are an example of this new framework. DNA damage repair is a complex and multifaceted process that is critical to cell survival. Members of the PARP family are central to specific DNA damage repair pathways, particularly the base excision repair (BER) pathway. PARP inhibition, with subsequent impairment of the BER mechanism, may enhance the cytotoxicity of agents that generate single-strand breaks in DNA, such as radiation and certain chemotherapy drugs. In addition, PARP inhibitors may induce death through "synthetic lethality" if the DNA repair mechanisms that rescue BER-deficient cells are themselves impaired. This mechanism is thought to underlie the impressive results of PARP inhibition in BRCA-associated breast and ovarian cancer, and may also account for the reported benefit of this approach in "triple-negative" breast cancer. This review will examine the current understanding of PARP inhibition as a treatment for breast cancer, ongoing clinical trials, and future directions for this new approach.
Defective DNA methylation and CD70 overexpression in CD4+ T cells in MRL/lpr lupus‐prone mice (2007)

We have determined that abnormal DNA methylation in T cells coincides with the development of autoimmunity, using a mouse model that exhibits an age-dependent lupus-like disease (MRL/lpr mice). Splenic CD4(+) T cells were isolated from these mice at 5 and 16 wk of age (before and after autoimmunity is established) and the expression of DNA methyltransferase 1 (Dnmt1) and the methylation-sensitive gene Tnfsf7 (CD70) was measured. Bisulfite DNA sequencing was used to monitor the methylation status of the Tnfsf7 gene. We found that Dnmt1 steady-state mRNA levels were significantly lower in 16-wk-old MRL/lpr mice, which had established autoimmunity, compared to the 5-wk-old MRL/lpr mice. Furthermore, the expression of CD70 was higher in MRL/lpr mice at 16 wk. CD70 was overexpressed in MRL/lpr mice compared to age- and sex-matched MRL(+/+) controls. Bisulfite DNA sequencing of the Tnfsf7 gene in MRL/lpr mice revealed that at 16 wk, CG pairs were hypomethylated compared to 5-wk-old mice, and that Tnfsf7 from MRL/lpr mice was hypomethylated at 16 wk relative to age-matched MRL(+/+) controls. Our data indicate that decreased expression of Dnmt1 and the corresponding T cell DNA hypomethylation correlate with the development of age-dependent autoimmunity in MRL/lpr mice.
Atlas of Internal Medicine (2002)

1.Cardiology2.Pulmonary and Critical Care Medicine 3.Endocriniology4.Dermatology5.Rheumatology6.Allergy and Immunology7.Infectious Diseases8.Neurology9.Oncology10.Hematology11.Gastroenterology 12.Hepatology 13.Nephrology
Colorectal carcinoma-specific antigen: detection by means of monoclonal antibodies. (1979)

Fusion of P3 X 63 Ag8 mouse myeloma cells with splenocytes obtained from mice immunized with cells derived from human colorectal carcinomas resulted in the production of antibody-secreting hybridomas. Two hybridomas (1083-17 and 1116-56) and their clones secreted antibodies binding specifically to human colorectal carcinoma cells either grown in culture or obtained from patients, but did not bind to normal colonic mucosa or other normal and malignant human cells. The binding specificity was consistent in three assays: radioimmunoassay, mixed hemadsorption, and immunofluorescence. Adsorption of these antibodies to colorectal carcinoma cell lines totally eliminated their specific binding.
Regulatory elements in the 5'-flanking region and the first intron contribute to transcriptional control of the mouse alpha 1 type I collagen gene. (1989)

We have identified two blocks of regulatory sequences located in the 5'-flanking region and the first intron of the mouse alpha 1 type I collagen (COL1A1) gene. Both blocks were found to contain positive as well as negative regulatory elements. Sequences located within 222 base pairs upstream of the transcription start site showed a strong stimulatory effect on the COL1A1 promoter and were sufficient for tissue-specific regulation of the COL1A1 gene. The combined upstream and intron regulatory sequences showed a marked inhibition of COL1A1 promoter activity in fibroblasts. This finding suggests that additional, more remote regulatory sequences may be required for establishing the high level of activity of the endogenous COL1A1 gene in fibroblastoid cells.
Elastic LiDAR Fusion: Dense Map-Centric Continuous-Time SLAM (2018)

The concept of continuous-time trajectory representation has brought increased accuracy and efficiency to multi-modal sensor fusion in modern SLAM. However, regardless of these advantages, its offline property caused by the requirement of global batch optimization is critically hindering its relevance for real-time and life-long applications. In this paper, we present a dense map-centric SLAM method based on a continuous-time trajectory to cope with this problem. The proposed system locally functions in a similar fashion to conventional Continuous-Time SLAM (CT-SLAM). However, it removes the need for global trajectory optimization by introducing map deformation. The computational complexity of the proposed approach for loop closure does not depend on the operation time, but only on the size of the space it explored before the loop closure. It is therefore more suitable for long term operation compared to the conventional CT-SLAM. Furthermore, the proposed method reduces uncertainty in the reconstructed dense map by using probabilistic surface element (surfel) fusion. We demonstrate that the proposed method produces globally consistent maps without global batch trajectory optimization, and effectively reduces LiDAR noise by surfel fusion.
Biochemical studies on bovine adenovirus type 3. I. Purification and properties (1975)

Bovine adenovirus type 3 (BAV3) was purified and its properties were studied. On productive infection of CKT1 cells (a cell line derived from calf kidney) with BAV3, it was observed that viral DNA synthesis was initiated after about 24 h and its rate was maximal after about 40 h. Maturation of the virus occurred several hours after this. Purified BAV3 was separated into four discrete bands by CsCl density gradient centrifugation (complete, incomplete, empty, and degraded viruses). The complete BAV3 was similar in size and structure to human and avian adenoviruses. Polyacrylamide gel electrophoresis showed that the complete BAV3 virion contained at least 10 polypeptides. The total structural proteins of the virion had a similar amino acid composition to those of human adenoviruses. DNA of the complete virus was a linear duplex and its contour length was 12.3 +/- 0.9 mum. The So20,w value of the DNA was 32.9S and its buoyant density in CsCl was 1.717 g/ml. There was about 25% homology between the DNAs of BAV3 and human adenovirus type 5 by filter hybridization. It was also noted that BAV3 produced incomplete virus. The incomplete virus was similar in morphology to the complete virus and contained almost all the structural polypeptides of the latter, but lacked infectivity. However, its DNA had a deletion(s) (13%) which seemed to locate near a terminal.
Soil biodiversity and soil community composition determine ecosystem multifunctionality (2014)

Biodiversity loss has become a global concern as evidence accumulates that it will negatively affect ecosystem services on which society depends. So far, most studies have focused on the ecological consequences of above-ground biodiversity loss; yet a large part of Earth's biodiversity is literally hidden below ground. Whether reductions of biodiversity in soil communities below ground have consequences for the overall performance of an ecosystem remains unresolved. It is important to investigate this in view of recent observations that soil biodiversity is declining and that soil communities are changing upon land use intensification. We established soil communities differing in composition and diversity and tested their impact on eight ecosystem functions in model grassland communities. We show that soil biodiversity loss and simplification of soil community composition impair multiple ecosystem functions, including plant diversity, decomposition, nutrient retention, and nutrient cycling. The average response of all measured ecosystem functions (ecosystem multifunctionality) exhibited a strong positive linear relationship to indicators of soil biodiversity, suggesting that soil community composition is a key factor in regulating ecosystem functioning. Our results indicate that changes in soil communities and the loss of soil biodiversity threaten ecosystem multifunctionality and sustainability.
1H NMR-Based Metabolomic Analysis of Liver, Serum, and Brain Following Ethanol Administration in Rats (2007)

Ethanol is a widely used drug that is consumed in large amounts for pharmacologic effects. Elimination of ethanol alters metabolism in the liver and throughout an organism. Ethanol's effect on metabolites can influence the regulation of key pathways such as gluconeogenesis. We adopted a proton NMR-based metabolomic approach to study ethanol-induced metabolic changes in liver, blood, and brain tissue from rats exposed to either a single dose of ethanol or a chronic 4 day binge-ethanol protocol. Both acute and binge ethanol caused (i) decreased glucose, lactate, and alanine in liver and serum; (ii) increased acetate in liver and serum; and (iii) increased acetoacetate in serum. Binge-ethanol increased liver beta-hydroxybutyrate and decreased betaine. Pretreatment with the antioxidant butylated hydroxytoluene (BHT) increased betaine and reduced ethyl glucuronide (EtG) in livers of binge-ethanol animals, as compared to those not pretreated with BHT. We found no change in brain metabolites after a single dose of ethanol. Unsupervised principal component (PC) analysis of spectral data from liver and serum successfully discriminated treatment groups, based largely on the biochemical differences outlined above, confirming the results of manual analysis. To explain the observed lack of gluconeogenesis following ethanol treatment and to resolve apparently discordant results from previous studies, we propose a model in which decreased hepatic alanine removes inhibition on pyruvate kinase, thus permitting a futile cycle that diverts phosphoenolpyruvate away from gluconeogenesis. This is a new mechanism that biochemically elucidates the well-known, yet unexplained, "empty calorie" phenomenon of ethanol. Reduction of EtG by pretreatment with BHT suggests that BHT and perhaps other compounds may alter the pharmacokinetics of EtG so that EtG may not always be a sensitive marker for ethanol abuse.
Antitumor Effects of Nonconjugated Murine Lym-2 and Human-Mouse Chimeric CLL-1 Monoclonal Antibodies Against Various Human Lymphoma Cell Lines In Vitro and In Vivo (1997)

Lym-2 is a murine monoclonal antibody (MoAb) directed towards a human class II molecule variant reactive with both normal and neoplastic human B lymphocytes. Previous studies have shown that signals transmitted by class II molecules that stimulate normal lymphocytes can be inhibitory for B-cell lymphoma growth by signaling activation-induced cell death. Therefore, we sought to evaluate the effects of nonconjugated murine Lym-2 and a human-mouse chimeric Lym-2 (chCLL-1; with murine variable regions and human constant regions) MoAb on the growth of various human lymphomas by using both in vitro and in vivo assays. Cell lines derived from Burkitt's lymphomas, diffuse large cell B-cell lymphomas, anaplastic large-cell lymphomas, and Epstein-Barr virus-induced B-cell lymphomas were incubated with Lym-2 or chCLL-1 in vitro, and effects on proliferation were determined by [3H]-thymidine incorporation. The effects of Lym-2 in vitro were also compared with those of Lym-1, which is a similar MoAb that has been evaluated clinically. After immobilization, which enhances crosslinking of the MoAbs, both Lym-2 and chCLL-1 were capable of directly inhibiting the growth of various lymphoma lines in vitro. These human lymphomas were then transferred into mice with severe combined immunodeficiency to evaluate the efficacy of these MoAbs in vivo. Treatment with either murine Lym-2 or the chimeric chCLL-1 were significantly effective in improving the survival of tumor-bearing mice. These results indicate that stimulation by nonconjugated chCLL-1 may offer a biological approach to the treatment of various human lymphomas.
MicroRNA-30e regulates neuroinflammation in MPTP model of Parkinson’s disease by targeting Nlrp3 (2017)

Accumulating evidences suggest that neuroinflammation is a pathological hallmark of Parkinson's disease (PD), a neurodegenerative disorder characterized by loss of dopaminergic neurons in substantia nigra pars compacta (SNpc). MicroRNAs have been recently recognized as crucial regulators of inflammatory responses. Here, we found significant downregulation of microRNA-30e (miR-30e) in SNpc of MPTP-induced PD mice. Next, we employed miR-30e agomir to upregulate miR-30e expression in MPTP-treated mice. Our results showed that delivery of miR-30e agomir remarkably improved motor behavioral deficits and neuronal activity, and inhibited the loss of dopamine neurons. Moreover, the increased α-synuclein protein expression in SNpc of MPTP-PD mice was alleviated by the upregulation of miR-30e. Further, miR-30e agomir administration also attenuated the marked increase of inflammatory cytokines, such as TNF-α, COX-2, iNOS, and restored the decreased secretion of BDNF in SNpc. In addition, we demonstrated for the first time that miR-30e directly targeted to Nlrp3, thus suppressing Nlrp3 mRNA and protein expression. Finally, miR-30e upregulation significantly inhibited the activation of Nlrp3 inflammasome as evident from the decreased Nlrp3, Caspase-1 and ASC expressions and IL-18 and IL-1β secretions. Taken together, our study demonstrates that miR-30e ameliorates neuroinflammation in the MPTP model of PD by decreasing Nlrp3 inflammasome activity. These findings suggesting that miR30e may be a key inflammation-mediated molecule that could be a potential target for PD therapeutics.
Two distinctly regulated genes are required for ferric reduction, the first step of iron uptake in Saccharomyces cerevisiae. (1994)

Iron uptake in Saccharomyces cerevisiae involves at least two steps: reduction of ferric to ferrous ions extracellularly and transport of the reduced ions through the plasma membrane. We have cloned and molecularly characterized FRE2, a gene which is shown to account, together with FRE1, for the total membrane-associated ferric reductase activity of the cell. Although not similar at the nucleotide level, the two genes encode proteins with significantly similar primary structures and very similar hydrophobicity profiles. The FRE1 and FRE2 proteins are functionally related, having comparable properties as ferric reductases. FRE2 expression, like FRE1 expression, is induced by iron deprivation, and at least part of this control takes place at the transcriptional level, since 156 nucleotides upstream of the initiator AUG conferred iron-dependent regulation when fused to a heterologous gene. However, the two gene products have distinct temporal regulation of their activities during cell growth.
Complete nucleotide sequence of human mammary gland lactoferrin (1990)

Journal Article Complete nucleotide sequence of human mammary gland lactoferrin Get access Michael W. Rey, Michael W. Rey Search for other works by this author on: Oxford Academic PubMed Google Scholar Shelley L. Woloshuk, Shelley L. Woloshuk 1GenePharming Europe B.V., Einsteinweg 5, 2333 CC Leiden, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Herman A. deBoer, Herman A. deBoer 1GenePharming Europe B.V., Einsteinweg 5, 2333 CC Leiden, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Frank R. Pieper Frank R. Pieper * 1GenePharming Europe B.V., Einsteinweg 5, 2333 CC Leiden, The Netherlands *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 17, 11 September 1990, Page 5288, https://doi.org/10.1093/nar/18.17.5288 Published: 11 September 1990 Article history Received: 26 July 1990 Published: 11 September 1990
Blood Flow Imaging by Cine Magnetic Resonance (1986)

A technique for measuring blood flow by whole body nuclear magnetic resonance is described. This method uses imaging gradient profiles that combine even echo rephasing with a field echo sequence to overcome the problem of signal loss from flowing blood. The flow velocity component in any desired direction may be measured by appropriate gradient profile modifications, producing velocity dependent phase shifts that can be displayed by phase mapping. The sequence allows for fast repetition so that flow information may be acquired rapidly from many points in the cardiac cycle and has been used in this mode to observe and measure blood flow in the heart chambers and great vessels. Flow measurements in the femoral artery were also carried out using the same technique; these were compared with similar measurements obtained by Doppler ultrasound. The technique can readily be applied using standard imaging equipment and should prove useful in the clinical assessment of many diseases of the cardiovascular system.
Percutaneous coronary interventions in Europe 1992?2001 (2004)

Interventional cardiology in Europe is still expanding, mainly due to rapid growth in countries with lower socio-economical levels. Most central European countries reported only minor increases in procedures performed. Coronary stenting remains the only noteworthy adjunctive strategy to balloon angioplasty.
Cloning and Overexpression of Glycosyltransferases That Generate the Lipopolysaccharide Core of Rhizobium leguminosarum (1998)

The lipopolysaccharide (LPS) core of the Gram-negative bacterium Rhizobium leguminosarum is more amenable to enzymatic study than that of Escherichia coli because much of it is synthesized from readily available sugar nucleotides. The inner portion of the R. leguminosarum core contains mannose, galactose, and three 3-deoxy-D-manno-octulosonate (Kdo) residues, arranged in the order: lipid A-(Kdo)2-Man-Gal-Kdo-[O antigen]. A mannosyltransferase that uses GDP-mannose and the conserved precursor Kdo2-[4'-32P]lipid IVA (Kadrmas, J. L., Brozek, K. A., and Raetz, C. R. H. (1996) J. Biol. Chem. 271, 32119-32125) is proposed to represent a key early enzyme in R. leguminosarum core assembly. Conditions for demonstrating efficient galactosyl- and distal Kdo-transferase activities are now described using a coupled assay system that starts with GDP-mannose and Kdo2-[4'-32P]lipid IVA. As predicted, mannose incorporation precedes galactose addition, which in turn precedes distal Kdo transfer. LPS core mutants with Tn5 insertions in the genes encoding the putative galactosyltransferase (lpcA) and the distal Kdo-transferase (lpcB) are shown to be defective in the corresponding in vitro glycosylation of Kdo2-[4'-32P]lipid IVA. We have also discovered the new gene (lpcC) that encodes the mannosyltransferase. The gene is separated by several kilobase pairs from the lpcAB cluster. All three glycosyltransferases are carried on cosmid pIJ1848, which contains at least 20 kilobase pairs of R. leguminosarum DNA. Transfer of pIJ1848 into R. meliloti 1021 results in heterologous expression of all three enzymes, which are not normally present in strain 1021. Expression of the lpc genes individually behind the T7 promoter results in the production of each R. leguminosarum glycosyltransferase in E. coli membranes in a catalytically active form, demonstrating that lpcA, lpcB, and lpcC are structural genes.
The role of calcitonin gene‐related peptide in gastric mucosal protection in the rat (1991)

The presence of circulating antibodies to calcitonin gene-related peptide (CGRP) enhanced the damaging effect of ethanol on the rat gastric mucosa. Taken together with previous experimental and morphological data the results suggest that CGRP released from the peripheral terminals of visceral afferent fibres plays a role in mediating gastric mucosal defence mechanisms.
Some chlorinated hydroxyphenoxyacetic acids (1955)

J. P. Brown and E. B. McCall, J. Chem. Soc., 1955, 3681 DOI: 10.1039/JR9550003681
Replication of Norovirus in Cell Culture Reveals a Tropism for Dendritic Cells and Macrophages (2004)

Noroviruses are understudied because these important enteric pathogens have not been cultured to date. We found that the norovirus murine norovirus 1 (MNV-1) infects macrophage-like cells in vivo and replicates in cultured primary dendritic cells and macrophages. MNV-1 growth was inhibited by the interferon-alphabeta receptor and STAT-1, and was associated with extensive rearrangements of intracellular membranes. An amino acid substitution in the capsid protein of serially passaged MNV-1 was associated with virulence attenuation in vivo. This is the first report of replication of a norovirus in cell culture. The capacity of MNV-1 to replicate in a STAT-1-regulated fashion and the unexpected tropism of a norovirus for cells of the hematopoietic lineage provide important insights into norovirus biology.