gebhart/patrepeval huggingface dataset:
Mef2c deletion in osteocytes results in increased bone mass (2011)

Myocyte enhancer factors 2 (MEF2) are required for expression of the osteocyte bone formation inhibitor Sost in vitro, implying these transcription factors in bone biology. Here, we analyzed the in vivo function of Mef2c in osteocytes in male and female mice during skeletal growth and aging. Dmp1-Cre-induced Mef2c deficiency led to progressive decreases in Sost expression by 40% and 70% in femoral cortical bone at 3.5 months and 5 to 6 months of age. From 2 to 3 months onward, bone mass was increased in the appendicular and axial skeleton of Mef2c mutant relative to control mice. Cortical thickness and long bone and vertebral trabecular density were elevated. To assess whether the increased bone mass was related to the decreased Sost expression, we characterized 4-month-old heterozygous Sost-deficient mice. Sost heterozygotes displayed similar increases in long bone mass and density as Mef2c mutants, but the relative increases in axial skeletal parameters were mostly smaller. At the cellular level, bone formation parameters were normal in 3.5-month-old Mef2c mutant mice, whereas bone resorption parameters were significantly decreased. Correspondingly, cortical expression of the anti-osteoclastogenic factor and Wnt/β-catenin target gene osteoprotegerin (OPG) was increased by 70% in Mef2c mutant males. Furthermore, cortical expression of the Wnt signaling modulators Sfrp2 and Sfrp3 was strongly deregulated in both sexes. In contrast, heterozygous Sost deficient males displayed mildly increased osteoblastic mineral apposition rate, but osteoclast surface and cortical expression of osteoclastogenic regulators including OPG were normal and Sfrp2 and Sfrp3 were not significantly changed. Together, our data demonstrate that Mef2c regulates cortical Sfrp2 and Sfrp3 expression and is required to maintain normal Sost expression in vivo. Yet, the increased bone mass phenotype of Mef2c mutants is not directly related to the reduced Sost expression. We identified a novel function for Mef2c in control of adult bone mass by regulation of osteoclastic bone resorption.
Online and off-line handwriting recognition: a comprehensive survey (2000)

Handwriting has continued to persist as a means of communication and recording information in day-to-day life even with the introduction of new technologies. Given its ubiquity in human transactions, machine recognition of handwriting has practical significance, as in reading handwritten notes in a PDA, in postal addresses on envelopes, in amounts in bank checks, in handwritten fields in forms, etc. This overview describes the nature of handwritten language, how it is transduced into electronic data, and the basic concepts behind written language recognition algorithms. Both the online case (which pertains to the availability of trajectory data during writing) and the off-line case (which pertains to scanned images) are considered. Algorithms for preprocessing, character and word recognition, and performance with practical systems are indicated. Other fields of application, like signature verification, writer authentification, handwriting learning tools are also considered.
Targeting the von Hippel–Lindau E3 Ubiquitin Ligase Using Small Molecules To Disrupt the VHL/HIF-1α Interaction (2012)

E3 ubiquitin ligases, which bind protein targets, leading to their ubiquitination and subsequent degradation, are attractive drug targets due to their exquisite substrate specificity. However, the development of small-molecule inhibitors has proven extraordinarily challenging as modulation of E3 ligase activities requires the targeting of protein-protein interactions. Using rational design, we have generated the first small molecule targeting the von Hippel-Lindau protein (VHL), the substrate recognition subunit of an E3 ligase, and an important target in cancer, chronic anemia, and ischemia. We have also obtained the crystal structure of VHL bound to our most potent inhibitor, confirming that the compound mimics the binding mode of the transcription factor HIF-1α, a substrate of VHL. These results have the potential to guide future development of improved lead compounds as therapeutics for the treatment of chronic anemia and ischemia.
Sources of degradation of speech recognition in the telephone network (2002)

We compare speech recognition accuracy for high-quality speech recorded under controlled conditions with speech as it appears over long-distance telephone lines. In addition to comparing recognition accuracy we use telephone-channel simulation to identify the sources of degradation of speech over telephone lines that have the greatest impact on speech recognition accuracy. We first compare the performance of the CMU SPHINX-I system on the TIMIT and NTIMIT databases. We found that other factors beyond a mere decrease in bandwidth cause the observed degradation in recognition accuracy, and that the environmental compensation algorithms RASTA and CDCN fail to compensate completely for degradations introduced by the telephone network. We identify the most problematic telephone-channel impairments using a commercial telephone channel simulator and the SPHINX-II system. Of the various effects considered, additive noise and linear filtering appear to have the greatest impact on recognition accuracy. Finally, we examined the performance of three cepstral compensation algorithms in the presence of the most damaging conditions. We found the compensation algorithms to be effective except for the worst 1% of the telephone channels.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Overexpression of c-Myc inhibits p21WAF1/CIP1 expression and induces S-phase entry in 12-O-tetradecanoylphorbol-13-acetate (TPA)-sensitive human cancer cells. (1999)

The c-Myc oncoprotein is a transcription factor involved in cellular transformation. We previously found (M. V. Blagosklonny, et al., Cancer Res., 57: 320-325, 1997) that exposure of human SkBr3 breast cancer and LNCaP prostate cancer cells to 12-O-tetradecanoylphorbol-13-acetate (TPA) led to a growth arrest associated with the up-regulation of the cyclin-dependent kinase inhibitor p21(WAF1/cIP1) and the inhibition of c-Myc expression. We show here that exogenous c-Myc inhibits p21 expression in SkBr3 and LNCaP cells induced to enter into S-phase. p27 expression was not increased from basal levels in TPA-treated growth-arrested cells. A time course after infection of TPA-arrested cells using a c-Myc-expressing adenovirus revealed that the inhibition of p21 expression preceded entry into S-phase. In contrast, after infection by E2F-1-expressing adenovirus, p21 expression was reduced after the cells entered S-phase. Overexpression of c-Myc reduced the levels of endogenous p21 mRNA, and transfection of c-Myc repressed p21-promoter luciferase-reporter gene expression. The results suggest that the down-regulation of p21 expression may contribute to c-Myc-dependent entry into S-phase, possibly in situations in which growth arrest is associated with increased p21 expression.
Putative role of γ ‐aminobutyric acid (GABA) as a long‐distance signal in up‐regulation of nitrate uptake in Brassica napus L. (2004)

ABSTRACT The relationship between nitrate influx, BnNrt2 nitrate transporter gene expression and amino acid composition of phloem exudate was investigated during N‐deprivation (short‐term experiment) and over a growth cycle (long‐term experiment) in Brassica napus L. The data showed a positive correlation between γ ‐aminobutyric acid (GABA) in phloem exudate and nitrate uptake in the short‐ and the long‐term experiments. The hypothesis that this non‐protein amino acid could up‐regulate nitrate uptake via a long‐distance signalling pathway was tested by providing an exogenous GABA supply to the roots. The effect of GABA was compared with the effects of Gln, Glu and Asn, each known to be inhibitors of nitrate uptake. The results showed that GABA treatment induced a significant increase of BnNrt2 mRNA expression, but had less effect on nitrate influx. By contrast, Gln, Glu and Asn significantly reduced nitrate influx and BnNrt2 mRNA expression compared with the control plants. This study provides the first evidence that GABA may act as a putative long‐distance inter‐organ signal molecule in plants in conjunction with negative control exerted by Gln. The up‐regulation effect of GABA on nitrate uptake is discussed in the context of its role in N metabolism, nutritional stress and the recent discovery of a putative role of GABA as a signal molecule in plant development.
Cell-Free Co-Translational Approaches for Producing Mammalian Receptors: Expanding the Cell-Free Expression Toolbox Using Nanolipoproteins (2019)

Membranes proteins make up more than 60% of current drug targets and account for approximately 30% or more of the cellular proteome. Access to this important class of proteins has been difficult due to their inherent insolubility and tendency to aggregate in aqueous solutions. Understanding membrane protein structure and function demands novel means of membrane protein production that preserve both their native conformational state as well as function. Over the last decade, cell-free expression systems have emerged as an important complement to cell-based expression of membrane proteins due to their simple and customizable experimental parameters. One approach to overcome the solubility and stability limitations of purified membrane proteins is to support them in stable, native-like states within nanolipoprotein particles (NLPs), aka nanodiscs. This has become common practice to facilitate biochemical and biophysical characterization of proteins of interest. NLP technology can be easily coupled with cell-free systems to achieve functional membrane protein production for this purpose. Our approach involves utilizing cell-free expression systems in the presence of NLPs or using co-translation techniques to perform one-pot expression and self-assembly of membrane protein/NLP complexes. We describe how cell-free reactions can be modified to render control over nanoparticle size and monodispersity in support of membrane protein production. These modifications have been exploited to facilitate co-expression of full-length functional membrane proteins such as G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). In particular, we summarize the state of the art in NLP-assisted cell-free coexpression of these important classes of membrane proteins as well as evaluate the advances in and prospects for this technology that will drive drug discovery against these targets. We conclude with a prospective on the use of NLPs to produce as well as deliver functional mammalian membrane-bound proteins for a range of applications.
CIC inactivating mutations identify aggressive subset of 1p19q codeleted gliomas (2015)

CIC mutations result in protein inactivation with upregulation of CIC target genes, activation of proliferative pathways, inhibition of differentiation, and poorer outcome in patients with a 1p19q codeleted glioma.
Dynamic Cell and Microparticle Control via Optoelectronic Tweezers (2007)

This paper reports on cell and microparticle manipulation using optically induced dielectrophoresis. Our novel optoelectronic tweezers (OET) device enables optically controlled trapping, transportation, and sorting via dielectrophoretic forces. By integrating a spatial light modulator and using direct imaging, arbitrary dynamic manipulation patterns are obtained. Here, we demonstrate manipulation functions, including particle collectors, single-particle traps, individually addressable single-particle arrays, light-defined particle channels, and size-based particle sorting. OET-induced particle manipulation velocities are analyzed as a function of the applied voltage, optical pattern linewidth, and single-particle trap dimensions.
Synthesis Of 2-Acyltetrahydro-β-Carbolines By An Intramolecular α-Amidoalkylation Reaction (1999)

Abstract 2-Acyltetrahydro-β-carbolines 7 have been obtained by cyclization of adducts 5 from imines 3 of tryptamine 1 and aldehydes 2 with acyl chlorides 4 as a result of an intramolecular a-amidoalkylation reaction in the presence of bases as N,N-dimethylaniline or Et3N.
Cytotoxic Glycosides from Albizia julibrissin (1997)

During the course of a study of leguminous plants, cytotoxicity was demonstrated by the crude saponin fraction of Albizia julibrissin. Following chromatographic purification, the structures of three novel saponins, julibrosides I-III (1-3), inclusive of a cytotoxic principle, were elucidated. A comparison of the cytotoxicity of julibrosides (1-3) and their prosapogenins (4-15) prepared by alkaline hydrolysis clearly indicated that both an alpha-L-arabinofuranosyl-(1-->4)-[beta-D-glucopyranosyl-(1-->3)]-alpha- L-rhamnopyranosyl-(1-->2)-beta-D-glucopyranosyl ester unit and a monoterpene-quinovopyranosyl moiety are crucial substituents for cytotoxicity among this class of compounds. The hydroxy group at C-16 of aglycon may play an important role in mediating cytotoxicity, and the N-acetyl-glucosamine moiety at C-3 seems to enhance activity because 3 showed the strongest cytotoxicity.
Genomic organization of the selectin family of leukocyte adhesion molecules on human and mouse chromosome 1. (1990)

A structurally and functionally related group of genes, lymph node homing receptor (LHR), granule membrane protein 140 (GMP-140), and endothelial leukocyte adhesion molecule 1 (ELAM-1) are shown to constitute a gene cluster on mouse and human chromosome 1. In situ hybridization mapped GMP-140 to human chromosome 1 bands 21-24 consistent with chromosomal localization of LHR. Gene linkage analysis in the mouse indicated that these genes and serum coagulation factor V (FV) all map to a region of distal mouse chromosome 1 that is syntenic with human chromosome 1, with no crossovers identified between these four genes in 428 meiotic events. Moreover, long range restriction site mapping demonstrated that these genes map to within 300 kb in both the human and mouse genomes. These data suggest that LHR, ELAM-1, and GMP-140 comprise an adhesion protein family, the selectins, that arose by multiple gene duplication events before divergence of mouse and human. Furthermore, the location of these genes on mouse and human chromosome 1 is consistent with a close evolutionary relationship to the complement receptor-related genes, which also are positioned on the same chromosomes in both species and with which these genes share a region of sequence homology. These data characterize the organization of a genomic region that may be critical for intercellular communication within the immune system.
Sterilization by dry heat (1961)

The advantages and disadvantages of three forms of dry heat sterilization are discussed. In addition a fourth method, consisting of heating by infrared rays in vacuo, is described. This method is particularly suitable for instruments used in the operating theatre, since it can replace an autoclave where a supply of steam is not available. Recommended times and temperatures for dry heat sterilization are detailed, and are related to the thermal death point of Cl. tetani. The dangers of recontamination during the cooling process are discussed.
Mechanisms for induction of acquired host immunity by neutrophil peptide defensins (1999)

Human neutrophil peptide (HNP) defensins were studied to determine their potential effects on adaptive mucosal immunity. Intranasal delivery of HNPs plus ovalbumin (OVA) enhanced OVA-specific serum IgG antibody (Ab) responses. However, OVA-specific IgA Abs were not induced in mucosal secretions or in serum. CD4(+) T cells of intranasally immunized mice displayed higher OVA-specific proliferative responses and elevated production of interferon gamma, interleukin (IL) 5, IL-6, and IL-10 when compared with control groups receiving OVA alone. In vitro, HNPs also enhanced both proliferative responses and T helper (Th) cytokine secretion profiles of CD3epsilon-stimulated spleen- and Peyer's patch-derived naive CD4(+) T cells. HNPs modulated the expression of costimulatory molecules by lipopolysaccharide- or CD3epsilon-stimulated splenic and Peyer's patch B or T cell populations, respectively. These studies show that defensins enhance systemic IgG, but not IgA, Ab responses through help provided by CD4(+) Th1- and Th2-type cytokines and foster B and T cell interactions to link innate immunity with the adaptive immune system.
Culture-Negative Endocarditis Probably Due to Chlamydia pneumoniae (1990)

Journal Article Culture-Negative Endocarditis Probably Due to Chlamydia pneumoniae Get access Thomas J. Marrie, Thomas J. Marrie Reprints and correspondence: Dr. Thomas 1. Marrie, Room 4090 A.C.C., Victoria General Hospital, 1278 Tower Rd., Halifax, NS, Canada B3H 2Y9 Search for other works by this author on: Oxford Academic PubMed Google Scholar Martha Harczy, Martha Harczy Search for other works by this author on: Oxford Academic PubMed Google Scholar O. Elizabeth Mann, O. Elizabeth Mann Search for other works by this author on: Oxford Academic PubMed Google Scholar Roderick W. Landymore, Roderick W. Landymore Search for other works by this author on: Oxford Academic PubMed Google Scholar A. Raza, A. Raza Search for other works by this author on: Oxford Academic PubMed Google Scholar San-pin Wang, San-pin Wang Search for other works by this author on: Oxford Academic PubMed Google Scholar J. Thomas Grayston J. Thomas Grayston Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 161, Issue 1, January 1990, Pages 127–129, https://doi.org/10.1093/infdis/161.1.127 Published: 01 January 1990 Article history Received: 04 May 1989 Revision received: 21 July 1989 Published: 01 January 1990
Mammalian cytidine 5′-monophosphate N -acetylneuraminic acid synthetase: A nuclear protein with evolutionarily conserved structural motifs (1998)

Sialic acids of cell surface glycoproteins and glycolipids play a pivotal role in the structure and function of animal tissues. The pattern of cell surface sialylation is species- and tissue-specific, is highly regulated during embryonic development, and changes with stages of differentiation. A prerequisite for the synthesis of sialylated glycoconjugates is the activated sugar-nucleotide cytidine 5'-monophosphate N-acetylneuraminic acid (CMP-Neu5Ac), which provides a substrate for Golgi sialyltransferases. Although a mammalian enzymatic activity responsible for the synthesis of CMP-Neu5Ac has been described and the enzyme has been purified to near homogeneity, sequence information is restricted to bacterial CMP-Neu5Ac synthetases. In this paper, we describe the molecular characterization, functional expression, and subcellular localization of murine CMP-Neu5Ac synthetase. Cloning was achieved by complementation of the Chinese hamster ovary lec32 mutation that causes a deficiency in CMP-Neu5Ac synthetase activity. A murine cDNA encoding a protein of 432 amino acids rescued the lec32 mutation and also caused polysialic acid to be expressed in the capsule of the CMP-Neu5Ac synthetase negative Escherichia coli mutant EV5. Three potential nuclear localization signals were found in the murine synthetase, and immunofluorescence studies confirmed predominantly nuclear localization of an N-terminally Flag-tagged molecule. Four stretches of amino acids that occur in the N-terminal region are highly conserved in bacterial CMP-Neu5Ac synthetases, providing evidence for an ancestral relationship between the sialylation pathways of bacterial and animal cells.
Rapid Extraction of Genomic DNA from Medically Important Yeasts and Filamentous Fungi by High-Speed Cell Disruption (1998)

Current methods of DNA extraction from different fungal pathogens are often time-consuming and require the use of toxic chemicals. DNA isolation from some fungal organisms is difficult due to cell walls or capsules that are not readily susceptible to lysis. We therefore investigated a new and rapid DNA isolation method using high-speed cell disruption (HSCD) incorporating chaotropic reagents and lysing matrices in comparison to standard phenol-chloroform (PC) extraction protocols for isolation of DNA from three medically important yeasts (Candida albicans, Cryptococcus neoformans, and Trichosporon beigelii) and two filamentous fungi (Aspergillus fumigatus and Fusarium solani). Additional extractions by HSCD were performed on Saccharomyces cerevisiae, Pseudallescheria boydii, and Rhizopus arrhizus. Two different inocula (10(8) and 10(7) CFU) were compared for optimization of obtained yields. The entire extraction procedure was performed on as many as 12 samples within 1 h compared to 6 h for PC extraction. In comparison to the PC procedure, HSCD DNA extraction demonstrated significantly greater yields for 10(8) CFU of C. albicans, T. beigelii, A. fumigatus, and F. solani (P < or = 0.005), 10(7) CFU of C. neoformans (P < or = 0.05), and 10(7) CFU of A. fumigatus (P < or = 0.01). Yields were within the same range for 10(8) CFU of C. neoformans and l0(7) CFU of C. albicans for both HSCD extraction and PC extraction. For 10(7) CFU of T. beigelii, PC extraction resulted in a greater yield than did HSCD (P < or = 0.05). Yields obtained from 10(8) and 10(7) CFU were significantly greater for filamentous fungi than for yeasts by the HSCD extraction procedure (P < 0.0001). By the PC extraction procedure, differences were not significant. For all eight organisms, the rapid extraction procedure resulted in good yield, integrity, and quality of DNA as demonstrated by restriction fragment length polymorphism, PCR, and random amplified polymorphic DNA. We conclude that mechanical disruption of fungal cells by HSCD is a safe, rapid, and efficient procedure for extracting genomic DNA from medically important yeasts and especially from filamentous fungi.
A novel monoclonal antibody (FUN‐1) identifies an activation antigen in cells of the B‐cell lineage and Reed—Sternberg cells (1993)

The characterization of a new monoclonal antibody (MoAb) recognizing a human B-cell activation antigen, designated FUN-1, is described in this paper. Immunoprecipitation revealed that FUN-1 recognizes an antigen with a molecular weight (MW) of 75kD. FUN-1 reacts with pokeweed mitogen-activated B lymphocytes and monocytes of peripheral blood, but not with unstimulated lymphocytes or granulocytes. It also reacts with large lymphoid cells in germinal centres, Epstein-Barr virus-transformed B cell lines, large B-cell lymphomas, Ki-1-positive anaplastic large-cell lymphomas, and Reed-Sternberg cells of Hodgkin's disease, but not with Concanavalin A-activated T cells, acute lymphoblastic leukaemias, T-cell lymphomas, or low-grade B-cell leukaemias. These findings indicate that FUN-1 recognizes a previously unreported B-cell activation antigen. This MoAb appears to be useful for the study of maturation and differentiation in the B-cell lineage as well as for the immunohistochemical diagnosis of B-cell lymphomas and Hodgkin's disease.
New and Convergent Synthesis of Osimertinib (2017)

New and convergent synthetic route of osimertinib is described on a dozen of grams scale. A key cyclization of 1‐(4‐((2‐(dimethylamino)ethyl)(methyl)amino)‐2‐methoxy‐5‐nitrophenyl)guanidine and 3‐(dimethylamino)‐1‐(1‐methyl‐1 H ‐indol‐3‐yl)prop‐2‐en‐1‐one is adopted to give the 4‐(1 H ‐indol‐3‐yl)‐ N ‐phenylpyrimidin‐2‐amine structure. Osimertinib is prepared in 40.4% yield over six steps and 99.1% purity (HPLC). Purification methods of the intermediates involved in the route are also given.
Selective reduction and recovery of invariant Valpha24JalphaQ T cell receptor T cells in correlation with disease activity in patients with systemic lupus erythematosus. (2001)

The selective reduction of DN invariant Valpha24JalphaQ T cells is related to the disease progression of SLE, while DN TCR Valpha24 T cells other than Valpha24JalphaQ T cells constitute autoaggressive T cells in SLE.