gebhart/patrepeval huggingface dataset:
Rapid creation of Arabidopsis doubled haploid lines for quantitative trait locus mapping (2012)

Quantitative trait loci (QTL) mapping is a powerful tool for investigating the genetic basis of natural variation. QTL can be mapped using a number of different population designs, but recombinant inbred lines (RILs) are among the most effective. Unfortunately, homozygous RIL populations are time consuming to construct, typically requiring at least six generations of selfing starting from a heterozygous F(1). Haploid plants produced from an F(1) combine the two parental genomes and have only one allele at every locus. Converting these sterile haploids into fertile diploids (termed "doubled haploids," DHs) produces immortal homozygous lines in only two steps. Here we describe a unique technique for rapidly creating recombinant doubled haploid populations in Arabidopsis thaliana: centromere-mediated genome elimination. We generated a population of 238 doubled haploid lines that combine two parental genomes and genotyped them by reduced representation Illumina sequencing. The recombination rate and parental allele frequencies in our population are similar to those found in existing RIL sets. We phenotyped this population for traits related to flowering time and for petiole length and successfully mapped QTL controlling each trait. Our work demonstrates that doubled haploid populations offer a rapid, easy alternative to RILs for Arabidopsis genetic analysis.
Peripheral blood stem cells: In vivo biology and therapeutic potential (1994)

Peripheral blood stem cells (PBSC) have been studied for their use after high-dose chemotherapy. The combination of a standard-dose chemotherapy [VIP: VP16 (etoposide), ifosfamide, cisplatin] in combination with hematopoietic growth factors was shown to provide effective anti-cancer activity as well as to enable sufficient stem cell mobilization for clinical use. Different growth factor regimens [granulocyte-colony-stimulating factor (G-CSF), granulocyte-macrophage (GM)-CSF, interleukin (IL)-3/GM-CSF] resulted in a differential induction of high levels of circulating PBSC after VIP chemotherapy, with the sequential combination of IL-3 and GM-CSF inducing maximal numbers of CD34+ cells as well as clonogenic progenitors. Our studies revealed a correlation between prior treatment and PBSC recruitment: the highest numbers of PBSC were mobilized in untreated patients whereas stem cell harvest was considerably impeded in heavily pretreated patients. Phase I/II trials demonstrated that transplantation of PBSC collected after VIP plus growth factor mobilization was safe, and engraftment was rapid and sustained. However, PBSC mobilization carried the risk of concomitant tumor cell recruitment in patients with detectable levels of tumor cells prior to therapy and in 21% of patients without circulating tumor cells. Positive selection of CD34+ cells by immunoadsorption that leads to an approximately three-log depletion of contaminating tumor cells therefore was investigated with regard to feasibility and capability as a source for PBSC transplantation. Twenty-one patients with advanced malignancies received autologous CD34+ cell transplantation after high-dose chemotherapy. Hematological recovery was as rapid as recorded for unseparated PBSC preparations, indicating that CD34+ cells can be safely used for autologous PBSC transplantation.(ABSTRACT TRUNCATED AT 250 WORDS)
Synthesis of 2′,3′-didehydro-2′,3′-dideoxy-2′-fluoro apionucleosides as potential antiviral agents (2002)

Synthesis of novel 2′,3′-didehydro-2′,3′-dideoxy-2′-fluoro apionucleosides which combine the properties of 2′,3′-didehydro-2′,3′-dideoxy nucleosides and apionucleosides on the basis of a bioisosteric rationale is described.
New STIFF-FLOP module construction idea for improved actuation and sensing (2015)

MRI compatibility, which often is a requirement for the new medical soft robot projects, greatly reduces available actuation methods and sensors. An example of such project is STIFF-FLOP, which aims to develop a soft silicone manipulator actuated by pressure. The current arm construction and method of actuation cause several undesirable effects, which pose problems for actuation and sensing. In this paper, the authors identify the source of those negative effects and propose improvements over the current construction to eliminate or limit their influence. The new construction concept is tested and compared with the current one. Possible ideas for further development are also proposed.
Is PM1 similar to PM2.5? A new insight into the association of PM1 and PM2.5 with children’s lung function (2020)

Experimental data suggests that PM<sub>1</sub> is more toxic than PM<sub>2.5</sub> although the epidemiologic evidence suggests that the health associations are similar. However, few objective exposure data are available to compare the associations of PM<sub>1</sub> and PM<sub>2.5</sub> with children lung function. Our objectives are a) to evaluate associations between long-term exposure to PM<sub>1</sub>, PM<sub>2.5</sub> and children's lung function, and b) to compare the associations between PM<sub>1</sub> and PM<sub>2.5</sub>. From 2012 to 2013, we enrolled 6,740 children (7-14 years), randomly recruited from primary and middle schools located in seven cities in northeast China. We measured lung function including forced vital capacity (FVC), forced expiratory volume in 1 s (FEV1), peak expiratory flow (PEF), and maximal mid-expiratory flow (MMEF) utilizing two portable electronic spirometers. We dichotomized continuous lung function measures according the expected values for gender and age. The spatial resolution at which PM<sub>1</sub> and PM<sub>2.5</sub> estimated were estimated using a machine learning method and the temporal average concentrations were averaged from 2009 to 2012. A multilevel regression model was used to estimate the associations of PM<sub>1</sub>, PM<sub>2.5</sub> exposure and lung function measures, adjusted for confounding factors. Associations with lower lung function were consistently larger for PM<sub>1</sub> than for PM<sub>2.5</sub>. Adjusted odds ratios (OR) per interquartile range greater PM<sub>1</sub> ranged from 1.53 for MMEF (95% confidence interval [CI]: 1.20-1.96) to 2.14 for FEV1 (95% CI: 1.66-2.76) and ORs for PM<sub>2.5</sub> ranged from 1.36 for MMEF (95%CI: 1.12-1.66) to 1.82 for FEV1 (95%CI: 1.49-2.22), respectively. PM<sub>1</sub> and PM<sub>2.5</sub> had significant associations with FVC and FEV1 in primary school children, and on PEF and MMEF in middle school children. Long-term PM<sub>1</sub> and PM<sub>2.5</sub> exposure can lead to decreased lung function in children, and the associations of PM<sub>1</sub> are stronger than PM<sub>2.5</sub>. Therefore, PM<sub>1</sub> may be more hazardous to children's respiratory health than PM<sub>2.5</sub> exposure.
High-throughput construction method for expression vector of peptides for NMR study suited for isotopic labeling (2004)

Fusion protein constructs for labeled peptides were generated with the 114 amino acid thioredoxin (TRX), coupled with the incorporation of a histidine tag for affinity purification. Two tandem AhdI sites were designed in the multiple cloning site of the fusion vector according to our novel unidirectional TA cloning methodology named PRESAT-vector, allowing one-step background-free cloning of DNA fragments. Constructs were designed to incorporate the four residue sequence Ile-Asp-Gly-Arg to generate pure peptides following Factor Xa cleavage of the fusion protein. The system is efficient and cost-effective for isotopic labeling of peptides for heteronuclear NMR studies. Seven peptides of varying length, including pituitary adenylate cyclase activating polypeptide (PACAP), vasoactive intestinal peptide (VIP) and ubiquitin interacting motif (UIM), were expressed using this TRX fusion system to give soluble fusion protein constructs in all cases. Three alternative methods for the preparation of DNA fragments were applied depending on the length of the peptides, such as polymerase chain reaction, chemical synthesis or a 'semi-synthetic method', which is a combination of chemical synthesis and enzymatic extension. The ability easily to construct, express and purify recombinant peptides in a high-throughput manner will be of enormous benefit in areas of biomedical research and drug discovery.
Optical Control of Insulin Secretion Using an Incretin Switch (2015)

Incretin mimetics are set to become a mainstay of type 2 diabetes treatment. By acting on the pancreas and brain, they potentiate insulin secretion and induce weight loss to preserve normoglycemia. Despite this, incretin therapy has been associated with off-target effects, including nausea and gastrointestinal disturbance. A novel photoswitchable incretin mimetic based upon the specific glucagon-like peptide-1 receptor (GLP-1R) agonist liraglutide was designed, synthesized, and tested. This peptidic compound, termed LirAzo, possesses an azobenzene photoresponsive element, affording isomer-biased GLP-1R signaling as a result of differential activation of second messenger pathways in response to light. While the trans isomer primarily engages calcium influx, the cis isomer favors cAMP generation. LirAzo thus allows optical control of insulin secretion and cell survival.
Activation of serum- and glucocorticoid-regulated protein kinase by agonists that activate phosphatidylinositide 3-kinase is mediated by 3-phosphoinositide-dependent protein kinase-1 (PDK1) and PDK2 (1999)

The PtdIns(3,4,5)P3-dependent activation of protein kinase B (PKB) by 3-phosphoinositide-dependent protein kinases-1 and -2 (PDK1 and PDK2 respectively) is a key event in mediating the effects of signals that activate PtdIns 3-kinase. The catalytic domain of serum- and glucocorticoid-regulated protein kinase (SGK) is 54% identical with that of PKB and, although lacking the PtdIns(3,4, 5)P3-binding pleckstrin-homology domain, SGK retains the residues that are phosphorylated by PDK1 and PDK2, which are Thr256 and Ser422 in SGK. Here we show that PDK1 activates SGK in vitro by phosphorylating Thr256. We also show that, in response to insulin-like growth factor-1 (IGF-1) or hydrogen peroxide, transfected SGK is activated in 293 cells via a PtdIns 3-kinase-dependent pathway that involves the phosphorylation of Thr256 and Ser422. The activation of SGK by PDK1 in vitro is unaffected by PtdIns(3,4,5)P3, abolished by the mutation of Ser422 to Ala, and greatly potentiated by mutation of Ser422 to Asp (although this mutation does not activate SGK itself). Consistent with these findings, the Ser422Asp mutant of SGK is activated by phosphorylation (probably at Thr256) in unstimulated 293 cells, and activation is unaffected by inhibitors of PtdIns 3-kinase. Our results are consistent with a model in which activation of SGK by IGF-1 or hydrogen peroxide is initiated by a PtdIns(3,4, 5)P3-dependent activation of PDK2, which phosphorylates Ser422. This is followed by the PtdIns(3,4,5)P3-independent phosphorylation at Thr256 that activates SGK, and is catalysed by PDK1. Like PKB, SGK preferentially phosphorylates serine and threonine residues that lie in Arg-Xaa-Arg-Xaa-Xaa-Ser/Thr motifs, and SGK and PKB inactivate glycogen synthase kinase-3 similarly in vitro and in co-transfection experiments. These findings raise the possibility that some physiological roles ascribed to PKB on the basis of the overexpression of constitutively active PKB mutants might be mediated by SGK.
Affinity purification of antibodies using antigens immobilized on solid supports (1988)

Conference Article| April 01 1988 Affinity purification of antibodies using antigens immobilized on solid supports PAUL A. FISHER; PAUL A. FISHER 1Department of Pharmacological Sciences, Health Sciences Center, State University of New York at Stony Brook, Stony Brook, NY 11794, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar DAVID E. SMITH DAVID E. SMITH 1Department of Pharmacological Sciences, Health Sciences Center, State University of New York at Stony Brook, Stony Brook, NY 11794, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1988) 16 (2): 134–138. https://doi.org/10.1042/bst0160134 Article history Received: October 10 1987 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation PAUL A. FISHER, DAVID E. SMITH; Affinity purification of antibodies using antigens immobilized on solid supports. Biochem Soc Trans 1 April 1988; 16 (2): 134–138. doi: https://doi.org/10.1042/bst0160134 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: SDS/PAGE, SDS/polyacrylamide gel electrophoresis, CNBr, cyanogen bromide This content is only available as a PDF. © 1988 Biochemical Society1988 Article PDF first page preview Close Modal You do not currently have access to this content.
Promyelocytic Leukemia Protein Mediates Interferon-Based Anti-Herpes Simplex Virus 1 Effects (2003)

Herpes simplex virus (HSV) 1 disaggregates the nuclear domain 10 (ND10) nuclear structures and disperses its organizing promyelocytic leukemia protein (PML). An earlier report showed that ectopic overexpression of PML precludes the disaggregation of ND10 but has no effect on viral replication. PML has been reported to mediate the effects of interferon (IFN) and viral mutants lacking ICP0 (Delta alpha 0 mutants). To test the hypothesis that HSV disaggregates ND10 structures and disperses PML to preclude IFN-mediated antiviral effects, we tested the accumulation of viral proteins and virus yields from murine PML(+/+) and PML(-/-) cells mock treated or exposed to IFN-alpha, IFN-gamma, or both and infected with the wild-type or Delta alpha 0 mutant virus. We report the following results. (i) The levels of growth of wild-type and mutant viruses and of accumulation of viral proteins were not significantly different in untreated PML(+/+) and PML(-/-) cells. (ii) Major effects of IFN-alpha and -gamma were observed in PML(+/+) cells infected with the Delta alpha 0 mutant virus, and more minor effects were observed in cells infected with the wild-type virus. The effects of the IFNs on either wild-type or the mutant virus in PML(-/-) cells were minimal. (iii) The mixture of IFN-alpha and -gamma was more effective than either IFN alone, but again, the effect was more drastic in PML(+/+) cells than in PML(-/-) cells. We concluded that the anti-HSV state induced by exogenous IFN is mediated by PML and that the virus targets the ND10 structures and disseminates PML in order to preclude the establishment of the antiviral state induced by IFNs.
QTc Interval Screening in Methadone Treatment (2009)

Expert panel members reviewed and discussed the following sources regarding methadone: pertinent English-language literature identified from MEDLINE and EMBASE searches (1966 to June 2008), national substance abuse guidelines from the United States and other countries, information from regulatory authorities, and physician awareness of adverse cardiac effects. RECOMMENDATION 1 (DISCLOSURE): Clinicians should inform patients of arrhythmia risk when they prescribe methadone. RECOMMENDATION 2 (CLINICAL HISTORY): Clinicians should ask patients about any history of structural heart disease, arrhythmia, and syncope. RECOMMENDATION 3 (SCREENING): Obtain a pretreatment electrocardiogram for all patients to measure the QTc interval and a follow-up electrocardiogram within 30 days and annually. Additional electrocardiography is recommended if the methadone dosage exceeds 100 mg/d or if patients have unexplained syncope or seizures. RECOMMENDATION 4 (RISK STRATIFICATION): If the QTc interval is greater than 450 ms but less than 500 ms, discuss the potential risks and benefits with patients and monitor them more frequently. If the QTc interval exceeds 500 ms, consider discontinuing or reducing the methadone dose; eliminating contributing factors, such as drugs that promote hypokalemia; or using an alternative therapy. RECOMMENDATION 5 (DRUG INTERACTIONS): Clinicians should be aware of interactions between methadone and other drugs that possess QT interval-prolonging properties or slow the elimination of methadone.
Fast model predictive control of sheet and film processes (2000)

Sheet and film processes are prevalent in the chemical and pulp and paper industries, and include paper coating, polymer film extrusion, and papermaking. A model predictive control algorithm is developed which is based on an off-line singular value decomposition of the plant. The input constraints are approximated by an ellipsoid whose size is optimized online to reduce conservatism. The controller has a structure proven to be robust to model inaccuracies and is computationally efficient enough for real-time implementation on large scale sheet and film processes (e.g., manipulated variable settings computed for 200 actuators in less than ten CPU seconds). The algorithm is applied to a paper machine model constructed from industrial data.
[The antiepileptic effects of sodium valproate and the calcium antagonist riodipine when used jointly in a model of focal penicillin-induced epileptic activity]. (1992)

In experiments on 52 freely moving Wistar male rats, 200-220 g in weight, on the model of focal penicillin-induced epileptic activity (EpA) in brain cortex the efficacy of combined application of drugs influencing different mechanisms of epileptogenesis: sodium valproate enhancing GABA-ergic processes, and the calcium antagonist ryodipine (1,4-dihydropyridine) have been studied. It was shown that valproate and ryodipine when used in combination at relatively small doses (150 and 0.8 mg/kg l.p., respectively) produced a more marked antiepileptic effect than each of these drugs given alone. These and previously reported results of studies on the model of generalized pentylenetetrazol-induced EpA, suggest that complex pathogenic therapy (CPT) as a combination of the antiepileptic drugs acting on the corresponding basic pathogenic mechanisms of respective form of epilepsy is reasonable to be used. CPT allows to obtain a better curative effect with a lower dose of each drug used and to reduce the risk of side effects of the drugs applied at large doses in case of monotherapy.
Synthesis of substituted thieno[2,3‐b]pyrroles (1974)

Abstract A relatively simple route for synthesis of substituted thieno[2,3‐ b ]pyrroles from readily available starting material and data for structural assignment are reported.
Association of ABCB1/MDR1 and OPRM1 Gene Polymorphisms With Morphine Pain Relief (2007)

The pharmacokinetics and pharmacodynamics of morphine are under the control of several polymorphic genes, which can account for part of the observed interindividual variation in pain relief. We focused on two such genes: ABCB1/MDR1, a major determinant of morphine bioavailability, and OPRM1, which encodes for the mu-opioid receptor, the primary site of action for morphine. One hundred and forty-five patients of Italian origin undergoing morphine therapy were genotyped for the single-nucleotide polymorphism (SNP) C3435T of ABCB1/MDR1 and for the A80G SNP of OPRM1. Pain relief variability was significantly (P<0.0001) associated with both polymorphisms. Combining the extreme genotypes of both genes, the association between patient polymorphism and pain relief improved (P<0.00001), allowing the detection of three groups: strong responders, responders, and non-responders, with sensitivity close to 100% and specificity more than 70%. This study provides a good example of the possible clinical use of pharmacogenetics.
Group sparsity for mimo speech dereverberation (2015)

Reverberation can severely affect the speech signals recorded in a room, possibly leading to a significantly reduced speech quality and intelligibility. In this paper we present a batch algorithm employing a signal model based on multi-channel linear prediction in the short-time Fourier transform domain. Aiming to achieve multiple-input multiple-output (MIMO) speech dereverberation in a blind manner, we propose a cost function based on the concept of group sparsity. To minimize the obtained nonconvex function, an iteratively reweighted least-squares procedure is used. Moreover, it can be shown that the derived algorithm generalizes several existing speech dereverberation algorithms. Experimental results for several acoustic systems demonstrate the effectiveness of nonconvex sparsity-promoting cost functions in the context of dereverberation.
Plant compounds insecticide activity against Coleoptera pests of stored products (2007)

The objective of this work was to screen plants with insecticide activity, in order to isolate, identify and assess the bioactivity of insecticide compounds present in these plants, against Coleoptera pests of stored products: Oryzaephilus surinamensis L. (Silvanidae), Rhyzopertha dominica F. (Bostrichidae) and Sitophilus zeamais Mots. (Curculionidae). The plant species used were: basil (Ocimum selloi Benth.), rue (Ruta graveolens L.), lion's ear (Leonotis nepetifolia (L.) R.Br.), jimson weed (Datura stramonium L.), baleeira herb (Cordia verbenacea L.), mint (Mentha piperita L.), wild balsam apple (Mormodica charantia L.), and billy goat weed or mentrasto (Ageratum conyzoides L.). The insecticide activity of hexane and ethanol extracts from those plants on R. dominica was evaluated. Among them, only hexane extract of A. conyzoides showed insecticide activity; the hexane extract of this species was successively fractionated by silica gel column chromatography, for isolation and purification of the active compounds. Compounds 5,6,7,8,3',4',5'-heptamethoxyflavone; 5,6,7,8,3'-pentamethoxy-4',5'-methilenedioxyflavone and coumarin were identified. However, only coumarin showed insecticide activity against three insect pests (LD50 from 2.72 to 39.71 mg g-1 a.i.). The increasing order of insects susceptibility to coumarin was R. dominica, S. zeamais and O. surinamensis.
Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli (2009)

Despite recent advances in sequencing, complete finishing of large genomes and analysis of novel proteins they encode typically require cloning of specific regions. However, many of these fragments are extremely difficult to clone in current vectors. Superhelical stress in circular plasmids can generate secondary structures that are substrates for deletion, particularly in regions that contain numerous tandem or inverted repeats. Common vectors also induce transcription and translation of inserted fragments, which can select against recombinant clones containing open reading frames or repetitive DNA. Conversely, transcription from cloned promoters can interfere with plasmid stability. We have therefore developed a novel Escherichia coli cloning vector (termed 'pJAZZ' vector) that is maintained as a linear plasmid. Further, it contains transcriptional terminators on both sides of the cloning site to minimize transcriptional interference between vector and insert. We show that this vector stably maintains a variety of inserts that were unclonable in conventional plasmids. These targets include short nucleotide repeats, such as those of the expanded Fragile X locus, and large AT-rich inserts, such as 20-kb segments of genomic DNA from Pneumocystis, Plasmodium, Oxytricha or Tetrahymena. The pJAZZ vector shows decreased size bias in cloning, allowing more uniform representation of larger fragments in libraries.