gebhart/patrepeval huggingface dataset:
Ligase-based detection of mononucleotide repeat sequences (1999)

Up to 15% of all colorectal cancers are considered to be replication error positive (RER(+)) and contain mutations at hundreds of thousands of microsatellite repeat sequences. Recently, a number of intragenic mononucleotide repeat sequences have been demonstrated to be targets for inactivating genes in RER(+)colorectal tumors. In this study, thermostable DNA ligases were tested for the ability to detect alterations in microsatellite sequences in colon tumor samples. Ligation profiles on mononucleotide repeat sequences were determined for four related thermostable DNA ligases, Thermus thermophilus ( Tth ) ligase, Thermus sp. AK16D ligase, Aquifex aeolicus ligase and the K294R mutant of the Tth ligase. While the limit of detection for point mutations was one mutation in 1000 wild-type sequences, the ability to detect a single base deletion in a 10 base mononucleotide repeat was one mutation in 100 wild-type sequences. Furthermore, the misligation error increased exponentially as the length of the mono-nucleotide repeat increased, and was 10% of the correct signal for a 19 base mononucleotide repeat. A fluorescent ligase-based assay [polymerase chain reaction/ligase detection reaction (PCR/LDR)] correlated with results obtained using a radioactive assay to detect instability within the TGF-beta Type II receptor gene. PCR/LDR was also used to detect the APCI1307K mononucleotide repeat allele which has a carrier frequency of 6.1% in Ashkenazi Jewish individuals. In a blind study, 30 samples that had been typed for the presence of the APCI1307K allele were tested. The PCR/LDR results correlated with those obtained using sequencing and allele-specific oligonucleotide hybridization for 16 samples carrying the mutation and 13 wild-type samples. Ligation assays that characterize mononucleotide repeats can be used to rapidly detect somatic mutations in tumors, and to screen for individuals who have a hereditary predisposition to develop colon cancer.
Structure and gene expression of theE. coliMn-superoxide dismutase gene (1986)

Superoxide dismutase is an enzyme which converts superoxide O2- to hydrogen peroxide. Using a single synthetic oligonucleotide 33mer, we screened the E. coli DNA library and isolated a clone containing the E. coli manganese-superoxide dismutase gene. We determined the DNA sequence. The analysis of the DNA sequence and in vivo as well as in vitro transcription has shown the following. The DNA sequence suggests two possible promoters. However, only one of them seems active during normal aerobic growth. Purified RNA polymerase initiates in vitro transcription from the same promoter. It is not clear whether the second promoter is functional. It is possible that this promoter could be activated under different growth conditions. There is an inverted repeat sequence which could form a stem-loop structure downstream of the translation stop codon TAA of the Mn-SOD gene. The results of the analysis of in vivo and in vitro RNA have shown that this is the transcription termination signal. Thus, the Mn-SOD gene constitutes a single gene operon. There is an almost perfect 19 base palindrome at the -35 region. The position and the size of the palindrome suggest that this could be a regulatory site.
Effect of parasitic element on the characteristics of microstrip antenna (1991)

The variations in the sizes and position of a parasitic element with the input impedance and bandwidth of a rectangular microstrip antenna are investigated by the method of moments. An integral equation for the unknown patch current densities is formulated in the spectral domain. The Galerkin procedure is employed to solve for the unknowns. It is found that the input impedance varies significantly with the size and position of the parasitic patch. The result is important for bandwidth enhancement and impedance matching of the microstrip antenna.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A novel deletion in the GTPase domain of OPA1 causes defects in mitochondrial morphology and distribution, but not in function (2008)

Autosomal dominant optic atrophy (ADOA), the commonest cause of inherited optic atrophy, is caused by mutations in the ubiquitously expressed gene optic atrophy 1 (OPA1), involved in fusion and biogenesis of the inner membrane of mitochondria. Bioenergetic failure, mitochondrial network abnormalities and increased apoptosis have all been proposed as possible causal factors. However, their relative contribution to pathogenesis as well as the prominent susceptibility of the retinal ganglion cell (RGC) in this disease remains uncertain. Here we identify a novel deletion of OPA1 gene in the GTPase domain in three patients affected by ADOA. Muscle biopsy of the patients showed neurogenic atrophy and abnormal morphology and distribution of mitochondria. Confocal microscopy revealed increased mitochondrial fragmentation in fibroblasts as well as in myotubes, where mitochondria were also unevenly distributed, with clustered organelles alternating with areas where mitochondria were sparse. These abnormalities were not associated with altered bioenergetics or increased susceptibility to pro-apoptotic stimuli. Therefore, changes in mitochondrial shape and distribution can be independent of other reported effects of OPA1 mutations, and therefore may be the primary cause of the disease. The arrangement of mitochondria in RGCs, which degenerate in ADOA, may be exquisitely sensitive to disturbance, and this may lead to bioenergetic crisis and/or induction of apoptosis. Our results highlight the importance of mitochondrial dynamics in the disease per se, and point to the loss of the fine positioning of mitochondria in the axons of RGCs as a possible explanation for their predominant degeneration in ADOA.
Total Synthesis of (+)-Narciclasine (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTTotal Synthesis of (+)-NarciclasineJames H. Rigby and Mary E. MateoView Author Information Department of Chemistry Wayne State University Detroit, Michigan 48202-3489 Cite this: J. Am. Chem. Soc. 1997, 119, 51, 12655–12656Publication Date (Web):December 24, 1997Publication History Received22 August 1997Published online24 December 1997Published inissue 1 December 1997https://pubs.acs.org/doi/10.1021/ja972950zhttps://doi.org/10.1021/ja972950zrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views2127Altmetric-Citations60LEARN 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 SUBJECTS:Chemical synthesis,Cyclization,Hydroxyls,Organic synthesis,Photocyclization Get e-Alerts
Quantifying distortions in soft lithography (1998)

This article describes a moiré technique for determining distortions in soft lithography. We use the technique to investigate distortions when soft lithography is performed in a variety of configurations; a method is identified for limiting maximum distortions to less than 1 μm over areas ∼1 cm2. We also suggest an approach for actively controlling these distortions, and we demonstrate in a simple way its feasibility.
Mouse mammary tumor virus-related sequences in mouse lymphocytes are inducible by 12-O-tetradecanoyl phorbol-13-acetate (1984)

cDNA libraries from EL-4 cells treated with 12-O-tetradecanoyl phorbol-13-acetate (TPA) were screened for TPA-inducible sequences by differential hybridization. The most abundant inducible species was a sequence similar to that of mouse mammary tumor virus (MMTV). Induction of the mRNA corresponding to the MMTV-related sequences was already evident 30 min after TPA treatment, whereas the maximum accumulation occurred after 20 h of exposure to TPA. TPA also increased levels of MMTV-related RNA in the normal spleen cells of BALB/c and C57BL/6 mice. The level of RNA expression corresponding to MMTV-related sequences, however, was markedly elevated in EL-4 cells as compared with normal spleen cells. Southern blots of EL-4 cell DNA showed that the MMTV-related sequences were inserted into multiple locations of the EL-4 genome. Sequence analysis revealed that the MMTV-related cDNA clones included a part of the env gene and the right long terminal repeat of MMTV. However, the cDNA sequences were substantially different from published MMTV proviral sequences, most notably because of a contiguous deletion of 491 base pairs in the open reading frame within the U3 region.
MultiSpace: Enabling Electronic Document Micro-mobility in Table-Centric, Multi-Device Environments (2006)

Although electronic media has changed how people interact with documents, today's electronic documents and the environments in which they are used are still impoverished relative to traditional paper documents when used by groups of people and across multiple computing devices. Vertical interfaces (e.g., walls and monitors) afford a less democratic style of interaction than generally observed when people are working around a table. In this paper, we introduce MultiSpace, a research effort which explores the role of the table as a central hub to support ad hoc collaboration in a multidevice environment. The table centric approach offers new interaction techniques to provide egalitarian access and shared transport of data, supporting mobility and micromobility (Luff and Heath, 1998) of electronic content between tables and other devices. Our observations show how people use these techniques, and how tabletop technology can support and augment collaborative tasks.
Acquisition of HIV-1 Resistance in T Lymphocytes Using an ACA-Specific E. coli mRNA Interferase (2010)

Transcriptional activation of gene expression directed by the long terminal repeat (LTR) of HIV-1 requires both the transactivation response element (TAR) and Tat protein. HIV-1 mutants lacking a functional tat gene are not able to proliferate. Here we take a genetic approach to suppress HIV-1 replication based on Tat-dependent production of MazF, an ACA-specific endoribonuclease (mRNA interferase) from Escherichia coli. When induced, MazF is known to cause Bak- and NBK-dependent apoptotic cell death in mammalian cells. We first constructed a retroviral vector, in which the mazF (ACA-less) gene was inserted under the control of the HIV-1 LTR, which was then transduced into CD4+ T-lymphoid CEM-SS cells in such a way that, upon HIV-1 infection, the mazF gene is induced to destroy the infecting HIV-1 mRNA, preventing HIV-1 replication. Indeed, when the transduced cells were infected with HIV-1 IIIB, the viral replication was effectively inhibited, as HIV-1 IIIB p24 could not be detected in the culture medium. Consistently, not only cell growth but also the CD4 level was not affected by the infection. These results suggest that the HIV-1-LTR-regulated mazF gene was effectively induced upon HIV-1 IIIB infection, which is sufficient enough to destroy the viral mRNA from the infected HIV-1 IIIB to completely block viral proliferation in the cells, but not to affect normal cell growth. These results indicate that the T cells transduced with the HIV-1-LTR-regulated mazF gene acquire HIV-1 resistance, providing an intriguing potential for the use of the HIV-1-LTR-regulated mazF gene in anti-HIV gene therapy.
Regulation of apoptosis by viral gene products (1997)

Free access1 March 1997 Share on Regulation of apoptosis by viral gene productsAuthors: J G Teodoro, P E BrantonAuthors Info & AffiliationsDOI: https://doi.org/10.1128/jvi.71.3.1739-1746.1997 PDF/EPUB
Regulation of apoptosis and T cell activation by Fas-specific mAb (1994)

Fas was initially described as a molecule expressed on the surface of certain cell lines that could mediate programmed cell death (apoptosis) subsequent to ligation by specific mAb. To determine whether mAb to other epitopes on the Fas molecule might mediate other functions, we generated a panel of mAb to the extracellular portion of human Fas. Significant lysis of Fas-expressing target cells was only observed when the new mAb were first bound to a solid-phase support and not when the mAb were added in solution. However, several of these mAb inhibited the killing of target cells induced by the prototypic Fas-specific mAb, CH-11. Those mAb that inhibited apoptosis of target cells mediated by the CH-11 mAb also blocked lysis of target cells mediated by cells expressing Fas ligand. Finally, some of the Fas-specific mAb were found to co-stimulate proliferation of peripheral blood T cells in the presence of immobilized CD3 mAb. Thus, the data indicate the existence of a complex set of interactions mediated by Fas in both normal and transformed lymphoid cells that may have important implications regarding the role(s) of this molecule in regulation of immune responses.
Initial clinical experience with perducer® device: Promising new tool in the diagnosis and treatment of pericardial disease (1999)

According to the present experience, we believe that, with minor modifications, the PerDUCER device could be successfully implemented for pericardial entry in patients with pericardial disease. Further studies are needed to evaluate the feasibility and safety of this new instrument in patients with a normal pericardium. This could open a most exciting spectrum of possible implementations of the device in the future.
Shaping a femtosecond pulse with a programmable thermo-optically driven phase modulator (2007)

A femtosecond pulse shaping apparatus based on a thermo-optically driven spatial phase modulator is presented. The modulator cell is illuminated by a standard projector and is easily controllable with a computer. In principle the setup allows for two dimensional pulse shaping, however, all initial demonstrations reported here, such as feedback controlled dispersion compensation or pulse train generation, are performed in a one dimensional phase-only shaping geometry.
CpG methylation has differential effects on the binding of YY1 and ETS proteins to the bi-directional promoter of the Surf-1 and Surf-2 genes (1995)

The divergently transcribed Surf-1 and Surf-2 housekeeping genes are separated by a bi-directional, TATA-less promoter which lies within a CpG-rich island. Here we show that CpG methylation severely reduces transcription in the direction of both Surf-1 and Surf-2. Previous work has identified three promoter elements (Su1, Su2 and Su3) which are conserved between the human and mouse Surf-1/Surf-2 promoters. These elements bind transcription factors present in human and mouse cell nuclear extracts in vitro and mutations which prevent factor binding also reduce promoter activity in vivo. Transcription initiation factor YY1 binds to the Su1 site and stimulates transcription in the direction of Surf-1 and, to a lesser extent, Surf-2. Here we show that members of the ETS family of transcription factors bind to the Su2 site. Although the Su1 factor binding site contains three CpG dinucleotides, the binding of YY1 is not affected by CpG methylation. In contrast, CpG methylation abolishes the binding of ETS proteins to the Su2 site; methylation of a single cytosine, at position 3 of the consensus ETS site, is sufficient to prevent factor binding. This direct effect on the binding of ETS proteins is, however, not in itself sufficient to explain the repression of this promoter by CpG methylation. A mutation of the Su2 site which removes the sequence CpG, but which does not prevent ETS factor binding, fails to relieve this promoter from repression by CpG methylation.
Autonomous MAV flight in indoor environments using single image perspective cues (2011)

We consider the problem of autonomously flying Miniature Aerial Vehicles (MAVs) in indoor environments such as home and office buildings. The primary long range sensor in these MAVs is a miniature camera. While previous approaches first try to build a 3D model in order to do planning and control, our method neither attempts to build nor requires a 3D model. Instead, our method first classifies the type of indoor environment the MAV is in, and then uses vision algorithms based on perspective cues to estimate the desired direction to fly. We test our method on two MAV platforms: a co-axial miniature helicopter and a toy quadrotor. Our experiments show that our vision algorithms are quite reliable, and they enable our MAVs to fly in a variety of corridors and staircases.
PSIC: profile extraction from sequence alignments with position-specific counts of independent observations (1999)

Sequence weighting techniques are aimed at balancing redundant observed information from subsets of similar sequences in multiple alignments. Traditional approaches apply the same weight to all positions of a given sequence, hence equal efficiency of phylogenetic changes is assumed along the whole sequence. This restrictive assumption is not required for the new method PSIC (position-specific independent counts) described in this paper. The number of independent observations (counts) of an amino acid type at a given alignment position is calculated from the overall similarity of the sequences that share the amino acid type at this position with the help of statistical concepts. This approach allows the fast computation of position-specific sequence weights even for alignments containing hundreds of sequences. The PSIC approach has been applied to profile extraction and to the fold family assignment of protein sequences with known structures. Our method was shown to be very productive in finding distantly related sequences and more powerful than Hidden Markov Models or the profile methods in WiseTools and PSI-BLAST in many cases. The profile extraction routine is available on the WWW (http://www.bork.embl-heidelberg. de/PSIC or http://www.imb.ac.ru/PSIC).
Adeno-Associated Virus (AAV) gene therapy for cystic fibrosis: current barriers and recent developments (2017)

Since the cystic fibrosis (CF) gene was discovered in 1989, researchers have worked to develop a gene therapy. One of the most promising and enduring vectors is the AAV, which has been shown to be safe. In particular, several clinical trials have been conducted with AAV serotype 2. All of them detected viral genomes, but identification of mRNA transduction was not consistent; clinical outcomes in Phase II studies were also inconsistent. The lack of a positive outcome has been attributed to a less-than-efficient viral infection by AAV2, a weak transgene promoter and the host immune response to the vector. Areas covered: Herein, the authors focus on AAV gene therapy for CF, evaluating past experience with this approach and identifying ways forward, based on the progress that has already been made in identifying and overcoming the limitations of AAV gene therapy. Expert opinion: Such progress makes it clear that this is an opportune time to push forward toward the development of a gene therapy for CF. Drugs to treat the basic defect in CF represent a remarkable advance but cannot treat a significant cohort of patients with rare mutations. Thus, there is a critical need to develop a gene therapy for those individuals.
The safety and efficacy of high dose ferric carboxymaltose in patients with chronic kidney disease: A single center study (2015)

Ferric carboxymaltose (FCM) is a parenteral, dextran-free iron formulation designed to overcome the limitations of existing intravenous (IV) iron preparations. We investigated the safety and efficacy of high dose administration of FCM in our anemic chronic kidney disease (CKD) patients. It was a prospective observational study from June 2011 to August 2013. FCM was administered as IV infusion 1000 mg in 250 ml of normal saline over 15-30 min. Efficacy was evaluated by comparing the Hb and/or serum iron status at the first follow-up visit after the infusion with that at the baseline. A total of 500 infusions were administered to 450 patients. All patients had a successful administration of the FCM. None of the patients had any serious drug-related AE. AE of mild to moderate severity observed or reported after the infusion were: accelerated hypertension (0.2%), feeling abnormal (0.6%), headache and bodyaches (0.6% each), and infusion site reaction (0.8%). 261 patients had a follow up Hb, which showed an increase of 1.7 ± 1.5 g/dl after a period of 11 ± 7.2 weeks (P = 0.001); 188 (72%) patients had a rise in Hb of ≥1 g/dl. The increase in Hb was observed uniformly across all stages of CKD. Proportions of patients with an Hb of above 10 and 11 g/dl increased from 30.2% to 62.8% and 16.1% to 37.9%, respectively (P = 0.001). Iron status evaluation done in 44 patients after a follow up period of 15.1 ± 11.5 weeks showed increases in Hb of 1.6 ± 2.2 g/dl (P = 0.001), transferrin saturation of 9.1 ± 16.9% (P = 0.001), and ferritin of 406 ± 449 ng/ml (P = 0.001). We conclude high dose administration of FCM is safe and well-tolerated. It was effective in the treatment of iron deficiency in nondialysis and peritoneal dialysis CKD patients.
The Enamine Alkylation and Acylation of Carbonyl Compounds (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Enamine Alkylation and Acylation of Carbonyl CompoundsGilbert. Stork, A. Brizzolara, H. Landesman, J. Szmuszkovicz, and R. TerrellCite this: J. Am. Chem. Soc. 1963, 85, 2, 207–222Publication Date (Print):January 1, 1963Publication History Published online1 May 2002Published inissue 1 January 1963https://pubs.acs.org/doi/10.1021/ja00885a021https://doi.org/10.1021/ja00885a021research-articleACS PublicationsRequest reuse permissionsArticle Views14792Altmetric-Citations913LEARN 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