gebhart/patrepeval huggingface dataset:
A Dual Benefit of Sacral Neuromodulation (2008)

Sacral neuromodulation is a therapeutic option for women with detrusor overactivity and more recently has been used in patients with fecal incontinence and slow-transit constipation. A 47-year-old woman presented with chronic constipation since childhood. She used multiple laxatives, fiber supplements, and enemas, all without success, and defecated only once per week. Extensive investigations, including barium enema, colonoscopy, defecating proctography, pelvic magnetic resonance imaging, and anorectal manometry all were normal. A transit study showed delayed small-bowel emptying. Colonic transit could not be accurately interpreted because of the marked delayed in proximal transit. An ileostomy was being considered to defunction the colon after the patient become desperate for a better quality of life. She also complained of severe urinary frequency and incomplete emptying. A cystoscopy was normal, and a temporary sacral neuromodulation device was inserted as a staged procedure to improve her urinary symptoms. From the day of device placement and thereafter, the patient defecated without difficulty and has also been free of bladder symptoms. Repeat colonic transit has shown normalization of the stomach, small bowel, and colon.
Nuclease activity of 1,10-phenanthroline-copper ion (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNuclease activity of 1,10-phenanthroline-copper ionDavid S. SigmanCite this: Acc. Chem. Res. 1986, 19, 6, 180–186Publication Date (Print):June 1, 1986Publication History Published online1 May 2002Published inissue 1 June 1986https://doi.org/10.1021/ar00126a004RIGHTS & PERMISSIONSArticle Views1597Altmetric-Citations528LEARN 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 InReddit PDF (4 MB) Get e-Alertsclose Get e-Alerts
Quantitation of Glycosylated Hemoglobin by Boronate Affinity Chromatography (1984)

Total hemoglobin glycosylation and the contribution of glycosylation at the N-terminus of the beta-chains and at "non"-beta-N-terminal positions were quantitated by use of boronate affinity and ion exchange chromatography. Glycohemoglobin (y) was found to correlate linearly (y = 1.92x + 0.53; r = 0.96) with HbA1c (x) and to contain approximately 50% beta-N-terminally glycosylated hemoglobin. This result is in agreement with the binding on boronate agarose of the various hemoglobin components resolved by cation exchange chromatography. An amount of glycohemoglobin similar to that of HbA1c was isolatable from HbA. A slope of less than 2 results because HbA1c is retained only to 93% and the intercept of the regression line reflects the partial adherence (65%) of HbA1a + b to the resin. These results confirm the occurrence of significant "non"-beta-N-terminal glycosylation and show that under optimal chromatographic conditions total glycohemoglobin can be determined with boronate affinity chromatography.
Neisseria gonorrhoeae multi-antigen sequence typing using non-cultured clinical specimens (2009)

The NG-MAST system can successfully be applied directly to non-cultured urogenital samples, but is less suitable for extragenital specimens, particularly throat swabs, due to cross-reaction with commensal Neisseria species.
IL-2 Mediates Protection Against Abscess Formation in an Experimental Model of Sepsis (1999)

Little is known regarding the mechanism by which T cells control intraabdominal abscess formation. Treating animals with polysaccharide A (PS A) from Bacteroides fragilis shortly before or after challenge protects against abscess formation subsequent to challenge with different abscess-inducing bacteria. Although bacterial polysaccharides are considered to be T cell-independent Ags, T cells from PS A-treated animals mediate this protective activity. In the present study, we demonstrate that CD4+ T cells transfer PS A-mediated protection against abscess formation, and that a soluble mediator produced by these cells confers this activity. Cytokine mRNA analysis showed that T cells from PS A-treated animals produced transcript for IL-2, IFN-gamma, and IL-10, but not for IL-4. The addition of IL-2-specific Ab to T cell lysates taken from PS A-treated animals abrogated the ability to transfer protection, whereas the addition of Abs specific for IFN-gamma and IL-10 did not affect protection. Finally, administration of rIL-2 to animals at the time of bacterial challenge prevented abscess formation in a dose-dependent manner. These data demonstrate that PS A-mediated protection against abscess formation is dependent upon a CD4+ T cell-dependent response, and that IL-2 is essential to this immune mechanism.
Intraocular grafts of fresh and freeze‐stored rat hippocampal tissue: A comparison of survivability and histological and connective organization (1984)

Intraocular grafts of rat hippocampal tissue, grafted either directly from the immature donor brains (fresh) or after storage in liquid nitrogen at -196 degrees C (freeze-stored), were compared with regard to survivability and histological and connective organization. For direct grafting, pieces of hippocampal tissue from rat embryos (embryonic day 19, E21) and newborn rats (PO) were placed in the anterior eye chamber of adult rats immediately after dissection. For grafting after deep-freeze storage, pieces of hippocampal tissue were taken from rat embryos (E16-E21) and newborn rats (PO), frozen at a cooling rate of 1 degrees C/min in CO2 or N2 vapours after addition of the cryoprotective agent dimethylsolfoxide (DMSO), and stored in liquid nitrogen for 1 to 33 days before thawing and intraocular grafting. From 20 to 68 days after grafting, the recipient rats were sacrificed, their eyes sectioned, and the sections stained with thionine for cell bodies, Timm's sulphide silver method for hippocampal fiber systems and terminal fields, and acetylcholinesterase (AChE) for cholinergic fibers and AChE-positive neurons. When examining the 101 grafted eyes (34 grafted with fresh and 67 with freeze-stored tissue) a significantly lower survival rate of the freeze-stored tissue was found (28 vs. 88%). The survivability of the freeze-stored tissue was age-dependent with no survival at donor ages E16 and PO, while tissue from E18-E21 had a 50% survival rate. The grafts of the freeze-stored tissue were also smaller and showed an increased tendency for fragmentation. When evaluating the structure of the grafts, the deep-freeze storage was found primarily to have been harmful to the dentate granule cells and their precursors. The organization of intrinsic fiber connections followed the pattern known from lesion and intracerebral transplant studies. While demonstrating that immature brain tissue can survive deep-freeze storage and subsequent intraocular grafting, the study also indicates that different schemes may have to be used to get optimal survival of different neuronal populations.
Biochemistry of airway mucus secretions. (1980)

Tracheobronchial secretions are a complex mixture of secretory fluids derived from sources within the lung. Important constituents include the mucous glycoproteins, other secretory proteins, serum proteins, lipids, salts; water makes up 95% of mucus by weight. These secretions form two phases at the epithelial surface: a mucous gel and an aqueous layer (periciliary fluid). Polymerization and aggregation of mucous glycoproteins create the gel matrix. Other macromolecules such as lysozyme, albumin, and immunoglobulin A also may participate in the process of gelation. Intermolecular forces contributing to gelation include disulfide bonding, sugar-sugar interactions between adjacent glycoproteins, and ionic interactions between the glycoprotein anionic groups (sialic acid carboxyl and sulfate) and cationic components in the secretions. Respiratory tract mucous glycoproteins are large, extended molecules, which have a high carbohydrate content. They are polydisperse, with variation occurring largely in the content of sulfated sugars and sialic acid. Factors such as cell of origin, chronic lung disease, and pharmacologic effects influence the density of these anionic (acidic) groups. Variation in acidic properties may influence the physical and virus-binding properties of mucus. Little information is available concerning the biosynthetic mechanisms in airway epithelium through which these variations are effected.
Improving Defences at the Portal of HIV Entry: Mucosal and Innate Immunity (2008)

The Policy Forum allows health policy makers around the world
Conversion of betulin into careyagenolide (2α,3β-dihydroxy-18α,19βH-ursan-28,20β-olide) (1989)

Careyagenolide ( I ) and its respective 2β,3α- and 2β,3β-isomers XVII and XIV were prepared from 3-oxo-18α,19β H -ursan-28,20β-olide ( IX ), accessible from betulin ( II ). The key step of the synthesis was hydroxylation of ketones IX and X with 3-chloroperoxybenzoic acid and reduction of ketones XI-XIII .
Automated, integrated modules for fluid handling, thermal cycling and purification of DNA samples for high throughput sequencing and analysis (2002)

The Genomation Laboratory at the University of Washington has developed an automated fluid handling system called "Acapella" to prepare microliter reactions for genome analysis. Reactions such as restriction enzyme digests, polymerase chain reactions (PCRs), and sequencing reactions are prepared in glass capillaries, one per sample, with an automated system that can process 5000 samples in 8 hours. A DNA sample is aspirated from a microplate well with a novel piezoelectric aspirator/mixer actuator, reagents are dispensed into the end of the capillary with piezoelectric reagent dispensers, all fluids inside the capillary are mixed with the piezoelectric aspirator/mixer actuator, and the capillary is off-loaded to a capillary cassette for further processing. On-going development includes new, automated modules for thermal processing of capillaries, real-time DNA quantitation, and purification of DNA inside of capillaries to prepare the samples for DNA sequencing. Applications of the technology include minimal residual disease quantification and sample preparation for DNA sequencing.
Fluorous Synthesis with Fewer Fluorines (Light Fluorous Synthesis):  Separation of Tagged from Untagged Products by Solid-Phase Extraction with Fluorous Reverse-Phase Silica Gel (1999)

Fluorous synthesis involves tagging an organic substrate with a fluorinated tag for the purposes of separation. To date, techniques of fluorous synthesis have relied on liquid−liquid extractions. This paper applies a simple solid−liquid extraction procedure over fluorous reverse-phase silica gel (silica with a fluorocarbon bonded phase) for use in fluorous synthesis. Four amino acids were tagged on nitrogen with the C9F19CO− group, and the resulting acids were coupled in a parallel experiment with an excess of four amines. The resulting 16 crude fluorous amide products were separated from all the coupling reagents and excess amine by two-stage filtration through fluorous silica. In 15 of the 16 cases, the products were isolated in good to excellent yield and purity. All of the products are soluble in organic solvents and none is expected to have any significant solubility in fluorous solvents, so the experiment dramatically illustrates the advantages of the solid−liquid extraction over the liquid−liquid extraction. Future prospects for application of fluorous silica are briefly discussed.
Interleukin-8 is associated with circulating CD133+ progenitor cells in acute myocardial infarction (2006)

In AMI, IL-8 is associated with circulating progenitor cells. In addition to the pro-angiogenic functions of IL-8 and VEGF, this mechanism may contribute to new vessel generation and, thereby, improve myocardial function.
A Novel Dnmt3a Isoform Produced from an Alternative Promoter Localizes to Euchromatin and Its Expression Correlates with Activede Novo Methylation (2002)

Previous studies have shown that the Dnmt3b gene encodes multiple variants via alternative splicing. However, only one form of Dnmt3a has been identified to date. We report here the discovery of a small form of Dnmt3a, denoted Dnmt3a2, from both human and mouse. The transcript encoding Dnmt3a2 is initiated from a downstream intronic promoter. As a result, the Dnmt3a2 protein lacks the N-terminal 223 (human) or 219 (mouse) amino acid residues of the full-length Dnmt3a. Recombinant Dnmt3a2 protein displayed similar cytosine methyltransferase activity as Dnmt3a in vitro. However, Dnmt3a and Dnmt3a2 exhibited strikingly different subcellular localization patterns. Unlike Dnmt3a, which was concentrated on heterochromatin, Dnmt3a2 displayed a localization pattern suggestive of euchromatin association. Dnmt3a2 is the predominant form in embryonic stem cells and embryonal carcinoma cells and can also be detected from testis, ovary, thymus, and spleen, whereas Dnmt3a is expressed at low levels ubiquitously. Comparison of human embryonal carcinoma cell lines with breast/ovarian cancer cell lines indicates that DNMT3A2 expression correlates with high de novo methylation activity. These findings suggest that Dnmt3a and Dnmt3a2 may have distinct DNA targets and different functions in development.
Glycosylation Defect in Lec1 Chinese Hamster Ovary Mutant Is Due to a Point Mutation in N-Acetylglucosaminyltransferase I Gene (1996)

The Lec1 Chinese hamster ovary (CHO) mutant is a leuco-phytohemagglutinin resistant cell line unable to synthesize complex and hybrid N-glycans due to the lack of N-acetylglucosaminyltransferase I (GnTI) activity. Here we have identified the lec1 mutation. Using specific antibodies to GnTI we demonstrate that Lec1 cells synthesize an inactive GnTI protein identical in size to the wild-type CHO enzyme. We have cloned and sequenced the gene coding GnTI from parental CHO and Lec1 mutant cells. Comparison of GnTI sequences detected three mutations within the luminal domain of Lec1 GnTI, each resulting in an amino acid substitution. The effect of each mutation on enzyme activity was analyzed by site-directed mutagenesis of wild-type rabbit GnTI and transient expression in COS cells. One of the three mutations (Cys123 --> Arg123) resulted in complete loss of activity, whereas the other two mutations had no apparent effect on enzyme activity. This conclusion was confirmed by expression of GnTI mutants in the GnTI null background of Saccharomyces cerevisiae. Both Lec1 GnTI and the GnTI mutant (Cys123 --> Arg123) are correctly localized to the Golgi apparatus, indicating that the inactive GnTI molecules are sufficiently well folded for efficient transport from the endoplasmic reticulum. These results demonstrate that the lec1 mutation is a point mutation and that Cys123 is a critical residue for GnTI activity.
JPred: a consensus secondary structure prediction server. (1998)

geoff@ebi.ac.uk
Studies on Ribonucleic Acid Ligase (1974)

Abstract RNA ligase, isolated from bacteriophage T4-infected Escherichia coli, catalyzes the conversion of synthetic [5'-32P]polyribonucleotides to a form resistant to alkaline phosphatase. The reaction requires ATP and leads to the formation of AMP and PPi. The purification procedure for T4-induced RNA ligase has been modified to yield stable enzyme preparations. The influence of secondary structure on the RNA ligase reaction has been investigated with these fractions. The conversion of synthetic polynucleotides to complex secondary structures was either without effect or inhibitory in the RNA ligase system. Purified RNA ligase was shown to catalyze an exchange reaction between ATP and PPi, but not between ATP and AMP. The ATP-PPi exchange reaction occurred in the absence of a polyribonucleotide substrate. The formation of an RNA ligase-adenylate complex was demonstrated by gel filtration, polyacrylamide gel electrophoresis, and ultracentrifugation in a glycerol gradient. The complex was dissociated by 5'-P-poly(A) to yield AMP while ATP was generated in the presence of PPi. These findings suggest that an enzyme-AMP intermediate occurs during the course of the RNA ligase reaction. Evidence is presented for the occurrence of an RNA ligase activity in eukaryotic cells.
Robustly detecting differential expression in RNA sequencing data using observation weights (2014)

A popular approach for comparing gene expression levels between (replicated) conditions of RNA sequencing data relies on counting reads that map to features of interest. Within such count-based methods, many flexible and advanced statistical approaches now exist and offer the ability to adjust for covariates (e.g. batch effects). Often, these methods include some sort of 'sharing of information' across features to improve inferences in small samples. It is important to achieve an appropriate tradeoff between statistical power and protection against outliers. Here, we study the robustness of existing approaches for count-based differential expression analysis and propose a new strategy based on observation weights that can be used within existing frameworks. The results suggest that outliers can have a global effect on differential analyses. We demonstrate the effectiveness of our new approach with real data and simulated data that reflects properties of real datasets (e.g. dispersion-mean trend) and develop an extensible framework for comprehensive testing of current and future methods. In addition, we explore the origin of such outliers, in some cases highlighting additional biological or technical factors within the experiment. Further details can be downloaded from the project website: http://imlspenticton.uzh.ch/robinson_lab/edgeR_robust/.
Effect of ecteinascidin-743 on the interaction between DNA binding proteins and DNA. (1999)

Ecteinascidin-743 (ET-743) is a tetrahydroisoquinoline alkaloid isolated from Ecteinascidia turbinata, a tunicate growing in mangrove roots in Caribbean. It has been shown to bind in the minor groove of DNA forming covalent adducts by reaction of the N2 of guanine with the carbinolamine moiety. We investigated ET-743 ability to inhibit the binding of different transcription factors to their consensus sequences by using gel shift assays. We have selected three types of factors: (i) oncogene products such as MYC, c-MYB and Maf; (ii) transcriptional activators regulated during the cell cycle as E2F and SRF; and (iii) general transcription factors such as TATA binding protein (TBP), Sp1 and NF-Y. We observed no inhibition of the binding of Sp1, Maf, MYB and MYC. Inhibition of DNA binding was observed for TBP, E2F, SRF at ET-743 concentrations ranging from 50 to 300 microM. The inhibition of binding of NF-Y occurs at even lower concentrations (i.e. 10-30 microM) when the recombinant subunits of NF-Y are preincubated with the drug, indicating that the inhibition of NF-Y binding does not require previous ET-743 DNA binding. Since NF-Y is a trimer containing two subunits with high resemblance to histones H2B and H2A, we have investigated the effect of ET-743 on nucleosome reconstitution. ET-743 caused a decrease of the nucleosomal band at 100 nM, with the complete disappearance of the band at 3-10 microM. These data suggest that the mode of action of this novel anticancer drug is related to its ability to modify the interaction between some DNA binding proteins and DNA.
Neurotensin Receptor 1 Is Expressed in Gastrointestinal Stromal Tumors but Not in Interstitial Cells of Cajal (2011)

Gastrointestinal stromal tumors (GIST) are thought to derive from the interstitial cells of Cajal (ICC) or an ICC precursor. Oncogenic mutations of the KIT or PDGFRA receptor tyrosine kinases are present in the majority of GIST, leading to ligand-independent activation of the intracellular signal transduction pathways. We previously investigated the gene expression profile in the murine Kit(K641E) GIST model and identified Ntsr1 mRNA, encoding the Neurotensin receptor 1, amongst the upregulated genes. Here we characterized Ntsr1 mRNA and protein expression in the murine Kit(K641E) GIST model and in tissue microarrays of human GIST. Ntsr1 mRNA upregulation in Kit(K641E) animals was confirmed by quantitative PCR. Ntsr1 immunoreactivity was not detected in the Kit positive ICC of WT mice, but was present in the Kit positive hyperplasia of Kit(K641E) mice. In the normal human gut, NTSR1 immunoreactivity was detected in myenteric neurons but not in KIT positive ICC. Two independent tissue microarrays, including a total of 97 GIST, revealed NTSR1 immunoreactivity in all specimens, including the KIT negative GIST with PDGFRA mutation. NTSR1 immunoreactivity exhibited nuclear, cytoplasmic or mixed patterns, which might relate to variable levels of NTSR1 activation. As studies using radio-labeled NTSR1 ligand analogues for whole body tumor imaging and for targeted therapeutic interventions have already been reported, this study opens new perspectives for similar approaches in GIST.
Cell and Environment Interactions in Tumor Microregions: The Multicell Spheroid Model (1988)

Abnormal vascularization of malignant tumors is associated with the development of microregions of heterogeneous cells and environments. Experimental models such as multicell spheroids and a variety of new techniques are being used to determine the characteristics of these microregions and to study the interactions of the cells and microenvironments. The special cellular microecology of tumors influences responsiveness to therapeutic agents and has implications for future directions in cancer research.
A Systematic Approach to the Plain Radiographic Evaluation of the Young Adult Hip (2008)

Clohisy, John C. MD; Carlisle, John C. MD; Beaulé, Paul E. MD; Kim, Young-Jo MD; Trousdale, Robert T. MD; Sierra, Rafael J. MD; Leunig, Michael MD; Schoenecker, Perry L. MD; Millis, Michael B. MD Author Information
Motorola field programmable analogue arrays, present hardware and future trends (1998)

The Motorola MPAA020 Field Programmable Analogue Array (FPAA) is an integrated array of undedicated programmable analogue cells, based upon switched capacitor technology. Programming data is held in SRAM in each cell, and it is possible to configure and re-configure the implemented circuit without limit. The chip is capable of supporting a diverse range of analogue signal processing functions, such as data conversion, linear signal processing, filtering and non-linear functions. The MPAA020 chip is mounted within a development board which provides support functions such as clock generation, voltage regulation and I/O pins. This board connects to the serial port of a PC to provide easy download of configurations from the design support software, Easy AnalogTM. This software fully abstracts the design process away from component level to system level. At system level, design entry is performed by inter-connection of user-parameterised macro-cells and then downloaded directly to the device. Very rapid prototyping of switched capacitor circuits is possible with the MPAA020 array, reducing time to market by months when compared with a full custom ASIC implementation. A full configuration of the chip may be accomplished in 5 μS and a partial update of the function may be done in 200 nS per 8 bit data word. (5 pages)