gebhart/patrepeval huggingface dataset:
Equivalent genetic roles for bmp7/snailhouse and bmp2b/swirl in dorsoventral pattern formation (2000)

A bone morphogenetic protein (BMP) signaling pathway acts in the establishment of the dorsoventral axis of the vertebrate embryo. Here we demonstrate the genetic requirement for two different Bmp ligand subclass genes for dorsoventral pattern formation of the zebrafish embryo. From the relative efficiencies observed in Bmp ligand rescue experiments, conserved chromosomal synteny, and isolation of the zebrafish bmp7 gene, we determined that the strongly dorsalized snailhouse mutant phenotype is caused by a mutation in the bmp7 gene. We show that the original snailhouse allele is a hypomorphic mutation and we identify a snailhouse/bmp7 null mutant. We demonstrate that the snailhouse/bmp7 null mutant phenotype is identical to the presumptive null mutant phenotype of the strongest dorsalized zebrafish mutant swirl/bmp2b, revealing equivalent genetic roles for these two Bmp ligands. Double mutant snailhouse/bmp7; swirl/bmp2b embryos do not exhibit additional or stronger dorsalized phenotypes, indicating that these Bmp ligands do not function redundantly in early embryonic development. Furthermore, overexpression experiments reveal that Bmp2b and Bmp7 synergize in the ventralization of wild-type embryos through a cell-autonomous mechanism, suggesting that Bmp2b/Bmp7 heterodimers may act in vivo to specify ventral cell fates in the zebrafish embryo.
Adaptive response of the enterohepatic circulation of bile acids to extrahepatic cholestasis (1996)

Experimental cholestasis induced by ligation of the common bile duct results in morphological and functional changes in the rat hepatocyte. The aim of this study was to evaluate the adaptive response of the transport process involved in the enterohepatic circulation of bile salts to obstructive cholestasis. Male Sprague-dawley rats with common bile duct ligation were killed after 48 and 72 hours. Portal and systemic blood and duodenal aspirates were collected. Taurocholate transport was measured in isolated ileal brush border (BBM) and liver basolateral membranes (BLM). Drastic reduction in intraluminal bile salt concentrations in ligated rats accompanied decreases in saturable taurocholate uptake by ileal BBMs. Kinetic analysis indicated that the decrease was attributable to reduction in transporter density and alteration in affinity for the substrate, both of which accentuated with increase in postligation time. In contrast, despite 20-fold higher portal venous bile salt concentrations, taurocholate uptake by hepatic sinusoidal membrane was lower in rats. Kinetic analysis and immunoblots developed using polyclonal antisera to the liver BLM bile acid transporter demonstrated a gradual decrease in transporter density with increase in postligation time accompanied by reduced taurocholate uptake by basolateral membrane. These results further support the concept that the ileal brush border membrane transporter is regulated by the availability of the substrate, whereas regulation of the bile salt transport across the liver BLM is independent of portal venous bile acid concentration.
Common dental infections in the primary care setting. (2008)

Family physicians commonly encounter patients with dental infections, such as dental caries and periodontal disease. Dental caries is caused by bacteria that destroy the enamel and dentin; it can be detected by an oral examination that shows stained pits or fissures on the tooth surface. Use of fluoride is the most effective prevention measure for dental caries. Untreated caries may progress to pulpitis and, eventually, to necrosis of the pulp. In irreversible pulpitis, the tooth dies and the patient may have a localized abscess that can spread to surrounding tissue. Periodontal infections are caused by bacteria in the subgingival dental plaque. In gingivitis, the inflamed gums bleed easily with brushing or flossing; the condition can be controlled with good oral hygiene. Periodontitis is characterized by a loss of supportive bone structure caused by chronic gingivitis; it is also associated with some systemic diseases. Localized periodontitis is treated with mechanical debridement and good oral hygiene, whereas generalized periodontitis requires adjunct antibiotic therapy. Pericoronitis results when food particles become trapped under the gum of an impacted tooth. This condition can be controlled by removal of food debris and good oral hygiene. For patients in whom dental infections are disseminated and have invaded the deeper oral spaces, antibiotic treatment should be initiated at the time of referral.
Structural Profiling of Individual Glycosphingolipids in a Single Thin-Layer Chromatogram by Multiple Sequential Immunodetection Matched with Direct IR-MALDI-o-TOF Mass Spectrometry (2009)

The thin-layer chromatography (TLC) immunoenzyme overlay assay is a widely used tool for antibody-mediated identification of glycosphingolipids (GSLs) in mixtures. However, because the majority of GSLs is left unexamined in a chromatogram of a single assay, we developed a novel method that permits detection of various GSLs by sequential multiple immunostaining combined with individual coloring of GSLs in the same chromatogram. Specific staining was achieved by means of primary anti-GSL antibodies, directed against lactosylceramide, globotriaosylceramide, and globotetraosylceramide, in conjunction with alkaline phosphatase (AP)- or horseradish peroxidase (HRP)-conjugated secondary antibodies together with the appropriate chromogenic substrates. Triple coloring with 5-bromo-4-chloro-3-indolyl phosphate (BCIP)-AP, Fast Red-AP, and 3,3'-diaminobenzidine (DAB)-HRP resulted in blue, red, and black precipitates, respectively, following three sequential immunostaining rounds. Structures of antibody-detected GSLs were determined by direct coupling of TLC with infrared matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometry. This combinatorial technique was used to demonstrate structural GSL profiling of crude lipid extracts from human hepatocellular cancer. This powerful technology allows efficient structural characterization of GSLs in small tissue samples and marks a further step forward in the emerging field of glycosphingolipidomics.
Adhesion and Fitness in the Bean Phyllosphere and Transmission to Seed of Xanthomonas fuscans subsp. fuscans (2009)

Deciphering the mechanisms enabling plant-pathogenic bacteria to disperse, colonize, and survive on their hosts provides the necessary basis to set up new control methods. We evaluated the role of bacterial attachment and biofilm formation in host colonization processes for Xanthomonas fuscans subsp. fuscans on its host. This bacterium is responsible for the common bacterial blight of bean (Phaseolus vulgaris), a seedborne disease. The five adhesin genes (pilA, fhab, xadA1, xadA2, and yapH) identified in X. fuscans subsp. fuscans CFBP4834-R strain were mutated. All mutants were altered in their abilities to adhere to polypropylene or seed. PilA was involved in adhesion and transmission to seed, and mutation of pilA led to lower pathogenicity on bean. YapH was required for adhesion to seed, leaves, and abiotic surfaces but not for in planta transmission to seed or aggressiveness on leaves. Transmission to seed through floral structures did not require any of the known adhesins. Conversely, all mutants tested, except in yapH, were altered in their vascular transmission to seed. In conclusion, we showed that adhesins are implicated in the various processes leading to host phyllosphere colonization and transmission to seed by plant-pathogenic bacteria.
Response criteria for phase II studies of supratentorial malignant glioma. (1990)

We suggest "new" response criteria for phase II studies of supratentorial malignant glioma and favor rigorous criteria similar to those in medical oncology, with important modifications. Four response categories are proposed: complete response (CR), partial response (PR), stable disease (SD), and progressive disease (PD). Response in this scheme is based on major changes in tumor size on the enhanced computed tomographic (CT) or magnetic resonance imaging (MRI) scan. Scan changes are interpreted in light of steroid use and neurologic findings. We advocate careful patient selection, emphasize pitfalls in the assessment of response, and suggest guidelines to minimize misinterpretations of response.
Bacterial DNA and immunostimulatory CpG oligonucleotides trigger maturation and activation of murine dendritic cells (1998)

Bacterial DNA and immunostimulatory (i.s.) synthetic CpG-oligodeoxynucleotides (ODN) act as adjuvants for Th1 responses and cytotoxic T cell responses to proteinaceous antigens. Dendritic cells (DC) can be referred to as "nature's adjuvant" since they display the unique capacity to sensitize naive T cells. Here, we demonstrate that bacterial DNA or i.s. CpG-ODN cause simultaneous maturation of immature DC and activation of mature DC to produce cytokines. These events are associated with the acquisition of professional antigen-presenting cell (APC) function. Unfractionated murine bone marrow-derived DC and FACS-fractionated MHC class IIlow (termed immature DC) or MHC class IIhigh populations (termed mature DC) were stimulated with bacterial DNA or i.s. CpG-ODN. Similar to lipopolysaccharide, i.s. CpG-ODN caused up-regulation of MHC class II, CD40 and CD86, but not CD80 on immature and mature DC. In parallel both DC subsets were activated to produce large amounts of IL-12, IL-6 and TNF-alpha. CpG-ODN-activated DC displayed professional APC function in allogeneic mixed lymphocyte reaction and in staphylococcal enterotoxin B-driven naive T cell responses. We interpret these findings to mean that bacterial DNA and i.s. CpG-ODN cause maturation (first step) and activation (second step) of DC to bring about conversion of immature DC into professional APC.
Nonenzymatic Deamidation of Asparaginyl and Glutaminyl Residues in Protein (1991)

Some asparagine and glutamine residues in proteins undergo deamidation to aspartate and glutamate with rates that depend upon the sequence and higher-order structure of the protein. Functional groups within the protein can catalyze this reaction, acting as general acids, bases, or stabilizers of the transition state. Information from specific proteins that deamidate and analysis of protein sequence and structure data bases suggest that asparagine and glutamine lability has been a selective pressure in the evolution of protein sequence and folding. Asparagine and glutamine deamidation can affect protein structure and function in natural and engineered mutant sequences, and may play a role in the regulation of protein folding, protein breakdown, and aging.
Regeneration of mouse liver after partial hepatectomy. (1953)

Summary Extirpation of 65 per cent of the mouse liver results in rapid growth of the remaining lobes, so that the original mass, in terms of percentage of liver to body weight, is essentially restored by the sixth day. However, the original total liver weight, nitrogen, and desoxyribonucleic acid are not completely recovered until the eighth day. The total number of nuclei increases more slowly and reaches 87 per cent of the normal value at 28 days after hepatectomy. Parenchymal nuclei comprise only 56 per cent of the total nuclei of normal mouse liver, the remainder belonging to bile duct, Kupffer, connective tissue, smooth muscle, and mesothelial cells and also to macrophages and leukocytes. These nonparenchymal elements are increased between the third and 45th days of regeneration. Substantial individual variation is observed in the response of mice to partial hepatectomy. The time interval after operation is not a satisfactory, uniform criterion of the degree of restoration of the liver remnant in individual mice.
Flexible aliphatic-bridged bisphenol-based polybenzoxazines (2012)

In this paper, we report the synthesis of a series of novel aliphatic-bridged bisphenol-based benzoxazine monomers comprising four to ten methylene unit spacers (BZ(n)BA). Cationic ring-opening polymerization of these monomers provides flexible polybenzoxazine thermosets with good film forming characteristics under solvent-free processing conditions. The effects of aliphatic bisphenol chain length on polymerization behavior, thermomechanical transitions, and mechanical properties of the polybenzoxazine thermosets are reported. Fourier transform-infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC) show the ring-opening polymerization proceeds to high conversion with minimal dependence on spacer chain length. Thermomechanical properties of the pBZ(n)BA thermosets, such as rubbery storage modulus and glass transition temperature (Tg), show a strong dependence on the length of the aliphatic-bridged bisphenol linker where both properties decrease with increasing linker length. In particular, changing the length of the aliphatic-bridged bisphenol linker enables tailoring the Tg of the pBZ(n)BA series from 67 °C to 101 °C, as determined by dynamic mechanical analysis (DMA). Tensile properties of the pBZ(n)BA series exhibit similar trends with Young's modulus decreasing and elongation at break increasing with increasing aliphatic-bridged bisphenol linker length. The pBZ(n)BA materials all show a similar three mode degradation process by thermogravimetric analysis (TGA) consistent with other bisphenol based polybenzoxazines, and additionally exhibit a decrease in char yield with increasing aliphatic chain length owing to a decrease in aromatic content in the thermoset network.
A pulmonary influenza virus infection in SCID mice can be cured by treatment with hemagglutinin-specific antibodies that display very low virus-neutralizing activity in vitro (1997)

We have previously shown that a pulmonary influenza virus infection in SCID mice can be cured by treatment with monoclonal antibodies (MAbs) specific for the viral transmembrane protein hemagglutinin (HA) but not for matrix 2. Since both types of MAbs react with infected cells but only the former neutralizes the virus, it appeared that passive MAbs cured by neutralization of progeny virus rather than reaction with infected host cells. To prove this, we selected a set of four HA-specific MAbs, all of the immunoglobulin G2a isotype, which reacted well with native HA expressed on infected cells yet differed greatly (>10,000-fold) in virus neutralization (VN) activity in vitro, apparently because of differences in antibody avidity and accessibility of the respective determinants on the HA of mature virions. Since the VN activities of these MAbs in vitro were differentially enhanced by serum components, we determined their prophylactic activities in vivo and used them as measures of their actual VN activities in vivo. The comparison of therapeutic and prophylactic activities indicated that these MAbs cured the infection to a greater extent by VN activity (which was greatly enhanced in vivo) and to a lesser extent by reaction with infected host cells. Neither complement- nor NK cell-dependent mechanisms were involved in the MAb-mediated virus clearance.
Molecular and functional analysis of PRKAR1A and its locus (17q22-24) in sporadic adrenocortical tumors: 17q losses, somatic mutations, and protein kinase A expression and activity. (2003)

Germ-line protein kinase A (PKA) regulatory-subunit type-Ialpha (RIalpha; PRKAR1A)-inactivating mutations and loss-of-heterozygosity (LOH) of its 17q22-24 locus have been found in Cushing syndrome (CS) caused by primary pigmented nodular adrenocortical disease (PPNAD). We examined whether somatic 17q22-24, PRKAR1A, or PKA changes are present in 44 sporadic adrenocortical tumors (29 adenomas and 15 cancers); 26 of these tumors were responsible for CS. A probe containing the PRKAR1A gene-mapped by fluorescent in situ hybridization to 17q22-24-and corresponding microsatellite markers were used to study allelic losses; PRKAR1A was sequenced in all samples. 17q22-24 losses were seen in 23 and 53% of adenomas and cancers, respectively. In three tumors, somatic, PRKAR1A-inactivating mutations were identified: (a) a nonsense mutation in exon 6 (A751G); (b) a splicing mutation (9IVS-1G/A); and (c) a transition (1050T>C) followed by a 22-bp deletion, also in exon 9; all predicted premature RIalpha protein terminations. Quantitative message and protein studies showed RIalpha down-regulation in tumors with genetic changes; their cortisol secretion pattern was similar to that of PPNAD, and they had higher PKA activity by enzymatic studies. We conclude that somatic allelic losses of the 17q22-24 region, PRKAR1A-inactivating mutations or down-regulation, and corresponding PKA activity changes are present in at least some sporadic adrenocortical tumors, especially those with a PPNAD-like clinical presentation of CS.
Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. (2003)

In modern clinical neuro-oncology, histopathological diagnosis affects therapeutic decisions and prognostic estimation more than any other variable. Among high-grade gliomas, histologically classic glioblastomas and anaplastic oligodendrogliomas follow markedly different clinical courses. Unfortunately, many malignant gliomas are diagnostically challenging; these nonclassic lesions are difficult to classify by histological features, generating considerable interobserver variability and limited diagnostic reproducibility. The resulting tentative pathological diagnoses create significant clinical confusion. We investigated whether gene expression profiling, coupled with class prediction methodology, could be used to classify high-grade gliomas in a manner more objective, explicit, and consistent than standard pathology. Microarray analysis was used to determine the expression of approximately 12000 genes in a set of 50 gliomas, 28 glioblastomas and 22 anaplastic oligodendrogliomas. Supervised learning approaches were used to build a two-class prediction model based on a subset of 14 glioblastomas and 7 anaplastic oligodendrogliomas with classic histology. A 20-feature k-nearest neighbor model correctly classified 18 of the 21 classic cases in leave-one-out cross-validation when compared with pathological diagnoses. This model was then used to predict the classification of clinically common, histologically nonclassic samples. When tumors were classified according to pathology, the survival of patients with nonclassic glioblastoma and nonclassic anaplastic oligodendroglioma was not significantly different (P = 0.19). However, class distinctions according to the model were significantly associated with survival outcome (P = 0.05). This class prediction model was capable of classifying high-grade, nonclassic glial tumors objectively and reproducibly. Moreover, the model provided a more accurate predictor of prognosis in these nonclassic lesions than did pathological classification. These data suggest that class prediction models, based on defined molecular profiles, classify diagnostically challenging malignant gliomas in a manner that better correlates with clinical outcome than does standard pathology.
Multi-Magnetometer Based Perturbation Mitigation for Indoor Orientation Estimation (2011)

ABSTRACT: Determining orientation with respect to a known reference plays an important role in almost all modes of navigation. As the sensors required for measuring magnetic field have found their way into portable navigation devices, researchers have started investigating their application to orientation estimation in different environments. Nevertheless, the success of these sensors for orientation estimation is conditioned by their capacity to sense Earth's magnetic field in environments full of magnetic anomalies like urban canyons and indoors. These artificial fields contaminate Earth's magnetic field measurements, making orientation estimation very difficult in heavily perturbed areas. To overcome the effect of magnetic anomalies, a perturbation mitigation technique is proposed that utilizes multiple magnetometers. This mitigation technique is then used for estimating Earth's magnetic field indoors thus providing users with better magnetic orientation estimates. Performance of the proposed mitigation technique is assessed for pedestrian navigation in a shopping mall.
Modification of polysiloxane polymers for biomedical applications: a review (2001)

Abstract This paper reviews methods of modifying polydimethylsiloxane (PDMS) polymers to improve their properties for biomedical applications. The modification methods are discussed under three different categories: bulk, surface and other modification techniques. Surface modification techniques include physical and chemical techniques to modify polymer surfaces. Bulk modification techniques include blending, copolymerization, interpenetrating polymer networks (IPNs) and functionalization. The third category includes less common modification techniques. © 2001 Society of Chemical Industry
Harnessing human ADAR2 for RNA repair – Recoding a PINK1 mutation rescues mitophagy (2016)

Site-directed A-to-I RNA editing is a technology for re-programming genetic information at the RNA-level. We describe here the first design of genetically encodable guideRNAs that enable the re-addressing of human ADAR2 toward specific sites in user-defined mRNA targets. Up to 65% editing yield has been achieved in cell culture for the recoding of a premature Stop codon (UAG) into tryptophan (UIG). In the targeted gene, editing was very specific. We applied the technology to recode a recessive loss-of-function mutation in PINK1 (W437X) in HeLa cells and showed functional rescue of PINK1/Parkin-mediated mitophagy, which is linked to the etiology of Parkinson's disease. In contrast to other editing strategies, this approach requires no artificial protein. Our novel guideRNAs may allow for the development of a platform technology that requires only the administration or expression of a guideRNA to recode genetic information, with high potential for application in biology and medicine.
Synthesis of new amino acids mimicking sulfated and phosphorylated tyrosine residues (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of new amino acids mimicking sulfated and phosphorylated tyrosine residuesI. Marseigne and B. P. RoquesCite this: J. Org. Chem. 1988, 53, 15, 3621–3624Publication Date (Print):July 1, 1988Publication History Published online1 May 2002Published inissue 1 July 1988https://pubs.acs.org/doi/10.1021/jo00250a043https://doi.org/10.1021/jo00250a043research-articleACS PublicationsRequest reuse permissionsArticle Views690Altmetric-Citations76LEARN 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