gebhart/patrepeval huggingface dataset:
3D Interconnected Ionic Nano-Channels Formed in Polymer Films: Self-Organization and Polymerization of Thermotropic Bicontinuous Cubic Liquid Crystals (2011)

Thermotropic bicontinuous cubic (Cub(bi)) liquid-crystalline (LC) compounds based on a polymerizable ammonium moiety complexed with a lithium salt have been designed to obtain lithium ion-conductive all solid polymeric films having 3D interconnected ionic channels. The monomer shows a Cub(bi) phase from -5 to 19 °C on heating. The complexes retain the ability to form the Cub(bi) LC phase. They also form hexagonal columnar (Col(h)) LC phases at temperatures higher than those of the Cub(bi) phases. The complex of the monomer and LiBF(4) at the molar ratio of 4:1 exhibits the Cub(bi) and Col(h) phases between -6 to 19 °C and 19 to 56 °C, respectively, on heating. The Cub(bi) LC structure formed by the complex has been successfully preserved by in situ photopolymerization through UV irradiation in the presence of a photoinitiator. The resultant nanostructured film is optically transparent and free-standing. The X-ray analysis of the film confirms the preservation of the self-assembled nanostructure. The polymer film with the Cub(bi) LC nanostructure exhibits higher ionic conductivities than the polymer films obtained by photopolymerization of the complex in the Col(h) and isotropic phases. It is found that the 3D interconnected ionic channels derived from the Cub(bi) phase function as efficient ion-conductive pathways.
Direct Detection of Membrane Channels from Gels Using Water-in-Oil Droplet Bilayers (2007)

We form planar lipid bilayers between an aqueous droplet and a hydrogel support immersed in a lipid-oil solution. By scanning the bilayer over the surface of an SDS-PAGE gel, we are able to directly detect membrane proteins from gels using single-channel recording. Using this technique, we are able to examine low levels of endogenous protein from cell extracts without the need for over-expression. We also use droplet bilayers to detect small molecules from hydrogels. The bilayers show enhanced stability compared to conventional planar lipid bilayers, and both bilayer size and position can be controlled during an experiment. Hydrogel scanning with droplet bilayers provides a new method for the discovery and characterization of ion channels with the potential for high-throughput screening.
Transmission-blocking activity of antibodies to Plasmodium falciparum GLURP.10C chimeric protein formulated in different adjuvants (2015)

The combined data provide a strong basis for entering the next phase of clinical grade R0.10C production and testing.
Insertional mutagenesis and marker rescue in a protozoan parasite: cloning of the uracil phosphoribosyltransferase locus from Toxoplasma gondii. (1995)

Nonhomologous integration vectors have been used to demonstrate the feasibility of insertional mutagenesis in haploid tachyzoites of the protozoan parasite Toxoplasma gondii. Mutant clones resistant to 5-fluorouracil were identified at a frequency of approximately 10(-6) (approximately 2 x 10(-5) of the stable transformants). Four independent mutants were isolated, all of which were shown to lack uracil phosphoribosyl-transferase (UPRT) activity and harbor transgenes integrated at closely linked loci, suggesting inactivation of the UPRT-encoding gene. Genomic DNA flanking the insertion point (along with the integrated vector) was readily recovered by bacterial transformation with restriction-digested, self-ligated total genomic DNA. Screening of genomic libraries with the recovered fragment identified sequences exhibiting high homology to known UPRT-encoding genes from other species, and cDNA clones were isolated that contain a single open reading frame predicted to encode the 244-amino acid enzyme. Homologous recombination vectors were exploited to create genetic knock-outs at the UPRT locus, which are deficient in enzyme activity but can be complemented by transient transformation with wild-type sequences--formally confirming identification of the functional UPRT gene. Mapping of transgene insertion points indicates that multiple independent mutants arose from integration at distinct sites within the UPRT gene, suggesting that nonhomologous integration is sufficiently random to permit tagging of the entire parasite genome in a single transformation.
Sluggish Development of Parallel Lamellae at the Strongly Interacting Interface in Thin Films of Symmetric Diblock Copolymers (2002)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTSluggish Development of Parallel Lamellae at the Strongly Interacting Interface in Thin Films of Symmetric Diblock CopolymersByeong-Hyeok Sohn, Byung-Wook Seo, Seong Il Yoo, and Wang-Cheol ZinView Author Information Department of Materials Science and Engineering, Polymer Research Institute, Pohang University of Science and Technology, Pohang 790-784, Korea Cite this: Langmuir 2002, 18, 26, 10505–10508Publication Date (Web):December 2, 2002Publication History Received12 September 2002Revised23 October 2002Published online2 December 2002Published inissue 1 December 2002https://pubs.acs.org/doi/10.1021/la026538vhttps://doi.org/10.1021/la026538vbrief-reportACS PublicationsCopyright © 2002 American Chemical SocietyRequest reuse permissionsArticle Views172Altmetric-Citations12LEARN 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 SUBJECTS:Atmospheric chemistry,Interfaces,Layers,Silicon,Thin films Get e-Alerts
Recurrent BRAF Gene Fusions in a Subset of Pediatric Spindle Cell Sarcomas (2017)

Infantile fibrosarcomas (IFS) represent a distinct group of soft tissue tumors occurring in patients under 2 years of age and most commonly involving the extremities. Most IFS show recurrent ETV6-NTRK3 gene fusions, sensitivity to chemotherapy, and an overall favorable clinical outcome. However, outside these well-defined pathologic features, no studies have investigated IFS lacking ETV6-NTRK3 fusions, or tumors with the morphology resembling IFS in older children. This study was triggered by the identification of a novel SEPT7-BRAF fusion in an unclassified retroperitoneal spindle cell sarcoma in a 16-year-old female by targeted RNA sequencing. Fluorescence in situ hybridization screening of 9 additional tumors with similar phenotype and lacking ETV6-NTRK3 identified 4 additional cases with BRAF gene rearrangements in the pelvic cavity (n=2), paraspinal region (n=1), and thigh (n=1) of young children (0 to 3 y old). Histologically, 4 cases including the index case shared a fascicular growth of packed monomorphic spindle cells, with uniform nuclei and fine chromatin, and a dilated branching vasculature; while the remaining case was composed of compact cellular sheets of short spindle to ovoid cells. In addition, a minor small blue round cell component was present in 1 case. Mitotic activity ranged from 1 to 9/10 high power fields. Immunohistochemical stains were nonspecific, with only focal smooth muscle actin staining demonstrated in 3 cases tested. Of the remaining 5 BRAF negative cases, further RNA sequencing identified 1 case with EML4-NTRK3 in an 1-year-old boy with a foot IFS, and a second case with TPM3-NTRK1 fusion in a 7-week-old infant with a retroperitoneal lesion. Our findings of recurrent BRAF gene rearrangements in tumors showing morphologic overlap with IFS expand the genetic spectrum of fusion-positive spindle cell sarcomas, to include unusual presentations, such as older children and adolescents and predilection for axial location, thereby opening new opportunities for kinase-targeted therapeutic intervention.
Nucleolin, the major nucleolar protein of growing eukaryotic cells: an unusual protein structure revealed by the nucleotide sequence. (1987)

Nucleolin (also called C23) is the major nucleolar protein of exponentially growing eukaryotic cells. It is found associated with intranucleolar chromatin and preribosomal particles. Through use of a polyclonal antiserum, nucleolin cDNA clones were isolated from a Chinese hamster ovary cell library constructed in the expression vector lambda gt11. The isolated cDNAs encoded a polypeptide containing 679 residues of the 713 amino acids of nucleolin. The amino acid sequence presents several unusual features: in particular, repetitive sequences are found at both ends of the molecule. A repeat, Hy-Thr-Pro-Hy-Lys-Lys-Hy-Hy, in which Hy is a nonpolar residue, is found six times in the NH2-end proximal portion, followed by three acidic stretches containing 25, 25, and 33 glutamic acid or aspartic acid residues. Four potential phosphorylation sites (serines) are also observed in this region. The COOH-terminal proximal portion of the protein carries a glycine-rich region with fairly regularly interspersed phenylalanine and dimethylarginine residues. The two terminal portions of the molecule exhibit unique potential secondary structures: alpha-helix (NH2 terminus) and extended (COOH terminus). The central region exhibits alternating hydrophobic and hydrophilic stretches. Five potential N glycosylation sites are detected. The structure of this protein may reflect two functions in preribosome biogenesis: interaction with chromatin (NH2 terminus) and with preribosomes (COOH terminus).
Expression and localization of activin receptors during endochondral bone development (2001)

The expression and localization of activins (dimeric protein of inhibin beta subunit) and activin receptors in skeletal tissue were examined. RT-PCR revealed that cultured chondrocytes expressed mRNAs of inhibin/activin betaA and four activin receptors (two type I (ActRI and ActRIB) and two type II (ActRII and ActRIIB)). Immunohistochemical analyses showed that activin betaA, ActRI and ActRII were localized in proliferating chondrocytes and osteoblasts in tibiae of neonatal rats, and in implants of demineralized bone matrix, a well-established model of ectopic bone formation. The immunoreactivities of osteoblasts were decreased with aging in the tibiae and with progressing endochondral bone development in the implants. The strong expression of ActRI was also detected in hypertrophic chondrocytes both in the tibial growth plate and in the implants, whereas immunoreactive ActRII was lower in hypertrophic chondrocytes. Western blot analysis also showed that immunoreactive ActRI, migrating at 52 kDa, was detected only in the implants on days 9 and 11, the period of conversion from cartilage to bone. In view of the sharing of type II receptors between activins and bone morphogenetic proteins (BMPs), our findings suggest that activin/BMP activity involves in bone modeling, especially during active chondro- and osteogenesis and during the conversion from cartilage to bone.
Single Ketamine Infusion and Neurocognitive Performance in Bipolar Depression (2014)

We estimated neurocognitive performance using the trail making test (TMT) and the Stroop color-word interference test before, and on the 3(rd) day after a single infusion of ketamine, in 18 bipolar depressed patients receiving mood-stabilizing drugs. The performance on all tests significantly improved on the 3(rd) day after ketamine infusion which correlated positively with baseline intensity of neuropsychological impairment and was not associated either with baseline intensity of depression or reduction of depressive symptoms after 3 or 7 days. The results suggest that in such population of patients, single ketamine infusion may improve neuropsychological performance independently of antidepressant effect.
Calcitonin Gene-Related Peptide: Physiology and Pathophysiology (2014)

Calcitonin gene-related peptide (CGRP) is a 37-amino acid neuropeptide. Discovered 30 years ago, it is produced as a consequence of alternative RNA processing of the calcitonin gene. CGRP has two major forms (α and β). It belongs to a group of peptides that all act on an unusual receptor family. These receptors consist of calcitonin receptor-like receptor (CLR) linked to an essential receptor activity modifying protein (RAMP) that is necessary for full functionality. CGRP is a highly potent vasodilator and, partly as a consequence, possesses protective mechanisms that are important for physiological and pathological conditions involving the cardiovascular system and wound healing. CGRP is primarily released from sensory nerves and thus is implicated in pain pathways. The proven ability of CGRP antagonists to alleviate migraine has been of most interest in terms of drug development, and knowledge to date concerning this potential therapeutic area is discussed. Other areas covered, where there is less information known on CGRP, include arthritis, skin conditions, diabetes, and obesity. It is concluded that CGRP is an important peptide in mammalian biology, but it is too early at present to know if new medicines for disease treatment will emerge from our knowledge concerning this molecule.
Shape-Controlled Synthesis of Pt Nanocrystals: The Role of Metal Carbonyls (2012)

Well-controlled synthesis of nanocrystals is necessary to unambiguously correlate the structural properties of nanocrystals with the catalytic properties. The most common low-index surfaces are (111) and (100). Therefore, model materials with {111} and {100} facets are highly desirable, in order to understand the catalytic properties of (111) and (100) surfaces for various structure-sensitive reactions. We report a solution-phase synthesis using metal carbonyls as additives. This synthetic method produces highly monodisperse Pt octahedra and icosahedra as the model of Pt{111}, Pt cubes as the model of Pt{100}, respectively. Several other morphologies, such as truncated cubes, cuboctahedra, spheres, tetrapods, star-shaped octapods, multipods, and hyper-branched structure, are produced, as well. A bifunctional role of metal carbonyl in the synthesis is identified: zerovalent transition metal decomposed from metal carbonyl acts as a shape-directing agent, while CO provides the reducing power. These high-quality shape-controlled Pt nanocrystals are suitable for model catalyst studies.
Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region (1993)

Hepatitis C virus (HCV) showed substantial nucleotide sequence diversity distributed throughout the viral genome, with many variants showing only 68 to 79% overall sequence similarity to one another. Phylogenetic analysis of nucleotide sequences derived from part of the gene encoding a non-structural protein (NS-5) has provided evidence for six major genotypes of HCV amongst a worldwide collection of 76 samples from HCV-infected blood donors and patients with chronic hepatitis. Many of these HCV types comprised a number of more closely related subtypes, leading to a current total of 11 genetically distinct viral populations. Phylogenetic analysis of other regions of the viral genome produced relationships between published sequences equivalent to those found in NS-5, apart from the more highly conserved 5' non-coding region in which only the six major HCV types, but not subtypes, could be differentiated. A new nomenclature for HCV variants is proposed in this communication that reflects the two-tiered nature of sequence differences between different viral isolates. The scheme classifies all known HCV variants to date, and describes criteria that would enable new variants to be assigned within the classification as they are discovered.
Self‐assembly of carbon nanotube field‐effect transistors by ac‐dielectrophoresis (2006)

Abstract We report an entirely self‐assembly based method for the bottom‐up fabrication of carbon nanotube (CNT) field effect transistors (FETs). First, the single‐walled CNTs are dispersed in water by means of single‐stranded DNA. Thereafter, CNT connects are grown between adjacent metal electrodes by ac‐dielectrophoresis. Finally, to obtain high‐performance FETs, the metallic CNTs are eliminated by burning them through applying an intensive current while the semiconducting ones are switched off. In this way, we were able to produce multi‐tube CNT‐FETs with on/off ratios larger than 1000. Here we describe the preparation of the devices along with their microscopic and electrical characterization. Possible applications of the fabricated CNT‐FETs are gas‐ or biosensors. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
A Nongastrin Malignant Ampullary Tumor Causing Gastric Acid and Pepsin Hypersecretion A Case Report (1990)

We report a case of multiple duodenal ulcers with gastric hypersecretion due to a nongastrin secretagogue produced by a malignant tumor of the pancreas in a 78-year-old man. The case resembled a Zollinger-Ellison syndrome (ZES) with high acid output (basal acid output 27, sham meal-stimulated 37, maximum acid output 47 mEq/h), but with fasting gastrin 43 pg/ml, nonresponsive to secretin. As in ZES, pepsin output was comparatively low, and secretion was inhibitable by atropine (50% inhibited by 1 microM). The tumor removed at surgery contained less than 1 ng gastrin per gram, but was many times more potent than pentagastrin in stimulating acid from a lumen-perfused rat stomach. The tumor also contained cholecystokinin (CCK-8 and CCK-33), motilin, insulin, and somatostatin, which were also present in adjacent normal pancreas; in addition, the tumor contained pancreatic polypeptide and pancreatic cancer-associated antigen. This case represents a rare syndrome due to an as yet undefined peptide secreted by a (frequently malignant) pancreatic endocrine tumor and masquerading as ZES. This is the first report of studies of pepsin secretion and of the effect of atropine, suggesting that the physiologic effects of the secretagogue resemble that of gastrin.
Alzheimer’s-related endosome dysfunction in Down syndrome is Aβ-independent but requires APP and is reversed by BACE-1 inhibition (2009)

An additional copy of the beta-amyloid precursor protein (APP) gene causes early-onset Alzheimer's disease (AD) in trisomy 21 (DS). Endosome dysfunction develops very early in DS and AD and has been implicated in the mechanism of neurodegeneration. Here, we show that morphological and functional endocytic abnormalities in fibroblasts from individuals with DS are reversed by lowering the expression of APP or beta-APP-cleaving enzyme 1 (BACE-1) using short hairpin RNA constructs. By contrast, endosomal pathology can be induced in normal disomic (2N) fibroblasts by overexpressing APP or the C-terminal APP fragment generated by BACE-1 (betaCTF), all of which elevate the levels of betaCTFs. Expression of a mutant form of APP that cannot undergo beta-cleavage had no effect on endosomes. Pharmacological inhibition of APP gamma-secretase, which markedly reduced Abeta production but raised betaCTF levels, also induced AD-like endosome dysfunction in 2N fibroblasts and worsened this pathology in DS fibroblasts. These findings strongly implicate APP and the betaCTF of APP, and exclude Abeta and the alphaCTF, as the cause of endocytic pathway dysfunction in DS and AD, underscoring the potential multifaceted value of BACE-1 inhibition in AD therapeutics.
Evaluation of DNA extraction methods and real time PCR optimization on formalin-fixed paraffin-embedded tissues. (2007)

Formalin-fixed, paraffin-embedded (FFPE) tissues are the most invaluable source of diagnostic material for studying pathogenesis of cancer and a variety of other diseases. Unfortunately, DNA extracted from formalin fixed tissues is highly degraded due to cross-linking between nucleic acid strands. Real Time PCR has become the standard for gene copy as well as RNA transcript determination. Thus, optimum standardization of Real Time PCR is crucial for obtaining accurate quantification for both research as well as for clinical diagnosis. However there are various factors which have negative impact . The aim of our study was to establish a simpler method of extraction and Real Time PCR Optimization for FFPE extracted DNA. Five breast cancer tissues that were formalin fixed and paraffin embedded were used for DNA extraction with four different methods. Extracted DNA was amplified with different primer sets that gave amplimers of different size. Optimization of Real Time PCR for EMSY, cyclin D1 and beta-globin genes was carried out on DNA obtained using heat treatment protocol for annealing temperature, primer concentration and template concentration. Highest quantity of DNA was obtained without the use of expensive reagents and in short time frame. PCR positivity was observed in case of shorter amplimer up to 250 bp in length. Amplimers of higher length failed to amplify with paraffin extracted DNA. Optimum annealing temperature for EMSY, Cyclin D1 and beta-globin genes were 60 degrees C, 60 degrees C and 61 degrees C respectively. Good results were seen with a primer concentration of 300 nM and 5 ng of template DNA. This study indicates that DNA obtained from formalin fixed paraffin embedded tissue is highly fragmented and can be used for successful amplification of shorter amplification products up to 250 bp in length. Optimization of real time PCR is important, especially while using SYBR green dye chemistry.
Three pathways between the sacroiliac joint and neural structures. (1999)

Three pathways between the SIJ and neural structures exist.
Dynamic Interplay between O-Glycosylation and O-Phosphorylation of Nucleocytoplasmic Proteins (2002)

Previously, we reported that c-Myc is glycosylated by O-linked N-acetylglucosamine at Thr-58, a known phosphorylation site and a mutational hot spot in lymphomas. In this paper, we describe the production and characterization of two Thr-58 site-specific antibodies and use them to examine the modification of Thr-58 in living cells. One antibody specifically reacts with the Thr-58-glycosylated form of c-Myc, and the other reacts only with unmodified Thr-58 in c-Myc. Using these antibodies together with a commercial anti-Thr-58-phosphorylated c-Myc antibody, we simultaneously detected three forms of c-Myc (Thr-58-unmodified, -phosphorylated, and -glycosylated). It has been reported that Thr-58 phosphorylation is dependent on a prior phosphorylation of Ser-62. Mutagenesis of Ser-62 to Ala showed a marked decrease of Thr-58 phosphorylation and a marked increase of Thr-58 glycosylation. Growth inhibition of HL60 cells by serum starvation increases Thr-58 glycosylation and correspondingly decreases its phosphorylation. Serum stimulation has the opposite effect upon the modification status of Thr-58. A candidate kinase responsible for Thr-58 phosphorylation is the glycogen synthase kinase 3 (GSK3). Lithium, a competitive inhibitor of GSK3, decreased Thr-58 phosphorylation and increased its glycosylation. Finally, we show that the Thr-58-phosphorylated form of c-Myc predominantly accumulates in the cytoplasm rather than the nucleus upon inhibition of proteasome activity. These data suggest that hierarchical phosphorylation of Ser-62 and Thr-58 and alternative glycosylation/phosphorylation of Thr-58 together regulate the myriad functions of c-Myc in cells.