gebhart/patrepeval huggingface dataset:
The Pangenome Structure ofEscherichia coli: Comparative Genomic Analysis ofE. coliCommensal and Pathogenic Isolates (2008)

Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of approximately 2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.
Unusual Regulatory Elements for Iron Deficiency Induction of the idiA Gene of Synechococcus elongatus PCC 7942 (2001)

Expression of a thylakoid membrane-associated protein called IdiA (iron-deficiency-induced protein A) is highly elevated and tightly regulated by iron limitation in Synechococcus elongatus PCC 6301 and PCC 7942. Although this protein is not essential for photosystem II (PSII) activity, it plays an important role in protecting the acceptor side of PSII against oxidative damage, especially under iron-limiting growth conditions, by an unknown mechanism. We defined the iron-responsive idiA promoter by using insertional inactivation mutagenesis and reporter gene assays. A 67-bp DNA region was sufficient for full iron deficiency-inducible idiA promoter activity. Within this fragment is a palindromic sequence 4 bp upstream of a putative -35 promoter element, which resembles the binding site of FNR/CAP-type helix-turn-helix transcription factors. The absence of this palindromic sequence or a 3-bp mutation in a putative -10 region eliminated promoter activity completely. A previously identified candidate for a positively acting transcription factor is the IdiB protein, whose gene lies immediately downstream of idiA. IdiB shows strong similarity to helix-turn-helix transcription factors of the FNR/CAP family. A His(6x)-tagged IdiB that was overexpressed in Escherichia coli bound to a 59-bp fragment of the idiA regulatory region that included the palindrome. Although the idiA promoter lacks a consensus binding site for the iron-sensing regulator Fur, we attempted to inactivate fur in order to investigate the potential role of this factor. The resulting merodiploid mutants showed constitutive partial derepression of IdiA expression under iron-sufficient growth conditions. We concluded that IdiB is a specific iron-responsive regulator of idiA and that Fur has an indirect role in influencing idiA expression.
Surgical technique of meniscal replacement (1993)

Meniscal replacement by allograft and prosthesis is under laboratory and investigational clinical practice. In order to succeed, a replacement must duplicate the exact mechanical function of the original meniscal cartilage. The technique of replacement described in this article permits minimal disruption of the joint tissues, accurate placement of the meniscal horns, and secure fixation of the meniscal synovial junction.
Treatment-Induced Cortical Reorganization After Stroke in Humans (2000)

This is the first demonstration in humans of a long-term alteration in brain function associated with a therapy-induced improvement in the rehabilitation of movement after neurological injury.
MR molecular imaging and fluorescence microscopy for identification of activated tumor endothelium using a bimodal lipidic nanoparticle (2005)

In oncological research, there is a great need for imaging techniques that specifically identify angiogenic blood vessels in tumors on the basis of differences in the expression level of biomolecular markers. In the angiogenic cascade, different cell surface receptors, including the alphavbeta3-integrin, are strongly expressed on activated endothelial cells. In the present study, we aimed to image angiogenesis by detecting the expression of alphavbeta3 in tumor bearing mice with a combination of magnetic resonance imaging (MRI) and fluorescence microscopy. To that end, we prepared MR-detectable and fluorescent liposomes, which carry approximately 700 alphavbeta3-specific RGD peptides per liposome. RGD competition experiments and RAD-conjugated liposomes were used as controls for specificity. In vivo, both RAD liposomes and RGD liposomes gave rise to signal increase on T1-weighted MR images. It was established by the use of ex vivo fluorescence microscopy that RGD liposomes and RAD liposomes accumulated in the tumor by different mechanisms. RGD liposomes were specifically associated with activated tumor endothelium, while RAD liposomes were located in the extravascular compartment. This study demonstrates that MR molecular imaging of angiogenesis is feasible by using a targeted contrast agent specific for the alphavbeta3-integrin, and that the multimodality imaging approach gave insight into the exact mechanism of accumulation in the tumor.
Synthesis, Characterization, and Electrochemistry of a Series of Iron(II) Complexes Containing Self-Assembled 1,5-Diaza-3,7-diphosphabicyclo[3.3.1]nonane Ligands (2009)

The reaction between PPh(CH(2)OH)(2), iron(II) sulfate, ammonium sulfate, and formaldehyde in aqueous solution gives the iron(II) complex [Fe(kappa(2)-O(2)SO(2))L(2)] (1), where L is the bidentate phosphine ligand 3,7-diphenyl-1,5-diaza-3,7-diphosphabicyclo[3.3.1]nonane. During the course of the reaction, the ligand L self-assembles on the metal center. The reaction between PPh(CH(2)OH)(2), iron(II) chloride, ammonium chloride, and formaldehyde under similar conditions gives cis-[FeCl(2)L(2)] (cis-2). The complex cis-2 is converted into trans-2 in Et(2)O, whereas in water it is converted into cis-[Fe(OH(2))(2)L(2)](2+), though both of these interconversions are reversible. The chloro ligands in cis-2 are readily displaced by reaction with thiocyanate, azide, and carbonate to give cis- and trans-[Fe(NCS)(2)L(2)] (cis- and trans-3), cis- and trans-[Fe(N(3))(2)L(2)] (cis- and trans-4), and [Fe(kappa(2)-O(2)CO)L(2)] (5), respectively. The complex cis-2 reacts with CO in water to give trans-[FeCl(CO)L(2)]Cl (trans-6), whereas trans-2 reacts with CO in diethyl ether to give cis-[FeCl(CO)L(2)]Cl (cis-6), though cis-6 isomerizes in water to form trans-6. The reaction of cis-2 with sodium borohydride gives the hydride chloride complex trans-[FeCl(H)L(2)] (7). Electrochemical studies have been undertaken on complexes 1, cis-2, and 7. These reveal reversible oxidations for cis-2 and 7, with the latter giving rise to an unusual 17-electron iron(III) hydride chloride complex. Crystal structures have been obtained for 1, trans-2, trans-3, 5, and 7.
Additive and supra-additive cytotoxicity of cisplatin-taxane combinations in ovarian carcinoma cell lines (1998)

The purpose of this study was to compare the growth-inhibitory effect of cisplatin-paclitaxel with that obtained with a cisplatin-docetaxel combination and to assess the type of interaction. Concomitant use of taxanes and cisplatin was studied in seven human ovarian carcinoma cell lines, using the 96-well plate clonogenic assay. Chemosensitivity was expressed in terms of IC50 values, the drug concentration causing 50% inhibition of clonogenic survival. The type of interaction was studied using the area under the survival curve ratios (AUC ratios) obtained by numerical integration. Comparison of the AUC ratio and the surviving fraction (SF) value after taxane alone was made using Student's t-test. The influence of the drug concentration was tested by one-way analysis of variance (Anova). A supra-additive or additive effect was seen when seven ovarian carcinoma cell lines were exposed to paclitaxel or docetaxel concomitantly with cisplatin. A supra-additive effect was found in four cell lines (UT-OC-3, UT-OC-4, UT-OC-5 and SK-OV-3) after simultaneous use of cisplatin with all docetaxel concentrations tested, and in two cell lines (UT-OC-4 and SK-OV-3) when cisplatin was used concomitantly with paclitaxel. A more pronounced supra-additive effect was seen with the combination of cisplatin and docetaxel. The degree of supra-additivity was dose dependent, with increasing synergy after a higher taxane dose. The data obtained in this study suggest that a supra-additive or additive effect can be achieved in ovarian carcinoma with the concomitant use of cisplatin and a taxane.
Stereochemistry of ribostamycin biosynthesis. Application of hydrogen-2 NMR spectroscopy (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemistry of ribostamycin biosynthesis. Application of hydrogen-2 NMR spectroscopyKatsumi Kakinuma, Yasuaki Ogawa, Tohru Sasaki, Haruo Seto, and Noboru OtakeCite this: J. Am. Chem. Soc. 1981, 103, 18, 5614–5616Publication Date (Print):September 1, 1981Publication History Published online1 May 2002Published inissue 1 September 1981https://pubs.acs.org/doi/10.1021/ja00408a076https://doi.org/10.1021/ja00408a076research-articleACS PublicationsRequest reuse permissionsArticle Views151Altmetric-Citations31LEARN 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
Fabrication of patterned surfaces by photolithographic exposure of DNA hairpins carrying a novel photolabile group (2010)

This article demonstrates a method for the fabrication of patterned surfaces using hairpin oligonucleotides carrying a novel photolabile group at the apex of the loop. Photolysis of surfaces carrying photolabile hairpin oligonucleotides results in the formation of areas carrying single-stranded DNA sequences that direct the deposition of the complementary sequence at the photolysed sites. The non-photolysed areas carrying the intact hairpin do not bind to complementary sequences due to the presence of the more stable intramolecular hairpin duplex. The photolithographic process was performed on silicon wafers and followed by atomic force microscopy and epi-fluorescent microscopy. The method described offers an attractive option for the fabrication of biologically interfaced patterned surfaces with specific recognition properties with potential uses in electronics and as biosensors.
Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children (2016)

The results of our studies in humans and mice indicate that the Amish environment provides protection against asthma by engaging and shaping the innate immune response. (Funded by the National Institutes of Health and others.).
Hydrolysis in Pharmaceutical Formulations (2002)

This literature review presents hydrolysis of active pharmaceutical ingredients as well as the effects on dosage form stability due to hydrolysis of excipients. Mechanisms and measurement methods are discussed and recommendations for formulation stabilization are listed.
Synthetic Models for Low-Molecular-Weight Chromium-Binding Substance: Synthesis and Characterization of Oxo-Bridged Tetranuclear Chromium(III) Assemblies (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthetic Models for Low-Molecular-Weight Chromium-Binding Substance: Synthesis and Characterization of Oxo-Bridged Tetranuclear Chromium(III) AssembliesTruitt Ellis, Miriam Glass, Anthony Harton, Kristen Folting, John C. Huffman, and John B. VincentCite this: Inorg. Chem. 1994, 33, 24, 5522–5527Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/ic00102a028https://doi.org/10.1021/ic00102a028research-articleACS PublicationsRequest reuse permissionsArticle Views163Altmetric-Citations40LEARN 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 Get e-Alerts
Multiple myeloma biology: lessons from the 5TMM models (2003)

Multiple myeloma (MM) is a B cell neoplasm characterized by the monoclonal proliferation of plasma cells in the bone marrow, the development of osteolytic lesions and the induction of angiogenesis. These different processes require three-dimensional interactions, with both humoral and cellular contacts. The 5TMM models are suitable models to study these interactions. These murine models originate from spontaneously developed myeloma in elderly mice, which are propagated by in vivo transfer of the myeloma cells into young syngeneic mice. In this review we report on studies performed in the 5TMM models with special emphasis on the homing of the myeloma cells, the characterization of the migrating and proliferating clone and the identification of the isotype switch variants. The bone marrow microenvironment was further targeted with osteoprotegerin (OPG) to block the RANK/RANKL/OPG system and with potent bisphosphonates. Both treatments resulted in a significant protection against myeloma-associated bone disease, and they decreased myeloma disease, as evidenced by a lower tumor load and an increased survival of the mice. These different studies demonstrate the strength of these models, not only in unraveling basic biological processes but also in the testing of potentially new therapeutic targets.
Electrochemical polymerization of pyrrole on polymer-coated electrodes (1984)

O. Niwa and T. Tamamura, J. Chem. Soc., Chem. Commun., 1984, 817 DOI: 10.1039/C39840000817
GSK3β, But Not GSK3α, Inhibits the Neuronal Differentiation of Neural Progenitor Cells As a Downstream Target of Mammalian Target of Rapamycin Complex1 (2014)

Glycogen synthase kinase 3 (GSK3) acts as an important regulator during the proliferation and differentiation of neural progenitor cells (NPCs), but the roles of the isoforms of this molecule (GSK3α and GSK3β) have not been clearly defined. In this study, we investigated the functions of GSK3α and GSK3β in the context of neuronal differentiation of murine NPCs. Treatment of primary NPCs with a GSK3 inhibitor (SB216763) resulted in an increase in the percentage of TuJ1-positive immature neurons, suggesting an inhibitory role of GSK3 in embryonic neurogenesis. Downregulation of GSK3β expression increased the percentage of TuJ1-positive cells, while knock-down of GSK3α seemed to have no effect. When primary NPCs were engineered to stably express either isoform of GSK3 using retroviral vectors, GSK3β, but not GSK3α, inhibited neuronal differentiation and helped the cells to maintain the characteristics of NPCs. Mutant GSK3β (Y216F) failed to suppress neuronal differentiation, indicating that the kinase activity of GSK3β is important for this regulatory function. Similar results were obtained in vivo when a retroviral vector expressing GSK3β was delivered to E9.5 mouse brains using the ultrasound image-guided gene delivery technique. In addition, SB216763 was found to block the rapamycin-mediated inhibition of neuronal differentiation of NPCs. Taken together, our results demonstrate that GSK3β, but not GSK3α, negatively controls the neuronal differentiation of progenitor cells and that GSK3β may act downstream of the mammalian target of rapamycin complex1 signaling pathway.
Molecular Cloning of an Insect Aminopeptidase N That Serves as a Receptor for Bacillus thuringiensis CryIA(c) Toxin (1995)

The Bacillus thuringiensis CryIA(c) insecticidal delta-endotoxin binds to a 120-kDa glycoprotein receptor in the larval midgut epithelia of the susceptible insect Manduca sexta. This glycoprotein has recently been purified and identified as aminopeptidase N. We now report the cloning of aminopeptidase N from a M. sexta midgut cDNA library. Two overlapping clones were isolated, and their combined 3095-nucleotide sequence contains an open reading frame encoding a 990-residue pre-pro-protein. The N-terminal amino acid sequence derived from the glycoprotein is present in the open reading frame, immediately following a predicted cleavable signal peptide and a pro-peptide. There are four potential N-linked glycosylation sites. The C-terminal sequence contains a possible glycosylphosphatidylinositol (GPI) anchor signal peptide, which suggests that, unlike most other characterized aminopeptidases, the lepidopteran enzyme is anchored in the membrane by a GPI anchor. This was confirmed by partial release of aminopeptidase N activity from M. sexta midgut brush border membranes by phosphatidylinositol-specific phospholipase C. The deduced amino acid sequence shows significant similarity to the zinc-dependent aminopeptidase gene family, particularly in the region surrounding the consensus zinc-binding motif characteristic of these enzymes.
Preparation and structural characterization of large heparin-derived oligosaccharides (1995)

Porcine mucosal heparin was partially depolymerized with heparin lyase I and then fractionated into low-molecular-weight (< 5000) and high-molecular-weight (> 5000) oligosaccharides by pressure filtration. The high-molecular-weight oligosaccharide mixture (approximately 50 wt% of the starting heparin) also contained intact heparin. This intact polymer complicates oligosaccharide purification. Thus, the low-molecular-weight fraction was used to prepare homogeneous oligosaccharides for structural characterization. The low-molecular-weight oligosaccharide mixture was first fractionated by low-pressure gel permeation chromatography into size-uniform mixtures of disaccharides, tetrasaccharides, hexasaccharides, octasaccharides, decasaccharides, dodecasaccharides, tetradecasaccharides and higher oligosaccharides. Each size-fractionated mixture was then purified on the basis of charge by repetitive semi-preparative strong-anion-exchange high-performance liquid chromatography. This approach has led to the isolation of 14 homogeneous oligosaccharides from disaccharide to tetradecasaccharide. The purity of these heparin-derived oligosaccharides was determined by gradient polyacrylamide gel electrophoresis, analytical strong-anion-exchange high-performance liquid chromatography, capillary electrophoresis and one-dimensional nuclear resonance spectroscopy. The structure of these oligosaccharides was established using 600 MHz two-dimensional nuclear resonance spectroscopy. The spectral methods used included homonuclear correlation spectroscopy, nuclear Overhauser effect spectroscopy and heteronuclear multiple quantum coherence spectroscopy. The 1H/1H connectivities of the protons of each sugar residue in an oligosaccharide were established by two-dimensional homonuclear correlation spectroscopy, while 1H/13C assignments were made using 1H inverse detection. One- and two-dimensional nuclear resonance spectroscopic analysis of these heparin oligosaccharides showed two closely related groups of heparin-oligosaccharides are afforded by enzymatic depolymerization of heparin. One group is fully sulphated, having the structures delta UAp2S(1[-->4)-alpha-D-GlcNpS6S(1-->4)-alpha-L-IdoAp2S( 1]n-->4)-alpha- D-GlcNpS6S, where delta UAp is 4-deoxy-alpha-L-threo-hex-4-eno-pyranosyluronic acid, GlcNp is 2-deoxy-2-aminoglucopyranose, IdoAp is idopyranosyluronic acid, S is sulphate and n = 0-6. The other group of oligosaccharides differ in that they contain beta-D-glucuronic acid in place of the alpha-L-iduronic acid residue nearest to the reducing end. The present study describes the isolation and structural elucidation of seven new oligosaccharides: an octasaccharide, two decasaccharides, two dodecasaccharides and two tetradecasaccharides. The utility of two-dimensional nuclear resonance spectroscopy to determine the structure of complex heparin oligosaccharides is also illustrated.
Practical procedures for genetic manipulation systems for medermycin‐producing Streptomyces sp. AM‐7161 (2010)

Streptomyces sp. AM-7161 is a producer of an aromatic polyketide medermycin with strong antibacterial and antitumor activity. It has been inefficient to perform genetic manipulations in this strain, which heavily hinders the genetic analysis of some interesting problems concerning tailoring modifications in medermycin biosynthesis. Here, condition optimizations of sporulation and mycelium growth of this strain as well as protoplast preparation and regeneration were conducted systematically. Based on these results, protoplast transformation system was established, and two types of foreign plasmids (integrative and auto-replicating) were efficiently introduced into this strain. Additionally, a conjugation system to mediate plasmid transfer between Escherichia coli and Streptomyces sp. AM-7161 was also optimized and established. These results provide the practical procedures to perform more convenient genetic analysis of medermycin biosynthesis in this strain.