gebhart/patrepeval huggingface dataset:
Oligonucleotides containing flexible nucleoside analogs (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOligonucleotides containing flexible nucleoside analogsK. Christian Schneider and Steven A. BennerCite this: J. Am. Chem. Soc. 1990, 112, 1, 453–455Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://doi.org/10.1021/ja00157a073RIGHTS & PERMISSIONSArticle Views507Altmetric-Citations149LEARN 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 (492 KB) Get e-Alerts Get e-Alerts
Lithium metal anodes for rechargeable batteries (2013)

Lithium (Li) metal is an ideal anode material for rechargeable batteries due to its extremely high theoretical specific capacity (3860 mA h g−1), low density (0.59 g cm−3) and the lowest negative electrochemical potential (−3.040 V vs. the standard hydrogen electrode). Unfortunately, uncontrollable dendritic Li growth and limited Coulombic efficiency during Li deposition/stripping inherent in these batteries have prevented their practical applications over the past 40 years. With the emergence of post-Li-ion batteries, safe and efficient operation of Li metal anodes has become an enabling technology which may determine the fate of several promising candidates for the next generation energy storage systems, including rechargeable Li–air batteries, Li–S batteries, and Li metal batteries which utilize intercalation compounds as cathodes. In this paper, various factors that affect the morphology and Coulombic efficiency of Li metal anodes have been analyzed. Technologies utilized to characterize the morphology of Li deposition and the results obtained by modelling of Li dendrite growth have also been reviewed. Finally, recent development and urgent need in this field are discussed.
PCNA binding through a conserved motif (1998)

Proliferating cell nuclear antigen (PCNA) has recently been identified as a target for the binding of several proteins. The cell cycle regulatory protein, p21, and the replication endonuclease, Fen1, have already been described as competing for PCNA binding. Two recent reports have identified DNA (cytosine-5)methyltransferase (MCMT) and the DNA repair endonuclease XPG as binding to PCNA. The remarkable thing about these interactions is that they all seem to occur through a conserved motif that is likely to contact the same site on PCNA. This has fascinating implications for a regulatory network linking these diverse protein functions.
Iterative Fourier transform algorithm for phase-only pulse shaping (2001)

We demonstrate the adaptation of an iterative Fourier transform algorithm for the calculation of theoretical spectral phase functions required for pulse shaping applications. The algorithm is used to determine the phase functions necessary for the generation of different temporal intensity profiles. The performance of the algorithm is compared to two exemplary standard approaches. i.e. a Genetic Algorithm and a combination of a Simplex Downhill and a Simulated Annealing algorithm. It is shown that the iterative Fourier transform algorithm converges much faster than both alternative methods.
Slow allotypic variants of the NAT2 gene and susceptibility to early-onset Parkinson's disease (1998)

Slow-acetylation-mutated alleles may be considered low-penetrance genes in early-onset PD pathogenesis, with a relative risk ratio for individuals with slow-acetylation genotype of 2.92 (95% CI, 1.26 to 6.78). This study provides evidence for the interaction of genetic and environmental factors in the etiology of sporadic PD.
Anti-Tat MTT Assay: A Novel Anti-HIV Drug Screening System Using the Viral Regulatory Network of Replication (1995)

Since the recognition of its pivotal role in viral replication, Tat activity has become an interesting target for chemotherapeutic intervention of HIV infection. Here, we report a sensitive and simple colorimetric assay for the screening of Tat inhibitors. We have constructed a plasmid that contains the hygromycin B phosphotransferase gene under the control of the HIV-1 long terminal repeat (LTR) and HIV-1 tat gene constitutively expressed from the cytomegalovirus promoter. This plasmid has been stably transfected to the CD4+ T cell line CEM, which is rendered resistant to hygromycin B through the action of Tat. The inhibitory activity of the anti-Tat drugs was assessed by the extent of cytotoxicity in the presence of hygromycin B as a consequence of the suppressed expression of the hygromycin B phosphotransferase gene. Spectrophotometric quantitation of cell viability was done utilizing 3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyltetrazolium bromide (MTT) dye as the indicator. Using this assay system, we have confirmed that known anti-Tat compound Ro5-3335 and its derivative Ro24-7429 could inhibit Tat-mediated gene expression although their selectivities (anti-Tat activity versus nonselective cytotoxicity) were narrow. Since this method offers the advantage of not handling infectious particles or radioactive materials, it can offer wide applicability as a screening system for anti-Tat compounds.
Nucleotide sequence and the encoded amino acids of human serum albumin mRNA. (1982)

The complete nucleotide sequence of human serum albumin mRNA has been determined from recombinant cDNA clones and from a primer-extended cDNA synthesis on the mRNA template. The sequence is composed of 2078 nucleotides, starting upstream from a potential ribosome binding site in the 5' untranslated region. It contains all the translated codons and extends into the poly(A) at the 3' terminus. Part of the translated sequence codes for a hydrophobic prepeptide, Met-Lys-Trp-Val-Thr-Phe-Ile-Ser-Leu-Leu-Phe-Leu-Phe-Ser-Ser-Ala-Tyr-Ser, followed by a basic propeptide, Arg-Gly-Val-Phe-Arg-Arg. These signal peptides are absent from mature normal serum albumin and, so far, have not been identified in their nascent state in humans. A remaining 1755 nucleotides of the translated mRNA sequence code for 585 amino acids, which are in agreement, with few exceptions, with the published amino acid sequence for human serum albumin. The mRNA sequence verifies and refines the repeating homology in the triple-domain structure of the serum albumin molecule.
Complexity analysis of spontaneous EEG (2000)

The aim of the present paper is the assessment of the overall complexity of spontaneous and non-paroxysmal EEG signals obtained from three groups of human subjects, e.g., healthy, seizure and mania. Linear complexity measure suitable for multi-variate signals, along with nonlinear measures such as approximate entropy (ApEn) and Taken's estimator are considered. The degree of linear complexity is significantly reduced for the pathological groups compared with healthy group. The nonlinear measures of complexity are significantly decreased in the seizure group for most of the electrodes, whereas a distinct discrimination between the maniac and healthy groups based on these nonlinear measures is not evident.
Purification of &alpha;<sub>1</sub> Proteinase Inhibitor from Human Plasma Fraction IV-1 by Ion Exchange Chromatography (1998)

Background and Objectives: α-proteinase inhibitor (PI) protects the lungs from proteolytic damage caused by elastase and can be used to treat congenital emphysema. We describe an improved method of purification of α1 PI from redissolved fraction IV-1 paste. Materials and Methods: The process used dimethylaminoethy1 anion exchange chromatography, sulfopropyl cation exchange chromatography, virus inactivation by dry heat, and tri-n-butyl-phosphate/cholate treatment, followed by a second strong cation exchange chromatography. Optimizations of loading conditions for ion exchange chromatography at small scale (20–60 ml of suspension) are described. Virus inactivation was adjusted to provide the best yield of α1 PI consistent with effective inactivation. The process has been effectively scaled up. Results: The final product was approximately 90% pure by SDS-PAGE, with a 60–70% yield from starting fraction IV-I paste. The process has been characterized by methods including nonreduced SDS-PAGE, α1 PI inhibition assay, and biuret protein assay. Conclusion: The method described is an effective way of preparing large quantities of α1 PI from fractionated plasma.
Onychomatricoma in the Light of the Microanatomy of the Normal Nail Unit (2011)

Onychomatricoma (OM) is an uncommon benign tumor of the nail thought to exhibit differentiation limited toward the nail matrix. Four recent articles from our laboratory have shown, in some respect, a morphological and immunohistochemical homology between the nail unit and the hair follicle at the level of the matrix and isthmus. The purposes of this article are as follows: to investigate whether the sequential pattern of hair keratin expression in the normal nail matrix is maintained in OM, to compare and contrast follicular tumors with matrix differentiation in OM, and to furnish morphological and immunohistochemical markers of the onychogenic capacity of OM. Formalin-fixed paraffin sections from 6 OM were examined using specific keratin (K) antibodies for the matrix, nail bed, and nail isthmus. Hair keratins were expressed in a sequential pattern similar to normal nail matrix. In 3 cases where the cavities were completely lined by the fibroepithelial projections, the morphological aspect and the pattern of expression of K5, K17, K6, K16, and K75 suggested a differentiation toward the nail bed and the nail isthmus. This study shows for the first time that OM can recapitulate the entire nail unit with differentiation toward the nail bed and the nail isthmus. We have identified new histopathological and immunohistochemical features in OM, and we have abridged the diversity of its histological presentation in 2 main patterns: a lobulated or foliated pattern, observed principally on transverse section, and a "glove-finger" mono- or multidigitate pattern, observed mainly on longitudinal section. We have also concluded that OM is not a nail variant of trichoblastoma, pilomatricoma, or other pilar tumors. The concept of epithelial onychogenic tumor with onychogenic mesenchyme could shed more light about the true nature of this peculiar mixed tumor. However, the term OM is short and sanctioned by usage, which justifies keeping it.
Purification and characterization of a cephalosporin esterase from Rhodosporidium toruloides (1997)

A novel cephalosporin esterase (EC 3.1.1.41) from Rhodosporidium toruloides was purified to gel electrophoretic homogeneity. The enzyme is a glycoprotein with a molecular mass of 80 kDa. Upon deglycosylation, several forms of the enzyme were observed with a molecular mass range between 60 and 66 kDa. The isoelectric point of the enzyme is approximately 5.6, with the pH optimum for activity occurring at 6.0. The optimal activity of the enzyme occurred at 25 degrees C, with the enzyme rapidly losing activity at temperatures above 25 degrees C. The enzyme deacetylated a variety of cephalosporin derivatives, including cephalosporin C; the Km for this substrate is 51.8 mM, and the Vmax is 7.9 mumol/min/mg. In addition to cephalosporins, the enzyme hydrolyzed short-chain p-nitrophenyl esters, with the activity decreasing with increasing ester chain length. The enzyme also has the ability to acetylate desacetyl cephalosporins in high yields under mild conditions in the presence of various acetyl donors. A comparison of the physical properties of the esterase with those of other well-characterized cephalosporin esterases indicates that the enzyme is unique in this class.
Haemopoietic and neuroglial progenitors are promoted during cord blood ex vivo expansion (2002)

Umbilical cord blood (UCB) has emerged as a promising source of haemopoietic stem/progenitor cells (HSPC) for human bone marrow reconstitution, the limitation being the low harvestable number of HSPC from a single UCB sample. In developing our UCB ex vivo expansion strategies, our group designed ‘negative’ immunomagnetic selection systems to deplete developing haemopoietic cells from HSPC. The resulting highly purified non-committed ‘lineage negative’ (LinNeg) cell population represents 0·12% (± 0·02 SEM, n = 9) of original UCB mononuclear cells. In liquid culture (Iscove's modified Dulbecco's medium – 10% fetal calf serum, supplemented with thrombopoietin, Flt-3 ligand and c-Kit-ligand), LinNeg cells proliferated and maintained haemopoietic colonies for at least 5 weeks. In three independent experiments, LinNeg cells also produced a distinct adherent cell population showing neuroglial cell morphology. Further analysis with laser-scanning confocal microscopy revealed (i) active cell–cell communication through extensive membrane projections from these adherent cells (top image) and (ii) positivity for Glial Fibrillary Acidic Protein, a neuroglial marker (immuno-fluorescence bottom image). These results support the existence of a cell population with multi-tissue differentiation ability within UCB. Our findings widen the potential of UCB as an accessible and ethically sound stem cell source for treatment of haematological diseases, and possibly for certain neurological disorders.
Synthesis, chemical and rheological characterization of new hyaluronic acid-based hydrogels (2000)

New hyaluronic acid-based hydrogels have been synthesized. The carboxylate groups of hyaluronan were activated in order to bind the amino terminal groups of the di-amine cross-linking reagent. Different hydrogels were obtained according to the different di-amine cross-linking agents (1,3-diaminepropane, 1.6-diaminohexane, PEG500 di-amine. and PEG800 di-amine). The cross-linked polymer (C.L.Hyal) was then sulphated (C.L.HyalS) by a heterogeneous reaction using sulphur trioxide pyridine complex (SO3-Py). The thermo-mechanical properties and swelling degree were evaluated and are discussed in relation to the chemical structure and the hydrophilic character of the gels. The different behaviours of C.L.Hyal and C.L.HyalS indicate the important role of sulphated groups.
Microstructure of GaAs/GaN interfaces produced by direct wafer fusion (2002)

Results of a transmission electron microscopy (TEM) study of directly bonded GaAs/GaN structures obtained by wafer fusion are presented. A large fraction of the interface area was found to be well bonded, with the presence of a thin (1–2 nm) amorphous layer of a native oxide at the bonded interface. The dominant defects found in nonbonded areas were cavities elongated along the [110]GaAs direction. Plan-view TEM study of well-bonded regions showed the presence of two dislocation networks. The first, formed at the interface to accommodate an unintentional tilt between the fused crystals, consists of a one-dimensional array of wavy dislocations located at interface steps. The second dislocation network, formed to relieve additional strain from the thermal processing of the samples, consists of a two-dimensional, irregularly spaced grid of dislocations formed on the GaAs side that runs parallel to either the [110]GaAs or [11_0]GaAs directions.
Primary structure of human placental 5′‐nucleotidase and identification of the glycolipid anchor in the mature form (1990)

A cDNA was cloned coding for human placental 5'-nucleotidase. The 3547-bp cDNA contains an open reading frame that encodes a 574-residue polypeptide with calculated size of 63 375 Da. The NH2-terminal 26 residues comprise a signal peptide, which is followed by the NH2-terminal sequence of the purified protein. four potential N-linked glycosylation sites are found in the molecule, accounting for a larger mass of the mature form (71 kDa). The predicted structure contains a hydrophobic amino acid sequence at the COOH terminus, a possible signal for the post-translational modification by glycophospholipid. To confirm this possibility, we tried to isolate and characterize the membrane-anchoring domain of 5'-nucleotidase. BrCN-cleaved fragments of the protein were extracted with hexane and subjected to HPLC, resulting in purification of a single component of 2.3 kDa. Chemical analyses revealed that the purified fragment contains the tetradecapeptide Lys-Val-Ile-Tyr-Pro-Ala-Val-Glu-Gly-Arg-Ile-Lys-Phe-Ser, ethanolamine, glucosamine, mannose, inositol, palmitic acid, and stearic acid. The peptide sequence determined is identified at positions 510-523 in the primary structure deduced from the cDNA sequence, which predicts a further extension to position 548, containing the hydrophobic amino acid sequence. Thus, it is concluded that the mature 5'-nucleotidase lacks the predicted COOH-terminal peptide extension (524-548), which has been replaced by the glycophospholipid functioning as the membrane anchor of 5'-nucleotidase.
Taloside Inhibitors of Galectin‐1 and Galectin‐3 (2011)

Galectin-1 and galectin-3 have roles in cancer and inflammation. Galectin-1 has recently emerged as a significant protein produced by tumour cells to promote tumour development, angiogenesis and metastasis and consequently represents an important target to inhibit. The design of inhibitors targeting the carbohydrate recognition domain that is known to recognize galactose is an important approach in the fight against cancer. Based on the analysis of crystal structures, we pursued the concept that if the galactose was replaced with talose (the C2 epimer of galactose) as a scaffold, then O2 substituents would be directed closer to the protein surface and provide opportunity to design inhibitors that are more specific towards particular galectins. Our elucidation of X-ray crystal structures of two of our synthesized talosides in complex with galectin-1 and galectin-3 provides the first atomic information on the interactions of galectins, and indeed any protein, with talosides. These results have enabled a structure-based rationale for the specificity differences shown by galectin-1 and galectin-3 towards these talosides and demonstrate new opportunities for further exploitation as specific inhibitors of galectins.
dbQSNP: A database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods (2005)

We present a database, dbQSNP (http://qsnp.gen.kyushu-u.ac.jp/), that provides sequence and allele frequency information for single-nucleotide polymorphisms (SNPs) located in the promoter regions of human genes, which were defined by the 5' ends of full-length cDNA clones. We searched for the SNPs in these regions by sequencing or single-strand conformation polymorphism (SSCP) analysis. The allele frequencies of the identified SNPs in two ethnic groups were quantified by SSCP analyses of pooled DNA samples. The accuracy of our estimation is supported by strong correlations between the frequencies in our data and those in other databases for the same ethnic groups. The frequencies vary considerably between the two ethnic groups studied, suggesting the need for population-based collections and allele frequency determination of SNPs, in, e.g., association studies of diseases. We show profiles of SNP densities that are characteristic of transcription start site regions. A fraction of the SNPs revealed a significantly different allele frequency between the groups, suggesting differential selection of the genes involved.
Interactions between integrin receptors and fibronectin are required for calvarial osteoblast differentiation in vitro (1997)

We previously showed that anti-fibronectin antibodies or soluble fibronectin fragments containing the central cell-binding domain inhibit formation of mineralized nodules by fetal calvarial osteoblasts in vitro. These findings suggest a critical role for fibronectin in osteoblast differentiation and morphogenesis. In this study we tested the hypothesis that fibronectin's effects on osteogenesis are mediated via direct interactions with integrin receptors for fibronectin on osteoblasts. Immunocytochemical analysis identified the integrin fibronectin receptor alpha5ss1 in fetal rat calvarial tissue and in cultured osteoblasts at all stages of differentiation. Three other integrins, alpha3ss1, alpha8ss1 and alphavss3, which can bind fibronectin, as well as other matrix components, were also identified in tissue and at all stages of cell culture. Immunoprecipitation data showed that alpha5ss1 levels are constant throughout osteoblast differentiation whereas levels of alpha3ss1 and alpha8ss1 decline in mature mineralized cultures. To determine whether integrin fibronectin receptors are required for osteoblast formation of mineralized nodules, we examined the extent of nodule formation in the presence and absence of function-perturbing anti-integrin antibodies. The antibodies were present continuously in cultures beginning at confluence (day 3), and nodule formation was measured at days 10 and 20. An anti-alpha5 integrin subunit antibody reduced nodule formation to less than 5% of control values at both time points. Inhibition of nodule formation was reversible and did not affect cell attachment and viability. Function-perturbing antibodies against alpha3ss1 and alpha8ss1 also reduced nodule formation, to less than 20% of control values. In contrast, function-perturbing antibodies to alphavss3 and alphavss5 did not affect nodule formation, indicating that the inhibitions noted were indeed specific. To determine the effect of antibody treatment on gene expression, steady-state mRNA expression was examined and found to be suppressed for osteoblast markers alkaline phosphatase and osteocalcin. Together, these results indicate that direct osteoblast interactions with the extracellular matrix are mediated by a select group of integrin receptors that includes alpha5ss1, alpha3ss1 and alpha8ss1. We further conclude that the specific alpha5ss1 fibronectin receptor mediates critical interactions between osteoblasts and fibronectin required for both bone morphogenesis and osteoblast differentiation.