gebhart/patrepeval huggingface dataset:
X‐ray and primary structure of horse serum albumin (Equus caballus) at 0.27‐nm resolution (1993)

The amino-acid sequence and three-dimensional structure of equine serum albumin have been determined. The amino-acid sequence was deduced from cDNA isolated from equine liver. Comparisons of the primary structure of equine serum albumin with human serum albumin and bovine serum albumin reveal 76.1% and 73.9% sequence identity, respectively. The three-dimensional structure was determined crystallographically by the molecular-replacement method using molecular coordinates from the previously determined structure of human serum albumin, to a resolution of 0.27 nm. In accordance with the primary structure, the three-dimensional structures are highly conserved. There is a root-mean-square difference between alpha-carbons of the two structures of 0.201 nm. The association constants (Ka) for the binding of 2,3,5-triiodobenzoic acid were determined by ultrafiltration methods for equine and human serum albumins to be approximately 10(4) M-1 and 10(5) M-1, respectively. Crystallographic studies of equine serum albumin reveal two binding sites for 2,3,5-triiodobenzoic acid identical with those previously reported for human serum albumin which are located within subdomains in IIA and IIIA. Details and comparisons of the binding chemistry are discussed.
High-Resolution Genotyping of Campylobacter Species by Use of PCR and High-Throughput Mass Spectrometry (2008)

In this work we report on a high-throughput mass spectrometry-based technique for the rapid high-resolution identification of Campylobacter jejuni strain types. This method readily distinguishes C. jejuni from C. coli, has a resolving power comparable to that of multilocus sequence typing (MLST), is applicable to mixtures, and is highly automated. The strain typing approach is based on high-performance mass spectrometry, which "weighs" PCR amplicons with enough mass accuracy to unambiguously determine the base composition of each amplicon (i.e., the numbers of A's, G's, C's, and T's). Amplicons are derived from PCR primers which amplify short (<140-bp) regions of the housekeeping genes used by conventional MLST strategies. The results obtained with a challenge panel that comprised 25 strain types of C. jejuni and 25 strain types of C. coli are presented. These samples were parsed and resolved with demonstrated sensitivity down to 10 genomes/PCR from pure isolates.
Productive Replication of Adeno-Associated Virus Can Occur in Human Papillomavirus Type 16 (HPV-16) Episome-Containing Keratinocytes and Is Augmented by the HPV-16 E2 Protein (2000)

We used a sensitive assay to test whether an adeno-associated virus (AAV) productive replication cycle can occur in immortalized human keratinocytes carrying episomal human papillomavirus type 16 (HPV-16) DNA. Following transfection with cloned AAV DNA, infectious AAV was produced, and the infectivity was blocked by anti-AAV antiserum. The HPV-16 E2 protein substantially increased the yield of AAV. Other HPV early proteins did not, in our experiments, show this ability. E2 has been shown to be able to affect p53 levels and to block cell cycle progression at mitosis. We tested the effect of changes in p53 expression on AAV replication and found that large differences in the level of p53 did not alter AAV DNA replication. In extension of this, we found that cellular help for AAV in response to stress was also independent of p53. To test if a mitotic block could trigger AAV DNA replication, we treated the cells with the mitotic inhibitor nocodazole. AAV DNA replication was stimulated by the presence of nocodazole in these and a number of other cell types tested. Yields of infectious virus, however, were not increased by this treatment. We conclude that the HPV-16 E2 protein stimulates AAV multiplication in these cells and propose that this occurs independently of the effects of E2 on p53 and cell cycle progression. Since the effect of E2 was not seen in keratinocytes lacking the HPV-16 episome, we suggest that E2 can help AAV by working in concert with other HPV-16 proteins.
Percutaneous Reinsertion of the Nucleus Pulposus (1998)

Early reinsertion of the nucleus pulposus (fresh or cryopreserved) delays degeneration of such disc materials as the anulus fibrosus, endplate, and remaining nucleus pulposus.
Identification of new genes required for meiotic recombination in Saccharomyces cerevisiae. (1993)

Mutants defective in meiotic recombination were isolated from a disomic haploid strain of Saccharomyces cerevisiae by examining recombination within the leu2 and his4 heteroalleles located on chromosome III. The mutants were classified into two new complementation groups (MRE2 and MRE11) and eight previously identified groups, which include SPO11, HOP1, REC114, MRE4/MEK1 and genes in the RAD52 epistasis group. All of the mutants, in which the mutations in the new complementation groups are homozygous and diploid, can undergo premeiotic DNA synthesis and produce spores. The spores are, however, not viable. The mre2 and mre11 mutants produce viable spores in a spo13 background, in which meiosis I is bypassed, suggesting that these mutants are blocked at an early step in meiotic recombination. The mre2 mutant does not exhibit any unusual phenotype during mitosis and it is, thus, considered to have a mutation in a meiosis-specific gene. By contrast, the mre11 mutant is sensitive to damage to DNA by methyl methanesulfonate and exhibits a hyperrecombination phenotype in mitosis. Among six alleles of HOP1 that were isolated, an unusual pattern of intragenic complementation was observed.
PERCS: The IBM POWER7-IH high-performance computing system (2011)

In 2001, the Defense Advanced Research Projects Agency called for the creation of commercially viable computing systems that would not only perform at very high levels but also be highly productive. The forthcoming POWER7®-IH system known as Productive, Easy-to-use, Reliable Computing System (PERCS) was IBM's response to this challenge. Compared with state-of-the-art high-performance computing systems in existence today, PERCS has very high performance and productivity goals and achieves them through tight integration of computing, networking, storage, and software. This paper describes the PERCS hardware and software, along with many of the design decisions that went into its creation.
APOE genotypes and disease severity in multiple sclerosis (2002)

Apolipoprotein E (opoE) is involved in the transport of lipids necessary for membrane repair and is encoded by a gene on chromosome 19q13, a region positive for linkage in two multiple sclerosis (MS) genome-wide screens. The APOE epsilon4 allele confers susceptibility to both familial and sporadic Alzheimer's disease (AD). Carriage of epsilon4 is associated with defective dendritic remodeling in AD, and with unfavorable clinical outcome in head trauma and cerebrovascular disease. According to the results of previous studies, APOE epsilon4 does not increase the risk of developing MS, but it may influence disease progression and ultimate disability. From a total cohort of over 900 MS patients, we compared APOE epsilon2-4 genotypes in, roughly, the cohort's least disabled and most disabled septiles. 'Benign MS' (n=124) was defined as an Expanded Disability Status Scale (EDSS) score of 3.0 or less, despite at least 10 years of disease duration, and 'severe MS' (n=140) as the attainment of an EDSS score of 6.0 within 8 years of disease onset. We found no significant differences in genotype or phenotype frequencies between the benign-MS and severe-MS septiles; however, the risk conferred by epsilon4 rose progressively upon comparison of carriage rates in more narrowly defined anti-podal quantiles.
Interaction between nanoparticles and cytokine proteins: impact on protein and particle functionality (2010)

There is increased use of nanomaterials in many applications due to their unique properties, such as their high surface area and surface reactivity. However, the potential health effects to workers, consumers and the environment exposed to nanoparticles (NPs) is unknown. The aim of this study was to investigate whether NPs which may enter the body could adsorb proteins and whether this interaction affects both the particle and the protein function. The cytokines IL-8 and TNF-alpha were adsorbed significantly more by 14 nm carbon black (CB) compared with a similar dose of 260 nm CB. Uncoated 14 nm CB particles produced a significant increase in intracellular calcium [Ca(2 + )](i) which was greater than a similar mass dose of 260 nm CB. The 260 nm CB produced an increase in ICAM-1 expression in A549 epithelial cells at a comparable dose of 14 nm CB, and after coating with TNF-alpha 260 nm CB produced significantly more ICAM-1 expression compared with control cells. TNF-alpha bound to 14 nm CB induced a level of ICAM-1 expression that was no greater than the control level, suggesting that the TNF-alpha activity may be inhibited. These results suggest that NP-protein interaction results both in a decrease in protein function and particle activity in the cellular assays tested and this is currently being investigated.
Binding of dolastatin 10 to tubulin at a distinct site for peptide antimitotic agents near the exchangeable nucleotide and vinca alkaloid sites. (1990)

Dolastatin 10, a potent antimitotic peptide from a marine animal, strongly inhibits microtubule assembly, tubulin-dependent GTP hydrolysis, and the binding of vinca alkaloids to tubulin. In studies of the binding of [3H]vincristine to the protein, with vinblastine as a control for competitive inhibition (Ki, 6.6 microM), we found that the macrolide antimitotic agents maytansine and rhizoxin were also competitive inhibitors (Ki values, 3.1 and 12 microM). Dolastatin 10 and an unrelated peptide antimitotic, phomopsin A, were more potent but noncompetitive inhibitors (Ki values, 1.4 and 2.8 microM). Since maytansine and, to a much lesser extent, vinblastine interfere with nucleotide exchange on tubulin, all drugs were examined for effects on nucleotide interactions at the exchangeable GTP site. Rhizoxin had effects intermediate between those of vinblastine and maytansine. Both peptides inhibited binding of radiolabeled GTP to tubulin even more strongly than did maytansine, but no drug displaced nucleotide from tubulin. The drugs were evaluated for stabilizing effects on the colchicine binding activity of tubulin. The peptides prevented loss of this activity, and vinblastine provided partial protection, while rhizoxin and maytansine did not stabilize tubulin. A tripeptide segment of dolastatin 10 also effectively inhibits tubulin polymerization and GTP hydrolysis. The tripeptide did not significantly inhibit either vincristine binding or nucleotide exchange, nor did it stabilize colchicine binding. These findings are rationalized in terms of a model with two distinct drug binding sites in close physical proximity to each other and to the exchangeable GTP site on beta-tubulin.
Is pantetheinase the actual identity of mouse and human vanin‐1 proteins? (1999)

Pantetheinase is an amidohydrolase involved in the dissimilative pathway of CoA, allowing the turnover of the pantothenate moiety. We have determined the N-terminal sequence as well as the sequences of a number of tryptic and chymotryptic peptides of the protein isolated from pig kidney. These sequence stretches were used as probes to search in the SwissProt database and significant similarities were found with a GPI-anchored protein (mouse vanin-1, with a suggested role in lymphocyte migration), with two putative proteins encoded by human cDNAs (VNN1 and VNN2) and with human biotinidase. On the basis of sequence similarity, we propose that vanin-1 and VNN1 should be identified as pantetheinase.
Targeting in Gene Therapy for Gliomas (1999)

Cancer is a disease of a series of genes. Thus, theoretically, brain tumors could be treated by targeting their fundamental molecular defects. Currently, most of the approved clinical protocols for gene therapy involve cancer patients. Several of these protocols are designed to improve the treatment of brain tumors. In this brief report, we analyze the rationale, advantages, and disadvantages of a series of gene therapy approaches against brain tumors that include transfer of tumor suppressor genes and cell-cycle modulators; suicide or prodrug strategies; immunogene therapy; antiangiogenesis; and oncolytic virus therapy. In summary, in this review, we highlight the translational advances in molecular medicine that broaden our battery of therapies for patients with brain tumors.
Synthesis of Oligoinosinates with 2′–5′ Internucleotide Linkage in Aqueous Solution Using Pb2+ Ion (1981)

Abstract Oligoinosinates up to a pentamer were synthesized by the polymerization of inosine-5′-phosphorimidazolide in aqueous solution using Pb2+ ion. 2′–5′ Internucleotide linkage was preferentially formed. The yields of the 2′–5′ linked dimer, trimer, and tetramer were 14.8, 4.5, and 1.6%, respectively. A small amount of linkage isomers of oligoinosinates with 3′–5′ linkage was obtained. The products were characterized by sequential enzyme tests.
Wettability of Surface Oxyfluorinated Polypropylene Fibres and Its Effect on Interfacial Bonding with Cementitious Matrix (1997)

Abstract The surface of high molecular weight polypropylene monofilament fibre was modified using a oxyfluorination method. The oxyfluorination treatment level was varied and a hydrolysis post-treatment was also applied. Contact angles of oxyfluorinated, hydro-lyzed oxyfluorinated and unmodified polypropylene fibres were obtained by dynamic contact angle (DCA) measurement using three liquids of known dispersion, acid and base surface free energy components. The surface free energies were then calculated according to the acid-base theory developed by Good, van Oss and Chaudhury. Surface oxyfluorination largely increased the acid and base components of the fibres' surface free energy compared with unmodified polypropylene fibres. The oxyfluorinated and unmodified polypropylene fibre surfaces were observed by Scanning Electronic Microscopy and Photoacoustic Infrared Spectroscopy. It was found that the surface oxyfluorination largely increases the roughness of the polypropylene surfaces and the carbonyl group content increases as the treatment level increases. The interfacial shear bond strengths between the cementitious matrix and the polypropylene fibres treated under various conditions were determined by embedded fibre pull-out tests. Results showed that the fibre surface oxyfluorination treatments increase the interfacial bond strengths. The correlations between the shear bond strengths and surface free energy components were established. Results showed that fibre/concrete interfacial bonding was best correlated with the acid component of surface free energy of polypropylene fibres.
Anaerobes as Normal Oral Flora (1984)

The human mouth provides a suitable habitat for numerous bacterial genera. Anaerobic genera or genera that include anaerobic members found in the oral cavity are Actinomyces, Arachnia, Bacteroides, Bifidobacterium, Eubacterium, Fusobacterium, Lactobacillus, Leptotrichia, Peptococcus, Peptostreptococcus, Propionibacterium, Selenomonas, Treponema, and Veillonella. The incidence of anaerobes varies with age of the individual and with specific sites sampled. In edentulous infants, the incidence of anaerobes is relatively low. In adults, anaerobes are invariably present but are more prevalent in samples from the gingival sulcus than they are in samples from the gingival margin, tooth surfaces, buccal mucosa, tongue, or saliva. In samples from the healthy gingival sulcus, anaerobic, gram-positive bacilli are found in the range of 5%-14%; gram-negative bacilli in the range of 13%-29%; Veillonella in the range of 2%-8%; and gram-positive cocci in the range of 1%-15% of the cultivable flora. From marginal plaque and plaque from the tooth surface, gram-positive bacilli, gram-positive cocci, and Veillonella appear to be the predominant anaerobes. In saliva, Veillonella are the most numerous anaerobes.
Unique Toxicities and Resistance Mechanisms Associated with Monoclonal Antibody Therapy (2005)

Anti-CD20 therapy has had a truly dramatic impact on treatment and outcome of patients with follicular lymphoma. Unfortunately, the majority of responses to single-agent rituximab are incomplete, and all patients with follicular lymphoma will experience disease progression at some point following rituximab therapy. Rituximab has multiple mechanisms of inducing in vivo cytotoxicity, including antibody-dependent cell-mediated cytotoxicity, complement-dependent cytotoxicity, direct apoptotic signaling, and possible vaccinal effects. The cellular microenvironment within follicular lymphoma has a profound impact on which mechanism is dominant, and confers resistance in many situations. Both tumor-associated and host-associated factors also contribute to rituximab resistance. There are multiple potential approaches to overcoming rituximab resistance, including rational biologic combination immunotherapy, engineered antibodies, and radioimmunoconjugates. Improved ability to overcome resistance will require further elucidation of critical signaling pathways involved in rituximab induced cytotoxicity and a comprehensive understanding of interactions between its multiple mechanisms of action.
Dosage-sensitive requirement for mouse Dll4 in artery development (2004)

Involvement of the Notch signaling pathway in vascular development has been demonstrated by both gain- and loss-of-function mutations in humans, mice, and zebrafish. In zebrafish, Notch signaling is required for arterial identity by suppressing the venous fate in developing artery cells. In mice, the Notch4 receptor and the Delta-like 4 (Dll4) ligand are specifically expressed in arterial endothelial cells, suggesting a similar role. Here we show that the Dll4 ligand alone is required in a dosage-sensitive manner for normal arterial patterning in development. This implicates Dll4 as the specific mammalian endothelial ligand for autocrine endothelial Notch signaling, and suggests that Dll4 may be a suitable target for intervention in arterial angiogenesis.
Quantum measurements performed with a single-electron transistor (1998)

Low-capacitance Josephson junction systems as well as coupled quantum dots, in a parameter range where single charges can be controlled, provide physical realizations of quantum bits, discussed in connection with quantum computing. The necessary manipulation of the quantum states can be controlled by applied gate voltages. In addition, the state of the system has to be read out. Here we suggest to measure the quantum state by coupling a single-electron transistor to the $q$-bit. As long as no transport voltage is applied, the transistor influences the quantum dynamics of the $q$-bit only weakly. We have analyzed the time evolution of the density matrix of the transistor and $q$-bit when a voltage is turned on. For values of the capacitances and temperatures which can be realized by modern nanotechniques, the process constitutes a quantum measurement process.
ChemInform Abstract: Total Synthesis of (+)‐Duocarmycin A, epi‐(+)‐Duocarmycin A and Their Unnatural Enantiomers: Assessment of Chemical and Biological Properties. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Upregulation of SGLT-1 transport activity in rat jejunum induced by GLP-2 infusion in vivo (1997)

The effect of in vivo infusion of the peptide hormone glucagon-like peptide 2 (GLP-2) on glucose transport across the rat jejunal brush-border membrane (BBM) was assessed using isolated membrane vesicles. A 2-h infusion of GLP-2 produced a marked acceleration of sodium-dependent glucose uptake into BBM vesicles with a significant overshoot. There was no change in vesicle space or permeability resulting from the hormone infusion. Kinetic analysis showed this stimulation to be the result of a three-fold increase in the maximal rate of transport, with no consistent change in the affinity constant (Km). The time course of this response showed that the effect was observable, but smaller, after only 30 min of hormone infusion and was maximal after 1 h. Sodium-dependent phloridzin binding to the membrane vesicles showed a parallel increase in maximal binding after 1 and 2 h of hormone infusion. Western blotting showed a similar increase in sodium-dependent glucose transporter 1 (SGLT-1) abundance. The effect of GLP-2 could be blocked by luminal brefeldin A or wortmannin. These results indicate that GLP-2 is able to induce trafficking of SGLT-1 from an intracellular pool into the BBM within 60 min and that phosphoinositol 3-kinase may well be involved in the intracellular signaling pathway in this response.
Human vitamin D receptor is selectively phosphorylated by protein kinase C on serine 51, a residue crucial to its trans-activation function. (1991)

The vitamin D receptor (VDR) is known to be a phosphoprotein and inspection of the deduced amino acid sequence of human VDR (hVDR) reveals the conservation of three potential sites of phosphorylation by protein kinase C (PKC)--namely, Ser-51, Ser-119, and Ser-125. Immunoprecipitated extracts derived from a rat osteoblast-like osteosarcoma cell line that contains the VDR in high copy number were incubated with the alpha, beta, and gamma isozymes of PKC, and VDR proved to be an effective substrate for PKC-beta, in vitro. When hVDR cDNAs containing single, double, and triple mutations of Ser-51, Ser-119, and Ser-125 were expressed in CV-1 monkey kidney cells, immunoprecipitated and phosphorylated by PKC-beta, in vitro, the mutation of Ser-51 selectively abolished phosphorylation. Furthermore, when transfected CV-1 cells were treated with phorbol 12-myristate 13-acetate, a PKC activator, phosphorylation of wild-type hVDR was enhanced, whereas that of the Ser-51 mutant hVDR was unaffected. Therefore, Ser-51 is the site of hVDR phosphorylation by PKC, both in vitro and in vivo. To evaluate the functional role of Ser-51 and its potential phosphorylation, hVDR-mediated transcription was tested using cotransfection with expression plasmids and a reporter gene that contained a vitamin D response element. Mutation of Ser-51 markedly inhibited transcriptional activation by the vitamin D hormone, suggesting that phosphorylation of Ser-51 by PKC could play a significant role in vitamin D-dependent transcriptional activation. Therefore, the present results link the PKC signal transduction pathway of growth regulation and tumor promotion to the phosphorylation and function of VDR.
Partial Hepatectomy in the Mouse: Technique and Perioperative Management (2003)

Hepatic surgery in mice is challenging because of the delicate nature of the liver, lack of intravenous access, and risk of hemorrhage. In order to study the ability of the liver to regenerate after surgical resection, we developed a novel, rapid, and safe technique for partial hepatectomy in mice. We determined the relative contributions of the seven lobes of the mouse liver and resected the three most anterior lobes for a 68% hepatectomy. We used general anesthesia, a small upper midline incision, silk suture to tie off the lobes to be resected, warming pads and lights, as well as subcutaneous saline injection to ensure minimal morbidity. We have performed a safe two-thirds hepatic resection in 288 of 300 C57BL6 mice (96%). Perioperative mortality was due to technical error. Minimal long-term morbidity was appreciated. This technique may be applied to any type of hepatic resection in mice. In addition, the general operative technique and perioperative management of these mice may be applied to all types of murine intra-abdominal procedures used for surgical research.