gebhart/patrepeval huggingface dataset:
Crystal Structure of Yeast Cytosine Deaminase (2003)

Yeast cytosine deaminase is an attractive candidate for anticancer gene therapy because it catalyzes the deamination of the prodrug 5-fluorocytosine to form 5-fluorouracil. We report here the crystal structure of the enzyme in complex with the inhibitor 2-hydroxypyrimidine at 1.6-A resolution. The protein forms a tightly packed dimer with an extensive interface of 1450 A2 per monomer. The inhibitor was converted into a hydrated adduct as a transition-state analog. The essential zinc ion is ligated by the 4-hydroxyl group of the inhibitor together with His62, Cys91, and Cys94 from the protein. The enzyme shares similar active-site architecture to cytidine deaminases and an unusually high structural homology to 5-aminoimidazole-4-carboxamide-ribonucleotide transformylase and thereby may define a new superfamily. The unique C-terminal tail is involved in substrate specificity and also functions as a gate controlling access to the active site. The complex structure reveals a closed conformation, suggesting that substrate binding seals the active-site entrance so that the catalytic groups are sequestered from solvent. A comparison of the crystal structures of the bacterial and fungal cytosine deaminases provides an elegant example of convergent evolution, where starting from unrelated ancestral proteins, the same metal-assisted deamination is achieved through opposite chiral intermediates within distinctly different active sites.
A prototype closed aquaculture system for controlled ecological life support applications (1991)

Biopsy specimens of cervico-scutular muscles obtained from animals injected with bee crude venom were prepared for electron microscopy studies. At 6 h from Apis mellifera venom injection, in mice under transmission electron microscopy, the muscular fibres presented different atrophy levels with increment of the intermyofibrillar spaces. Tubules and sarcoplasmic reticulum elements were altered, in some places only tubular fragments and an increment of the intermyofibrillar spaces were noticed as well as loss of fibre regularity and prominent triads. In subsarcolemma region, areas lacking myofibrils and mitochondria damages were observed. Muscular segmental necrosis and atrophy areas were observed. Neuromuscular junctions were altered. The number of synaptic vesicles was very variable and synaptic clefts showed irregularities. A decrease in the number and arrangement of the synaptic clefts, as well as free polysomes, suggesting regeneration processes, were also observed. The myelinic nerves exhibited in the axon or in the wall vacuolisation areas. The presence of severe muscular lesions, the finding of venom activities in the presynaptic region and the detection of damages in the neuromuscular junctions at different chronological stages of our experiments indicate that the bee venom is highly toxic for neuromuscular structures.
Peptide functionalised discotic amphiphiles and their self-assembly into supramolecular nanofibres (2011)

The multicomponent co-assembly of discotic amphiphiles provides a modular and versatile approach to prepare RGDS- and PHSRN-peptide functionalised supramolecular nanofibres, bearing pendant paramagnetic Gd(III)-chelates.
Comparison of Methods for Accurate Quantification of DNA Mass Concentration with Traceability to the International System of Units (2010)

Accurate estimation of total DNA concentration (mass concentration, e.g., ng/muL) that is traceable to the International System of Units (SI) is a crucial starting point for improving reproducible measurements in many applications involving nucleic acid testing and requires a DNA reference material which has been certified for its total DNA concentration. In this study, the concentrations of six different lambda DNA preparations were determined using different measurement platforms: UV Absorbance at 260 nm (A(260)) with and without prior sodium hydroxide (NaOH) treatment of the DNA, PicoGreen assay, and digital polymerase chain reaction (dPCR). DNA concentration estimates by A(260) with and without prior NaOH treatment were significantly different for five of the six samples tested. There were no significant differences in concentration estimates based on A(260) with prior NaOH treatment, PicoGreen analysis, and dPCR for two of the three samples tested using dPCR. Since the measurand in dPCR is amount (copy number) concentration (copies/muL), the results suggest that accurate estimation of DNA mass concentration based on copy number concentration is achievable provided the DNA is fully characterized and in the double-stranded form or amplification is designed to be initiated from only one of the two complementary strands.
Synthesis and properties of oligonucleotides having a chemically stable 2-(trimethylsilyl)benzoyl group (2008)

Acyl groups such as benzoyl and phenoxyacetyl have been used as a fundamental tool for protection of reactive hydroxyl and amino groups in chemical synthesis of DNA and RNA oligomers. It is well known that such protecting groups can be easily cleaved under basic conditions. Here we report 2-(trimethylsilyl)benzoyl (TMSBz), i.e., a chemically stabilized benzoyl group that is substituted with a trimethylsilyl group at its 2-position. To the best of our knowledge, the TMSBz group is the most resistant to basic conditions as an acyl group in nucleic acid chemistry.
Isolation and mapping of 62 new RFLP markers on human chromosome 11. (1991)

To obtain new RFLP markers on human chromosome 11 for a high-resolution map, we constructed a cosmid library from a Chinese hamster x human somatic hybrid cell line that retains only human chromosome 11 in a Chinese hamster genomic background. A total of 3,500 cosmids were isolated by colony hybridization with labeled human genomic DNA. DNA was prepared from 130 of these cosmid clones and examined for RFLP. In 62 of them, polymorphism was detected with one or more enzymes; four RFLPs were VNTR systems. All polymorphic clones were assigned to one of 22 intervals obtained by mapping on a deletion panel of 15 somatic hybrid cell lines containing parts of chromosome 11; 11 clones were finely mapped by in situ hybridization. Although RFLP markers were scattered on the whole chromosome, they were found predominantly in the regions of R-banding. These DNA markers will contribute to fine mapping of genes causing inherited disorders and tumor-suppressor genes that reside on chromosome 11. Furthermore, as one-third of the cosmid clones revealed a band or bands in Chinese hamster DNA, indicating sequence conservation, this subset of clones may be useful for isolating biologically important genes on chromosome 11.
The transforming growth factor-beta receptor type III is a membrane proteoglycan. Domain structure of the receptor. (1988)

The transforming growth factor-beta (TGF-beta) receptor type III is a low abundance cell surface component that binds TGF-beta 1 and TGF-beta 2 with high affinity and specificity, and is present in many mammalian and avian cell types. Type III TGF-beta receptors affinity-labeled with 125I-TGF-beta migrate in sodium dodecyl sulfate-polyacrylamide electrophoresis gels as diffuse species of 250-350 kDa. Here we show that type III receptors deglycosylated by the action of trifluoromethanesulfonic acid yield affinity-labeled receptor cores of 110-130 kDa. This marked decrease in molecular weight is also achieved by combined treatment of type III receptors with heparitinase and chondroitinase ABC. Digestion of receptor-linked glycosaminoglycans by treatment of intact cell monolayers with heparitinase and chondroitinase does not prevent TGF-beta binding to the type III receptor core polypeptide and does not release the receptor polypeptide from the membrane. The type III TGF-beta receptor binds tightly to DEAE-Sephacel and coelutes with cellular proteoglycans at a characteristically high salt concentration. Thus, the type III TGF-beta receptor has the properties of a membrane proteoglycan that carries heparan and chondroitin sulfate glycosaminoglycan chains. The binding site for TGF-beta appears to reside in the 100-120-kDa core polypeptide of this receptor. The type III receptor is highly sensitive to cleavage by trypsin. Trypsin action releases the glycosaminoglycan-containing domain of the receptor leaving a 60-kDa membrane-associated domain that contains the cross-linked ligand. A model for the domain structure of the TGF-beta receptor type III is proposed based on these results.
Alzheimer disease: Time to improve its diagnosis and treatment (2009)

Basic research is bringing a much-needed infusion of optimism and urgency to the clinical diagnosis and treatment of Alzheimer disease. Some of its risk factors may be modifiable, and although current drugs offer only modest benefit, true disease-modifying drugs are on the horizon. This review is aimed at primary care physicians, who are the first clinicians to see patients with Alzheimer disease and are responsible for their ongoing care throughout the course of their dementia.
Tetrahydrofolate Recognition by the Mitochondrial Folate Transporter (2011)

A mitochondrial carrier family (MCF) of transport proteins facilitates the transfer of charged small molecules across the inner mitochondrial membrane. The human genome has ∼50 genes corresponding to members of this family. All MCF proteins contain three repeats of a characteristic and conserved PX(D/E)XX(K/R) motif thought to be central to the mechanism of these transporters. The mammalian mitochondrial folate transporter (MFT) is one of a few MCF members, known as the P(I/L)W subfamily, that have evolved a tryptophan residue in place of the (D/E) in the second conserved motif; the function of this substitution (Trp-142) is unclear. Molecular dynamics simulations of the MFT in its explicit membrane environment identified this tryptophan, as well as several other residues lining the transport cavity, to be involved in a series of sequential interactions that coordinated the movement of the tetrahydrofolate substrate within the transport cavity. We probed the function of these residues by mutagenesis. The mutation of every residue identified by molecular dynamics to interact with tetrahydrofolate during simulated transit into the aqueous channel severely impaired folate transport. Mutation of the subfamily-defining tryptophan residue in the MFT to match the MCF consensus at this position (W142D) was incompatible with cell survival. These studies indicate that MFT Trp-142, as well as other residues lining the transporter interior, coordinate tetrahydrofolate descent and positioning of the substrate in the transporter basin. Overall, we identified residues in the walls and at the base of the transport cavity that are involved in substrate recognition by the MFT.
Characterization of class II apurinic/apyrimidinic endonuclease activities in the human malaria parasite, Plasmodium falciparum (2000)

We have reported that the human malaria parasite, Plasmodium falciparum, repairs apurinic/apyrimidinic (AP) sites on DNA by a long-patch base excision repair (BER) pathway. This biology is different from that in mammalian cells, which predominantly repair AP sites by a DNA-polymerase-β-dependent, one-nucleotide patch BER pathway. As a starting point for the identification and biochemical characterization of the enzymes involved in the parasite DNA BER pathway, we chose characterization of the AP endonuclease activity in a P. falciparum cell-free lysate. Evidence is provided for the presence of class II, Mg2+-dependent and independent AP endonucleases in the parasite lysate. The investigation of the processing of AP sites in Plasmodium will provide new information about long-patch BER pathways; if they are different from those in the human host they might provide a new target for anti-malarial chemotherapy.
Cloning and Targeted Deletion of the Mouse Fetuin Gene (1997)

We proposed that the alpha2-Heremans Schmid glycoprotein/fetuin family of serum proteins inhibits unwanted mineralization. To test this hypothesis in animals, we cloned the mouse fetuin gene and generated mice lacking fetuin. The gene consists of seven exons and six introns. The cystatin-like domains D1 and D2 of mouse fetuin are encoded by three exons each, whereas a single terminal exon encodes the carboxyl-terminal domain D3. The promoter structure is well conserved between rat and mouse fetuin genes within the regions shown to bind transcription factors in the rat system. Expression studies demonstrated that mice homozygous for the gene deletion lacked fetuin protein and that mice heterozygous for the null mutation produced roughly half the amount of fetuin protein produced by wild-type mice. Fetuin-deficient mice were fertile and showed no gross anatomical abnormalities. However, the serum inhibition of apatite formation was compromised in these mice as well as in heterozygotes. In addition, some homozygous fetuin-deficient female ex-breeders developed ectopic microcalcifications in soft tissues. These results corroborate a role for fetuin in serum calcium homeostasis. The fact that generalized ectopic calcification did not occur in fetuin-deficient mice proves that additional inhibitors of phase separation exist in serum.
Investigation of Sheath Flow Chambers for Flow Cytometers (Micro Machined Flow Chamber with Low Pressure Loss). (1997)

A new type of sheath flow chamber with low pressure loss was developed using micro-machining. The chamber was formed by laminating three 100-μm-thick, photoetched, metal plates. The device uses sheath-flow geometry : particles in suspension, which enter the chamber via an axial specimen nozzle, are enveloped by a buffering sheath flow and transported to a square capillary tube with cross-section of 300 μm×300μm. Finite element viscous-flow analysis is used to examine the flow behavior in the quasi-two-dimensional passage configuration which produces the fluid-dynamic focusing flow. Experimental measurement showed a smooth constricted sheath flow, and pressure loss was reduced to one-tenth of that which occurs with conventional glass flow chambers.
Vascular Endothelial Growth Factor Effect on Endothelial Cell Proliferation, Migration, and Platelet-activating Factor Synthesis Is Flk-1-dependent (1999)

Vascular endothelial growth factor (VEGF) is a potent inducer of endothelial cell (EC) proliferation and migration in vitro as well as inflammation in vivo. We showed recently that VEGF effect on vascular permeability was dependent on the synthesis of platelet-activating factor (PAF) by EC. Consequently, we sought to evaluate by antisense knockdown of gene expression the contribution of VEGF receptors (Flt-1 and Flk-1) on these events. VEGF (10(-11) to 10(-8) M) elicited a dose-dependent increase of bovine aortic EC proliferation, migration, and PAF synthesis by up to 2.05-, 1.31- and 35.9-fold above basal levels, respectively. A treatment with two modified antisense oligomers (1-5 x 10(-7) M) directed against Flk-1 mRNA blocked by 100, 91, and 85% the proliferation, migration, and PAF synthesis mediated by VEGF, respectively. A treatment with two antisense oligomers directed against Flt-1 mRNA failed to modulate these activities. The use of placenta growth factor (up to 10(-8) M), an Flt-1-specific agonist, induced only a slight increase (0.6-fold) of PAF synthesis. These data illustrate the crucial role of Flk-1 in EC stimulation by VEGF. The capacity to inhibit the protein synthesis of Flt-1 and Flk-1 by antisense oligonucleotides provides a new approach to block VEGF pathological effects in vivo.
TRMSim-WSN, Trust and Reputation Models Simulator for Wireless Sensor Networks (2009)

Trust and reputation models research and development for distributed systems such as P2P networks, wireless sensor networks (WSNs) or multi-agent systems has arisen and taken importance in the last recent years among the international research community. However it is not always easy to check the correctness and accuracy of a model and even more, to compare it against other trust and reputation models. This paper presents TRMSim-WSN, a Java-based trust and reputation models simulator aimed to provide an easy way to test a trust and/or reputation model over WSNs and to compare it against other models. It allows the user to adjust several parameters such as the percentage of malicious nodes or the possibility of forming a collusion, among many others.
Molecular cloning, expression, and uses of mammalian glycosyltransferases. (1991)

Lineage specific expression patterns of mammalian oligosaccharides are regulated largely by glycosyltransferases. Several distinct glycosyltransferase genes have recently been isolated by gene transfer and traditional cloning approaches. These each maintain a type II transmembrane topology, that yields a COOH-terminal, Golgi-resident catalytic domain. However, significant primary sequence similarities between cloned glycosyltransferases have been found only between enzymes with substantial functional similarity. These cloned DNA segments, and their cognate enzymes, have been used to determine glycosyltransferase expression patterns, characterize the molecular basis for mutant glycosyltransferase alleles, and identify oligosaccharide ligands for members of the Selectin family of cell adhesion molecules. They have also shown promise for use in the preparative synthesis of defined oligosaccharide molecules, and for transgenic animal approaches designed to explore the function(s) of oligosaccharides in mammalian organisms.
Quantifying Colorimetric Assays in Paper-Based Microfluidic Devices by Measuring the Transmission of Light through Paper (2009)

This article describes a point-of-care (POC) system--comprising a microfluidic, paper-based analytical device (micro-PAD) and a hand-held optical colorimeter--for quantifying the concentration of analytes in biological fluids. The micro-PAD runs colorimetric assays, and consists of paper that has been (i) patterned to expose isolated regions of hydrophilic zones and (ii) wet with an index-matching fluid (e.g., vegetable oil) that is applied using a disposable, plastic sleeve encasement. Measuring transmittance through paper represents a new method of quantitative detection that expands the potential functionality of micro-PADs. This prototype transmittance colorimeter is inexpensive, rugged, and fully self-contained, and thus potentially attractive for use in resource-limited environments and developing countries.
The New Biology of Gastrointestinal Hormones (1998)

The classic concept of gastrointestinal endocrinology is that of a few peptides released to the circulation from endocrine cells, which are interspersed among other mucosal cells in the upper gastrointestinal tract. Today more than 30 peptide hormone genes are known to be expressed throughout the digestive tract, which makes the gut the largest endocrine organ in the body. Moreover, development in cell and molecular biology now makes it feasible to describe a new biology for gastrointestinal hormones based on five characteristics. 1) The structural homology groups the hormones into families, each of which is assumed to originate from a common ancestral gene. 2) The individual hormone gene is often expressed in multiple bioactive peptides due to tandem genes encoding different hormonal peptides, alternative splicing of the primary transcript, or differentiated processing of the primary translation product. By these mechanisms, more than 100 different hormonally active peptides are produced in the gastrointestinal tract. 3) In addition, gut hormone genes are widely expressed, also outside the gut. Some are expressed only in neuroendocrine cells, whereas others are expressed in a multitude of different cells, including cancer cells. 4) The different cell types often express different products of the same gene, "cell-specific expression." 5) Finally, gastrointestinal hormone-producing cells release the peptides in different ways, so the same peptide may act as an acute blood-borne hormone, as a local growth factor, as a neurotransmitter, and as a fertility factor. The new biology suggests that gastrointestinal hormones should be conceived as intercellular messengers of general physiological impact rather than as local regulators of the upper digestive tract.
Autoantibodies in neoplasia an unresolved enigma (1990)

One hundred sixty-four sera samples of patients with malignant diseases were analyzed for the presence of autoantibodies to ssDNA, dsDNA, poly(I), Poly(G), cardiolipin, histones, RNP, Sm, Ro(SSA), and La (SSB). No distinction could be made between these patients and a comparative group composed of age-adjusted healthy subjects when measuring antibody levels to these autoantigens by the ELISA technique. This finding remained valid after further subgrouping of the patients according to age, sex, and histologic origin of the tumor. The authors conclude that in contrast to the known clinical coexistence of neoplasia in autoimmune states, there is no increased incidence of antinuclear autoantibodies in malignant conditions.
Modular artificial neural network for prediction of petrophysical properties from well log data (2002)

This paper reports the application of Kohonen's Self-Organizing Map (SOM) and Learning Vector Quantization (LVQ) algorithms, and the commonly used Back Propagation Neural Network (BPNN) to the prediction of petrophysical properties from well log data. Recently, the use of artificial neural networks (ANN) in the field of petrophysical properties prediction has received increasing attentions. In this paper, a modular ANN comprises of a complex network made up of a number of sub-networks is introduced. In this approach, the SOM algorithm is first applied to classify the well log data into a pre-defined number of classes. This gives an indication of the lithology of the given well. The LVQ algorithm is then applied to train the network under supervised learning. A set of BPNN which corresponds to different classes is then developed for the prediction of petrophysical properties. Once the network is trained if is then used as the classification and prediction model for subsequent input data. Results obtained from example studies using this proposed method have shown to be fast and accurate as compared to a single BPNN network.
CD47–signal regulatory protein-α (SIRPα) interactions form a barrier for antibody-mediated tumor cell destruction (2011)

Monoclonal antibodies are among the most promising therapeutic agents for treating cancer. Therapeutic cancer antibodies bind to tumor cells, turning them into targets for immune-mediated destruction. We show here that this antibody-mediated killing of tumor cells is limited by a mechanism involving the interaction between tumor cell-expressed CD47 and the inhibitory receptor signal regulatory protein-α (SIRPα) on myeloid cells. Mice that lack the SIRPα cytoplasmic tail, and hence its inhibitory signaling, display increased antibody-mediated elimination of melanoma cells in vivo. Moreover, interference with CD47-SIRPα interactions by CD47 knockdown or by antagonistic antibodies against CD47 or SIRPα significantly enhances the in vitro killing of trastuzumab-opsonized Her2/Neu-positive breast cancer cells by phagocytes. Finally, the response to trastuzumab therapy in breast cancer patients appears correlated to cancer cell CD47 expression. These findings demonstrate that CD47-SIRPα interactions participate in a homeostatic mechanism that restricts antibody-mediated killing of tumor cells. This provides a rational basis for targeting CD47-SIRPα interactions, using for instance the antagonistic antibodies against human SIRPα described herein, to potentiate the clinical effects of cancer therapeutic antibodies.