gebhart/patrepeval huggingface dataset:
Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members (2005)

We report an in-depth computational study of the protein sequences and structures of the superfamily of archaeo-eukaryotic primases (AEPs). This analysis greatly expands the range of diversity of the AEPs and reveals the unique active site shared by all members of this superfamily. In particular, it is shown that eukaryotic nucleo-cytoplasmic large DNA viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses and the mimivirus, encode AEPs of a distinct family, which also includes the herpesvirus primases whose relationship to AEPs has not been recognized previously. Many eukaryotic genomes, including chordates and plants, encode previously uncharacterized homologs of these predicted viral primases, which might be involved in novel DNA repair pathways. At a deeper level of evolutionary connections, structural comparisons indicate that AEPs, the nucleases involved in the initiation of rolling circle replication in plasmids and viruses, and origin-binding domains of papilloma and polyoma viruses evolved from a common ancestral protein that might have been involved in a protein-priming mechanism of initiation of DNA replication. Contextual analysis of multidomain protein architectures and gene neighborhoods in prokaryotes and viruses reveals remarkable parallels between AEPs and the unrelated DnaG-type primases, in particular, tight associations with the same repertoire of helicases. These observations point to a functional equivalence of the two classes of primases, which seem to have repeatedly displaced each other in various extrachromosomal replicons.
Synthetic Natural Product Inspired Cyclic Peptides (2021)

Natural products are a bountiful source of bioactive molecules. Unfortunately, discovery of novel bioactive natural products is challenging due to cryptic biosynthetic gene clusters, low titers, and arduous purifications. Herein, we describe SNaPP (<u>S</u>ynthetic <u>Na</u>tural <u>P</u>roduct Inspired Cyclic <u>P</u>eptides), a method for identifying NP-inspired bioactive peptides. SNaPP expedites bioactive molecule discovery by combining bioinformatics predictions of nonribosomal peptide synthetases with chemical synthesis of the predicted natural products (pNPs). SNaPP utilizes a recently discovered cyclase, the penicillin binding protein-like cyclase, as the lynchpin for the development of a library of head-to-tail cyclic peptide pNPs. Analysis of 500 biosynthetic gene clusters allowed for identification of 131 novel pNPs. Fifty-one diverse pNPs were synthesized using solid phase peptide synthesis and solution-phase cyclization. Antibacterial testing revealed 14 pNPs with antibiotic activity, including activity against multidrug-resistant Gram-negative bacteria. Overall, SNaPP demonstrates the power of combining bioinformatics predictions with chemical synthesis to accelerate the discovery of bioactive molecules.
Enhanced Reliability in Silver Impregnation of Terminal Axonal Degeneration-Original Nauta Method (1960)

Brains of rat with surgical lesions 3-5 days old are fixed in 10% neutralized formalin (excess of CaCO3), 20 μ serial frozen sections cut therefrom and kept in neutralized formalin for an additional 24-48 hr. The sections are soaked in distilled water 12-24 hr, transferred to 50% alcohol containing 0.75 ml of concentrated NH4OH (sp. gr. 0.91) per 100 ml 12-24 hr, placed in distilled water 2-3 hr and then in silver-pyridine solution (AgNO3 3% aq., 20 ml; pyridine, 1 ml) for 48 hr. Test sections are transferred directly to each one of 3 ammoniated silver-solutions, pH 12.8, 13.0 and 13.2, made as follows: To 200 ml of solution 1 (silver nitrate, 6.4 gm; alcohol 96%, 220 ml; NH4OH (sp. gr. 0.91), 28 ml and distilled water, 440 ml) is added respectively 8-12 ml, 12-16 ml and 16-20 ml of solution 2 (2% NaOH) to give the pH desired. The test sections are studied and the optimal ammoniated silver solution chosen. Two baths of ammoniated silver are used, the section placed with continuous agitation into the first bath for 30 sec and the second bath for 60 sec. The sections are then transferred directly into a reducing bath (formalin 10%, 2ml; alcohol 96%, 5 ml; citric acid 1%, 1.5 ml and distilled water, 4.5 ml) for 2 min and from there to 5% Na2S2O3 for 1 min, rinsed in 3 changes of distilled water, dehydrated and mounted.
Human plasma extrinsic pathway inhibitor activity: II. Plasma levels in disseminated intravascular coagulation and hepatocellular disease (1989)

Plasma or serum extrinsic pathway inhibitor (EPI) activity was measured in 24 patients with disseminated intravascular coagulation (DIC) and in 23 patients with severe hepatocellular disease. EPI was measured as activity in a test sample that inhibited factor VIIa/tissue factor (TF)-catalyzed activation of 3H-factor IX (activation peptide release) in the presence of factor X. Of the 24 patients with DIC, 13 had sepsis and five had metastatic carcinoma, disorders in which tissue factor is believed to initiate DIC. EPI activity ranged from 68% to 300% (mean 134% +/- 50%). Serial measurements in nine patients failed to show depletion of EPI activity coincident with worsening DIC. DIC induced by tissue factor or other activating materials may progress despite normal EPI levels. In the patients with liver disease, of whom 15 had decompensated chronic hepatocellular disease (two fatal cases) and eight had acute fulminant liver failure (seven fatal cases), plasma or serum EPI activity varied from less than 20% to 194%. Values were distributed in a bimodal fashion. EPI activity could not be correlated with either the etiology of the liver disease or the degree of prolongation of the prothrombin time. Patients with chronic hepatocellular disease who survived had normal or elevated EPI activity. Patients with fatal hepatic dysfunction had low, normal, or high values for EPI activity. This must mean that secretion of EPI from cells other than hepatocytes can maintain normal plasma EPI levels.
Isocyanates derived from fatty acids by the trimethylsilyl azide modification of the curtius rearrangement (1972)

Abstract Five fatty acid chlorides—myristoyl (14:0), palmitoyl (16:0), linoleoyl (18:2), oleyl (18:1) and stearoyl (18:0)—were smoothly converted in a one‐pot, one‐step reaction to the isocynates with one less carbon atom in the alkyl chain by treatment with trimethylsilyl azide in aromatic solvents at 100 C. The yields were consistently greater than 70%, and NMR and IR spectra of the products were consistent with the assigned isocyanate structures.
Temperature-dependent Azide Sensitivity of Growth and ATPase Activity in the Facultative Thermophile, Bacillus coagulans (1984)

Inhibition by sodium azide of the growth of Bacillus coagulans decreased but the cytochrome content, particularly cytochrome d, increased with increasing growth temperature. Higher cytochrome d content correlated with increased cyanide resistance of NADH oxidase, but azide resistant activity was found in mesophilic and thermophilic cultures. Anaerobic growth at 37 °C was totally inhibited by 1 mm-azide. At 55 °C; growth occurred with 4 mm-azide, but the cell yield was reduced by 60%. ATPase activity was sensitive to azide but inhibition varied with both growth and assay temperatures. ATPase from cells grown at 55 °C; was least sensitive when assayed at 55 °C;. Possible changes in ATPase which could account for the temperature-dependent azide sensitivity are discussed.
Dynamic Vegas (2008)

i-manager's Journal on Future Engineering and Technology, i-manager's Journal on Software Engineering, i-manager's Journal on Electrical Engineering, i-manager's Journal on Electronics Engineering, i-manager's Journal of Educational Technology, i-manager's Journal on Educational Psychology, i-manager's Journal on School Educational Technology, i-manager's Journal on English Language Teaching, i-manager's Journal on Mechanical Engineering, i-manager's Journal on Civil Engineering, i-manager's Journal on Embedded Systems, i-manager's Journal on Information Technology, i-manager's Journal on Structural Engineering, i-manager's Journal on Communication Engineering and Systems, i-manager's Journal on Wireless Communication Networks, i-manager's Journal on Instrumentation and Control Engineering, i-manager's Journal on Circuits and Systems, i-manager's Journal on Digital Signal Processing, i-manager's Journal on Power Systems Engineering, i-manager's Journal on Computer Science, i-manager's Journal on Material Science, i-manager's Journal on Cloud Computing, i-manager's Journal on Image Processing, i-manager's Journal on Mobile Applications and Technologies, i-manager's Journal on Pattern Recognition, i-manager's Journal on Mathematics, i-manager's Journal on Management, i-manager's Journal on Nursing, i-manager's Journal on Physical Sciences, i-manager's Journal on Chemical Sciences, i-manager's Journal on Economics & Commerce , i-manager's Journal on Humanities & Social Sciences, i-manager's Journal on Life Sciences , i-manager's Journal on Construction Management, i-manager's Oyla , ,India best Journal Publication Website,World Best Plication SIte,Free atrticle published website,Journal Publised,Published Journal,Research Paper Published,indian research paper publications,how to published your article/research paper in india for free,journal’s instructions for authors
Study on Security Problems of the Internet of Things (2013)

Internet of things is a worldwide network which based on mass micro-devices, using the new generation as the backbone, and will be used in traditional and emerging industries. The possibility of seamlessly merging the real and the virtual world, through the massive deployment of embedded devices, opens up new exciting directions for both research and business. In this survey article, we provided an overview of the key issues such as security problems related to the development of IoT technologies and services.
Spam over Internet telephony: Prototype implementation (2008)

This paper presents a prototype implementation of the reputation-based spam detection scheme, first presented in. Different components were developed, in particular the reputation manager (RM) that collects the appropriate information from the contact lists of the SIP subscribers and builds a social network. The latter provides the possible paths that might exist between any two SIP subscribers. This social network is endowed with a metric that allows to assign reputation values to the mentioned paths. Based on these scored paths, a decision is taken for accepting or rejecting calls. The result of our implementation is a working mechanism that tolerates zero false acceptance and an average of 4% false rejection. Our work demonstrates the scalability of the suggested solution as well as the feasibility of using the reputation concept for detecting SIP spam.
A COMPARATIVE GENOMIC ANALYSIS OF CHLORELLA NC64A VIRUS NY-2A AND CHLORELLA Pbi VIRUS MT325 FROM THE FAMILY PHYCODNAVIRIDAE (2006)

The family Phycodnaviridae consists of a morphologically similar but genetically diverse group of large dsDNA viruses which infect both fresh and marine water eukaryotic algae. Two viruses, the 370 kb Chlorella NC64A virus NY-2A and the 313 kb Chlorella Pbi virus MT325, from the family Phycodnaviridae, genus Chlorovirus, were sequenced, analyzed, and compared to the prototype chlorella virus PBCV-1. The NY-2A genome, the largest chlorella viral genome sequenced to date, contains 886 open reading frames (ORFs) of 65 codons or larger and encodes 404 putative proteins and 7 tRNAs. The MT325 genome, the smallest chlorella viral genome sequenced to date, contains 845 ORFs and encodes 331 putative proteins and 10 tRNAs. The protein-encoding genes are evenly distributed on both strands, and the intergenic space is minimal. Approximately 50% of the viral gene products have been identified, including some which are the first of their type to be detected in a virus. Domain scatter plots revealed that NY-2A and MT325 are mosaics of both prokaryotic- and eukaryotic-like proteins. A comparison of the three chlorella viruses sequenced, NY-2A, MT325, and the previously sequenced PBCV-1, revealed that ~75% of the viral encoded proteins are homolgous. However, 64% of these homologs are classified as unknowns based on a lack of sequence similarity to proteins in public databases. In addition to the genomic annotations, I conducted an extensive comparison of the chloroviruses to other phycodnavirus members as well as other large dsDNA viruses. Surprisingly, only 10 (~3%) of the chlorovirus genes are encoded by all six of the sequenced phycodnaviruses. Adviser: James L. Van Etten
Patterns of protein synthesis following heat shock in pupae of Drosophila melanogaster (1979)

Abstract Pupae of Drosophila melanogaster were heat‐shocked under conditions required to induce phenocopies in more than 90% of the flies that subsequently emerge. The effects of these treatments on protein synthesis in two tissues (thoracic epithelium and brain) were followed for several hours after the heat treatments. Results from pulse‐labeling and protein separations on sodium dodecylsulfate (SDS) acrylamide gels showed a virtually complete cessation of protein synthesis immediately after the shock, followed by a noncoordinate resumption of the starting pattern. Similar experiments following double heat shocks demonstrated a more rapid resumption of synthesis of heat shock proteins after two successive heat treatments than after a single one.
Kinematic Precise Point Positioning Using Multi-Constellation Global Navigation Satellite System (GNSS) Observations (2017)

Multi-constellation global navigation satellite systems (GNSSs) are expected to enhance the capability of precise point positioning (PPP) by improving the positioning accuracy and reducing the convergence time because more satellites will be available. This paper discusses the performance of multi-constellation kinematic PPP based on a multi-constellation kinematic PPP model, Kalman filter and stochastic models. The experimental dataset was collected from the receivers on a vehicle and processed using self-developed software. A comparison of the multi-constellation kinematic PPP and real-time kinematic (RTK) results revealed that the availability, positioning accuracy and convergence performance of the multi-constellation kinematic PPP were all better than those of both global positioning system (GPS)-based PPP and dual-constellation PPP. Multi-constellation kinematic PPP can provide a positioning service with centimetre-level accuracy for dynamic users.
Functional Characterization of a Maize Purine Transporter by Expression in Aspergillus nidulans (2001)

Eleftheria Argyrou, Vicky Sophianopoulou, Neil Schultes, George Diallinas, Functional Characterization of a Maize Purine Transporter by Expression in Aspergillus nidulans, The Plant Cell, Vol. 13, No. 4 (Apr., 2001), pp. 953-964
Low-Temperature Effects on Photosynthesis and Correlation with Freezing Tolerance in Spring and Winter Cultivars of Wheat and Rye (1993)

Winter cultivars of rye (Secale cereale L., cv Musketeer) and wheat (Triticum aestivum L. cvs Kharkov and Monopol), but not a spring cultivar of wheat (Glenlea), grown at cold-hardening temperatures showed, at high irradiances, a higher proportion of oxidized to reduced primary, stable quinone receptor (QA) than did the same cultivars grown under nonhardening conditions. In addition, there was a positive correlation between the effects of low-growth temperature on this increased proportion of oxidized QA, and a concomitant increase in the capacity for photosynthesis, and LT50, the temperature at which 50% of the seedlings are killed, in cultivars showing different freezing tolerances. This suggests that low-temperature modulation of the photosynthetic apparatus may be an important factor during the induction of freezing resistance in cereals. Finally, the control of photosystem II photochemistry by nonphotochemical quenching of excitation energy was identical for nonhardened and cold-hardened winter rye. However, examination of measuring temperature effects per se revealed that, irrespective of growth temperature, nonphotochemical quenching exerted a stronger control on photosystem II photochemistry at 10[deg] C rather than at 20[deg] C.
p49, a putative HLA class I-specific inhibitory NK receptor belonging to the immunoglobulin superfamily (1998)

NK cells display several killer inhibitory receptors (KIR) specific for different alleles of MHC class I molecules. A family of KIR are represented by type I transmembrane proteins belonging to the immunoglobulin superfamily (Ig-SF). Besides cDNA encoding for these KIR, additional cDNA have been identified which encode for Ig-SF receptors with still undefined specificity. Here we analyze one of these cDNA, termed cl.15.212, which encodes a type I transmembrane protein characterized by two extracellular Ig-like domains and a 115-amino acid cytoplasmic tail containing a single immuno-receptor tyrosine-based inhibitory motif (ITIM) which is typical of KIR. cl.15.212 cDNA displays approximately 50 % sequence homology with other Ig-SF members. Different from the other KIR, cl.15.212 mRNA is expressed by all NK cells and by a fraction of KIR+ T cell clones. cl.15.212 cDNA codes for a membrane-bound receptor displaying an apparent molecular mass of 49 kDa, thus termed p49. To determine the specificity of the cl.15.212-encoded receptor, we generated soluble fusion proteins consisting of the ectodomain of p49 and the Fc portion of human IgG1. Soluble molecules bound efficiently to 221 cells transfected with HLA-G1, -A3, -B46 alleles and weakly to -B7 allele. On the other hand, they did not bind to 221 cells either untransfected or transfected with HLA-A2, -B51, -Cw3 or -Cw4. The binding specificity of soluble p49-Fc was confirmed by competition experiments using an anti-HLA class I-specific monoclonal antibody. Finally, different cDNA encoding for molecules homologous to cl.15.212 cDNA have been isolated, two of which lack the sequence encoding the transmembrane portion, thus suggesting they may encode soluble molecules.
Sphingosine 1-Phosphate Distribution in Human Plasma: Associations with Lipid Profiles (2012)

The physiological significance of sphingosine 1-phosphate (S1P) transport in blood has been debated. We have recently reported a comprehensive sphingolipid profile in human plasma and lipoprotein particles (VLDL, LDL, and HDL) using HPLC-MS/MS (Hammad et al., 2010). We now determined the relative concentrations of sphingolipids including S1P in the plasma subfraction containing lipoproteins compared to those in the remaining plasma proteins. Sphingomyelin and ceramide were predominantly recovered in the lipoprotein-containing fraction. Total plasma S1P concentration was positively correlated with S1P concentration in the protein-containing fraction, but not with S1P concentration in the lipoprotein-containing fraction. The percentage of S1P transported in plasma lipoproteins was positively correlated with HDL cholesterol (HDL-C) concentration; however, S1P transport in lipoproteins was not limited by the concentration of HDL-C in the individual subject. Thus, different plasma pools of S1P may have different contributions to S1P signaling in health and disease.
Rotary Clamp in Uniaxial and Biaxial Extensional Rheometry of Polymer Melts (1981)

The rotary clamp consisting of a pair of gears is a basic construction element for the design of various types of extensional rheometers for polymer melts. With the most recent model of the uniaxial extensional rheometer, built with rotary clamps, homogeneous deformations of Hencky strains up to ε=7 have been performed with a low‐density polyethylene melt. For the evaluation and discussion of results from tests with large deformations, it is vital that parameters which characterize the quality of each test be defined and measured. Otherwise, the measured force and the rotational speed of the clamps might be of little relevance for the stress, strain, and strain rate within the sample. The biaxial extensional rheometer consists of eight rotary clamps in a circular arrangement. With this new instrument, extensional Hencky strains up to ε11=ε22=2.2 can be achieved for a polyisobutylene sample. Such a high deformation corresponds to a compression in the third direction of ε33=−4.4. The material within the samples is deformed homogeneously. The samples are shaped as flat circular disks. During the test they are cut periodically at the rim between the clamps in order to keep the "active" diameter constant within a narrow range. Hence, from the forces measured at the clamps, the tensile stress can be determined.
Nasal amphotericin irrigation in chronic rhinosinusitis (2008)

The use of amphotericin for patients with chronic rhinosinusitis is not substantiated by the majority of publications. Although some studies found improvement on radiographic images, the symptoms of the disorder were not improved even with fungal eradication. Further studies need to be carried out to determine if changes in dosage, treatment time or route of administration could improve results.
Protein Processing in Herpes Viruses (1993)

The gene encoding cytomegalovirus assembly protein (AP) has been cloned, sequenced and found to be organized within a nested set of four in-frame, 3′-coterminal genes. These genes code for a precursor of the enzyme (assemblin) 64 kDa, a pre-45 kDa protein 46 kDa, a pre-assembly protein 34 kDa, and a 27 kDa protein. A new approach to protein sequencing that combines enzymatic and chemical digestion with high sensitivity molecular weight measurements by mass spectrometry was developed. In particular it involved mass-mapping of unfractionated enzymatic digests using plasma desorption mass spectrometery (PDMS), purification of peptides, transfer of peptides to the mass spectrometer using blotting techniques, and mass analysis following in situ digestion with carboxypeptidases to reveal amino acid sequence, post translational modifications and/or cleavage sites. This approach is a 100 fold more sensitive than those which rely upon fragmentation in tandem mass spectrometers, and enables the analysis of proteins available in very small quantities (10 to 50 picomoles). PDMS was used to determine the exact cleavage site of the pre-assembly protein. C-terminal peptide fragments were generated by Endoproteinase-Lys C and Endoproteinase-Glu C. A nitrocellulose coated sample foil was used for on foil digestion of the carboxy terminal fragment of the AP with carboxypeptidase. The identification of alanine 277 as the carboxy terminal amino acid of the mature AP enabled the recognition of a consensus proteinase cleavage sequence of V/L-X-A↓-S/V at the carboxylic end of all herpes viruses AP homologs. This finding also predicts that the mature enzyme is generated by cleavage at YVKA S. In addition PDMS was used to determine phosphorylation sites on the AP. Our results suggest a single site at S144. The sequence RS144GALKRRR is a concensus sequence for cellular protein kinase C. AP from other herpes viruses also have a consensus sequence that could be phosphorylated by protein kinase C. This area is conserved in all Herpes viruses, strongly suggesting that phosphorylation of the AP might play a role in its function.
An algorithm for weighted bilinear regression (1997)

Bilinear models in which the expectation of a two-way array is the sum of products of parameters are widely used in spectroscopy. In this paper we present an algorithm called combined-vector successive overrelaxation (COV-SOR) for bilinear models, and compare it with methods like alternating least squares, singular value decomposition, and the Marquardt procedure. Comparisons are done for missing data also.