gebhart/patrepeval huggingface dataset:
Ancylostoma caninum anticoagulant peptide: a hookworm-derived inhibitor of human coagulation factor Xa. (1995)

Human hookworm infection is a major cause of gastrointestinal blood loss and iron deficiency anemia, affecting up to one billion people in the developing world. These soil-transmitted helminths cause blood loss during attachment to the intestinal mucosa by lacerating capillaries and ingesting extravasated blood. We have isolated the major anticoagulant used by adult worms to facilitate feeding and exacerbate intestinal blood loss. This 8.7-kDa peptide, named the Ancylostoma caninum anticoagulant peptide (AcAP), was purified by using a combination of ion-exchange chromatography, gel-filtration chromatography, and reverse-phase HPLC. N-terminal sequencing of AcAP reveals no homology to any previously identified anticoagulant or protease inhibitor. Single-stage chromogenic assays reveal that AcAP is a highly potent and specific inhibitor of human coagulation, with an intrinsic K*i for the inhibition of free factor Xa of 323.5 pM. In plasma-based clotting time assays, AcAP was more effective at prolonging the prothrombin time than both recombinant hirudin and tick anticoagulant peptide. These data suggest that AcAP, a specific inhibitor of factor Xa, is one of the most potent naturally occurring anticoagulants described to date.
Exogenous GTP Enhances the Effects of Sodium Nitrite on Cyclic GMP Accumulation, Vascular Smooth Muscle Relaxation and Platelet Aggregation (1991)

Exogenous guanosine triphosphate (GTP) (1-2 x 10(-4)M) resulted in increased concentrations of cyclic GMP both in endothelium denuded rat mesenteric artery (RMA) and in human ADP-stimulated platelets. Sodium nitrite (3.3 x 10(-4)M) relaxed precontracted RMA by 34%. When the arteries were preincubated with GTP (2 x 10(-4)M) sodium nitrite administration resulted in a significantly greater relaxation (58%) of the RMA with concomitant 2-fold increase in cGMP. Sodium nitrite (1 x 10(-4)M) had an inhibitory effect on ADP-induced platelet aggregation. Preincubation with GTP enhanced significantly the sodium nitrite-induced inhibition of ADP-induced platelet aggregation with a simultaneous 5-fold increase in cGMP. These results indicate that exogenous GTP enhances the sodium nitrite-induced stimulation of guanylate cyclase and thus enhances the effects of sodium nitrite on arterial smooth muscle and platelets.
Spatiotemporal Data from Mobile Phones for Personal Mobility Assessment (2013)

Purpose — In this chapter, we will review several alternative methods of collecting data from mobile phones for human mobility analysis. We propose considering cellular network location data as a useful complementary source for human mobility research and provide case studies to illustrate the advantages and disadvantages of each method.Methodology/approach — We briefly describe cellular phone network architecture and the location data it can provide, and discuss two types of data collection: active and passive localization. Active localization is something like a personal travel diary. It provides a tool for recording positioning data on a survey sample over a long period of time. Passive localization, on the other hand, is based on phone network data that are automatically recorded for technical or billing purposes. It offers the advantage of access to very large user populations for mobility flow analysis of a broad area.Findings — We review several alternative methods of collecting data from mobile phone for human mobility analysis to show that cellular network data, although limited in terms of location precision and recording frequency, offer two major advantages for studying human mobility. First, very large user samples – covering broad geographical areas – can be followed over a long period of time. Second, this type of data allows researchers to choose a specific data collection methodology (active or passive), depending on the objectives of their study. The big mobile phone localization datasets have provided a new impulse for the interdisciplinary research in human mobility.Originality/value of chapter — We propose considering cellular network location data as a useful complementary source for transportation research and provide case studies to illustrate the advantages and disadvantages of each proposed method. Mobile phones have become a kind of “personal sensor” offering an ever-increasing amount of location data on mobile phone users over long time periods. These data can thus provide a framework for a comprehensive and longitudinal study of temporal dynamics, and can be used to capture ephemeral events and fluctuations in day-to-day mobility behavior offering powerful tools to transportation research, urban planning, or even real-time city monitoring.
An Experimental Evaluation of List Scheduling (1998)

While altering the scope of instruction scheduling has a rich heritage in compiler literature, instruction scheduling algorithms have received little coverage in recent times. The widely held belief is that greedy heuristic techniques such as list scheduling are &amp;quot;good&amp;quot; enough for most practical purposes. The evidence supporting this belief is largely anecdotal with a few exceptions.
A Study of the Active Site of Influenza Virus Sialidase:  An Approach to the Rational Design of Novel Anti-influenza Drugs (1996)

The development of sialidase inhibitor-based potential anti-influenza drugs using rational drug design techniques has been of recent interest. The present study details an investigation of the active site of influenza virus sialidase by using the program GRID in an attempt to design more potent inhibitors in the hope they will eventually lead to anti-influenza drugs. A number of different probes (amino, carboxy, hydroxy, methyl, etc.) have been used in an effort to determine the functional groups most likely to improve the binding of the starting template 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en). The data have correctly predicted the binding regions for the carboxylate, acetamido (NH and methyl), and glycerol (OH) groups of N-acetylneuraminic acid. Moreover, the data suggest that the addition of certain functionalities (amino group) at the C-4 position should enhance the overall binding.
Inventarisatie, voorspelling en beheersing zwarte vlekkenziekte in peen. Rhexocercosporidium carotae, een `nieuwe' veroorzaker van zwarte vlekkenziekte in bewaarpeen (2004)

Rhexocercosporidium carotae, een `nieuwe? veroorzaker van zwarte vlekkenziekte in bewaarpeen.
Superagonist IL-15-Armed Oncolytic Virus Elicits Potent Antitumor Immunity and Therapy That Are Enhanced with PD-1 Blockade (2018)

Oncolytic immunotherapy is a promising novel therapeutic for cancer, and further preclinical studies may maximize its therapeutic efficacy. In this study, we construct a novel oncolytic vaccinia virus (VV) expressing a superagoinst IL-15, a fusion protein of IL-15 and IL-15Ralpha. This virus, named vvDD-IL15-Rα, possesses similar replication efficiency as the parental virus vvDD yet leads to significantly more regression of the disease and extends the survival of mice bearing MC38 colon or ID8 ovarian cancer. This novel virus elicits potent adaptive antitumor immunity as shown by ELISPOT assays for interferon-gamma-secreting CD8<sup>+</sup> T cells and by the rejection of tumor implants upon re-challenge in the mice, which were previously cured by vvDD-IL15-Rα treatment. In vivo cell depletion assays with antibodies showed that this antitumor activity is highly dependent on CD8<sup>+</sup> T cells but much less so on CD4<sup>+</sup> T cells and NK cells. Finally, the combination of the oncolytic immunotherapy with anti-PD-1 antibody dramatically improves the therapeutic outcome compared to either anti-PD-1 alone or vvDD-IL15-Rα alone. These results demonstrate that the IL-15-IL-15Rα fusion protein-expressing OV elicits potent antitumor immunity, and rational combination with PD-1 blockade leads to dramatic tumor regression and prolongs the survival of mice bearing colon or ovarian cancers.
MAP Kinase Pathways (2012)

MAP kinases are activated within protein kinase cascades that regulate cell proliferation, differentiation, and death. In mammals, MAP kinases are grouped into three families: ERKs, JNKs, and p38/SAPKs.
Typing of Histoplasma capsulatum by restriction fragment length polymorphisms in a nuclear gene (1992)

We previously described yps-3, a Histoplasma-specific nuclear gene probe useful in the identification of Histoplasma capsulatum. By using restriction fragment length polymorphisms (RFLPs) of DNA detected by the yps-3 gene and mitochondrial DNA, 76 clinical and soil isolates of H. capsulatum were classified. The majority of North American isolates obtained from endemic regions of the midwestern United States were members of the previously characterized class 2, although four clinical isolates from different patients with AIDS from that region were grouped in class 1 with the temperature-sensitive Downs strain. A Florida soil isolate (FLS1) was placed in class 4 on the basis of RFLP with both probes. Two American Type Culture Collection strains (G184B and G186B) from Panama were grouped into class 3 by this analysis. A group of five H. capsulatum isolates obtained from patients with AIDS in New York City were typed into a new class 5 on the basis of yps-3 polymorphisms; those organisms fell into two broad mitochondrial DNA patterns, designated 5b and 5c. Two new isolates from Panama were also members of this broad yps-3 class 5 group, but they exhibited a distinct mitochondrial DNA profile (class 5a). A sixth class was detected in DNA obtained from a patient with AIDS from Panama; that DNA had unique RFLP profiles with respect to both probes. These observations suggest that the Histoplasma-specific yps-3 gene probe is a sensitive tool for typing H. capsulatum in clinical specimens. Additionally, these studies provide molecular support for the hypothesis that AIDS-associated histoplasmosis in nonendemic areas is due to reactivation of a previously acquired infection.
Identification of Three Highly Attenuated Salmonella typhimurium Mutants That Are More Immunogenic and Protective in Mice than a Prototypical aroA Mutant (1998)

A panel of Salmonella typhimurium 14028s mutants, which were previously shown to be highly attenuated in the BALB/c mouse model of infection, were analyzed for their potential as live Salmonella oral-vaccine candidates. A prototypical aroA mutant was chosen as a basis of comparison. From the panel of mutants initially chosen for this study, three mutants with comparable levels of attenuation elicited higher Salmonella-specific serum immunoglobulin G (IgG) and/or mucosal secretory-IgA antibody titers than the aroA vaccine strain. The three mutants, CL288, CL401, and CL554, also elicited a better protective immune response than the aroA control strain, after a single oral dose of 1 x 10(9) to 2 x 10(9) bacteria.
Localization of D-amino acid oxidase on the cell surface of human polymorphonuclear leukocytes (1978)

The ultrastructural localization of D-amino acid oxidase (DAO) was studied cytochemically by detecting sites of hydrogen peroxide production in human polymorphonuclear leukocytes (PMNs). Reaction product, which forms when cerous ions react with H2O2 to form an electron-dense precipitate, was demonstrated on the cell surface and within the phagosomes of phagocytically stimulated cells when D-amino acids were provided as substrate. Resting cells showed only slight activity. The competitive inhibitor D,L-2-hydroxybutyrate greatly reduced the D-amino acid-stimulated reaction while KCN did not. The cell surface reaction was abolished by nonpenetrating inhibitors of enzyme activity while that within the phagosome was not eliminated. Dense accumulations of reaction product were formed in cells which phagocytosed Staphylococcus aureus in the absence of exogenous substrate. No reaction product formed with Proteus vulgaris while an intermediate amount formed when Escherichia coli were phagocytosed. Variation in the amount of reaction product with the different bacteria correlated with the levels of D-amino acids in the bacterial cell walls which are available for the DAO of PMNs. An alternative approach utilizing ferricyanide as an electron acceptor was also used. This technique verified the results obtained with the cerium reaction, i.e., the DAO is located in the cell surface and is internalized during phagocytosis and is capable of H2O2 production within the phagosome. The present finding that DAO is localized on the cell surface further supports the concept that the plasma membrane is involved in peroxide formation in PMNs.
Distinct brain networks for adaptive and stable task control in humans (2007)

Control regions in the brain are thought to provide signals that configure the brain's moment-to-moment information processing. Previously, we identified regions that carried signals related to task-control initiation, maintenance, and adjustment. Here we characterize the interactions of these regions by applying graph theory to resting state functional connectivity MRI data. In contrast to previous, more unitary models of control, this approach suggests the presence of two distinct task-control networks. A frontoparietal network included the dorsolateral prefrontal cortex and intraparietal sulcus. This network emphasized start-cue and error-related activity and may initiate and adapt control on a trial-by-trial basis. The second network included dorsal anterior cingulate/medial superior frontal cortex, anterior insula/frontal operculum, and anterior prefrontal cortex. Among other signals, these regions showed activity sustained across the entire task epoch, suggesting that this network may control goal-directed behavior through the stable maintenance of task sets. These two independent networks appear to operate on different time scales and affect downstream processing via dissociable mechanisms.
Studies on the Substrate Specificity of Escherichia coli Galactokinase (2003)

In vitro glycorandomization (IVG) technology is dependent upon the ability to rapidly synthesize sugar phosphates. Compared with chemical synthesis, enzymatic (kinase) routes to sugar phosphates would be attractive for this application. This work focuses upon the development of a high-throughput colorimetric galactokinase (GalK) assay and its application toward probing the substrate specificity and kinetic parameters of Escherichia coli GalK. The demonstrated dinitrosalicylic assay should also be generally applicable to a variety of sugar-processing enzymes. [reaction: see text]
Rapid electrochemical detection on a mobile phone (2013)

We present a compact mobile phone platform for rapid, quantitative biomolecular detection. This system consists of an embedded circuit for signal processing and data analysis, and disposable microfluidic chips for fluidic handling and biosensing. Capillary flow is employed for sample loading, processing, and pumping to enhance operational portability and simplicity. Graphical step-by-step instructions displayed on the phone assists the operator through the detection process. After the completion of each measurement, the results are displayed on the screen for immediate assessment and the data is automatically saved to the phone's memory for future analysis and transmission. Validation of this device was carried out by detecting Plasmodium falciparum histidine-rich protein 2 (PfHRP2), an important biomarker for malaria, with a lower limit of detection of 16 ng mL(-1) in human serum. The simple detection process can be carried out with two loading steps and takes 15 min to complete each measurement. Due to its compact size and high performance, this device offers immense potential as a widely accessible, point-of-care diagnostic platform, especially in remote and rural areas. In addition to its impact on global healthcare, this technology is relevant to other important applications including food safety, environmental monitoring and biosecurity.
Hyperfractionated Irradiation with or without Concurrent Chemotherapy for Locally Advanced Head and Neck Cancer (1998)

Combined treatment for advanced head and neck cancer is more efficacious and not more toxic than hyperfractionated irradiation alone.
Isolation and Localization of the Antibiotic Gliotoxin Produced byGliocladium virensfrom Alginate Prill in Soil and Soilless Media (1992)

Gliocladium virens produced detectable levels of gliotoxin when grown with an alginate-wheat bran food base delivery system in peat mossvermiculite soilless medium (PV medium). The fungus also effectively controlled damping-off of zinnia seedlings caused by Pythium ultimum and Rhizoctonia solani in this same system. Gliotoxin was not detectable, and biocontrol effectiveness was greatly reduced when the fungus was grown in a medium containing bark ash (charcoal) (...)
Microplate and dot immunoassays for the serodiagnosis of tuberculosis. (1992)

A simple dot enzyme immunoassay based on the recognition of serum IgG antibody to a 30,000 dalton native antigen purified from culture filtrates of Mycobacterium tuberculosis was developed and compared with a standard plate enzyme-linked immunosorbent assay in the serodiagnosis of tuberculosis. The previously described favorable test characteristics of plate enzyme-linked immunoassay were confirmed; although the dot enzyme immunoassay was promising, it was less satisfactory. Dot enzyme immunoassay may have its most promising use as a screening test for situations of limited technical facilities. Both plate enzyme-linked immunoassay and dot enzyme immunoassay had markedly reduced sensitivities in persons with human immunodeficiency virus infection.
Role of p38 Mitogen-Activated Protein Kinase in Rhinovirus-Induced Cytokine Production by Bronchial Epithelial Cells (2000)

The stress-activated protein kinase p38 plays a central role in the regulation of cytokine biosynthesis by various cell types in response to a wide range of stimuli. Because the local inflammatory response and the infiltration of neutrophils is thought to contribute to the symptoms and sequelae of rhinovirus infection, we investigated the role of p38 kinase in cytokine and chemokine elaboration in airway epithelial cells infected with human rhinovirus. Rhinovirus-39 infection of BEAS-2B cells resulted in synthesis of cytokines (IL-1, IL-6, G-CSF, and GM-CSF) and CXC chemokines (IL-8, epithelial neutrophil-activating protein-78, and growth-related oncogene-alpha), evident 24-72 h postinfection. Rhinovirus infection induced a time- and dose-dependent increase in tyrosine phosphorylation of p38 kinase, which peaked 30 min postinfection and remained elevated for 1 h. Treatment of infected cells with SB 239063, a potent pyridinyl imidazole inhibitor of p38 kinase, resulted in up to 100% inhibition of mediator production and partially reduced levels of IL-8 mRNA as determined by quantitative RT-PCR. Treatment with SB 239063 had no effect on virus replication and was not cytotoxic at concentrations </= 70 microM. These studies provide the first evidence that early activation of p38 kinase by rhinovirus infection is a key event in regulation of virus-induced cytokine transcription, and may provide a new target for inhibition of symptoms and airway inflammation associated with rhinovirus infection.
Network edge services (2003)

NetEdge is a network edge device for the Internet that offloads the origin server by accommodating client capabilities and preferences locally. Services available include language translation, virus scanning, security and authentication, caching, image transcoding, and resolution of questions and ambiguity. We discuss how this new concept could be used as a virtual assistant to improve the client's view of available web services.
Light Intensity During Leaf Growth Affects Chlorophyll Concentration and CO2 Assimilation of a Soybean Chlorophyll Mutant1 (1974)

An evaluation was made of leaf diffusive resistance and chlorophyll concentrations of dark green (normal) and pale green (chlorophyll deficient) phenotypes of a soybean [ Glycine max (L.) Merrill] mutant when grown 10‐ and 30‐klux light intensities. When grown at the 10‐klux intensity the two leaf types had similar mesophyll and total CO 2 diffusive resistances and similar net photosynthetic rates per unit leaf area at normal ambient CO 2 concentrations (e.g., 300 µl/liter). Chloropyhll concentration of the pale green leaf was one‐fourth that of the dark green leaf. On a chlorophyll basis, rate of CO 2 fixation was four times faster in the pale green type than in the dark green type. The similarity in net photosynthetic rates per unit leaf area of the two phenotypes when grown at the 10‐klux light intensity was the result of (1) similar CO 2 diffusive resistances and (2) the ability of the photosynthetic apparatus of the pale green leaf to fix CO 2 as rapidly as that of the dark green leaf, in spite of a much lower amount of chlorophyll. When grown at the 30‐klux light intensity, chlorophyll concentration of the pale green phenotype progressively declined, to one‐tenth the amount at the 10‐klux intensity. Chlorophyll concentration of the dark green phenotype was not significantly affected by light intensity. Photosynthesis of the pale green leaf grown at the 30‐klux intensity became CO 2 saturated at concentrations well below 300 µl/liter. Therefore, light intensity during leaf growth strongly influenced the relative CO 2 assimilation rates of the dark green and pale green phenotypes.
Structure and Characterization of a cDNA Clone for Phenylalanine Ammonia-Lyase from Cut-Injured Roots of Sweet Potato (1989)

A cDNA clone for phenylalanine ammonia-lyase (PAL) induced in wounded sweet potato (Ipomoea batatas Lam.) root was obtained by immunoscreening a cDNA library. The protein produced in Escherichia coli cells containing the plasmid pPAL02 was indistinguishable from sweet potato PAL as judged by Ouchterlony double diffusion assays. The M(r) of its subunit was 77,000. The cells converted [(14)C]-l-phenylalanine into [(14)C]-t-cinnamic acid and PAL activity was detected in the homogenate of the cells. The activity was dependent on the presence of the pPAL02 plasmid DNA. The nucleotide sequence of the cDNA contained a 2121-base pair (bp) open-reading frame capable of coding for a polypeptide with 707 amino acids (M(r) 77, 137), a 22-bp 5'-noncoding region and a 207-bp 3'-noncoding region. The results suggest that the insert DNA fully encoded the amino acid sequence for sweet potato PAL that is induced by wounding. Comparison of the deduced amino acid sequence with that of a PAL cDNA fragment from Phaseolus vulgaris revealed 78.9% homology. The sequence from amino acid residues 258 to 494 was highly conserved, showing 90.7% homology.
Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells (2017)

CpG islands (CGIs) are primarily promoter-associated genomic regions and are mostly unmethylated within highly methylated mammalian genomes. The mechanisms by which CGIs are protected from de novo methylation remain elusive. Here we show that insertion of CpG-free DNA into targeted CGIs induces de novo methylation of the entire CGI in human pluripotent stem cells (PSCs). The methylation status is stably maintained even after CpG-free DNA removal, extensive passaging, and differentiation. By targeting the DNA mismatch repair gene <i>MLH1</i> CGI, we could generate a PSC model of a cancer-related epimutation. Furthermore, we successfully corrected aberrant imprinting in induced PSCs derived from an Angelman syndrome patient. Our results provide insights into how CpG-free DNA induces de novo CGI methylation and broaden the application of targeted epigenome editing for a better understanding of human development and disease.