gebhart/patrepeval huggingface dataset:
The Salmonella virulence plasmid spv genes are required for cytopathology in human monocyte-derived macrophages (2000)

The pathogenesis of serious systemic Salmonella infections is characterized by survival and proliferation of bacteria inside macrophages. Infection of human monocyte-derived macrophages in vitro with S. typhimurium or S. dublin produces cytopathology characterized by detachment of cells that contain large numbers of proliferating bacteria. This cytopathology is dependent on the expression of the bacterial spv genes, a virulence locus previously shown to markedly enhance the ability of Salmonella to produce systemic disease. After 24 h of infection, macrophage cultures contain two populations of bacteria: (i) proliferating organisms present in a detached cell fraction; and (ii) a static bacterial population in macrophages remaining attached to the culture well. Mutations in either the essential transcriptional activator SpvR or the key SpvB protein markedly reduce the cytopathic effect of Salmonella infection. The spv-dependent cytopathology in macrophages exhibits characteristics of apoptosis, with release of nucleosomes into the cytoplasm, nuclear condensation and DNA fragmentation. The current findings suggest that the mechanism of the spv effect is through induction of increased cytopathology in host macrophages.
The Arabidopsis CDPK-SnRK Superfamily of Protein Kinases (2003)

The CDPK-SnRK superfamily consists of seven types of serine-threonine protein kinases: calcium-dependent protein kinase (CDPKs), CDPK-related kinases (CRKs), phosphoenolpyruvate carboxylase kinases (PPCKs), PEP carboxylase kinase-related kinases (PEPRKs), calmodulin-dependent protein kinases (CaMKs), calcium and calmodulin-dependent protein kinases (CCaMKs), and SnRKs. Within this superfamily, individual isoforms and subfamilies contain distinct regulatory domains, subcellular targeting information, and substrate specificities. Our analysis of the Arabidopsis genome identified 34 CDPKs, eight CRKs, two PPCKs, two PEPRKs, and 38 SnRKs. No definitive examples were found for a CCaMK similar to those previously identified in lily (Lilium longiflorum) and tobacco (Nicotiana tabacum) or for a CaMK similar to those in animals or yeast. CDPKs are present in plants and a specific subgroup of protists, but CRKs, PPCKs, PEPRKs, and two of the SnRK subgroups have been found only in plants. CDPKs and at least one SnRK have been implicated in decoding calcium signals in Arabidopsis. Analysis of intron placements supports the hypothesis that CDPKs, CRKs, PPCKs and PEPRKs have a common evolutionary origin; however there are no conserved intron positions between these kinases and the SnRK subgroup. CDPKs and SnRKs are found on all five Arabidopsis chromosomes. The presence of closely related kinases in regions of the genome known to have arisen by genome duplication indicates that these kinases probably arose by divergence from common ancestors. The PlantsP database provides a resource of continuously updated information on protein kinases from Arabidopsis and other plants.
Flagellin Glycans from Two Pathovars of <i>Pseudomonas syringae</i> Contain Rhamnose in <scp>d</scp> and <scp>l</scp> Configurations in Different Ratios and Modified 4-Amino-4,6-Dideoxyglucose (2007)

Flagellins from Pseudomonas syringae pv. glycinea race 4 and Pseudomonas syringae pv. tabaci 6605 have been found to be glycosylated. Glycosylation of flagellin is essential for bacterial virulence and is also involved in the determination of host specificity. Flagellin glycans from both pathovars were characterized, and common sites of glycosylation were identified on six serine residues (positions 143, 164, 176, 183, 193, and 201). The structure of the glycan at serine 201 (S201) of flagellin from each pathovar was determined by sugar composition analysis, mass spectrometry, and (1)H and (13)C nuclear magnetic resonance spectroscopy. These analyses showed that the S201 glycans from both pathovars were composed of a common unique trisaccharide consisting of two rhamnosyl (Rha) residues and one modified 4-amino-4,6-dideoxyglucosyl (Qui4N) residue, beta-D-Quip4N(3-hydroxy-1-oxobutyl)2Me-(1-->3)-alpha-L-Rhap-(1-->2)-alpha-L-Rhap. Furthermore, mass analysis suggests that the glycans on each of the six serine residues are composed of similar trisaccharide units. Determination of the enantiomeric ratio of Rha from the flagellin proteins showed that flagellin from P. syringae pv. tabaci 6605 consisted solely of L-Rha, whereas P. syringae pv. glycinea race 4 flagellin contained both L-Rha and D-Rha at a molar ratio of about 4:1. Taking these findings together with those from our previous study, we conclude that these flagellin glycan structures may be important for the virulence and host specificity of P. syringae.
Dieting and Depression Reexamined (1974)

A survey of the literature on untoward responses to dieting has established that [1] there is a high incidence of symptoms of emotional illness in outpatients treated for obesity; [2] such responses occur also during prolonged inpatient treatment, whether by fasting or by caloric restriction; and [3] short-term fasting of inpatients is far less frequently associated with untoward responses. Three variables may affect the incidence of untoward responses: [1] persons with childhood onset of obesity seem more vulnerable than those with adulthood onset of obesity; [2] severe caloric restriction may produce symptoms more readily than total fast; and [3] outpatient treatment may be more stressful than inpatient treatment. These variables should be controlled during evaluation of new methods of treating obesity, and further controlled studies of their influence are needed.
Long-term effect of immunization with neural and nonneural antigens on the noradrenaline and serotonin levels of discrete brain areas in mice and the relationship between neurotransmitter levels and antibody production. (1991)

The effect of immunization with neural and nonneural antigens on hypothalamic and mesencephalic neurotransmission and antibody response have been investigated. Treatment of SJL/N mice with bovine myelin basic protein (BMBP), mouse spinal cord homogenate (MSCH) or bovine serum albumin (BSA) produced no significant changes in the average hypothalamic and mesencephalic noradrenaline (NA) or serotonin (5-HT) content. In Balb/c mice, however, treatment with BMBP caused a significant increase in mesencephalic NA, and treatment with MSCH caused a significant increase in hypothalamic 5-HT 3 weeks after the first antigenic challenge. The SJL/N strain showed a high antibody response to BMBP and BSA, and a moderate one to MSCH, while in Balb/c mice, there was a low response to BMBP, a moderate one to MSCH and a high response to BSA. Significant, positive correlations were found between the level of antigen-specific serum antibodies and the following neurotransmitters: hypothalamic NA in the BMBP and MSCH-treated groups, hypothalamic 5-HT in the MSCH-treated group, mesencephalic NA and 5-HT in the BMBP-treated group, and mesencephalic 5-HT in the MSCH-treated SJL/N animals. No significant correlations between the levels of antibodies and neurotransmitters have been found either in the BSA-immunized SJL/N animals, or in any of the groups of Balb/c mice treated with BMBP, MSCH or BSA.
Polycarbonates (2005)

Abstract Properties and Characterization Preparation Health and Safety Factors Uses Other Polycarbonates, Blends, and Copolymers
Pharmacokinetics of Pyrazinoyl-guanidine, 3-Aminopyrazinoyl-guanidine and Their Corresponding Pyrazinoic Acid Metabolites in Humans and Dogs (1992)

Pyrazinoylguanidine (PZG), 3-aminopyrazinoylguanidine (NH2PZG) and their pyrazinoic acid metabolites were measured by a new reverse-phase HPLC method in the serum of dogs and humans after administration of PZG, NH2PZG or 2-pyrazinoic acid (PZA). Kinetic properties of PZG and its principal metabolite, PZA, were studied in normal humans and also in azotemic patients, since PZG acts on renal tubules of patients with kidney failure to increase urea elimination. In humans and dogs, PZG was rapidly hydrolyzed to PZA. The serum half-life (t1/2) of PZG was 1 h. In turn, PZA was metabolized to 5-hydroxy-PZA, but no evidence appeared for conjugation of PZA with glycine. The apparent volume of distribution of PZG and its 3-amino analog, NH2PZG, exceeded that of total body water. In the dog the serum t1/2 for NH2PZG was twice that of PZG. Compared to PZG, NH2PZG and its metabolite, 3-aminopyrazinoic acid, were much stabler in vitro in serum and water.
Treatment of tissue extravasation by antitumor agents (1982)

Infiltration of antitumor agents into subcutaneous tissues may either result in a local area of self-resolving inflammation, or progress to full-thickness loss of skin and underlying vital structures. The immediate treatment of 50 extravasations occurring over a 20-month period resulted in our developing a protocol of appropriate care. Once extravasation is suspected, the intravenous line is removed, ice is applied intermittently for three days, and the wound is observed closely. No drugs are even given locally. If local pain persists or skin changes progress, the area of involvement is debrided and, a skin graft is applied two to three days later. As a result of this conservative approach, only 12 of 50 patients have required surgery. This method of treatment has minimized patient mortality, hospitalizations, and loss of synchronization of chemotherapy.
Cytoprotective actions of 2,4‐dimethoxybenzylidene anabaseine in differentiated PC12 cells and septal cholinergic neurons (1994)

Abstract The potential cytoprotective actions of a novel nicotinic agent 2,4‐dimethoxybenzilidene anabaseine (DMXB) were investigated in differentiated PC12 cells and transected rat septal cholinergic neurons in vivo. In NGF‐differentiated PC12 cells, removal of both NGF and serum led to cell loss, a reduced % of cells expressing neurites, the release of lactate dehydrogenase, and a decrease in total cellular protein. Cell loss was apparent within 24 h, and remained constant between 4–8 days post‐NGF removal. NGF alone (100 ng/ml), DMXB (10 μM), but not nicotine (10 μM), prevented these cell and neurite losses. DMXB‐induced cytoprotection was blocked by 1 μM mecamylamine. DMXB (1 mg/kg, ip) injected twice but not once per day protected cholinesterase‐staining septal neurons from retrograde degeneration following unilateral fimbrial transections. The twice per day DMXB injection‐protocol also decreased cell roundness among cholinesterase‐staining cells in the lesioned septal hemisphere compared to saline‐injected animals. These studies suggest that DMXB may exert cytoprotective activity in NGF‐sensitive neuronal populations. © 1994 Wiley‐Liss, Inc.
Interaction of water‐soluble triphenylphosphines with β‐cyclodextrin: a quantum chemistry study (2011)

Abstract The interaction of β‐cyclodextrin (β‐CD) with meta ‐trisulfonated triphenylphosphine derivatives bearing one or two methyl (or methoxy) groups on the aromatic rings has been investigated by PM3 calculations. The results show that phosphine molecules interact with β‐CD having either an unsubstituted sulfophenyl group or a substituted sulfophenyl group at the para and/or meta ‐position. The presence of one methyl or methoxy group in the ortho ‐position on each aromatic ring prevents the formation of an inclusion complex between meta ‐trisulfonated triphenylphosphine derivatives and β‐CD. The deeply included phosphines in the β‐CD cavity show significant van der Waals interactions with β‐CD. These interactions are at the origin of the high association constants between these molecules and β‐CD. Phosphines exhibiting small association constants interact with β‐CD by forming H‐bonds and weak (or null) van der Waals interactions. Copyright © 2011 John Wiley & Sons, Ltd.
The CMDB Imperative: How to Realize the Dream and Avoid the Nightmares (2009)

Implement Configuration Management Databases that Deliver Rapid ROI and Sustained Business ValueImplementing an enterprise-wide Configuration Management Database (CMDB) is one of the most influential actions an IT organization can take to improve service delivery and bridge the gap between technology and the business. With a well-designed CMDB in place, companies are better positioned to manage and optimize IT infrastructure, applications, and services; automate more IT management tasks; and restrain burgeoning costs. Now, theres an objective, vendor-independent guide to making a CMDB work in your organization. The CMDB Imperative presents a start-to-finish implementation methodology that works and describes how the CMDB is shifting to the superior Configuration Management System (CMS).Expert CMDB industry analyst Glenn ODonnell and leading-edge architect and practitioner Carlos Casanova first review the drivers behind a CMDB and the technical, economic, cultural, and political obstacles to success. Drawing on the experiences of hundreds of organizations, they present indispensable guidance on architecting and customizing CMDB solutions to your specific environment. Theyll guide you through planning, implementation, transitioning into production, day-to-day operation and maintenance, and much more. Coverage includesDefining the tasks and activities associated with configuration managementUnderstanding the CMDBs role in ITIL and the relationship between CMDBs and ITIL v3s CMSBuilding software models that accurately represent each entity in your IT environmentEnsuring information accuracy via change management and automated discoveryUnderstanding the state of the CMDB market and selling the CMDB within your organizationCreating federated CMDB architectures that successfully balance autonomy with centralized controlPlanning a deployment strategy that sets appropriate priorities and reflects a realistic view of your organizations maturityIntegrating systems and leveraging established and emerging standardsPreviewing the future of the CMDB/CMS and how it will be impacted by key trends such as virtualization, SOA, mobility, convergence, and flexi-sourcingForeword xi Prologue xiiiChapter 1: The Need for Process Discipline 1 Chapter 2: What Is a CMDB? 25 Chapter 3: Planning for the CMS 57 Chapter 4: The Federated CMS Architecture 91 Chapter 5: CMS Deployment Strategy 133 Chapter 6: IntegrationTheres No Way Around It! 177 Chapter 7: The Future of the CMS 197 Chapter 8: Continual Improvement for the CMS 241 Chapter 9: Leveraging the CMS 265 Chapter 10: Enjoy the Fruits of Success 297Glossary 313
Optimization of transmit signals to interfere eavesdropping in a wireless LAN (2014)

We consider physical-layer security of a wireless LAN where multiple receivers collude to eavesdrop the information from the base station to the intended receiver. To enhance the physical-layer security, we design the interference signals to combat the eavesdropping. Our design problems are resolved using semidefinite relaxation problems, which can be numerically solved efficiently by the existing convex optimization solvers. Simulation results are provided to demonstrate the efficiency of the proposed designs.
Radiolabeling and<i>in vitro</i>/<i>in vivo</i>evaluation of N‐(1‐adamantyl)‐8‐methoxy‐4‐oxo‐1‐phenyl‐1,4‐dihydroquinoline‐3‐carboxamide as a<scp>PET</scp>probe for imaging cannabinoid type 2 receptor (2013)

The cannabinoid type 2 (CB2) receptor plays an important role in neuroinflammatory and neurodegenerative diseases such as multiple sclerosis, amyotrophic lateral sclerosis, and Alzheimer’s disease and is therefore a very promising target for therapeutic approaches as well as for imaging. Based on the literature, we identified one 4-oxoquinoline derivative(designated KD2) as the lead structure. It was synthesized, radiolabeled and evaluated as a potential imaging tracer for CB2. [11C]KD2 was obtained in 99% radiochemical purity.Moderate blood–brain barrier (BBB) passage was predicted for KD2 from an in vitro transport assay with P-glycoprotein-transfected Madin Darby canine kidney cells. No efflux of KD2 by P-glycoprotein was detected. In vitro autoradiography of rat and mouse spleen slices demonstrated that [11C]KD2 exhibits high specific binding towards CB2. High spleen uptake of [11C]KD2 was observed in dynamic positron emission tomography(PET) studies with Wistar rats and its specificity was confirmed by displacement study with a selective CB2 agonist, GW405833. A pilot autoradiography study with post-mortem spinal cord slices from amyotrophic lateral sclerosis (ALS)patients with [11C]KD2 suggested the presence of CB2 receptors under disease conditions. Specificity of [11C]KD2 binding could also be demonstrated on these human tissues. In conclusion, [11C]KD2 shows good in vitro and in vivo properties as a potential PET tracer for CB2.
BRD4 degraders produce long-lasting loss of BRD4 Ppotein and robust efficacy in Burkitt’s lymphoma cells. (2015)

8557 Background: We have created specific BRD4 degraders using PROTAC (PROteolysis TArgeting Chimera) technology. This involves creating bi-functional molecules, with one end having a ligand for BRD4 and the other end a recruiting element for the E3 ligase cereblon. These PROTACs promote the interaction of BRD4 with cereblon, resulting in its degradation via the proteasome degradation machinery. Methods: Treatment of NAMALWA, Ramos, CA-46 and Daudi Burkitt’s lymphoma cells with BRD4 PROTACs leads to rapid loss of BRD4, with near complete loss observed within 4 hours. This effect is potent and long lasting, with the most effective molecules having DC50s in the pM range, and with 1 hour treatment of cells resulting in BRD4 loss over a 3 day period. We examined the functional effects of BRD4 PROTACs in several Burkitt’s lymphoma cell lines, comparing their effects to those observed with the clinical BRD4 inhibitor OTX015. Results: We found that treatment of cells with the BRD4 inhibitor OTX015 led to a rapid and robust hyper-accumulation of BRD4 that, together with the reversible nature of binding to BRD4, may have accounted for the observed moderate suppression of MYC expression, modest inhibition of cell proliferation and lack of cellular apoptosis. In contrast, BRD4 PROTACs maintained suppression of BRD4 protein throughout the several day experiment, maintained near complete MYC suppression and caused both pronounced suppression of proliferation and robust apoptotic responses, as measured by PARP cleavage. Conclusions: These data imply that degradation of BRD4 can provide a more robust therapeutic approach to MYC-driven hematological cancers.
Comparative Studies on the Amylase and Cellulase Production of Aspergillus and Penicillium (2011)

Filamentous fungi are important due to their high enzymes production potential. Many enzymes produced by fungi have related to biotechnological applications in several industrial sectors. The purpose of this study was to collect and isolate Penicillium and Aspergillus species from different sources and examined for their ability to produce cellulase and amylase. Ten fungal isolates of genera, Aspergilus and Penicillium were examined for their ability to produce industrial important enzymes. All fungal isolates exhibited high DCZ/DFC ratio in cellulase and amylayes activity. It was also evident that starch and cellulose medium effected the fungal growth. Four Penicillium species viz. Penicillium janthinellum (IK-48), Penicillium melinii (IK-49) and Penicillium velutinum (IK- 51) and Penicillium waskmanii (IK- 50) showed the increased growth in starch and cellulose medium as compare to control. P. waskmanii (IK- 50) showed the highest growth stimulation in the cellulose and starch medium. This study contributes to catalogue local fungal isolated in Pakistan, and provides additional information to support future research about the industrial potential of these microorganisms for enzymes and, eventually, also secondary metabolites with anti-microbial or anti-parasitic activities.
Removal of Manganese by Controlled Precipitation and Filtration (1965)

The work on manganese (Mn) removal on which this article is based is a logical outgrowth of the work on iron (Fe) removal described in an article published in the April 1965 JOURNAL (“Removal of Soluble Iron by Filtration,” George R. Bell, p.458‐471.) The work described in the present article was conducted under a jointly sponsored research and development contract with the Massachusetts Health Research Institute, Inc. (MHRI). The initial work under the MHRI contract was undertaken by the Massachusetts Department of Public Health, with George Coogan as principal investigator. Coogan's published report contains little reference to Mn removal, as such treatment was not originally an objective of the project. The MHRI pilot plant, however, was designed with sufficient flexibility to permit some Mn removal studies when this contaminant was found in the water supplies studied. These preliminary studies have since been improved upon in connection with other water supplies outside the scope of the original project.
<scp>JavAdaptor</scp>—Flexible runtime updates of Java applications (2012)

SUMMARY Software is changed frequently during its life cycle. New requirements come, and bugs must be fixed. To update an application, it usually must be stopped, patched, and restarted. This causes time periods of unavailability, which is always a problem for highly available applications. Even for the development of complex applications, restarts to test new program parts can be time consuming and annoying. Thus, we aim at dynamic software updates to update programs at runtime. There is a large body of research on dynamic software updates, but so far, existing approaches have shortcomings either in terms of flexibility or performance. In addition, some of them depend on specific runtime environments and dictate the program's architecture. We present JavAdaptor , the first runtime update approach based on Java that (a) offers flexible dynamic software updates, (b) is platform independent, (c) introduces only minimal performance overhead, and (d) does not dictate the program architecture. JavAdaptor combines schema changing class replacements by class renaming and caller updates with Java HotSwap using containers and proxies. It runs on top of all major standard Java virtual machines. We evaluate our approach's applicability and performance in non‐trivial case studies and compare it with existing dynamic software update approaches. Copyright © 2012 John Wiley & Sons, Ltd.
Electromagnetic response of an embedded cylinder for line current excitation (1981)

Abstract Numerical results obtained from an extension of D'Yakonov's (1959) exact solution for the case of a buried horizontal circular cylinder, excited by a horizontal line source of current above the surface of a uniform half-space and parallel to the axis of the buried cylinder, are analyzed. Results show the field impedance (E x /H y ), the ratio of the vertical magnetic component to the horizontal magnetic component (H z /H y ) as well as the corresponding phase differences at the surface for a range of periods (T = 0.25 to 2 hours), varying cylinder conductivity (sigma 2 = 1 to 100 Sm (super -1) ) and cylinder radii (a = 0.5 and 25 km). The results have possible application in the interpretation of long period magnetotelluric and geomagnetic measurements in auroral and equatorial electrojet regions.