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Cobra

Cobra is a type of venomous snake found in parts of Asia and Africa.
These snakes are known for their distinctive hooded appearance and powerful neurotoxic venom.
Cobras are an important subject of research, as their venom contains compounds with potential medical applications, such as in the treatment of pain, inflammation, and neurological disorders.
PubCompare.ai is an AI-driven platform that can help researchers easily locate and compare the best Cobra research protocols from literature, preprints, and patents, streamlining the research process and maximizing the value of Cobra-related studies.
With its advanced comparison tools and AI-driven analysis, PubCompare.ai is a valuable resource for scientists working in the field of Cobra research.

Most cited protocols related to «Cobra»

A stoichiometric matrix, S (m × n), was constructed for iAF1260, where m is the number of metabolites and n is the number of reactions. The corresponding entry in the stoichiometric matrix, Sij, represents the stoichiometric coefficient for the participation of the ith metabolite in the jth reaction. FBA was then used to solve the linear programming problem under steady-state criteria (Price et al, 2004 (link)) represented by the equation:

where v (n × 1) is a vector of reaction fluxes. Since the linear problem is normally an underdetermined system for genome-scale metabolic models, there exist multiple solutions for v that satisfy equation 2. To find a particular solution for v, the cellular objective of producing the maximal amount of biomass constituents, represented by the ratio of metabolites in the BOF, is optimized for in the linear system. Additionally, constraints that are imposed on the system are in the form of:

where α and β are the lower and upper limits placed on each reaction flux, vi, respectively. For reversible reactions, −∞⩽vi⩽∞, and for irreversible reactions, 0⩽vi⩽∞. The constraints on the reactions that allow metabolite entry into the extracellular space were set to 0⩽vi⩽∞ if the metabolite was not present in the medium, meaning that the compounds could leave, but not enter the system. For the metabolites that were in the medium, the constraints were set to −∞⩽vi⩽∞ for all except the limiting substrate(s) (e.g., glucose and/or oxygen). The reaction flux through the BOF was constrained from 0⩽vBOF⩽∞.
Linear programming calculations were performed using SimPheny™ (Genomatica, San Diego, CA) and the LINDO (Lindo Systems Inc., Chicago, IL) or TOMLAB (Tomlab Optimization Inc., San Diego, CA) solvers in MATLAB® (The MathWorks Inc., Natick, MA) with the COBRA Toolbox (Becker et al, 2007 (link)).
When comparing the flux distribution in central metabolism to experimentally reported values (Fischer et al, 2004 (link)), all of the comparisons were performed using computational results when optimal growth is predicted using the BOFCORE, the 152 regulated reactions under these conditions constrained to zero (see above), a split in the flux ratio between the two NADH dehydrogenases of 1:1, an NGAM value of 8.39 mmol ATP gDW−1 h−1, a GAM value of 59.81 mmol ATP gDW−1 and iAF1260. An FVA on the optimal flux distribution yielded no flexibility in the central metabolism pathways examined in this study. From the Fischer et al (2004) (link) study, data from E. coli growth in reactor conditions were used because the oxygen uptake and CO2 secretion rates were reported, and the flux values that were used were based off 13C-constrained flux balancing.
Publication 2007
Adjustment Disorders Biological Models Cloning Vectors Cobra Escherichia coli Extracellular Space Genome Glucose Metabolism NADH Cytochrome c Oxidoreductase Oxygen
The previously reconstructed iND750, a fully compartmentalized and elementally-balanced S. cerevisiae metabolic network, was used as the basis for reconstructing the iMM904 network [2 (link)]. The network was further expanded to include additional genes and reactions based on genomic, biochemical, and physiological information [see Additional file 1]. The details of existing reactions (substrate and cofactor specificity, reaction reversibility, and compartmentalization) in the iND750 network were also re-evaluated to update the model based on existing literature. The iMM904 network was reconstructed using the SimPheny® modeling software (Genomatica Inc, San Diego, CA). Existing gene-protein-reaction (GPR) associations from iND750 were also reviewed and several were modified to include additional genes and proteins. GPR associations are Boolean representations of the logical relationship between ORFs and their corresponding transcripts, proteins, and reactions to enable mapping of genes to their respective functions. The included model text files [see Additional file 2] are compatible for computation with the COBRA toolbox [13 (link)].
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Publication 2009
Cobra Gene Products, Protein Genes Genome Metabolic Networks Open Reading Frames Proteins
The ontology includes the major cell types from the major model organisms (for example, human, mouse, Drosophila, Caenorhabditis, zebrafish, Dictyostelium discoideum, Arabidopsis, fungi and prokaryotes). These cell types have been collated from our own knowledge, from major textbooks (for example [20 -22 ]), from the embryo and anatomy ontologies available on the OBO site [7 ], and from colleagues (who are thanked in the acknowledgements). The ontology currently holds some 680 cell types, together with their synonyms and, in most cases, text definitions.
The ontology was constructed using the open source Java tool OBO-Edit (previously known as DAG-Edit) [23 ], which is convenient for building ontologies that are consistent with the GO formalism. The resulting ontology is available in both the GO 'flat-file' format [24 ] and the newly defined 'OBO format' [25 ], and can easily be viewed using the OBO-Edit or the COBrA open source Java tool [26 ].
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Publication 2005
Arabidopsis Caenorhabditis Cells Cobra Dictyostelium discoideum Drosophila Embryo Fungi Homo sapiens Mus Prokaryotic Cells Zebrafish
We used 6 databases for this research: Premier, Optum, CPRD, CCAE, Truven Health MarketScan Medicaid (MDCD), and Truven Health MarketScan Medicare Supplemental (MDCR). Table 1 provides high-level information about each database. Optum, CCAE, MDCD, and MDCR are claims databases. Premier is a hospital billing database and CPRD is a UK general practitioners (GPs) database. Depending on the specific licensing agreement, it is possible to have data that spans more or less time than reported here. The use of Optum, Premier, CCAE, MDCD, and MDCR was reviewed by the New England Institutional Review Board and was determined to be exempt from broad Institutional Review Board approval as this project did not involve human subject research. Approval for CPRD was provided by the Independent Scientific Advisory Committee.

High-level Information about each dataset

StatisticPremier PerspectiveOptumCPRDTruven CCAETruven MDCRTruven MDCD
High-level DescriptionA hospital transactional database that includes emergency, inpatient, and outpatient visits for patients who visit a Premier hospital. Includes commercially insured, government plans, and charity care.An administrative health claims database for members of United Healthcare, who enrolled in commercial plans (including ASO, 36.31 M), Medicaid (prior to July 2010, 1.25 M), and Legacy Medicare Choice (prior to January 2006, 0.36 M) with both medical and prescription drug coverage.Anonymized longitudinal electronic health records from primary care practices in UK. Patient management system with many aspects of patient care covered, including diagnoses, prescriptions, signs and symptoms, procedures, labs, lifestyle factors, clinical, and administrative/social dataAn administrative health claims database for active employees, early retirees, COBRA continues, and their dependents insured by employer-sponsored plans (individuals in plans or product lines with fee-for-service plans and fully capitated or partially capitated plans).An administrative health claims database for Medicare-eligible active and retired employees and their Medicare-eligible dependents from employer-sponsored supplemental plans (predominantly fee-for-service plans). Only plans where both the Medicare-paid amounts and the employer-paid amounts were available and evident on the claims were selected for this database.An administrative health claims database for the pooled healthcare experience of Medicaid enrollees from multiple states.
Source Codes Used

Conditions

ICD9ICD9ReadICD9ICD9ICD9

Drugs

Premier Standard Charge CodeNDCs, HCPCs, ICD9-PROCMultilex, native immunization codesNDCs, HCPCs, ICD9-PROCNDCs, HCPCs, ICD9-PROCNDCs, HCPCs, ICD9-PROC

Lab Data

Premier Standard Charge CodeLOINCaNative test codesLOINCaLOINCa
RegionUnited StatesUnited StatesUnited Kingdom of Great BritainUnited StatesUnited StatesUnited States
Date RangesDecember 1998 - 2013October 2005 - December 2012January 1987 - July 2013January 2000 - October 2013January 2000 - October 2013January 2006 - October 2012
No. of Overall Patient Count100 092 90036 229 84911 485 373108 589 8668 216 67816 172 699
Age at Start in Database, mean (SD), y38.80 (24.33)31.43 (18.95)32.98 (23.07)31.20 (18.13)72.36 (8.10)22.45 (22.56)

Abbreviations: Optum, Optum Clinformatics DataMart; CPRD, Clinical Practice Research Datalink; Truven CCAE, Truven Health MarketScan Commercial Claims and Encounters; Truven MDCD, Truven Health MarketScan Medicaid; Truven MDCR, Truven Health MarketScan Medicare Supplemental; SD, Standard Deviation; ICD9, International Classification of Diseases, Ninth Revision; ICD9-PROC, International Classification of Diseases, Ninth Revision–Procedure Codes; LOINC, Logical Observation Identifiers Names and Codes; NDC, National Drug Code; HCPC, Healthcare Common Procedure Coding.

aResults for laboratory tests processed by large national lab vendors that provide data back to the data vendor.

Publication 2015
Cobra Diagnosis Emergencies enkephalin, Cys(2)-CysNH2(5)- Ethics Committees, Research General Practitioners Homo sapiens Immunization Infantile Neuroaxonal Dystrophy Inpatient O,O-diacetyl tartaric acid anhydride Outpatients Patient Care Management Patients Pharmaceutical Preparations Prescription Drugs Prescriptions Primary Health Care
The reconstructed metabolic network was converted into stoichiometric matrix (S = M * N) using the Matlab program, where M represents metabolites and N represents reactions [65 (link)]. The basic tools used for model analysis were flux balance analysis (FBA) and flux variability analysis (FVA). GLPK was used for linear programming [22 (link)], and Gurobi was used for quadratic programming [66 ]. In silico analysis included growth simulation, gene and reaction essentiality analysis, robustness analysis, and minimization of metabolic adjustment. Analyses were performed according to the instructions for the COBRA Toolbox [22 (link)]. Constraints used in each analysis are mentioned in the results section. To analyze model parameters relevant to cell growth, the biomass equation was selected as the objective function. For analysis of ARA production, the exchange reaction of ARA was the objective function.
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Publication 2015
Cells Cobra Genes Metabolic Networks

Most recents protocols related to «Cobra»

Venoms from Bitis arietans (Puff adder), Naja haje (Egyptian Cobra), and Naja pallida (Red spitting Cobra) were collected from wild-caught snakes at the East African Venom Supplies (Kenya). They were lyophilized and stored at −4°C at the Pharmacology and Toxicology Lab, Faculty of Veterinary Medicine, University of Nairobi. Each of the lyophilized venoms were accurately weighed (0.25 g) in an analytical balance and triturated using a pestle and mortar. The triturated venoms were transferred to 10 mL volumetric flasks and made up to the mark with phosphate buffered saline to make a 25 mg/mL concentration.
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Publication 2023
Bitis Cobra East African People Faculty Naja Naja haje Phosphates Saline Solution Snakes Venoms
This economic evaluation did not require evaluation by an institutional review board or patient informed consent because all data were publicly available and no human participants were involved (45 CFR part 46). This study followed Consolidated Health Economic Evaluation Reporting Standards (CHEERS) reporting guidelines for economic evaluations.6 (link) Merative MarketScan 2018 Commercial Claims and Encounters Databases were weighted to represent the non–Medicare eligible (aged <65 years) US ESI population (active employees, early retirees, and COBRA continuees plus dependents; Medicare supplemental plans not included). The databases report expenditures for inpatient services, outpatient services, and outpatient drugs from approximately 350 health insurance payers (large employers, health plans, and government and public organizations). Race and ethnicity are not reported in this database. By comparing total annual medical expenditures among similar enrollees with and without SUD diagnoses (referred to as control participants), this analysis aimed to estimate the cost that could be eliminated through prevention or successful treatment of SUD (referred to as the attributable cost). The main outcome measure was the annual attributable SUD medical cost in the ESI population overall and by substance type (eg, alcohol). The number of enrollees with an SUD diagnosis in the ESI population and the annual mean attributable cost of SUD diagnosis (any and by substance type) per affected enrollee are also reported. SUD diagnosis was defined by International Statistical Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) according to Clinical Classifications Software categories (alcohol-, cannabis-, hallucinogen-, inhalant-, opioid-, sedative-, stimulant-, and other substance-related disorders) on an inpatient or outpatient claim record (Table 1). Costs are reported in 2018 US dollars (unadjusted from data source); cost discounting was not applicable due to the 1-year analytic time horizon, which was selected to facilitate reporting in terms of annual cost, and the cost perspective was the health care payer.
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Publication 2023
Cannabis Cobra Diagnosis Ethanol Ethics Committees, Research Ethnicity Hallucinogens Health Insurance Health Planning Health Services, Outpatient Homo sapiens Infantile Neuroaxonal Dystrophy Inhalation Drug Administration Inpatient Opioids Outpatients Patients Pharmaceutical Preparations Sedatives Substance-Related Disorders
Flavone was purchased from Sigma-Aldrich chemicals
and used without
any purification. R2PI experiments have been performed employing a
molecular beam setup described previously.35 (link) (see also Supporting Information SI1).
Briefly, flavone was heated up to 150 °C within a glass container
in order to obtain sufficient vapor pressure and expanded using neon
at 1.5 bar as a carrier gas through a General Valve pulsed nozzle
with a 0.5 mm orifice diameter, which was kept 5 °C higher than
the main body in order to avoid clogging. After being skimmed by a
2 mm skimmer, the molecular beam entered an ionization chamber where
ions or electrons were detected using either a reflection time-of-flight
(R.M. Jordan Co.) setup for mass-resolved ion detection or a custom-built
setup (R.M. Jordan Co.) for electron detection.
(1 + 1′)
R2PI excitation spectra were recorded using a frequency-doubled
Sirah Cobra-Stretch dye laser operating on DCM/Pyrromethene 597 pumped
by a Spectra-Physics Lab 190 Nd/YAG laser for excitation and a Neweks
PSX-501 ArF excimer laser (193 nm, 6.42 eV) for ionization. Typically,
pulse energies of 10–50 μJ and 1 mJ were used for excitation
and ionization, respectively. For recording ionization threshold spectra,
the same pulsed dye laser system has been used in combination with
another pulsed dye laser system consisting of a frequency-doubled
Sirah Precision Scan dye laser operating on DCM or Pyrromethene 597
and pumped by a Spectra Physics Lab 190 Nd/YAG laser. In these experiments,
typical pulse energies were employed of 1 mJ for the pump laser and
2–4 mJ for the probe laser.
In order to analyze the observed
electronic transitions and to
determine the ionization energy of flavone and its complexes, DFT
has been used to determine the equilibrium geometries and harmonic
force fields of flavone in the electronic ground state of the neutral
(S0) and cation (D0), while time-dependent DFT
(TD-DFT) was employed to optimize the geometry of the molecule in
the first three electronically excited singlet states of the neutral
and to determine the associated harmonic force fields. Such calculations
have been performed at both the B3LYP/TVZP and wB97XD/cc-pVDZ level.36 (link)−39 (link) For comparison with the experimental results, the obtained equilibrium
geometries and force fields were used to obtain Franck–Condon
spectra at wB97XD/cc-pVDZ level for Sn ← S0 transitions for which vibrational frequencies
were scaled using a scaling factor of 0.953.40 (link),41 All calculations have been performed with the Gaussian16, Rev.C.01
suite of programs.42
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Publication 2023
A-factor (Streptomyces) Argon Fluoride Excimer Lasers Cobra Electrons factor A Flavones Human Body Lasers, Dye Neodymium-Doped Yttrium Aluminum Garnet Lasers Pulsed Dye Lasers Pulse Rate pyrromethene 597 Radionuclide Imaging Reflex Vapor Pressure Vibration
(2,2′,2″-(10-(1-Carboxy-4-((4-Isothiocyanatobenzyl)Amino)-4-Oxobutyl)-1,4,7,10-Tetraazacyclododecane-1,4,7-triyl)Triacetic Acid). p-NCS-Bn-DOTAGA was purchased from Chematech (Dijon, France) and cKNGRE from CASLO ApS (Lyngby, Denmark). Ultra-purified (u.p.) hydrochloric acid, NaOAc and water were purchased from Merck KGaA (Darmstadt, Germany). 68Ga radioisotope was eluted with 0.1 M u.p. HCl from a germanium-68/gallium-68 (68Ge/68Ga) isotope generator (Eckert-Ziegler, GalliaPharm®, Berlin, Germany). Activity measurements were carried out with a CAPINTEC CRC-15PET dose calibrator and a Perkin Elmer Packard Cobra gamma counter (Llantrisant, UK). Oasis HLB 1cc cartridge was purchased from Waters Corporation (Milford, MA, USA). All other reagents were purchased from Sigma-Aldrich.
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Publication 2023
Acids Cobra CREB3L1 protein, human Gallium Gallium-68 Gamma Rays Germanium Germanium-68 Hydrochloric acid Isotopes
The distribution of the radioactivity in n-octanol as well as water was determined by Gyuricza et al. in order to define the LogP value of [68Ga]Ga-DOTAGA-cKNGRE [31 (link)]. To have the two different layers separated, the mixture of 50 µL from the given radiotracer (approximately 2 MBq), 450 µL distilled water and 0.5 mL n-octanol was centrifuged for 5 min (9000× g). Then, the radioactivity was measured in 20 and 20 µL aliquots of n-octanol and water, respectively, with a Perkin Elmer Packard Cobra gamma-counter for the determination of the partition coefficient of the investigated probe. The LogP value was −4.13 for [68Ga]Ga-DOTAGA-cKNGRE.
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Publication 2023
1-Octanol Cobra Gamma Rays Octanols Radioactivity

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More about "Cobra"

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Cobras are a fascinating subject of study, as their venom contains a wealth of potentially valuable compounds for medical applications.
PubCompare.ai is an AI-powered platform that can help researchers easily locate and compare the best Cobra research protocols from a variety of sources, streamlining the research process and maximizing the impact of Cobra-related studies.
With its advanced comparison tools and intelligent analysis, PubCompare.ai is an indispensable resource for scientists working in the field of Cobra research.
Whether you're studying the venom's medicinal properties, exploring new treatment options, or investigating the biology of these remarkable snakes, PubCompare.ai can help you find the protocols and information you need to drive your research forward.