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Oxygen

Oxygen is a vital element essential for sustaining life.
It is a colorless, odorless gas that makes up approximately 21% of the Earth's atmosphere.
Oxygen plays a crucial role in various biological processes, including cellular respiration, where it is used by organisms to convert nutrients into energy.
It is also involved in the formation of water and many other important chemical compounds.
Oxygen is crucial for human health, as it is necessary for the proper functioning of the cardiovascular, respiratory, and nervous systems.
Deficiencies in oxygen can lead to serious health conditions, such as hypoxia and anoxia.
Researchers continue to explore the myriad ways in which oxygen influences living organisms and their environments.
Furthering our understanding of oxygen's role in biological systems is an area of active scientific inquiry.

Most cited protocols related to «Oxygen»

Simulations of the proteins in their crystal environments (Table 1), which were used previously during optimization of the C22/CMAP force field 40 (link), were performed using CHARMM on full unit cells with added waters and counterions to fill the vacuum space. Once the full unit cell was constructed based on the coordinates in the protein databank, a box of water with dimensions that encompassed the full unit cell was overlaid onto the crystal coordinates while preserving crystal waters, ions, and ligands. Water molecules with oxygen within 2.8 – 4.0 Å of any of the crystallographic non-hydrogen atoms were removed, as described below, as well as those occupying space beyond the full unit cell. To neutralize the total charge of each system, sodium or chloride ions were added to the system at random locations at least 3.0 Å from any crystallographic non-hydrogen atom or previously added ions and 0.5 Å from any water oxygen. Final selection of the water molecule deletion distance was performed by initially applying a 2.8 Å criteria to all systems followed by system equilibration and an NPT production run of 5 ns following which the lattice parameters were analyzed. The deletion distances were then increased and the equilibration and 5 ns production NPT simulation were repeated until the final lattice parameters were in satisfactory agreement with experimental data. The final water deletion distances and unit cell parameters from the full 40 ns production simulations are presented in Table S2 of the SI. For the minimization and MD simulations, electrostatic interactions were treated with PME using a real space cutoff of 10 Å. The LJ interactions were included with force switching from 8 Å to 10 Å, while the list of nonbonded atoms was kept for interatomic distances of up to 14 Å and updated heuristically. Each crystal system was first minimized with 100 steps of steepest-decent (SD) with non-water, non-ion crystallographic atoms held fixed followed by 200 steps of SD with harmonic positional restraints of 5 kcal/mol/Å2 on solute non-hydrogen atoms. The minimized system was then subject to an equilibration phase consisting of 100 ps of NVT simulation41 in the presence of harmonic positional restraints followed by 5 ns (100 ps for 135L and 3ICB) of fully relaxed NVT simulation with a time step of 2 fs. During the simulations all covalent bonds involving hydrogens were constrained using SHAKE42 . Production phase simulations were conducted for 40 ns in the isothermal and isobaric NPT ensemble43 . The only symmetry enforced was translational (i.e. periodic boundaries). Reference temperatures were set to match the crystallographic conditions (Table S2) and maintained by the Nosé-Hoover thermostat with a thermal piston mass of 1,000 kcal ps2/mol while a pressure mass of 600 amu was used with the Langevin piston. The first 5 ns of the production simulations were considered as equilibration and therefore discarded from analysis, which was performed on coordinate sets saved every 5 ps. The boundaries for α helices and β strands were obtained from a consensus of author annotations and structural assignments calculated by DSSP44 (link) and STRIDE45 (link) from the crystal structures.
Publication 2012
ARID1A protein, human Cells Chlorides Crystallography Deletion Mutation Deuterium Electrostatics Helix (Snails) Hydrogen Hydrogen-4 Ligands Oxygen Pressure Protein Biosynthesis Proteins Sodium STEEP1 protein, human Tritium Vacuum
The human metagenomic data we analyzed with MetaPhlAn are all available in public repositories. The 51 vaginal and 139 fecal samples from the HMP3 can be accessed at http://hmpdacc.org/HMASM, from which we used the "WGS" reads (not the "PGA" assemblies). The 16S rRNA profiling of HMP vaginal microbiomes used for comparison (Fig. 2) was performed from the mothur pipeline36 (link) data followed by phylotype profiling with the RDP classifier37 (link) (http://hmpdacc.org/HMMCP). The 85 fecal samples from MetaHIT4 (link) were downloaded from the European Nucleotide Archive (http://www.ebi.ac.uk/ena/, study accession number ERP000108), and the marine minimum oxygen zone samples10 (link) are available in the NCBI Sequence Read Archive under accession number SRA023632.
The full tables of results for the vaginal and gut metagenomes are available at http://huttenhower.sph.harvard.edu/metaphlan.
Publication 2012
Europeans Feces Homo sapiens Marines Metagenome Microbiome Nucleotides Oxygen RNA, Ribosomal, 16S Vagina

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Publication 2020
Adenovirus Infections Adrenal Cortex Hormones Antibiotics Bacteria Biological Assay Blood Bronchi Bronchoalveolar Lavage Fluid Complete Blood Count COVID 19 Creatine Kinase Electrolytes Feces Genes, env Influenza Influenza in Birds isolation Kidney Lactate Dehydrogenase Liver Mechanical Ventilation Methylprednisolone Middle East Respiratory Syndrome Coronavirus Nasal Cannula Nose Oligonucleotide Primers Oseltamivir Oxygen Parainfluenza Pathogenicity Patients Pharynx Physical Examination Physicians Pneumonia Real-Time Polymerase Chain Reaction Respiratory Rate Respiratory Syncytial Virus Respiratory System SARS-CoV-2 Serum Severe acute respiratory syndrome-related coronavirus Sputum Tests, Blood Coagulation Tests, Diagnostic Therapeutics Treatment Protocols Virus Virus Release
Another refinement in the C36m FF concerns improved description of salt bridge interactions involving guanidinium and carboxylate functional groups with a pair-specific non-bonded LJ parameter (NBFIX term in CHARMM) between the guanidinium nitrogen in arginine and the carboxylate oxygen in glutamate, aspartate as well as the C terminus. This salt bridge interaction was found to be too favorable in the CHARMM protein force fields as indicated by the overestimation of the equilibrium association constant of a guanidinium-acetate solution ,33 , 34 as well as the underestimation of its osmotic pressure (personal communication, Benoit Roux). The added NBFIX term increases the Rmin from the 3.55 Å based on the Lorentz-Berthelot rule to a larger value of 3.637 Å (Shen and Roux, personal communication), which we subsequently showed to improve the agreement with the experimental osmotic pressure of guanidinium acetate solutions (Supplementary Figure 19). We noted that the NBFIX approach employed here differs from Piana et al’s work27 where the CHARMM22 charges of the Arg, Asp and Glu side chains were reduced in magnitude, with both approaches leading to weaker and more realistic salt-bridge interactions. The NBFIX term makes sure only the specific interaction between Arg and Asp/Glu is modified, while the interaction of these residues with other amino acids, water, or ions are kept the same as in the C36 FF. Again, our aim is to improve the C36 FF with minimal changes in the model.
Publication 2016
Acetate Amino Acids Arginine Aspartate aspartylglutamate Glutamate Guanidine Ions Nitrogen Osmotic Pressure Oxygen Proteins Sodium Chloride

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Publication 2020
Bacteremia Blood Bronchoalveolar Lavage Fluid Congenital Abnormality Creatinine Echocardiography Electrocardiography Heart Heart Injuries Influenza in Birds Inhalation Kidney Diseases Kidney Injury, Acute Oxygen pathogenesis Patients Pneumonia, Hospital Acquired Respiratory Distress Syndrome, Acute Respiratory System SARS-CoV-2 Secondary Infections Serum Shock Sputum Troponin I Urine

Most recents protocols related to «Oxygen»

Example 4

3D design software and 3D drawing software were used to construct a 3D cylinder model with a diameter of 40 mm and a height of 15 mm, which was converted into an STL file and imported into SLM building software. The model was auto-sliced by the software and imported into an SLM printing system. After heating the substrate to 150° C., the René 104 nickel-based superalloy powder was added to a powder supply tank and then laid. Argon was introduced into the working chamber until the oxygen content was less than 0.1%. Then the printing procedure was carried out, and the steps of laying the powder and scanning the powder by laser were repeated until the printing was completed to obtain a cylinder.

The René 104 nickel-based superalloy powder has a particle size of 15-53 μm, a D10 of 17.5 μm, a D50 of 29.3 μm, and a D90 of 46.9 μm.

The process parameters for SLM are as follows: a laser power of 250 W, a spot diameter of 0.12 mm, a scanning speed of 500 mm/s, a scanning pitch of 0.12 mm, and a thickness of the laid powder layer being 0.03 mm.

The scanning strategy for SLM is a stripe scanning strategy. In the stripe scanning strategy, a layer-by-layer scanning method from bottom to top is adopted, the laser scanning direction is rotated by 67° between adjacent layers, the stripe width is 5 mm, and the overlap between stripes is 0.10 mm. (no contour+solid scanning method is adopted)

The stress relief annealing parameters are as follows: a temperature of 420° C. held for 90 min, and cooling within the furnace.

The SPS parameters are as follows: a graphite mold with a diameter of 40 mm, a heating rate of 60° C./min, a cooling rate of 60° C./min, a sintering pressure of 45 MPa, and a sintering temperature of 1020° C. held for 15 min.

Before and after post-treatments of the fabricated parts, the densities are 98.34% and 99.02%, respectively, and the mechanical properties at room temperature are 987 MPa and 1065 MPa.

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Patent 2024
Argon ARID1A protein, human Fungus, Filamentous Graphite Nickel Oxygen Powder Pressure

Example 5

113 g of sodium metal was melted and brought to 250° C. in an Inconel reactor vessel. The sodium was then stirred using a Cowles blade mixer rotating at 2000-2500 rpm. Powdered hafnium chloride (from Areva) was pulse-fed over approximately 1 hour into the stirred sodium, until 82 g of hafnium chloride had been added, at which point the reaction was halted. At the end of the reaction, the vortex in the sodium had substantially disappeared and the reactor temperature had increased to 301° C.

Once the reaction was completed, the reactor vessel was sealed, transferred to a furnace, and heated to 825° C. for four hours to reduce the surface area of the hafnium metal produced in the reaction. During this process step, unreacted sodium was removed from the hafnium metal to leave a hafnium-sodium chloride composite.

The hafnium and sodium chloride mixture was then transferred to a vacuum furnace and heated under vacuum to 2300° C., held at that temperature for one hour, and then cooled. This removed the sodium chloride and produced a button of solid hafnium.

The hafnium button was analyzed via glow discharge mass spectrometry (GDMS) and found to have 26 ppm oxygen content, 1690 ppm zirconium, and less than 150 ppm total transition metals. The results demonstrate the production of a low oxygen hafnium metal produced directly from hafnium powder consolidation.

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Patent 2024
ARID1A protein, human Blood Vessel Hafnium hafnium chloride Mass Spectrometry Metals Oxygen Patient Discharge Powder Pulse Rate Sodium Sodium Chloride Transition Elements Vacuum Zirconium
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Example 1

1 pound PTFE regrind, obtained from CSI Plastic (Millbury, Mass.), was inserted into a chamber. The chamber was heated using annular flow of hot oil at 200° C. for a nominal chamber temperature of 175° C. Oxygen was removed from the chamber using a nitrogen pressure swing inerting method. Gas flow of 20 vol % fluorine and 80% nitrogen was started at 0.4 scfm. The chamber pressure varied between 5 PSIA and 12 PSIA over the course of the experiment. The fluorine gas was fed through the chamber for 4 hours with the direction of gas flow alternated between top to bottom and bottom to top each hour. The amount of fluorine used was 4.99 pounds of fluorine per 1000 pounds of PTFE regrind. At the end of 4 hours, the oil heat was turned off and the chamber was again inerted using a nitrogen pressure swing method. Atmospheric air was fed through the chamber until the chamber temperature dropped below 55° C. The sample was tested for perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) using EPA method 3452A and EPA method 8321B. The sample was tested both before and after being treated with fluorine gas. The detection limit for PFOA and PFOS was 100 parts per trillion. No PFOS was detected either before or after the sample was treated. The results are shown in Table 1.

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Patent 2024
Fluorine Fluorocarbon Polymers Nitrogen Oxygen perfluorooctane sulfonic acid perfluorooctanoic acid Polytetrafluoroethylene Pressure

Example 7

The following Example is an exemplary assay to evaluate VGX-300 and VGX-301-ΔN2 for their ability to inhibit the onset of retinal neovascularization using the ROP model. In this model, postnatal day 7 (P7) mice are exposed to hyperoxia (75% oxygen) for 5 days (to P12). After hyperoxic exposure, P12 mice are returned to normoxia, and administered an intravitreal injection of human isotype control antibody, VGX-300, VGX-301-ΔN2, Eylea (VEGF-Trap), VGX-300+Eylea or VGX-301-ΔN2+Eylea. All mice are then housed under normoxic conditions for 5 days before sacrifice at P17, enucleation and fixation in 10% formalin/PBS. Vessels will be quantified in each group using H&E and/or IHC staining methods.

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Patent 2024
aflibercept Biological Assay Blood Vessel Cardiac Arrest eylea Formalin Homo sapiens Hyperoxia Immunoglobulin Isotypes Mus Oxygen Retinal Neovascularization Staining
Not available on PMC !

Example 9

A pediatric patient with Stage IV Wilms tumor is treated with dactinomycin, doxorubicin, cyclophosphamide and vincristine for 65 weeks. Doses of the drugs are as follows: dactinomycin (15 mcg/kg/d [IV]), vincristine (1.5 mg/m 2 wk [IV)), Adriamycin (doxorubicin 20 mg/m2/d [IV]), and cyclophosphamide (10 mg/kg/d [IV]). Dactinomycin courses are given postoperatively and at 13, 26, 39, 52, and 65 weeks. Vincristine is given on days 1 and 8 of each Adriamycin course. Adriamycin is given for three daily doses at 6, 19, 32, 45, and 58 weeks. Cyclophosphamide is given for three daily doses during each Adriamycin and each dactinomycin course except the postoperative dactinomycin course. During each administration of dactinomycin and vincristine a dose of 0.2 cc/kg of DDFPe is administered while the patient breathes supplemental oxygen. *D'angio, Giulio J., et al. “Treatment of Wilms' tumor. Results of the third national Wilms' tumor study.” Cancer 64.2 (1989): 349-360.

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Patent 2024
Adriamycin Cyclophosphamide Dactinomycin Doxorubicin Malignant Neoplasms Nephroblastoma Oxygen Patients Pharmaceutical Preparations Pharmacotherapy Radiotherapy Vincristine

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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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DMEM (Dulbecco's Modified Eagle's Medium) is a cell culture medium formulated to support the growth and maintenance of a variety of cell types, including mammalian cells. It provides essential nutrients, amino acids, vitamins, and other components necessary for cell proliferation and survival in an in vitro environment.
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The Vevo 2100 is a high-resolution, real-time in vivo imaging system designed for preclinical research. It utilizes advanced ultrasound technology to capture detailed images and data of small animal subjects.
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Sylgard 184 is a two-part silicone elastomer system. It is composed of a siloxane polymer and a curing agent. When mixed, the components crosslink to form a flexible, transparent, and durable silicone rubber. The core function of Sylgard 184 is to provide a versatile material for a wide range of applications, including molding, encapsulation, and coating.
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Penicillin/streptomycin is a commonly used antibiotic solution for cell culture applications. It contains a combination of penicillin and streptomycin, which are broad-spectrum antibiotics that inhibit the growth of both Gram-positive and Gram-negative bacteria.
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Isoflurane is a volatile anesthetic agent used in the medical field. It is a clear, colorless, and nonflammable liquid that is vaporized and administered through inhalation. Isoflurane is primarily used to induce and maintain general anesthesia during surgical procedures.
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The Oxygraph-2k is a high-performance respirometer designed for precise measurement of oxygen consumption and production in biological samples. It provides real-time monitoring of oxygen levels, making it a valuable tool for researchers in the fields of cell biology, physiology, and bioenergetics.
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The Clark-type oxygen electrode is a device used to measure the concentration of dissolved oxygen in a solution. It functions by using an electrochemical reaction to detect and quantify the amount of oxygen present in the sample.
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Glucose oxidase is an enzyme that catalyzes the oxidation of glucose to gluconic acid and hydrogen peroxide. It is commonly used in various laboratory applications, such as the detection and measurement of glucose levels in biological samples.
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Penicillin is a type of antibiotic used in laboratory settings. It is a broad-spectrum antimicrobial agent effective against a variety of bacteria. Penicillin functions by disrupting the bacterial cell wall, leading to cell death.

More about "Oxygen"

Oxygen (O₂) is a vital and indispensable element that sustains life on Earth.
This colorless, odorless gas makes up approximately 21% of the planet's atmosphere, playing a crucial role in numerous biological processes.
Cellular respiration, a fundamental metabolic pathway, relies on oxygen to help organisms convert nutrients into usable energy.
Oxygen also participates in the formation of water and various other essential chemical compounds.
For human health, oxygen is indispensable, as it is necessary for the proper functioning of the cardiovascular, respiratory, and nervous systems.
Deficiencies in oxygen, such as hypoxia and anoxia, can lead to serious health conditions.
Scientists continue to explore the myriad ways in which oxygen influences living organisms and their environments.
Researchers utilize a variety of tools and techniques to study oxygen's role in biological systems.
Common equipment includes the Oxygraph-2k, a high-resolution respirometry system, and the Clark-type oxygen electrode, which measures dissolved oxygen concentration.
Glucose oxidase, an enzyme that catalyzes the oxidation of glucose to gluconic acid and hydrogen peroxide, is also employed in oxygen-related research.
In cell culture experiments, researchers often supplement growth media like DMEM (Dulbecco's Modified Eagle Medium) and FBS (Fetal Bovine Serum) with antibiotics like Penicillin/Streptomycin to maintain sterile conditions.
Imaging techniques, such as those enabled by the Vevo 2100 ultrasound biomicroscopy system, allow for the visualization of oxygen-related processes in living organisms.
Additionally, the biocompatible polymer Sylgard 184 is commonly used to fabricate microfluidic devices for oxygen-sensitive applications.
By leveraging these tools and techniques, scientists can advance our understanding of oxygen's pivotal role in biological systems and develop innovative solutions to optimize oxygene research through AI-driven protocol comparison and other cutting-edge methods.