Gene Ontology

 CYSTEINE: (Kidney Stones)

Biological Processes:

·       apoptotic process

Definition: A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process and is typically characterized by rounding-up of the cell, retraction of pseudopods, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.

·       autophagy

Definition: The cellular catabolic process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.

·       mitophagy

Definition: The selective autophagy process in which a mitochondrion is degraded by macroautophagy.

·       protein delipidation

Definition: The breakage of covalent bonds to detach lipid groups from a protein.

·       protein localization to phagophore assembly site

Definition: Any process in which a protein is transported to, or maintained at, the phagophore assembly site (PAS).

·       protein transport

Definition: The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

·       proteolysis

Definition: The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.


TYPE IV COLLAGEN: (Alport Syndrome)

Biological Processes:

·         blood vessel development

Definition: The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.

·         bone trabecula formation

Definition: The process of creating a trabecula in the bone. A trabecula is a tissue element in the form of a small beam, strut or rod.

·         cartilage development involved in endochondral bone morphogenesis

Definition: The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones.

·         cellular response to amino acid stimulus

Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acid containing one or more amino groups.

·         cellular response to epidermal growth factor stimulus

Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epidermal growth factor stimulus.

·         cellular response to fibroblast growth factor stimulus

Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an fibroblast growth factor stimulus.

 

 

·         cellular response to fluoride

Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fluoride stimulus.

·         cellular response to mechanical stimulus

Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.

·         cellular response to retinoic acid

Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.

·         cellular response to transforming growth factor beta stimulus

Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus.

·         cellular response to tumor necrosis factor

Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.

·         cellular response to vitamin E

Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin E stimulus.

·         collagen-activated tyrosine kinase receptor signaling pathway

Definition: The series of molecular signals initiated by collagen binding to its receptor on the surface of a target cell where the receptor possesses tyrosine kinase activity, and ending with the regulation of a downstream cellular process, e.g. transcription.

·         collagen biosynthetic process

Definition: The chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).

·         collagen fibril organization Source:

Definition: Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix.

·         embryonic skeletal system development

Definition: The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure.

·         endochondral ossification

Definition: Replacement ossification wherein bone tissue replaces cartilage.

·         extracellular matrix organization

Definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.

·         face morphogenesis

Definition: The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head.

·         intramembranous ossification

Definition: Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells.

·         negative regulation of cell-substrate adhesion

Definition: Any process that decreases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.

·         Ossification

Definition: The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.

·         osteoblast differentiation

Definition: The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.

·         positive regulation of canonical Wnt signaling pathway

Definition: Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.

·         positive regulation of cell migration

Definition: Any process that activates or increases the frequency, rate or extent of cell migration.

·         positive regulation of epithelial to mesenchymal transition

Definition: Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.

·         positive regulation of transcription, DNA-templated

Definition: Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.

·         protein localization to nucleus

Definition: A process in which a protein transports or maintains the localization of another protein to the nucleus.

·         protein transport

Definition: The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

·         response to cAMP

Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.

·         response to corticosteroid

Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a corticosteroid hormone stimulus. A corticosteroid is a steroid hormone that is produced in the adrenal cortex. Corticosteroids are involved in a wide range of physiologic systems such as stress response, immune response and regulation of inflammation, carbohydrate metabolism, protein catabolism, blood electrolyte levels, and behavior. They include glucocorticoids and mineralocorticoids

·         response to estradiol

Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.

·         response to hydrogen peroxide

Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.

·         response to hyperoxia

Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating increased oxygen tension.

·         response to mechanical stimulus

Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.

·         response to peptide hormone

Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.

·         response to xenobiotic stimulus

Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a xenobiotic, a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.

·         sensory perception of sound

Definition: The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.

·         skeletal system development

Definition: The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).

·         skin development

Definition: The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue

·         skin morphogenesis

Definition: The process in which the anatomical structures of the skin are generated and organized. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner, sensitive and vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.

·         tooth eruption

Definition: The tooth development process in which the teeth enter the mouth and become visible.

·         tooth mineralization

Definition: The process in which calcium salts are deposited into calcareous tooth structures such as dental enamel, dentin and cementum.

·         visual perception

Definition: The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.

·         wound healing

Definition: The series of events that restore integrity to a damaged tissue, following an injury.


Polycystin-1:


GO - Biological process

 

 

·     anatomical structure morphogenesis

Definition:

The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.

·     branching morphogenesis of an epithelial tube

Definition:

The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.

·     calcium-independent cell-matrix adhesion

Definition:

The binding of a cell to the extracellular matrix via adhesion molecules that do not require the presence of calcium for the interaction.

·     calcium ion transmembrane transport

Definition:

A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.

·     calcium ion transport

Definition:

The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

·     cartilage condensation

Definition:

The condensation of mesenchymal cells that have been committed to differentiate into chondrocytes.

·     cartilage development

Definition:

The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.

·     cell-cell signaling by wnt

Definition:

Any process that mediates the transfer of information from one cell to another, medaited by a wnt family protein ligand. This process includes wnt signal transduction in the receiving cell, release of wnt ligand from a secreting cell as well as any processes that actively facilitate wnt transport and presentation to receptor on the recieving cell.

·     cell-matrix adhesion

Definition:

The binding of a cell to the extracellular matrix via adhesion molecules.

·     cytoplasmic sequestering of transcription factor

Definition:

The selective interaction of a transcription factor with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus.

·     detection of mechanical stimulus

Definition:

The series of events by which a mechanical stimulus is received and converted into a molecular signal.

·     digestive tract development

Definition:

The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.

·     embryonic placenta development

Definition:

The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.

·     establishment of cell polarity

Definition:

The specification and formation of anisotropic intracellular organization or cell growth patterns.

·     genitalia development

Definition:

The process whose specific outcome is the progression of the genitalia over time, from its formation to the mature structure.

·     heart development

Definition:

The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.

·     homophilic cell adhesion via plasma membrane adhesion molecules

Definition:

The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.

·     in utero embryonic development

Definition:

The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.

·     kidney development

Definition:

The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.

·     liver development

Definition:

The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.

·     lung epithelium development

Definition:

The biological process whose specific outcome is the progression of the lung epithelium from an initial condition to its mature state. This process begins with the formation of lung epithelium and ends with the mature structure. The lung epithelium is the specialized epithelium that lines the inside of the lung.

·     lymph vessel morphogenesis

Definition:

The process in which the anatomical structures of lymph vessels are generated and organized. The lymph vessel is the vasculature carrying lymph.

·     mesonephric duct development

Definition:

The process whose specific outcome is the progression of a mesonephric duct over time, from its initial formation to a mature structure. A mesonephric duct is a tube drains the mesonephros.

·     mesonephric tubule development

Definition:

The progression of a mesonephric tubule over time, from its initial formation to the mature structure. A mesonephric tubule is an epithelial tube that is part of the mesonephros.

·     metanephric ascending thin limb development

Definition:

The process whose specific outcome is the progression of a metanephric ascending thin limb over time, from its formation to the mature structure. The metanephric ascending thin limb is a segment of a nephron tubule in the metanephros lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent.

·     metanephric collecting duct development

Definition:

The process whose specific outcome is the progression of a metanephric ascending thin limb over time, from its formation to the mature structure. The metanephric ascending thin limb is a segment of a nephron tubule in the metanephros lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent.

·     metanephric distal tubule morphogenesis

Definition:

The progression of a mesonephric tubule over time, from its initial formation to the mature structure. A mesonephric tubule is an epithelial tube that is part of the mesonephros.

·     metanephric proximal tubule development

Definition:

The process whose specific outcome is the progression of the metanephric proximal tubule over time, from its formation to the mature structure. The metanephric proximal tubule is a metanephric nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle in the metanephros. It has a brush border epithelial morphology.

·     neural tube development

Definition:

The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium.

·     peptidyl-serine phosphorylation

Definition:

The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.

·     placenta blood vessel development

Definition:

The process whose specific outcome is the progression of a blood vessel of the placenta over time, from its formation to the mature structure

·     positive regulation of cyclin-dependent protein serine/threonine kinase activity

Definition:

Any process that activates or increases the frequency, rate or extent of CDK activity.

·     positive regulation of cytosolic calcium ion concentration

Definition:

Any process that increases the concentration of calcium ions in the cytosol.

·     positive regulation of protein binding

Definition:

Any process that activates or increases the frequency, rate or extent of protein binding.

·     positive regulation of transcription by RNA polymerase II

Definition:

Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.

·     protein export from nucleus

Definition:

The directed movement of a protein from the nucleus into the cytoplasm.

·     protein heterotetramerization

Definition:

The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.

·     receptor signaling pathway via JAK-STAT

Definition:

Any process in which STAT proteins (Signal Transducers and Activators of Transcription) and JAK (Janus Activated Kinase) proteins convey a signal to trigger a change in the activity or state of a cell. The receptor signaling pathway via JAK-STAT begins with activation of a receptor and proceeeds through STAT protein activation by members of the JAK family of tyrosine kinases. STAT proteins dimerize and subsequently translocate to the nucleus. The pathway ends with regulation of target gene expression by STAT proteins.

·     regulation of cell adhesion

Definition:

Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.

·     regulation of cell cycle

Definition:

Any process that modulates the rate or extent of progression through the cell cycle.

·     regulation of G1/S transition of mitotic cell cycle

Definition:

Any signalling pathway that modulates the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G1 phase to S phase of the mitotic cell cycle.

·     regulation of mitotic spindle organization

Definition:

Any process that modulates the rate, frequency or extent of the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.

·     regulation of proteasomal protein catabolic process

Definition:

Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.

·     response to fluid shear stress

Definition:

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface.

·     skin development

Definition:

The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.

·     spinal cord development

Definition:

The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues.


V2 vasopressin:

Biological process:

 

·     activation of adenylate cyclase activity

Definition:

Any process that initiates the activity of the inactive enzyme adenylate cyclase.

·     adenylate cyclase-modulating G protein-coupled receptor signaling pathway

Definition:

A G protein-coupled receptor signaling pathway in which the signal is transmitted via the activation or inhibition of adenylyl cyclase activity and a subsequent change in the intracellular concentration of cyclic AMP (cAMP).

·     G protein-coupled receptor signaling pathway

Definition:

The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane

·     hemostasis

Definition:

The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.

·     I-kappaB kinase/NF-kappaB signaling

Definition:

The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription

·     negative regulation of cell population proliferation

Definition:

Any process that stops, prevents or reduces the rate or extent of cell proliferation.

·     negative regulation of renal sodium excretion

Definition:

Any process that decreases the amount of sodium excreted in urine over a unit of time.

·     positive regulation of cell population proliferation

Definition:

Any process that activates or increases the rate or extent of cell proliferation.

·     positive regulation of gene expression

Definition:

Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).

·     positive regulation of systemic arterial blood pressure

Definition:

The process that increases the force with which blood travels through the systemic arterial circulatory system.

·     positive regulation of vasoconstriction

Definition:

Any process that activates or increases the frequency, rate or extent of vasoconstriction.

·     regulation of systemic arterial blood pressure by vasopressin

Definition:

The regulation of blood pressure mediated by the signaling molecule vasopressin. Vasopressin is produced in the hypothalamus, and affects vasoconstriction, and renal water transport.

·     renal water retention

Definition:

The process in which renal water excretion is decreased.

·     response to cytokine

Definition:

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.

·     telencephalon development

Definition:

The process whose specific outcome is the progression of the telencephalon over time, from its formation to the mature structure. The telencephalon is the paired anteriolateral division of the prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived.


Siderocalin: 

Biological process: 

 

Definition: 

A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. 

 

Definition: 

Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. 

 

Definition: 

Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. 

 

Definition: 

Any process that activates or increases the frequency, rate or extent of cold-induced thermogenesis 

 

Definition: 

The process of binding or confining iron ions such that they are separated from other components of a biological system. 

 

 

Definition: 

The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. 

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