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GLOSSARY (L-P)

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L


Ligands

In biochemistry and pharmacology, a ligand refers to a substance (generally a small molecule) that forms a complex with a biomolecule to serve a certain biological purpose. In protein-ligand binding, the ligand is usually a signal-triggering molecule, binding to a site on a target protein. In DNA-ligand binding studies, the ligand is usually any small molecule or ion, or even a protein that binds to the DNA double helix.

Binding occurs by intermolecular forces. This may include ionic bonds, hydrogen bonds and Van der Waals forces. The docking (or association) is usually reversible (or dissociation).  In biological systems irreversible covalent bonding between a ligand and its target molecule is rare. In contrast to the meaning in metalorganic and inorganic chemistry, it is irrelevant whether the ligand actually binds at a metal site, as is the case in hemoglobin.

In a specific binding action, the smaller of two molecules is generally considered to be the ligand.


Linker

The chemical structure connecting an antibody with a cytotoxic drug in an ADC.

Source: Chari RVJ. Targeted cancer therapy: conferring specificity to cytotoxic drugs. Acc Chem Res. 2008;41:98-107.


Light chain

A typical antibody is composed of two immunoglobulin (Ig) heavy chains and two Ig light chains. Each of these four subunits contain a constant region and a variable region. The constant region remains the same within each type of antibody. The variable region contains the antigen binding site.

A light chain is the small polypeptide subunit of an antibody. In humans there are two types of light chains

  • Kappa (κ) chain, encoded by the immunoglobulin kappa locus (IGK@) on chromosome 2
  • Lambda (λ) chain, encoded by the immunoglobulin lambda locus (IGL@) on chromosome 22

Antibodies are produced by B lymphocytes, each expressing only one class of light chain. Once set, light chain class remains fixed for the life of the B lymphocyte. In a healthy individual, the total kappa to lambda ratio is roughly 3:1 in serum (measuring intact whole antibodies) or 1:1.5 if measuring free light chains, with a highly divergent ratio indicative of neoplasm.

The exact normal ratio of kappa to lambda, according to a novel polyclonal free light chain assay, ranges from 0.26 to 1.65. Both the kappa and the lambda chains can increase proportionately, maintaining a normal ratio. This is usually indicative of something other than a blood cell dyscrasia, such as kidney disease.

Also see: Antibody


Lysis

Disruption, disintegration or breaking of the cellular membrane of the cell.  Lysis results in the release of cell contents and subsequent death of the cell.


Lysosomes

Lysosomes are cellular organelles contain a wide variety of hydrolytic enzymes (acid hydrolases) responsible for break down and degrading of macromolecules such as nucleic acids, proteins, and polysaccharides and other materials ingested by the cell and cell debris. These enzymes, active only in the lysosome’s acidic interior (an acidic environment of about pH 4.8), and act as waste disposal system of the cell by digesting unwanted materials in the cytoplasm, both from outside of the cell and obsolete components inside the cell.

Lysosomes digest excess or worn-out organelles, food particles, and engulfed viruses or bacteria. The membrane around a lysosome allows the digestive enzymes to work at the pH they require. They fuse with autophagic vacuoles (phagosomes) and dispense their enzymes into the autophagic vacuoles, digesting their contents.

The size of lysosomes varies from 0.1–1.2 μm.)


M


MAb

Abbreviation of Monoclonal Antibody.

Monoclonal Antibodies are highly specified and purified antibodies that recognize only a single epitope. They are produced via a recombinant process or by isolating a single B-cell from an immunized animal that recognizes a single epitope.

The production of monoclonal antibodies was pioneered by Georges Kohler and Cesar Milstein in 1975.

See Antibody


Macromolecules

In biochemistry, macromolecules are defined as very large molecules created by polymerization of smaller organic molecules. The term is used to identify three conventional biopolymers (nucleic acids, proteins, and carbohydrates) as well as non-polymeric molecules with large molecular mass such as lipids and macrocycles.

The term macromolecule was first coined by Nobel laureate Hermann Staudinger in the 1920s.


Maytansinoid

A derivative of the natural product originally derived from the African shrub Maytenus ovatus.

Source: Ricart AD, Tolcher AW. Technology insight: cytotoxic drug immunoconjugates for cancer therapy. Nat Clin Pract Oncol. 2007;4:245-255.  Also see: Maytansine


Methotrexate

A folic acid antagonist that inhibits the synthesis of DNA, RNA, thymidylates, and protein. It is used as a cytotoxic in a wide range of malignancies, including breast cancer.

Dorland’s Illustrated Medical Dictionary. 30th Edition. Philadelphia, Pennsylvania: Saunders, an imprint of Elsevier; 2007:1144-1145.


Metronomic chemotherapy (MCT)

The name metronomic comes from the idea of regular administration of chemotherapeutic drugs. 

The concept of Metronomic Chemotherapy or MCT, which is intended to prevent tumor angiogenesis, is based on research by Douglas Hanahan, Judah Folkman and Robert Kerbel and their respective colleagues. This approach stand in contradiction to traditional chemotherapy regimens which generally call for higher doses of chemotherapy and are often limited largely by the body’s own capacity to handle the adverse events as well as for limited campaigns of several weeks in order to avoid drug resistance and avoid harming the body’s organs beyond a certain limit. Hence, metronomic chemotherapy, which uses conventional cytotoxic drugs but counts on them to stop or slow blood vessel growth, makes reference to the chronic, equally spaced administration of low doses of various chemotherapeutic drugs without extended rest periods between cycles of therapy (a practice that may not only involve re-growth of tumour cells, but also growth of selected clones resistant to the therapy).

Metronomic Chemotherapy (MCT) contrasts the Maximum Tolerated Dose (MTD) method typically used in most clinical protocols.

References: Scharovsky OG, Mainetti LE, Rozados VR. Metronomic chemotherapy: changing the paradigm that more is better. Curr Oncol. 2009 Mar; 16(2): 7–15.

Pasquier E, Kavallaris M, André N. Metronomic chemotherapy: new rationale for new directions. Nat Rev Clin Oncol. 2010 Aug;7(8):455-65. doi: 10.1038/nrclinonc.2010.82. Epub 2010 Jun 8.


Microtubule inhibitors

Microtubule inhibitors or MTIs are a class of cytotoxic agents that act on microtubules, which play an important role in cell division and are therefore critical for rapidly dividing cancer cells. Microtubule inhibitors include agents such as taxanes, vinca alkaloids, and epothilones that are used against many solid and hematologic malignancies.

Perez EA. Microtubule inhibitors: differentiating tubulin-inhibiting agents based on mechanisms of action, clinical activity, and resistance. Mol Cancer Ther. 2009;9:2086-2095.


Monoclonal Antibodies

Monoclonal antibodies or monospecific antibodies are a class of antibodies produced in the laboratory by a single clone of a unique parent cells or a cell line and consisting of identical antibody molecules.

Monoclonal antibodies are proteins produced by the B lymphocytes of the immune system in response to foreign proteins, called antigens. Antibodies function as markers, binding to the antigen so that the antigen molecules can be recognized and destroyed by phagocytes. The part of the antigen that the antibody binds to is called the epitope, a short amino acid sequence that can be recognized by an antibody.

Two features of the antibody-epitope relationship are key:

  • Specificity: the antibody binds only to its particular epitope
  • Sufficiency: the epitope can bind to the antibody on its own, hence, the presence of the whole antigen is not necessary

Structurally antibodies are proteins consisting of four polypeptide chains. These four chains form a quaternary structure (resembling a Y shape).

See: MAb and Antibody


Myeloma

A lymphocytic cancer that arises in plasma cells, a type of white blood cell.

Myeloma, also known as multiple myeloma or plasma cell myeloma, is the third most common blood cancer (after lymphoma and leukemia) in the United States and constitutes approximately 1.4% of the estimated new cancer cases in 2014. Since 1975, overall myeloma incidence has increased nearly 1% annually. Overall mortality rates peaked in the mid-1990s and have fallen in recent years.

Men have a higher incidence of myeloma than women. In addition, African Americans have over twice the incidence and mortality rates of whites.

It is estimated that more than 24,000 individuals will be diagnosed with myeloma in the United States in 2014, and more than 11,000 will die from this disease.

Risk factors for myeloma include being middle aged or older, being black, being male, having been exposed to radiation or certain chemicals, and having a personal history of monoclonal gammopathy of undetermined significance (MGUS) or isolated plasmacytoma of the bone. There is no standard or routine screening test for myeloma. Standard treatments for myeloma include chemotherapy, corticosteroid therapy, targeted therapy, high-dose chemotherapy with stem cell transplant, biological therapy, radiation therapy, surgery, and watchful waiting.

Source: National Cancer Institute


N


Native

In the context of biopharmaceuticals, native general refers to a molecule’s normal, three-dimensional structure under optimal conditions.


NCI

Abbreviation of National Cancer Institute

The National Cancer Institute is part of the National Institutes of Health, which is one of 11 agencies that compose the U.S. Department of Health and Human Services. The NCI, established under the National Cancer Institute Act of 1937, is the Federal Government’s principal agency for cancer research and training. The National Cancer Act of 1971 broadened the scope and responsibilities of the NCI and created the National Cancer Program. Over the years, legislative amendments have maintained the NCI authorities and responsibilities and added new information dissemination mandates as well as a requirement to assess the incorporation of state-of-the-art cancer treatments into clinical practice.

The National Cancer Institute coordinates the National Cancer Program, which conducts and supports research, training, health information dissemination, and other programs with respect to the cause, diagnosis, prevention, and treatment of cancer, rehabilitation from cancer, and the continuing care of cancer patients and the families of cancer patients. Specifically, the Institute:

  • Supports and coordinates research projects conducted by universities, hospitals, research foundations, and businesses throughout this country and abroad through research grants and cooperative agreements;
  • Conducts research in its own laboratories and clinics;
  • Supports education and training in fundamental sciences and clinical disciplines for participation in basic and clinical research programs and treatment programs relating to cancer through career awards, training grants, and fellowships;
  • Supports research projects in cancer control;
  • Supports a national network of cancer centers;
  • Collaborates with voluntary organizations and other national and foreign institutions engaged in cancer research and training activities;
  • Encourages and coordinates cancer research by industrial concerns where such concerns evidence a particular capability for programmatic research;
  • Collects and disseminates information on cancer;
  • Supports construction of laboratories, clinics, and related facilities necessary for cancer research through the award of construction grants.

Source: National cancer Institute website; Last accessed November 12, 2014.


NDA

Abbreviation of New Drug Application.

In the United States the regulation and control of new drugs is been based on the New Drug Application (NDA). Since 1938, every new drug has been the subject of an approved NDA before commercialization. The NDA application is the mechanism used by drug sponsors (generally pharmaceutical companies) to formally propose that the U.S. Food and Drug Administration (FDA) approvea a new pharmaceutical for sale and marketing. The data gathered during the animal studies and human clinical trials of an Investigational New Drug (IND) become part of the NDA.

The purpose of a New Drug Application is to provide enough information to permit FDA reviewer to reach the following decision:

  • Is the drug safe and effective in its proposed use(s)
  • Do the benefits of the drug outweigh the risks
  • Is the drug’s proposed labeling (package insert) appropriate, and what it should contain.
  • Are the methods used in manufacturing the drug and the controls used to maintain the drug’s quality are adequate to preserve the drug’s identity, strength, quality, and purity.

The documentation required in an NDA is supposed to tell the drug’s whole story, including what happened during the clinical tests, what the ingredients of the drug are, the results of the animal studies, how the drug behaves in the body, and how it is manufactured, processed and packaged.

Source: FDA website; last accessed November 12, 2014


NIH

Abbreviation of National Institute of Health

The National Institutes of Health, is one of the eleven agencies that are part of the U.S. Department of Health and Human Services, is the nation’s medical research agency—making important discoveries that improve health and save lives.

The agency conducts and supports medical research and helps in the dissemination of information.

Thanks in large part to NIH-funded medical research, Americans today are living longer and healthier. Life expectancy in the United States has jumped from 47 years in 1900 to 78 years as reported in 2009, and disability in people over age 65 has dropped dramatically in the past 3 decades. In recent years, nationwide rates of new diagnoses and deaths from all cancers combined have fallen significantly.

Source: NCI website; last accessed November 12, 2014


N-terminal

The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) refers to the start of a protein or polypeptide terminated by an amino acid with a free amine group (-NH2).


Nucleic acids

Nucleic acids are polymeric macromolecules, or large biological molecules, essential for all known forms of life. They are made from monomers known as nucleotides and include deoxyribonucleic acid or DNA and ribonucleic acid or RNA, . Each nucleotide has three components: a 5-carbon sugar, a phosphate group, and a nitrogenous base.

If the sugar is deoxyribose, the polymer is DNA. If the sugar is ribose, the polymer is RNA.

Together with proteins, nucleic acids are the most important biological macromolecules. Each are found in abundance in living things where they function in encoding, transmitting and expressing genetic information. Strings of nucleotides strung together in a specific sequence are the mechanism for storing and transmitting hereditary, or genetic information via protein synthesis.

Nucleic acids were discovered by Friedrich Miescher in 1869. Experimental studies of nucleic acids constitute a major part of modern biological and medical research, and form a foundation for genome and forensic science, as well as the biotechnology and pharmaceutical industries.


Nucleosides

Nucleosides are glycosylamines consisting of a nucleobase (also known as a nitrogenous base) bound to a ribose or deoxyribose sugar. Examples of nucleosides include cytidine, uridine, adenosine, guanosine, thymidine and inosine.

In medicine several nucleoside analogues are used as antiviral or anticancer agents. The viral polymerase incorporates these compounds with non-canonical bases. These compounds are activated in the cells by being converted into nucleotides. They are administered as nucleosides since charged nucleotides cannot easily cross cell membranes.


Nucleoside analogues

Nucleoside analogues are molecules that act like nucleosides in DNA or RNA replication. They include a range of antiviral products used to prevent viral replication in infected cells.


Nucleotides

Nucleotides are organic molecules that serve as the monomers, or subunits (the basic structural units) of nucleic acids like DNA and RNA. The building blocks of nucleic acids, nucleotides are composed of a nitrogenous base, a 5-carbon sugar (ribose or deoxyribose), and at least one phosphate group.  The bases can be adenine (A), cytosine (C), guanine (G), thymine (T), or uracil (U).  A nucleoside plus a phosphate group yields a nucleotide.

Nucleotides serve to carry packets of energy within the cell in the form of the nucleoside triphosphates (ATP, GTP, CTP and UTP), playing a central role in metabolism. In addition, nucleotides participate in cell signaling (cGMP and cAMP), and are incorporated into important cofactors of enzymatic reactions (e.g. coenzyme A, FAD, FMN, NAD, and NADP+).


O


Oncogene

A gene that normally directs cell growth. If altered, an oncogene, when expressed, may induce cancer.

An oncogene is a sequence of deoxyribonucleic acid (DNA) that has been altered or mutated from its original form, the proto-oncogene.  In their normal, unaltered state, oncogenes (called porto-oncogenes) are positive growth regulators involved in promoting the differentiation and proliferation of normal cells.  A variety of these proto-oncogenes are involved in different crucial steps of cell growth, and a change in the proto-oncogene’s sequence or in the amount of protein it produces can interfere with its normal role in cellular regulation. Uncontrolled cell growth, or neoplastic transformation, can ensue, ultimately resulting in the formation of a cancerous tumor.


Organelle

An organelle is a specialized structurally discrete subunit within a cell that has a specific function inside an eukaryotic cell.


Organism

An autonomous living thing or any contiguous living system, such as a vertebrate, insect, plant or bacterium.


Orphan drugs

Orphan drugs are medicinal products intended for diagnosis, prevention or treatment of life-threatening or very serious diseases or disorders that are rare. In the United States a disease is considered a rare disease if it affects fewer than 200,000 people. In Europe, a disease or disorder is defined as rare when it affects less than 1 in 2,000 citizens.


P


PCR (history)

Abbreviation of Polymerase Chain Reaction.

The polymerase chain reaction is a biomedical technology in molecular biology used to amplify a single copy or a few copies of a piece of DNA from just one original strand across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.

Recognized as one of the most important scientific advances of the 20th century, copied DNA by polymerase chain reaction, can be used reliably in a wide variety of tests to diagnose or monitor diseases, or for basic molecular biology research.

In 1983, Kary Mullis, PhD (born:December 28, 1944), a scientist at the Cetus Corporation, one of the first biotechnology companies, conceived of PCR as a method to copy DNA and synthesize large amounts of a specific target DNA. Over the next two years, a team of Cetus scientists that recognized the potential impact PCR could have on molecular biology, researched, refined and made the theoretical process a reality.

The team presented the technology for the first time in 1985 at the American Society for Human Genetics annual meeting. Later the same year, Science, a journal of the American Association for the Advancement of Science, reported the results in the first-ever publication of the process.

In 1986, David H. Gelfand, PhD, a senior Cetus microbiologist, led a team that discovered the Yellowstone boiling mud pot bacterium, thermus aquaticus, that thrived at 100C. the scientists isolated and produced the key enzyme Taq polymerase needed to denature DNA at 90C in repeated cycles of the PCR process.

Because Taq could withstand high temperatures, it removed the need for human intervention during the reaction, streamlining and shortening the process. Without a heat-resistant enzyme like Taq polymerase, PCR could not be used on a large scale as the process would have been too cumbersome. Prior to Taq, DNA polymerase from E. coli, an enzyme that could not withstand rapid heating and cooling, was used in the second step of PCR. Using E. Coli, the polymerase was manually replaced at each step of the reaction as it degraded from the heat.

In 1987, PerkinElmer, another U.S.-based biotechnology company, launched a thermal cycler, an instrument that is programmed to regulate the temperature of a reaction, heating or cooling the samples as needed. Once again, this advance minimized human interaction in the reaction, leading to an elegant, efficient and streamlined process.

In 1991, Cetus received a PCR patent.  The same year F. Hoffmann-La Roche, Ltd. bought the rights to PCR from Cetus (allegedly for less than U.S. $ 200 million) and invested in refining the science for use in molecular diagnostics to detect diseases.

Kary Mullis received the 1993 Chemistry Nobel Prize for his work in developing the Polymerase Chain Reaction technology.

Source: Roche Molecular Systems Inc


PCR (Process)

Abbreviation of Polymerase Chain Reaction.

PCR

Schematic drawing of the Polymerase Chain Reaction cycle (design: Enzoklop)

The process of Polymerase Chain Reaction or PCR consists of a series of 20-40 repeated temperature changes, called cycles, with each cycle commonly consisting of 2-3 discrete temperature steps, usually three (See: Schematic drawing of the the Polymerase Chain Reaction cycle; above). The cycling is often preceded by a single temperature step at a high temperature (>90 °C), and followed by one hold at the end for final product extension or brief storage. The temperatures used and the length of time they are applied in each cycle depend on a variety of parameters. These include the enzyme used for DNA synthesis, the concentration of divalent ions and dNTPs in the reaction, and the melting temperature (Tm) of the primers.

Initialization (Only required for DNA polymerases that require heat activation by hot-start PCR.): This step consists of heating the reaction to a temperature of 94–96 °C (or 98 °C if extremely thermostable polymerases are used), which is held for 1–9 minutes.

Denaturation: This step is the first regular cycling event and consists of heating the reaction to 94–98 °C for 20–30 seconds. It causes DNA melting of the DNA template by disrupting the hydrogen bonds between complementary bases, yielding single-stranded DNA molecules.

Annealing: The reaction temperature is lowered to 50–65 °C for 20–40 seconds allowing annealing of the primers to the single-stranded DNA template. This temperature needs to be low enough to allow for hybridization of the primer to the strand, but high enough in order for the hybridization to be specific, i.e. the primer should only bind to a perfectly complementary part of the template. If the temperature is too low, the primer could bind imperfectly. If it is too high, the primer might not bind. Typically the annealing temperature is about 3–5 °C below the Tm of the primers used. Stable DNA–DNA hydrogen bonds are only formed when the primer sequence very closely matches the template sequence. The polymerase binds to the primer-template hybrid and begins DNA formation.

Extension/elongation: The temperature at this step depends on the DNA polymerase used; Taq polymerase has its optimum activity temperature at 75–80 °C,and commonly a temperature of 72 °C is used with this enzyme. At this step the DNA polymerase synthesizes a new DNA strand complementary to the DNA template strand by adding dNTPs that are complementary to the template in 5′ to 3′ direction, condensing the 5′-phosphate group of the dNTPs with the 3′-hydroxyl group at the end of the nascent (extending) DNA strand. The extension time depends both on the DNA polymerase used and on the length of the DNA fragment to be amplified. As a rule-of-thumb, at its optimum temperature, the DNA polymerase will polymerize a thousand bases per minute. Under optimum conditions, i.e., if there are no limitations due to limiting substrates or reagents, at each extension step, the amount of DNA target is doubled, leading to exponential (geometric) amplification of the specific DNA fragment.\

Final elongation: This single step is occasionally performed at a temperature of 70–74 °C (this is the temperature needed for optimal activity for most polymerases used in PCR) for 5–15 minutes after the last PCR cycle to ensure that any remaining single-stranded DNA is fully extended.

Final hold: This step at 4–15 °C for an indefinite time may be employed for short-term storage of the reaction.

Source: Roche Molecular Systems Inc


PEG

Abbreviation of Polyethylene glycol.

Polyethylene glycol, is s a polyether compound with many applications from industrial manufacturing to medicine. In biomedicine PEGs are used as dispersing agents, solvents, ointment and suppository bases, vehicles and excipients.


PEGylation

PEGylation is the process of covalent attachment of polyethylene glycol polymer chains to another molecule, normally a drug or therapeutic protein, which is then described as PEGylated.

PEGylation is routinely achieved by incubation of a reactive derivative of PEG with the target molecule. The covalent attachment of PEG to a drug or therapeutic protein can “mask” the agent from the host’s immune system (reduced immunogenicity and antigenicity), and increase the hydrodynamic size or size in solution of the agent which prolongs its circulatory time by reducing renal clearance. PEGylation can also provide water solubility to hydrophobic drugs and proteins.

All commercially available PEGylated pharmaceuticals contain methoxypoly(ethylene glycol) or mPEG.

An example of a PEGylated drug is peginterferon alfa-2a (Pegasys®; Genentech/Hoffmann-La Roche Inc), a prescription medication that is alone or in combination with ribavirin (Copegus®;Genentech/Hoffmann-La Roche Inc) indicated for the treatment of patients 5 years of age and older with chronic hepatitis C (CHC) virus infection with compensated liver disease and have not been previously treated with interferon alpha.


Peptide bioanalysis

An analytical technique to quantitatively measure peptide drugs and their metabolites in biological systems.


Peptide bond

A peptide bond or amide bond is a covalent chemical bond formed between two amino acid molecules.


Pyrrolobenzodiazepines (PBS)

Pyrrolobenzodiazepines, a class of natural products produced by actinomycetes, are sequence selective DNA alkylating compounds with significant antitumor properties. Some pyrrolobenzodiazepines (PBDs) have the ability to recognize and bond to specific sequences of DNA.

As DNA minor groove binding agents, pyrrolobenzodiazepines bind and cross-link specific sites of DNA of the cancer cell. This blocks the cancer cells’ division without distorting its DNA helix, thus potentially avoiding the common phenomenon of emergent drug resistance.

The first pyrrolobenzodiazepines antitumour antibiotic, anthramycin (not to be confused with anthracimycin), produced by streptomyces refuineus, was discovered in 1965. Since then, a number of naturally occurring PBDs have been reported, and over 10 synthetic routes have been developed to a variety of analogues. Other agents belonging to the pyrrolo(1,4)benzodiazepine antibiotic group include abbeymycin, chicamycin, DC-81, mazethramycin, neothramycins A and B , porothramycin prothracarcin, sibanomicin (D,C- 102) sibiromycin and tomamycin.

Spirogen, now part of AstraZeneca/Medimmune, which was founded in 2001 as a spin-out from several institutions including University College London and with partial funding by Cancer Research UK has developed a novel class of highly potent cytotoxic warheads based on its proprietary pyrrolobenzodiazepines (PBDs). The company has been developing its PBD technology for more than ten years, including a standalone PBD agent in a Phase II study in acute myeloid leukemia.

Li W, Khullar A, Chou S, Sacramo A, Gerratana B. Biosynthesis of sibiromycin, a potent antitumor antibiotic. Appl Environ Microbiol. 2009 May;75(9):2869-78. doi: 10.1128/AEM.02326-08. Epub 2009 Mar 6.

See: Pyrrolobenzodiazepines (PBDs)


 

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