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Journal of Clinical Oncology : Official... Sep 2014The purpose of this work was to modernize recommendations for evaluation, staging, and response assessment of patients with Hodgkin lymphoma (HL) and non-Hodgkin...
The purpose of this work was to modernize recommendations for evaluation, staging, and response assessment of patients with Hodgkin lymphoma (HL) and non-Hodgkin lymphoma (NHL). A workshop was held at the 11th International Conference on Malignant Lymphoma in Lugano, Switzerland, in June 2011, that included leading hematologists, oncologists, radiation oncologists, pathologists, radiologists, and nuclear medicine physicians, representing major international lymphoma clinical trials groups and cancer centers. Clinical and imaging subcommittees presented their conclusions at a subsequent workshop at the 12th International Conference on Malignant Lymphoma, leading to revised criteria for staging and of the International Working Group Guidelines of 2007 for response. As a result, fluorodeoxyglucose (FDG) positron emission tomography (PET)–computed tomography (CT) was formally incorporated into standard staging for FDG-avid lymphomas. A modification of the Ann Arbor descriptive terminology will be used for anatomic distribution of disease extent, but the suffixes A or B for symptoms will only be included for HL. A bone marrow biopsy is no longer indicated for the routine staging of HL and most diffuse large B-cell lymphomas. However, regardless of stage, general practice is to treat patients based on limited (stages I and II, nonbulky) or advanced (stage III or IV) disease, with stage II bulky disease considered as limited or advanced disease based on histology and a number of prognostic factors. PET-CT will be used to assess response in FDG-avid histologies using the 5-point scale. The product of the perpendicular diameters of a single node can be used to identify progressive disease. Routine surveillance scans are discouraged. These recommendations should improve evaluation of patients with lymphoma and enhance the ability to compare outcomes of clinical trials.
Topics: Bone Marrow Neoplasms; Fluorodeoxyglucose F18; Hodgkin Disease; Humans; International Cooperation; Liver Neoplasms; Lymphoma, Non-Hodgkin; Neoplasm Staging; Positron-Emission Tomography; Predictive Value of Tests; Prognosis; Radiopharmaceuticals; Tomography, X-Ray Computed; Treatment Outcome
PubMed: 25113753
DOI: 10.1200/JCO.2013.54.8800 -
Hepatology (Baltimore, Md.) Apr 2021Osteopontin (OPN) was first identified in 1986. The prefix osteo- means bone; however, OPN is expressed in other tissues, including liver. The suffix -pontin means... (Review)
Review
Osteopontin (OPN) was first identified in 1986. The prefix osteo- means bone; however, OPN is expressed in other tissues, including liver. The suffix -pontin means bridge and denotes the role of OPN as a link protein within the extracellular matrix. While OPN has well-established physiological roles, multiple "omics" analyses suggest that it is also involved in chronic liver disease. In this review, we provide a summary of the OPN gene and protein structure and regulation. We outline the current knowledge on how OPN is involved in hepatic steatosis in the context of alcoholic liver disease and non-alcoholic fatty liver disease. We describe the mechanisms whereby OPN participates in inflammation and liver fibrosis and discuss current research on its role in hepatocellular carcinoma and cholangiopathies. To conclude, we highlight important points to consider when doing research on OPN and provide direction for making progress on how OPN contributes to chronic liver disease.
Topics: Animals; Carcinoma, Hepatocellular; Disease Models, Animal; Extracellular Matrix; Gene Expression; Humans; Liver Cirrhosis; Liver Diseases, Alcoholic; Liver Neoplasms; Mice; Non-alcoholic Fatty Liver Disease; Osteopontin
PubMed: 32986864
DOI: 10.1002/hep.31582 -
The Computer Journal May 2018Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens...
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees.
PubMed: 29795706
DOI: 10.1093/comjnl/bxx108 -
Biophysical Reviews Dec 2018In this short review, I describe a brief history of the discovery of myosin I isolated from Acanthamoeba in 1973 by Tom Pollard and Ed Korn. Today, myosins form a large... (Review)
Review
In this short review, I describe a brief history of the discovery of myosin I isolated from Acanthamoeba in 1973 by Tom Pollard and Ed Korn. Today, myosins form a large "family tree" that includes more than 30 types of myosins. I discuss the importance of the relationship among actin, myosin, and other actin-binding proteins, many of which were pioneered by Pollard-san ("-san" is a Japanese honorific suffix showing respect, politeness and friendship). At the first conference devoted to actin, Pollard-san, Korn-san, and I discussed the importance of the nucleotide bound at the two ends of the actin filament. I conclude that life is a dynamic accumulation of molecule-molecule bindings, and although we do not yet know how they coordinate with each other to operate a living cell, many enthusiastic and excellent researchers like Pollard-san will unveil mechanisms that will show us what life really looks like.
PubMed: 30446945
DOI: 10.1007/s12551-018-0485-5 -
Human Genetics Apr 2021Cell-free DNA (cfDNA) has become widely recognized as a promising candidate biomarker for minimally invasive characterization of various genomic disorders and other... (Review)
Review
Cell-free DNA (cfDNA) has become widely recognized as a promising candidate biomarker for minimally invasive characterization of various genomic disorders and other clinical scenarios. However, among the obstacles that currently challenge the general progression of the research field, there remains an unmet need for unambiguous universal cfDNA nomenclature. To address this shortcoming, we classify in this report the different types of cfDNA molecules that occur in the human body based on its origin, genetic traits, and locality. We proceed by assigning existing terms to each of these cfDNA subtypes, while proposing new terms and abbreviations where clarity is lacking and more precise stratification would be beneficial. We then suggest the proper usage of these terms within different contexts and scenarios, focusing mainly on the nomenclature as it relates to the domains of oncology, prenatal testing, and post-transplant surgery surveillance. We hope that these recommendations will serve as useful considerations towards the establishment of universal cfDNA nomenclature in the future. In addition, it is conceivable that many of these recommendations can be transposed to cell-free RNA nomenclature by simply exchanging "DNA" with "RNA" in each acronym/abbreviation. Similarly, when describing DNA and RNA collectively, the suffix can be replaced with "NAs" to indicate nucleic acids.
Topics: Animals; Cell-Free Nucleic Acids; Humans; Terminology as Topic
PubMed: 33123832
DOI: 10.1007/s00439-020-02227-2 -
Research Square Oct 2023FM-indexes are a crucial data structure in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern. Ferragina...
FM-indexes are a crucial data structure in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer [1] observed in 2007 that word-based indexes often use fewer random accesses than character-based indexes, and thus support faster searches. Since DNA lacks natural word-boundaries, however, it is necessary to parse it somehow before applying word-based FM-indexing. Last year, Deng et al. [2] proposed parsing genomic data by induced suffix sorting, and showed the resulting word-based FM-indexes support faster counting queries than standard FM-indexes when patterns are a few thousand characters or longer. In this paper we show that using prefix-free parsing-which takes parameters that let us tune the average length of the phrases-instead of induced suffix sorting, gives a significant speedup for patterns of only a few hundred characters. We implement our method and demonstrate it is between 3 and 18 times faster than competing methods on queries to GRCh38, and is consistently faster on queries made to 25,000, 50,000 and 100,000 SARS-CoV-2 genomes. Hence, it seems our method accelerates the performance of count over all state-of-the-art methods with a minor increase in the memory. The source code for PFP-FM is available at https://github.com/marco-oliva/afm.
PubMed: 37961504
DOI: 10.21203/rs.3.rs-3487536/v1 -
BMC Medical Informatics and Decision... Jul 2023Diagnoses are crucial assets of clinical work and provide the foundation for treatment and follow up. They should be informative and customized to the patient's problem....
BACKGROUND
Diagnoses are crucial assets of clinical work and provide the foundation for treatment and follow up. They should be informative and customized to the patient's problem. Common prefixes, morphemes, and suffixes may aid the implementation of expressions that generate diagnoses.
RESULTS
Apt choices of symbols plays a major role in science. In this study, the variables e, o, and p are assigned to names of an etiological agent, a disorder, and a pathogenetic mechanism, respectively. The suffix -itis designates infections, allergies, inflammation, and/or immune reactions. Diagnoses (d) are generated by the formula d:= e&o&p where '&' means concatenation and ':= ' means assignment. Thus, with e:= 'Staphylococcus aureus ', o:= 'endocard', and p:= 'itis', d:= e&o&p generates the diagnosis d = 'Staphylococcus aureus endocarditis'. Diagnoses formed this way comply with common clinical diagnoses. Certain extensions generate complete, systematic medical diagnoses that are applicable to all medical specialties. For example, common medical prefixes, morphemes, and suffixes give rise to o = 'hypothyroidism', o = 'tachycardia', and o = 'hypophagocytosis'. The formula scales well with the developments in clinical medicine, systems biology, molecular biology, and microbiology. The diagnosis generating formula d:= e&o&p requires meticulous analysis of the components of diagnoses plus the introduction of appropriate variables and terms. Terms partition on established clinical categories and adhere to established clinical nomenclature. The syntax generates universal medical diagnoses.
CONCLUSIONS
The present study concerns a universal diagnosis syntax (UDS) that generates diagnoses using the formula d:= e&o&p with several extensions described in the study. The formula is easy to learn and covers diagnoses in all medical specialties. The present work succeeded in creating diagnoses from the formula. The fundamental insight is that no matter how complicated a diagnosis is it can be generated by a systematic process, which adds terms one by one. UDS may have implications for medical education and classifications. The formula lays a foundation for structured clinical decision-making. Formulas are hallmarks of hard science. So, d:= e&o&p anticipates a scientific medical revolution.
Topics: Humans; Medicine; Diagnosis; Terminology as Topic
PubMed: 37525189
DOI: 10.1186/s12911-023-02209-0