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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 -
Bioinformatics (Oxford, England) Jan 2013Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read...
MOTIVATION
Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases.
RESULTS
To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy.
AVAILABILITY AND IMPLEMENTATION
STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
Topics: Algorithms; Cluster Analysis; Gene Expression Profiling; Genome, Human; Humans; RNA Splicing; Sequence Alignment; Sequence Analysis, RNA; Software
PubMed: 23104886
DOI: 10.1093/bioinformatics/bts635 -
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 -
Behavioral Sciences (Basel, Switzerland) Feb 2023The current study investigated mixed-emotional memories in groups of young, young-old, and old-old participants. We used a "word-suffix approach" to simulate the...
The current study investigated mixed-emotional memories in groups of young, young-old, and old-old participants. We used a "word-suffix approach" to simulate the co-occurrence of positive and negative emotions. The participants engaged in a free-recall task for valenced words and mixed-emotional words (valenced words coupled with pejorative or endearment suffixes). Our results showed that the groups of older adults recalled higher numbers of suffixed words compared to their younger counterparts. Our findings highlighted older adults' tendency to perceive and remember emotionally ambivalent words to a greater extent than younger adults and showed that the young-old participants were particularly good at solving ambivalence by focusing on positive-dominant ambivalent words.
PubMed: 36829389
DOI: 10.3390/bs13020160 -
Molecules (Basel, Switzerland) Jun 2010This review provides a historical overview of the analog based drug discovery of miconazole and its congeners, and is focused on marketed azole antifungals bearing the... (Review)
Review
This review provides a historical overview of the analog based drug discovery of miconazole and its congeners, and is focused on marketed azole antifungals bearing the generic suffix "conazole". The antifungal activity of miconazole, one of the first broad-spectrum antimycotic agents has been mainly restricted to topical applications. The attractive in vitro antifungal spectrum was a starting point to design more potent and especially orally active antifungal agents such as ketoconazole, itraconazole, posaconazole, fluconazole and voriconazole. The chemistry, in vitro and in vivo antifungal activity, pharmacology, and clinical applications of these marketed conazoles has been described.
Topics: Antifungal Agents; Fluconazole; Itraconazole; Ketoconazole; Miconazole; Molecular Structure; Pyrimidines; Structure-Activity Relationship; Triazoles; Voriconazole
PubMed: 20657432
DOI: 10.3390/molecules15064129 -
BMC Genomic Data Jun 2022Several technological advancements and digitization of healthcare data have provided the scientific community with a large quantity of genomic data. Such datasets...
BACKGROUND
Several technological advancements and digitization of healthcare data have provided the scientific community with a large quantity of genomic data. Such datasets facilitated a deeper understanding of several diseases and our health in general. Strikingly, these genome datasets require a large storage volume and present technical challenges in retrieving meaningful information. Furthermore, the privacy aspects of genomic data limit access and often hinder timely scientific discovery.
METHODS
In this paper, we utilize the Generalized Suffix Tree (GST); their construction and applications have been fairly studied in related areas. The main contribution of this article is the proposal of a privacy-preserving string query execution framework using GSTs and an additional tree-based hashing mechanism. Initially, we start by introducing an efficient GST construction in parallel that is scalable for a large genomic dataset. The secure indexing scheme allows the genomic data in a GST to be outsourced to an untrusted cloud server under encryption. Additionally, the proposed methods can perform several string search operations (i.e., exact, set-maximal matches) securely and efficiently using the outlined framework.
RESULTS
The experimental results on different datasets and parameters in a real cloud environment exhibit the scalability of these methods as they also outperform the state-of-the-art method based on Burrows-Wheeler Transformation (BWT). The proposed method only takes around 36.7s to execute a set-maximal match whereas the BWT-based method takes around 160.85s, providing a 4× speedup.
Topics: Cloud Computing; Computer Security; Genomics; Outsourced Services; Privacy
PubMed: 35715724
DOI: 10.1186/s12863-022-01053-x