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Molecular classification

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https://www.readbyqxmd.com/read/30557098/minimalist-barcodes-for-sponges-a-case-study-classifying-african-freshwater-spongillida
#1
Dirk Erpenbeck, Markus Steiner, Astrid Schuster, Martin J Genner, Renata Manconi, Roberto Pronzato, Bernhard Ruthensteiner, Didier Van den Spiegel, Rob Wm van Soest, Gert Wörheide
African sponges, particularly freshwater sponges, are understudied relative to demosponges in most other geographical regions. Freshwater sponges (Spongillida) likely share a common ancestor; however, their evolutionary history, particularly during their radiation into endemic and allegedly cosmopolitan groups, is unclear. Freshwater sponges of at least 58 species of 17 genera and four families are described from Central and Eastern Africa, but the diversity is underestimated due to limited distinguishable morphological features...
December 17, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30556015/classification-of-hiv-1-protease-inhibitors-by-machine-learning-methods
#2
Yang Li, Yujia Tian, Zijian Qin, Aixia Yan
HIV-1 protease plays an important role in the processing of virus infection. Protease is an effective therapeutic target for the treatment of HIV-1. Our data set is based on a selection of 4855 HIV-1 protease inhibitors (PIs) from ChEMBL. A series of 15 classification models for predicting the active inhibitors were built by machine learning methods, including k -nearest neighors (K-NN), decision tree (DT), random forest (RF), support vector machine (SVM), and deep neural network (DNN). The molecular structures were characterized by (1) fingerprint descriptors including MACCS fingerprints and PubChem fingerprints and (2) physicochemical descriptors calculated by CORINA Symphony...
November 30, 2018: ACS Omega
https://www.readbyqxmd.com/read/30555750/design-and-clinical-validation-of-a-point-of-care-device-for-the-diagnosis-of-lymphoma-via-contrast-enhanced-microholography-and-machine-learning
#3
Hyungsoon Im, Divya Pathania, Philip J McFarland, Aliyah R Sohani, Ismail Degani, Matthew Allen, Benjamin Coble, Aoife Kilcoyne, Seonki Hong, Lucas Rohrer, Jeremy S Abramson, Scott Dryden-Peterson, Lioubov Fexon, Mikhail Pivovarov, Bruce Chabner, Hakho Lee, Cesar M Castro, Ralph Weissleder
The identification of patients with aggressive cancer who require immediate therapy is a health challenge in low-income and middle-income countries. Limited pathology resources, high healthcare costs and large-case loads call for the development of advanced standalone diagnostics. Here, we report and validate an automated, low-cost point-of-care device for the molecular diagnosis of aggressive lymphomas. The device uses contrast-enhanced microholography and a deep-learning algorithm to directly analyse percutaneously obtained fine-needle aspirates...
September 2018: Nature Biomedical Engineering
https://www.readbyqxmd.com/read/30555413/sex-related-differences-in-lactotroph-tumor-aggressiveness-are-associated-with-a-specific-gene-expression-signature-and-genome-instability
#4
Anne Wierinckx, Etienne Delgrange, Philippe Bertolino, Patrick François, Philippe Chanson, Emmanuel Jouanneau, Joël Lachuer, Jacqueline Trouillas, Gérald Raverot
Sex-related differences have been reported in various cancers, in particular men with lactotroph tumors have a worse prognosis than women. While the underlying mechanism of this sexual dimorphism remains unclear, it has been suggested that a lower estrogen receptor alpha expression may drive the sex differences observed in aggressive and malignant lactotroph tumors that are resistant to dopamine agonists. Based on this observation, we aimed to explore the molecular importance of the estrogen pathway through a detailed analysis of the transcriptomic profile of lactotroph tumors from 20 men and 10 women...
2018: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/30553171/molecular-alterations-in-meningiomas-literature-review
#5
REVIEW
Benedito Jamilson Araújo Pereira, Sueli Mieko Oba-Shinjo, Antônio Nogueira de Almeida, Suely Kazue Nagahashi Marie
Meningiomas, tumors that originate from meningothelial cells, account for approximately 30% of all new diagnoses of central nervous system neoplasms. According to the 2016 WHO classification of central nervous system tumors meningiomas are classified into three grades: I, II, and III. Past studies have shown that the risk of meningiomas recurrence is strongly correlated with the molecular profile of the tumor. Extensive whole-exome or whole-genome sequencing has provided a large body of information about the mutational landscape of meningiomas...
December 7, 2018: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/30552739/a-molecular-approach-combined-with-american-thyroid-association-classification-better-stratifies-recurrence-risk-of-classic-histology-papillary-thyroid-cancer
#6
Alexander J Lin, Pamela Samson, Todd DeWees, Lauren Henke, Thomas Baranski, Julie Schwarz, John Pfeifer, Perry Grigsby, Stephanie Markovina
BACKGROUND: Prognosis among patients with differentiated thyroid cancer is widely variable. Better understanding of biologic subtypes is necessary to stratify patients and improve outcomes. METHODS: In patients diagnosed with classic histology papillary thyroid cancer treated from 1973 to 2009, BRAF V600E mutation status was determined on surgical tumor specimens by restriction fragment length polymorphism analysis. A tissue microarray (TMA) was constructed from tumor specimens in triplicate and stained by immunohistochemistry for RET, phospho-MEK, MAPK(dpERK), PPARγ, and phospho-AKT(pAKT)...
December 14, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/30552188/molecular-identification-of-enteroviruses-from-cattle-and-goat-feces-and-environment-in-thailand
#7
Nicharee Income, Nathamon Kosoltanapiwat, Sarawut Taksinoros, Pornsawan Leaungwutiwong, Pannamas Maneekan, Irwin Fernandez Chavez
The identification and characterization of the viruses of the genus Enterovirus in healthy and infected livestock, including cattle and goats, have been increasing. Enterovirus E (EV-E) and F (EV-F) are commonly found in cattle, whereas Enterovirus G (EV-G) is found in goats. In this study, molecular and phylogenetic analyses were performed to determine the prevalence of EVs in cattle and goat feces from the Kanchanaburi Province, Thailand. The presence of EVs in water samples and feces of other animals collected from the areas surrounding cattle and goat farms was also investigated...
December 14, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/30551862/molecular-pathways-in-the-development-and-treatment-of-oesophageal-cancer
#8
REVIEW
Robert Charles Walker, Timothy James Underwood
The molecular pathways involved in the development and treatment of oesophageal cancer are complex. Recent large-scale genome sequencing studies have delivered novel insights into aetiology and possible targeted treatments. Oesophageal squamous cell carcinoma (OSCC) and adenocarcinoma (OAC) are distinct entities. At the molecular level OSCC is more similar to squamous cell cancers in other organs than OAC. Whilst considerable heterogeneity exists in both tumour types new data suggests that driver gene events and mutational signatures may be able to categorise tumours into potentially actionable subtypes...
October 2018: Best Practice & Research. Clinical Gastroenterology
https://www.readbyqxmd.com/read/30550977/three-monophyletic-clusters-in-retortamonas-species-isolated-from-vertebrates
#9
Joko Hendarto, Tetsushi Mizuno, Anggi P N Hidayati, Ismail E Rozi, Puji B S Asih, Din Syafruddin, Hisao Yoshikawa, Makoto Matsubayashi, Masaharu Tokoro
Retortamonas spp. has been reported as an intestinal parasite among various host organisms, including humans; however, its intra-genus molecular diversity has not yet been elucidated. Haplotypes of the 18S small subunit ribosomal RNA locus (1836-1899 bp) of Retortamonas spp. from humans (n = 8), pigs (n = 6), dogs (n = 1), goats (n = 16), water buffalos (n = 23), cattle (n = 7), rats (n = 3), and chickens (n = 5) were analyzed with references isolated from non-human mammals, amphibians, and insects...
December 11, 2018: Parasitology International
https://www.readbyqxmd.com/read/30550486/pathologic-prognostic-factors-in-endometrial-carcinoma-other-than-tumor-type-and-grade
#10
Naveena Singh, Lynn Hirschowitz, Richard Zaino, Isabel Alvarado-Cabrero, Maire A Duggan, Rouba Ali-Fehmi, Elizabeth Euscher, Jonathan L Hecht, Lars-Christian Horn, Olga Ioffe, Xavier Matias-Guiu, W Glenn McCluggage, Yoshiki Mikami, Jaume Ordi, Vinita Parkash, M Ruhul Quddus, Charles M Quick, Annette Staebler, Charles Zaloudek, Marisa Nucci, Anais Malpica, Esther Oliva
Although endometrial carcinoma (EC) is generally considered to have a good prognosis, over 20% of women with EC die of their disease, with a projected increase in both incidence and mortality over the next few decades. The aim of accurate prognostication is to ensure that patients receive optimal treatment and are neither overtreated nor undertreated, thereby improving patient outcomes overall. Patients with EC can be categorized into prognostic risk groups based on clinicopathologic findings. Other than tumor type and grade, groupings and recommended management algorithms may take into account age, body mass index, stage, and presence of lymphovascular space invasion...
January 2019: International Journal of Gynecological Pathology
https://www.readbyqxmd.com/read/30550227/-aspergillus-penicillioides-speg-implicated-in-keratomycosis
#11
Eulalia Machowicz-Matejko, Agnieszka Furmańczyk, Ewa Dorota Zalewska
The aim of the study was mycological examination of ulcerated corneal tissues from an ophthalmic patient. Tissue fragments were analyzed on potato-glucose agar (PDA) and maltose (MA) (Difco) media using standard laboratory techniques. Cultures were identified using classical and molecular methods. Macro- and microscopic colony morphology was characteristic of fungi from the genus Aspergillus (restricted growth series), most probably Aspergillus penicillioides Speg. Molecular analysis of the following rDNA regions: ITS1, ITS2, 5...
2018: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/30549365/quantitative-multi-locus-metabarcoding-and-waggle-dance-interpretation-reveal-honey-bee-spring-foraging-patterns-in-midwest-agroecosystems
#12
Rodney T Richardson, Hailey R Curtis, Emma G Matcham, Chia Hua Lin, Sreelakshmi Suresh, Douglas B Sponsler, Luke E Hearon, Reed M Johnson
We explored the pollen foraging behavior of honey bee colonies situated in the corn and soybean dominated agroecosystems of central Ohio over a month-long period using both pollen metabarcoding and waggle dance inference of spatial foraging patterns. For molecular pollen analysis we developed simple and cost-effective laboratory and bioinformatics methods. Targeting four plant barcode loci (ITS2, rbcL, trnL and trnH), we implemented metabarcoding library preparation and dual-indexing protocols designed to minimize amplification biases and index mis-tagging events...
December 14, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30549186/the-current-role-of-clinical-flow-cytometry-in-the-evaluation-of-mature-b-cell-neoplasms
#13
REVIEW
Adam C Seegmiller, Eric D Hsi, Fiona E Craig
Flow cytometry (FC) has a well-established role in the diagnostic evaluation of mature B-cell neoplasms. Effective assessment for lineage associated antigens, aberrant antigen expression, and immunoglobulin light chain restriction requires a well-designed, optimized, and controlled FC assay. However, it is important for hematopathologists to know when flow cytometry has a more limited role, and other modalities, such as immunohistochemistry, cytogenetic and molecular testing, are more important. This review will discuss the features of an optimal FC assay for the evaluation of mature B-cell neoplasms, and the current role of FC in the diagnosis and sub-classification, prognostic assessment, identification of therapeutic targets, and assessment for disease response to therapy...
December 13, 2018: Cytometry. Part B, Clinical Cytometry
https://www.readbyqxmd.com/read/30548619/tissue-based-transcriptomics-of-chionodraco-hamatus-sequencing-de-novo-assembly-annotation-and-marker-discovery
#14
Wei Song, Lingzhi Li, Hongliang Huang, Keji Jiang, Fengying Zhang, Luming Wang, Ming Zhao, Lingbo Ma
Here, we explored the liver, heart and muscle tissue transcriptome of the haemoglobinless Antarctic fish Chionodraco hamatus using the Illumina paired-end RNA sequencing. A total of 114,028 unigenes with a mean length of 794.24 bp was produced. Annotation of these unigenes showed that 29.16% and 35.52% of them had hits in the nucleotide (Nt) and protein (Nr) databases, respectively. In addition, 29.10% and 35.28% unigenes were annotated in the SwissProt and TrEMBL databases while 23.27% and 21.08% of unigenes were annotated in the conserved domain (CCD) and protein family (PFAM) databases, respectively...
December 13, 2018: Journal of Fish Biology
https://www.readbyqxmd.com/read/30546439/significance-of-the-epidermal-growth-factor-receptor-mutation-status-and-differences-among-molecular-subgroups-in-surgically-resected-lung-microinvasive-adenocarcinoma
#15
Ming Li, Chuanying Li, Li Ke, Mali Zhan, Min Cheng
Lung microinvasive adenocarcinoma (MIA) is a newly-defined subtype of early stage non-small cell lung cancer (NSCLC). However, its epidermal growth factor receptor (EGFR) mutation status and clinical significance remain unclear. The present study aimed to determine EGFR mutation characteristics and identify their significance in patients with resected lung MIA. The present study also analyzed clinicopathological differences between EGFR molecular subgroups defined as 19Del and L858R. The present study examined EGFR mutations in 79 consecutive lung MIA resection specimens and compared the differences in clinicopathological features between the EGFR wild-type and mutation groups, as well as between the 19Del and L858R subgroups...
December 2018: Oncology Letters
https://www.readbyqxmd.com/read/30545973/genetics-and-genomics-of-pulmonary-arterial-hypertension
#16
Nicholas W Morrell, Micheala A Aldred, Wendy K Chung, C Gregory Elliott, William C Nichols, Florent Soubrier, Richard C Trembath, James E Loyd
Since 2000 there have been major advances in our understanding of the genetic and genomics of pulmonary arterial hypertension (PAH), although there remains much to discover. Based on existing knowledge, around 25-30% of patients diagnosed with idiopathic PAH have an underlying Mendelian genetic cause for their condition and should be classified as heritable PAH (HPAH). Here, we summarise the known genetic and genomic drivers of PAH, the insights these provide into pathobiology, and the opportunities afforded for development of novel therapeutic approaches...
December 13, 2018: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/30545284/a-phylogenomic-resolution-of-the-sea-urchin-tree-of-life
#17
Nicolás Mongiardino Koch, Simon E Coppard, Harilaos A Lessios, Derek E G Briggs, Rich Mooi, Greg W Rouse
BACKGROUND: Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes...
December 13, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/30544742/rhabdomyosarcoma-and-extraosseous-ewing-sarcoma
#18
Juan P Gurria, Roshni Dasgupta
Rhabdomyosarcoma (RMS) is a malignant tumor that represents the most common form of pediatric soft tissue sarcoma. It arises from mesenchymal origin and forms part of the group of small round blue cell tumors of childhood. It has a constant annual incidence of 4.5 cases per 1,000,000 children. The known histological diagnosis of the two major subtypes (embryonal and alveolar) has been recently enhanced by tumor biological markers and molecular differentiation diagnostic tools that have improved not only the updated classification based on risk stratification, but also the treatment approach based on the clinical group...
December 10, 2018: Children
https://www.readbyqxmd.com/read/30544720/the-primary-causes-of-muscle-dysfunction-associated-with-the-point-mutations-in-tpm3-12-conformational-analysis-of-mutant-proteins-as-a-tool-for-classification-of-myopathies
#19
Yurii S Borovikov, Olga E Karpicheva, Armen O Simonyan, Stanislava V Avrova, Elena A Rogozovets, Vladimir V Sirenko, Charles S Redwood
Point mutations in genes encoding isoforms of skeletal muscle tropomyosin may cause nemaline myopathy, cap myopathy (Cap), congenital fiber-type disproportion (CFTD), and distal arthrogryposis. The molecular mechanisms of muscle dysfunction in these diseases remain unclear. We studied the effect of the E173A, R90P, E150A, and A155T myopathy-causing substitutions in γ-tropomyosin (Tpm3.12) on the position of tropomyosin in thin filaments, and the conformational state of actin monomers and myosin heads at different stages of the ATPase cycle using polarized fluorescence microscopy...
December 10, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/30542256/electrophysiological-profiling-of-neocortical-neural-subtypes-a-semi-supervised-method-applied-to-in-vivo-whole-cell-patch-clamp-data
#20
Parviz Ghaderi, Hamid Reza Marateb, Mir-Shahram Safari
A lot of efforts have been made to understand the structure and function of neocortical circuits. In fact, a promising way to understand the functions of cortical circuits is the classification of the neural types, based on their different properties. Recent studies focused on applying modern computational methods to classify neurons based on molecular, morphological, physiological, or mixed of these criteria. Although there are studies in the literature on in vitro /vivo extracellular or in vitro intracellular recordings, a study on the classification of neuronal types using in vivo whole-cell patch-clamp recordings is still lacking...
2018: Frontiers in Neuroscience
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