The Impact of Molecular Data in Fungal Systematics

2005 ◽  
pp. 33-67 ◽  
Author(s):  
P.D. Bridge ◽  
B.M. Spooner ◽  
P.J. Roberts
Keyword(s):  
Molecular Data ◽  
Fungal Systematics ◽  
The Impact

scholarly journals Examining Socioeconomic and Computational Aspects of Vaccine Pharmacovigilance

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Vasiliki Soldatou ◽  
Anastasios Soldatos ◽  
Theodoros Soldatos
Keyword(s):  
Adverse Event ◽  
Enrichment Analysis ◽  
Vaccine Safety ◽  
Molecular Data ◽  
Adverse Event Reporting ◽  
Computational Techniques ◽  
Behavioral Determinants ◽  
Clinical Patient ◽  
Adverse Event Data ◽  
The Impact

Background. Vaccine pharmacovigilance relates to the detection of adverse events, their assessment, understanding, and prevention, and communication of their risk to the public. These activities can be tedious and long lasting for regulatory authority scientists and may be affected by community practices and public health policies. To better understand underlying challenges, we examined vaccine adverse event reports, assessed whether data-driven techniques can provide additional insight in safety characterization, and wondered on the impact of socioeconomic parameters. Methods. First, we integrated VAERS content with additional sources of drug and molecular data and examined reaction and outcome occurrence by using disproportionality metrics and enrichment analysis. Second, we reviewed social and behavioral determinants that may affect vaccine pharmacovigilance aspects. Results. We describe our experience in processing more than 607000 vaccine adverse event reports and report on the challenges to integrate more than 95500 VAERS medication narratives with structured information about drugs and other therapeutics or supplements. We found that only 12.6% of events were serious, while 8.97% referred to polypharmacy cases. Exacerbation of serious clinical patient outcomes was observed in 8.88% VAERS cases in which drugs may interact with vaccinations or with each other, regardless of vaccine activity interference. Furthermore, we characterized the symptoms reported in those cases and summarized reaction occurrence among vaccine-types. Last, we examine socioeconomic parameters and cost-management features, explore adverse event reporting trends, and highlight perspectives relating to the use and development of digital services, especially in the context of personalized and collaborative health-care. Conclusions. This work provides an informative review of VAERS, identifies challenges and limitations in the processing of vaccine adverse event data, and calls for the better understanding of the socioeconomic landscape pertaining vaccine safety concerns. We expect that adoption of computational techniques for integrated safety assessment and interpretation is key not only to pharmacovigilance practice but also to stakeholders from the entire healthcare system.

scholarly journals OncoThreads: Visualization of Large Scale Longitudinal Cancer Molecular Data

2021 ◽  
Author(s):  
Theresa A Harbig ◽  
Sabrina Nusrat ◽  
Tali Mazor ◽  
Qianwen Wang ◽  
Alexander Thomson ◽  
...  
Keyword(s):  
Longitudinal Data ◽  
Large Scale ◽  
Cancer Genomics ◽  
Temporal Patterns ◽  
Molecular Data ◽  
Liquid Biopsies ◽  
Sequencing Technologies ◽  
Molecular Features ◽  
Wide Range ◽  
The Impact

Molecular profiling of patient tumors and liquid biopsies over time with next-generation sequencing technologies and new immuno-profile assays are becoming part of standard research and clinical practice. With the wealth of new longitudinal data, there is a critical need for visualizations for cancer researchers to explore and interpret temporal patterns not just in a single patient but across cohorts. To address this need we developed OncoThreads, a tool for the visualization of longitudinal clinical and cancer genomics and other molecular data in patient cohorts. The tool visualizes patient cohorts as temporal heatmaps and Sankey diagrams that support the interactive exploration and ranking of a wide range of clinical and molecular features. This allows analysts to discover temporal patterns in longitudinal data, such as the impact of mutations on response to a treatment, e.g. emergence of resistant clones. We demonstrate the functionality of OncoThreads using a cohort of 23 glioma patients sampled at 2-4 timepoints. OncoThreads is freely available at http://oncothreads.gehlenborglab.org and implemented in Javascript using the cBioPortal web API as a backend.

scholarly journals The dawn of phylogenetic research on Neotropical fishes: a commentary and introduction to Baskin (1973), with an overview of past progress on trichomycterid phylogenetics

2016 ◽  
Vol 14 (2) ◽  
Author(s):  
Mário C. C. de Pinna
Keyword(s):  
Quantitative Analysis ◽  
Molecular Data ◽  
Neotropical Fishes ◽  
Phylogenetic Methods ◽  
The Family ◽  
The Impact

ABSTRACT A review is made of the impact of the landmark Ph. D. Thesis of Jonathan N. Baskin from 1973 on the development of the phylogenetics of catfishes and some of its main subgroups and on neotropical ichthyology in general. Baskin's work is the first to propose a hypothesis of relationships for loricarioid catfishes and for the family Trichomycteridae on the basis of explicit Hennigian principles. It is arguably also the first application of phylogenetic methods to any group of neotropical fishes. The hypotheses presented by Baskin covered the monophyly of Siluriformes, the monophyly and relationships of loricarioid families and the relationships of Trichomycteridae (including the monophyly of the family and the relationships among its constituent genera). His discoveries are analyzed in view of the subsequent 40-odd years of progress on the understanding of the phylogeny of the respective groups. The ideas proposed in 1973 have resisted the test of time remarkably well, and a majority of them have been corroborated by additional characters and taxa (including molecular data and several taxa newly discovered in the meantime), as well as by modern quantitative analysis.

The Impact of Molecular Data on Our Understanding of Bee Phylogeny and Evolution

2013 ◽  
Vol 58 (1) ◽  
pp. 57-78 ◽  
Author(s):  
Bryan N. Danforth ◽  
Sophie Cardinal ◽  
Christophe Praz ◽  
Eduardo A.B. Almeida ◽  
Denis Michez
Keyword(s):  
Molecular Data ◽  
Phylogeny And Evolution ◽  
The Impact

Primary (1°) tumor location as an independent prognostic marker from molecular features for overall survival (OS) in patients (pts) with metastatic colorectal cancer (mCRC): Analysis of CALGB / SWOG 80405 (Alliance).

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 3503-3503 ◽  
Author(s):  
Alan P. Venook ◽  
Fang-Shu Ou ◽  
Heinz-Josef Lenz ◽  
Omar Kabbarah ◽  
Xueping Qu ◽  
...  
Keyword(s):  
Prognostic Marker ◽  
Molecular Subtype ◽  
Progression Free Survival ◽  
Molecular Data ◽  
Tumor Location ◽  
Tumor Burden ◽  
Independent Prognostic Marker ◽  
Molecular Features ◽  
Metastatic Sites ◽  
The Impact

3503 Background: 80405 found no OS or Progression Free Survival (PFS) difference when bevacizumab (BV) or cetuximab (Cet) was added to 1st-line FOLFOX or FOLFIRI in All RAS wild type (wt) mCRC pts. There was a significant 1° side by biologic interaction (P int: OS = 0.008, PFS = 0.001) favoring pts with left-sided (L) 1°. Analyses of 1° tumors beyond All RAS includes Consensus Molecular Subtype (CMS), BRAF and MSI. (CMS results - see Lenz et al; BRAF -see Innocenti et al) We asked whether 1° tumor location - L vs right (R) - is an independent prognostic marker when these other molecular features are considered. Methods: We used a Cox proportional hazard model stratified by prior XRT and +/- adjuvant chemo; adjusted for age, gender, synchronous vs metachronous, CMS, MSI and BRAF status. Pts with transverse (T) tumors were excluded in this analysis. Results: Sidedness was determined in 782 pts (L - 472; R - 256; T -54). Molecular data from 728 pts (with L - and R-sided 1°s) was available as follows: KRAS -- 291, NRAS -393, BRAF - 393, MSI - 378, CMS - 533. L vs R mOS: 32.9 v 19.6 months (mo) (p < 0.0001). See Table for OS results in All RAS / BRAF wt and BRAF mutant (mut) pts. Sidedness (R vs L) is an independent prognostic marker even after adjusting for all these molecular features: HR = 1.392 (1.032, 1.878), p = 0.031. Conclusions: Primary tumor location is an independent prognostic factor when adjusted for age, gender, synchronous/metachronous, CMS, MSI and BRAF status. We are exploring clinical variables such as tumor burden, metastatic sites and measurability of disease in an attempt to explain the impact of sidedness. Support: U10CA188021, U10CA180882. Eli Lilly and Co, Genentech/Roche, Pfizer, Sanofi. Clinical trial information: NCT002655850. [Table: see text]

Pre-transplant molecular minimal residual disease (MMRD) is associated with inferior outcomes in patients with acute myeloid leukemia undergoing allogeneic stem cell transplantation.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 7547-7547
Author(s):  
Muhammad Husnain ◽  
Krishna Komanduri ◽  
Jeremy Ramdial ◽  
Lazaros J. Lekakis ◽  
Trent Peng Wang ◽  
...  
Keyword(s):  
Stem Cell ◽  
Minimal Residual Disease ◽  
Residual Disease ◽  
Molecular Data ◽  
Cell Transplant ◽  
Post Transplant ◽  
Transplant Outcomes ◽  
Risk Patients ◽  
The Impact ◽  
Minimal Residual

7547 Background: Allogeneic Stem Cell Transplant (alloSCT) continues to be the optimal consolidation strategy for many patients with AML; cytogenetic and molecular abnormalities are known predictors of post-transplant outcomes. There is increasing evidence that Molecular Minimal Residual Disease (MMRD) following induction has important prognostic implications and its value in the prediction of post-transplant relapse continues to be elucidated. We aim to evaluate the impact of genetics and pre-transplant MMRD on clinical outcomes following alloSCT. Methods: We retrospectively evaluated eighty-nine patients, ≥18 years with a diagnosis of AML in complete morphologic remission (i.e. < 5% BM blasts by morphologic assessment) who received alloSCT between 01/2012-05/2018 at the University of Miami and for whom cytogenetic and comprehensive molecular data was available prior to transplantation. Patients were stratified into favorable, intermediate and poor-risk categories based on 2017 ELN criteria. MMRD was defined as persistent leukemia-specific mutations prior to transplantation (i.e. NPM1, FLT3, CEBPA, IDH1-2, RUNX1 and TP53). Persistence of DTA mutations (DNMT3A, TET2 and ASXL1) was not considered MMRD, patients with unavailable cytogenetic/molecular data at diagnosis were excluded. Results: Seventy-four (83%) patients were transplanted in CR1, myeloablative conditioning was used in 72% of patients. Two-year OS and LFS were 69.4% and 78.2%, respectively. Stratification by ELN criteria resulted in prognostic separation for patients transplanted in CR1: 2-year OS for favorable (87%), intermediate (68%) and adverse risk (51%) patients (p = 0.0417). The presence of MMRD was the strongest predictor of post-transplant outcomes for the whole cohort with 2-year OS and LFS of 29.4% and 37.1% (HR 5.45 [95%CI 2.43-12.3] p = 0.0001; HR 12.4 [95%CI: 3.76 to 39.8] p = 0.0001); respectively. Subgroup analysis confirmed that MMRD was associated with significantly inferior LFS for IM/favorable and adverse risk patients (HR: 6.76 [95% CI 1.12 to 40.9], p = 0.038). Conclusions: Pre-transplant MMRD was the most important prognostic factor for relapse and survival in our cohort of AML patients undergoing alloSCT. Correlation of MMRD with other transplant variables such as conditioning intensity, MRD status by MFC and the impact of pre-emptive/therapeutic strategies in high-risk patients continues to be explored.

scholarly journals Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

2016 ◽  
Vol 12 (5) ◽  
pp. 20151003 ◽  
Author(s):  
Thomas Guillerme ◽  
Natalie Cooper
Keyword(s):  
Data Collection ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Living Species ◽  
Anatomical Characters ◽  
The Impact

Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies.

The impact of multiple molecular and morphological data sets on the phylogenetic reconstruction of subtribe Neurachninae (Poaceae: Panicoideae: Paniceae)

2021 ◽  
Author(s):  
E. J. Thompson ◽  
Melodina Fabillo
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Plastid Markers ◽  
Morphological And Molecular Data ◽  
The Impact ◽  
Selection Of

The taxonomy of Neurachninane has been unstable, with its member genera consisting of Ancistrachne, Calyptochloa, Cleistochloa, Dimorphochloa, Neurachne, Paraneurachne and Thyridolepis, changing since its original circumscription that comprised only the latter three genera. Recent studies on the phylogeny of Neurachninae have focused primarily on molecular data. We analysed the phylogeny of Neurachninae on the basis of molecular data from seven molecular loci (plastid markers: matK, ndhF, rbcL, rpl16, rpoC2 and trnLF, and ribosomal internal transcribed spacer, ITS) and morphological data from 104 morphological characters, including new taxonomically informative micromorphology of upper paleas. We devised an impact assessment scoring (IAS) protocol to aid selection of a tree for inferring the phylogeny of Neurachninae. Combining morphological and molecular data resulted in a well resolved phylogeny with the highest IAS value. Our findings support reinstatement of subtribe Neurachninae in its original sense, Neurachne muelleri and Dimorphochloa rigida. We show that Ancistrachne, Cleistochloa and Dimorphochloa are not monophyletic and Ancistrachne maidenii, Calyptochloa, Cleistochloa and Dimorphochloa form a new group, the cleistogamy group, united by having unique morphology associated with reproductive dimorphism.

scholarly journals Gut health, stress, and immunity in neonatal dairy calves: the host side of host-pathogen interactions

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Johan. S. Osorio
Keyword(s):  
Bioactive Compounds ◽  
Late Pregnancy ◽  
Nutrient Content ◽  
Molecular Data ◽  
Recent Change ◽  
Future Research ◽  
Gut Health ◽  
Farm Level ◽  
Host Pathogen ◽  
The Impact

Abstract The cumulative evidence that perinatal events have long-lasting ripple effects through the life of livestock animals should impact future nutritional and management recommendations at the farm level. The implications of fetal programming due to malnutrition, including neonatal survival and lower birth weights, have been characterized, particularly during early and mid-gestation, when placental and early fetal stages are being developed. The accelerated fetal growth during late pregnancy has been known for some time, while the impact of maternal stressors during this time on fetal development and by extent its postnatal repercussions on health and performance are still being defined. Maternal stressors during late pregnancy cannot only influence colostrogenesis but also compromise adequate intestinal development in the fetus, thus, that further limits the newborn’s ability to absorb nutrients, bioactive compounds, and immunity (i.e., immunoglobulins, cytokines, and immune cells) from colostrum. These negative effects set the newborn calf to a challenging start in life by compromising passive immunity and intestinal maturation needed to establish a mature postnatal mucosal immune system while needing to digest and absorb nutrients in milk or milk replacer. Besides the dense-nutrient content and immunity in colostrum, it contains bioactive compounds such as growth factors, hormones, and cholesterol as well as molecular signals or instructions [e.g., microRNAs (miRNAs) and long non-coding RNAs (lncRNAs)] transferred from mother to offspring with the aim to influence postnatal gut maturation. The recent change in paradigm regarding prenatal materno-fetal microbiota inoculation and likely the presence of microbiota in the developing fetus intestine needs to be addressed in future research in ruminants. There still much to know on what prenatal or postnatal factors may predispose neonates to become susceptible to enteropathogens (e.g., enterotoxigenic Escherichia coli), causing diarrhea. From the host-side of this host-pathogen interaction, molecular data such as fecal RNA could, over time, help fill those gaps in knowledge. In addition, merging this novel fecal RNA approach with more established microbiome techniques can provide a more holistic picture of an enteropathogenesis and potentially uncover control points that can be addressed through management or nutrition at the farm level to minimize preweaning morbidity and mortality.

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