Finding needles in haystacks:Linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201

Analysis of shared heritability in common disorders of the brain

ience, this issue p. eaap8757 Structured Abstract INTRODUCTION Brain disorders may exhibit shared symptoms and substantial epidemiological comorbidity, inciting debate about their etiologic overlap. However, detailed study of phenotypes with different ages of onset, severity, and presentation poses a considerable challenge. Recently developed heritability methods allow us to accurately measure correlation of genome-wide common variant risk between two phenotypes from pools of different individuals and assess how connected they, or at least their genetic risks, are on the genomic level. We used genome-wide association data for 265,218 patients and 784,643 control participants, as well as 17 phenotypes from a total of 1,191,588 individuals, to quantify the degree of overlap for genetic risk factors of 25 common brain disorders. RATIONALE Over the past century, the classification of brain disorders has evolved to reflect the medical and scientific communities' assessments of the presumed root causes of clinical phenomena such as behavioral change, loss of motor function, or alterations of consciousness. Directly observable phenomena (such as the presence of emboli, protein tangles, or unusual electrical activity patterns) generally define and separate neurological disorders from psychiatric disorders. Understanding the genetic underpinnings and categorical distinctions for brain disorders and related phenotypes may inform the search for their biological mechanisms. RESULTS Common variant risk for psychiatric disorders was shown to correlate significantly, especially among attention deficit hyperactivity disorder (ADHD), bipolar disorder, major depressive disorder (MDD), and schizophrenia. By contrast, neurological disorders appear more distinct from one another and from the psychiatric disorders, except for migraine, which was significantly correlated to ADHD, MDD, and Tourette syndrome. We demonstrate that, in the general population, the personality trait neuroticism is significantly correlated with almost every psychiatric disorder and migraine. We also identify significant genetic sharing between disorders and early life cognitive measures (e.g., years of education and college attainment) in the general population, demonstrating positive correlation with several psychiatric disorders (e.g., anorexia nervosa and bipolar disorder) and negative correlation with several neurological phenotypes (e.g., Alzheimer's disease and ischemic stroke), even though the latter are considered to result from specific processes that occur later in life. Extensive simulations were also performed to inform how statistical power, diagnostic misclassification, and phenotypic heterogeneity influence genetic correlations. CONCLUSION The high degree of genetic correlation among many of the psychiatric disorders adds further evidence that their current clinical boundaries do not reflect distinct underlying pathogenic processes, at least on the genetic level. This suggests a deeply interconnected nature for psychiatric disorders, in contrast to neurological disorders, and underscores the need to refine psychiatric diagnostics. Genetically informed analyses may provide important "scaffolding" to support such restructuring of psychiatric nosology, which likely requires incorporating many levels of information. By contrast, we find limited evidence for widespread common genetic risk sharing among neurological disorders or across neurological and psychiatric disorders. We show that both psychiatric and neurological disorders have robust correlations with cognitive and personality measures. Further study is needed to evaluate whether overlapping genetic contributions to psychiatric pathology may influence treatment choices. Ultimately, such developments may pave the way toward reduced heterogeneity and improved diagnosis and treatment of psychiatric disorders

Finding needles in haystacks : linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201

Unsteady conjugate mass and heat transfer from/to a prolate spheroidal droplet in uniaxial extensional creeping flow

The unsteady conjugate mass/heat transfer from/to a prolate droplet suspended in uniaxial extensional creeping flow was numerically investigated. Based on the Stokes velocity field of a prolate droplet at small Reynolds numbers, a numerical algorithm combined with the finite difference method, the concentration transformation method and the level set approach was adopted to solve the convection-diffusion transport equations. The effects of Peclet number (1 <= Pe <= 1000), capillary number (0 <= Ca <= 0.1), viscosity ratio (0.01 <= lambda <= 1), diffusivity ratio (0.1 <= K <= 10) and distribution coefficient (0.1 <= m <= 10) on interphase transport process were examined in terms of numerical simulation. The results show that the conjugate mass transfer from/to a single prolate droplet in the uniaxial extensional flow is significantly influenced by these five parameters, and the local and total mass transfer rates of a deformable droplet are slightly different from that of a spherical one. Given Pe, Ca, lambda, K and m, an empirical correlation with an average relative deviation of 12.01% was proposed to predict Sh(1.infinity) of the prolate and spherical droplets suspended in uniaxial extensional creeping flow. (C) 2019 Elsevier Ltd. All rights reserved

Internal mass and heat transfer between a single deformable droplet and simple extensional creeping flow

This work studied numerically the internal mass/heat transfer of a deformable droplet immersed in a simple extensional flow. The droplet would deform gradually from prolate spheroid to 'peanut' in uniaxial extensional flow, or from oblate spheriod to 'red-blood-cell' in biaxial extensional flow. Based on the analytical solution of Stokes flow over a deformable droplet, the convection-diffusion transport equation was numerically solved by the finite difference method. The results show that the heat/mass transfer behaviors of a deformable droplet were different when compared with that of a spherical one. The effects of Pe (1 <= Pe <= 10000), capillary number Ca (0 <= Ca <= 0.5), viscosity ratio lambda (0.01 <= lambda <= 100) and the extensional flow direction on the Sh and mean concentration were numerically investigated. It shows that the internal mass/heat transfer rate was always enhanced with the increased degree of drop deformation in the diffusion-dominated case in both uniaxial/biaxial extensional flows. However, in the convection-dominated case, the flow direction has opposite influence on transport rates of mass/heat transfer with different deformation rates. The stabilized mass transfer rate decreased for droplets with different deformation in the order: 'red-blood-cell' shaped droplet, oblate droplet, prolate droplet and 'peanut' shaped droplet. At last, we proposed the empirical correlations to predict the internal mass/heat transfer rate of a deformable droplet (by adding the parameter Ca to represent the deformation of a droplet) in simple extensional flow. (C) 2018 Elsevier Ltd. All rights reserved

Visual dynamical measurement of the solute-induced Marangoni effect of a growing drop with a PLIF method

We present a visualized measurement of the transient Marangoni effect occurring in interfacial mass transfer processes by using a planner laser-induced fluorescence (PLIF) technique. Since acidity increased remarkably and linearly the fluorescent intensity of Rhodamine B, the concentration distribution of acidic solute inside a drop was obtained by PLIF. Thus, based on the concentration contours of solute, we could probe into the bulk flow and occurrence of the Marangoni effect. The Marangoni effect has been known to be affected by the physical properties of the test system, initial solute concentration, the operating conditions and device configurations. With existence of neutralization reaction in the extraction system, the Marangoni effect was declined as for the acetic acid being consumed rapidly. Last, we found that the density effect of solute coupled with Marangoni effect, which further affected the distribution of solute and then influenced the location and evolution of Marangoni effect. (C) 2021 Elsevier Ltd. All rights reserved

Development of a UPLC-MS/MS Method for Simultaneous Determination of Six Flavonoids in Rat Plasma after Administration of Maydis stigma Extract and Its Application to a Comparative Pharmacokinetic Study in Normal and Diabetic Rats

Maydis stigma is an important medicine herb used in many parts of the world for treatment of diabetes mellitus, which main bioactive ingredients are flavonoids. This paper describes for the first time a study on the comparative pharmacokinetics of six active flavonoid ingredients of Maydis stigma in normal and diabetic rats orally administrated with the decoction. Therefore, an efficient and sensitive ultra high performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) method for the simultaneous determination of six anti-diabetic ingredients (cynaroside, quercetin, luteolin, isorhamnetin, rutin and formononetin) of Maydis stigma in rat plasma has been developed and validated in plasma samples, which showed good linearity over a wide concentration range (r2 &gt; 0.99), and gave a lower limit of quantification of 1.0 ng·mL−1 for the analytes. The intra- and interday assay variability was less than 15% for all analytes. The mean extraction recoveries and matrix effect of analytes and IS from rats plasma were all more than 85.0%. The stability results showed the measured concentration for six analytes at three QC levels deviated within 15.0%. The results indicated that significant differences in the pharmacokinetic parameters of the analytes were observed between the two groups of animals, whereby the absorptions of these analytes in the diabetic group were all significantly higher than those in the normal group, which provides an experimental basis for the role of Maydis stigma in anti-diabetic treatment

Unsteady conjugate mass transfer of a 2D deformable droplet in a modest extensional flow in across-slot

This work aims to investigate the unsteady conjugate interphase mass transfer between a stationary deformed drop and the modest extensional flow in a cross-intersected 2D channel. It is very difficult to accurately quantify the transient mass transfer rate of solute in such a geometry. Therefore, we established a mathematical model on the basic of the Stokes equation and solved it by the boundary element method, which could deal precisely with a two-phase flow system with a deformable interface; meanwhile, the convection-diffusion equation was solved by the finite difference method to calculate the unsteady conjugate interphase mass transfer. The simulation results showed that the mass transfer rate, analyzed and characterized in terms of mean concentration variation and Sherwood number Sh, was affected by capillary number Ca, Peclet number Pe, viscosity ratio lambda, interior-to-exterior diffusivity ratio K, distribution coefficient m, and wall effect factor W

STRATEGY 1: DISTRIBUTED MILITARY STRATEGY EXPERT SYSTEM ON A MICROCOMPUTER ETHERNET

This paper introduces the STRATEGY 1, a Distributed Military Strategy Expert System on the ETHERNET used in the requirement prediction for Chinese defense. It describes the system architecture, the methodology of distributed problem solving by multiple expert systems using LISP, PROLOG and Fuzzy, the communication among workstations and graphic display of results by AUTOCAD and AUTOLISP. At the 5th International Conference on Distributed Computing Systems in 1985, Prof. J. B. Dennis pointed out that by now all programs of the Artificial Intelligence could only run on a single computer, but they should run on a distributed system in the future. Recently some scientists said that the Second Generation Expert System would be a distributed expert system.