234 research outputs found
dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture
Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within the reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of amplified sequence tags) by providing user-friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities.
Here, we present Version 2 of dartR. In this version, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting.
dartR provides many functions for importing, exporting and linking to other packages, to provide an easy-to-navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions.
As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice
Cluster expansion in the canonical ensemble
We consider a system of particles confined in a box \La\subset\R^d
interacting via a tempered and stable pair potential. We prove the validity of
the cluster expansion for the canonical partition function in the high
temperature - low density regime. The convergence is uniform in the volume and
in the thermodynamic limit it reproduces Mayer's virial expansion providing an
alternative and more direct derivation which avoids the deep combinatorial
issues present in the original proof
Langevin Equation for the Rayleigh model with finite-ranged interactions
Both linear and nonlinear Langevin equations are derived directly from the
Liouville equation for an exactly solvable model consisting of a Brownian
particle of mass interacting with ideal gas molecules of mass via a
quadratic repulsive potential. Explicit microscopic expressions for all kinetic
coefficients appearing in these equations are presented. It is shown that the
range of applicability of the Langevin equation, as well as statistical
properties of random force, may depend not only on the mass ratio but
also by the parameter , involving the average number of molecules in
the interaction zone around the particle. For the case of a short-ranged
potential, when , analysis of the Langevin equations yields previously
obtained results for a hard-wall potential in which only binary collisions are
considered. For the finite-ranged potential, when multiple collisions are
important (), the model describes nontrivial dynamics on time scales
that are on the order of the collision time, a regime that is usually beyond
the scope of more phenomenological models.Comment: 21 pages, 1 figure. To appear in Phys. Rev.
Phase transitions in the spinless Falicov-Kimball model with correlated hopping
The canonical Monte-Carlo is used to study the phase transitions from the
low-temperature ordered phase to the high-temperature disordered phase in the
two-dimensional Falicov-Kimball model with correlated hopping. As the
low-temperature ordered phase we consider the chessboard phase, the axial
striped phase and the segregated phase. It is shown that all three phases
persist also at finite temperatures (up to the critical temperature )
and that the phase transition at the critical point is of the first order for
the chessboard and axial striped phase and of the second order for the
segregated phase. In addition, it is found that the critical temperature is
reduced with the increasing amplitude of correlated hopping in the
chessboard phase and it is strongly enhanced by in the axial striped and
segregated phase.Comment: 17 pages, 6 figure
Sensoriamento remoto e geologia na região de Bojuru, porção média da planície costeira do RS, Brasil
Using the Wigner-Ibach Surmise to Analyze Terrace-Width Distributions: History, User's Guide, and Advances
A history is given of the applications of the simple expression generalized
from the surmise by Wigner and also by Ibach to extract the strength of the
interaction between steps on a vicinal surface, via the terrace width
distribution (TWD). A concise guide for use with experiments and a summary of
some recent extensions are provided.Comment: 11 pages, 4 figures, reformatted (with revtex) version of refereed
paper for special issue of Applied Physics A entitled "From Surface Science
to Device Physics", in honor of the retirements of Prof. H. Ibach and Prof.
H. L\"ut
Guest Charge and Potential Fluctuations in Two-Dimensional Classical Coulomb Systems
A known generalization of the Stillinger-Lovett sum rule for a guest charge
immersed in a two-dimensional one-component plasma (the second moment of the
screening cloud around this guest charge) is more simply retrieved, just by
using the BGY hierarchy for a mixture of several species; the zeroth moment of
the excess density around a guest charge immersed in a two-component plasma is
also obtained. The moments of the electric potential are related to the excess
chemical potential of a guest charge; explicit results are obtained in several
special cases.Comment: 21 pages. Latex. Appendix moved, with changes, to new subsection 2.3.
Description of the Appendix at the end of the Introduction, from an earlier
version, delete
Reply to Elmendorf and Ettinger: Photoperiod playsa dominantand irreplaceable role in triggering secondary growth resumption
In their Letter, Elmendorf and Ettinger (1) question the dominant role of photoperiod in driving secondary growth resumption (hereafter referred to as xylem formation onset) of the Northern Hemisphere conifers, recently reported by Huang et al. (2). Their opinions are grounded on the following three aspects, including 1) the seasonality of the photoperiod, 2) the dependence of the predictor variables (e.g., photoperiod, forcing, and chilling) on the response variable (the date of onset of xylem formation, day of the year [DOY]), and 3) the limited value of the obtained models for interannual forecasting. We think they bring up an interesting issue that deserves further discussion and clarification.
Photoperiod is acknowledged to regulate spring bud swelling while wood formation starts (3, 4). Although photoperiod seasonality occurs at each site, its influence is marginal in our study given that the analysis involved comparisons among sites across the Northern Hemisphere. Our conclusion that photoperiod plays a dominant role was built upon the combination of several coherent pieces of evidence, rather than “the crux of Huang et al….” as they pointed out. First, we clearly stated that model 2, which modeled DOY as a function of the mean annual temperature of the site (MAT), forcing, chilling, and soil moisture, was considered the best model in terms of parsimony according to minimum Akaike information criterion and Bayesian information criterion, rather than R2 as referred to in their Letter. Second, photoperiod interacted with MAT and can explain 61.7% of the variance of MAT alone (2). Therefore, we concluded that secondary growth resumption was driven primarily by MAT and photoperiod or by their interaction, which is challenging to be disentangled without experimental data, we agree. In terms of biological functioning, they play an ..
Development of a versatile laboratory experiment to teach the metabolic transformation of hydrolysis
In this paper we describe an easy, reliable, versatile and inexpensive laboratory experiment to teach the metabolic transformation of hydrolysis to Pharmacy students. The experiment does not require the sacrifice of any experimental animal, or any work with organs or tissues, and so can be implemented in a typical university chemistry laboratory. We used acetylsalicylic acid (ASA), hexyl salicylate (HS) and two enzymes, a lipase and an esterase. Since both ASS and HS liberate salicylic acid (SA) upon hydrolysis, students can evaluate the different enzymatic transformations by monitoring the amount of SA liberated. The learning outcomes are an enhanced student understanding of: (1) the process of hydrolysis; (2) the application of enzymatic transformations of molecules from food to xenobiotics; (3) the differences between the general specificity of substrate of both enzymes; (4) the concepts of the lipophilic pocket; (5) the catalytic triad and its regioselectivity in relation to the ester bond. A questionnaire was administered to participating students at three points in time: at the beginning of the module, after enzymatic hydrolysis was taught in class, and after the laboratory experiment. From an analysis of the questionnaire data we conclude that this practical helped Pharmacy students to understand these concepts
Germline MBD4-deficiency causes a multi-tumor predisposition syndrome
We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5′-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management
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