Miracle-dz/UniFAR-FTUs huggingface dataset:
AVES POLYOMAVIRUS 1 IN ARA CHLOROPTERA AND ECLECTUS RORATUS WITH DISCLOSURE OF FULL GENOMIC SEQUENCES

Abstract Aves polyomavirus 1 (APyV) is the causative agent of acute disease in birds and causes high mortality rates in nestlings. Infections have been reported worldwide in a significant number of caged bird species, such as parrots, caiques, budgerigars, lovebirds, and macaws. However, the number of complete viral sequences available in public databases is scarce, especially those with associated clinical histories. In this study, the clinical, pathological, epidemiological, and molecular characteristics of 2 APyV strains detected in Portugal are described. In the autumn of 2015, a 2‐month‐old female green‐winged macaw (Ara chloroptera) from a small breeder died with signs of dehydration, weight loss, and depression, raising the suspicion of polyomavirus infection. Histopathological analysis revealed lesions compatible with APyV infection, and the presence of polyomavirus in several organs was confirmed by polymerase chain reaction. From the cohabitants tested (n = 14), 1 eclectus parrot (Eclectus roratus), which was more than 1‐year‐old, was also APyV DNA‐positive. The full genomic sequences of the 2 strains were obtained and found identical, suggesting a single introduction in the premises and the occurrence of subsequent infections by the same virus. When compared with sequences of other APyVs available in public databases, high nucleotide similarity percentages were obtained, confirming the close genetic relationship among polyomaviruses worldwide. Interestingly, strain APV7, detected in a white‐bellied parrot in 2008 in Japan, was the closest strain to those isolated in this report. Attempts to isolate the virus in eggs and cell lines failed. Phylogenetic analysis was performed by the Bayesian method to determine the phylogenetic classification of the macaw and parrot strains. Both clustered into group V, together with other strains from different bird species with no host or spatial‐temporal relationships being observed.
Combining Smoothing Spline with Conditional Gaussian Graphical Model for Density and Graph Estimation.

Multivariate density estimation and graphical models play important roles in statistical learning. The estimated density can be used to construct a graphical model that reveals conditional relationships whereas a graphical structure can be used to build models for density estimation. Our goal is to construct a consolidated framework that can perform both density and graph estimation. Denote $\bm{Z}$ as the random vector of interest with density function $f(\bz)$. Splitting $\bm{Z}$ into two parts, $\bm{Z}=(\bm{X}^T,\bm{Y}^T)^T$ and writing $f(\bz)=f(\bx)f(\by|\bx)$ where $f(\bx)$ is the density function of $\bm{X}$ and $f(\by|\bx)$ is the conditional density of $\bm{Y}|\bm{X}=\bx$. We propose a semiparametric framework that models $f(\bx)$ nonparametrically using a smoothing spline ANOVA (SS ANOVA) model and $f(\by|\bx)$ parametrically using a conditional Gaussian graphical model (cGGM). Combining flexibility of the SS ANOVA model with succinctness of the cGGM, this framework allows us to deal with high-dimensional data without assuming a joint Gaussian distribution. We propose a backfitting estimation procedure for the cGGM with a computationally efficient approach for selection of tuning parameters. We also develop a geometric inference approach for edge selection. We establish asymptotic convergence properties for both the parameter and density estimation. The performance of the proposed method is evaluated through extensive simulation studies and two real data applications.
Utilizing random regression models for genomic prediction of a longitudinal trait derived from high‐throughput phenotyping

The accessibility of high-throughput phenotyping platforms in both the greenhouse and field, as well as the relatively low cost of unmanned aerial vehicles, have provided researchers with an effective means to characterize large populations throughout the growing season. These longitudinal phenotypes can provide important insight into plant development and responses to the environment. Despite the growing use of these new phenotyping approaches in plant breeding, the use of genomic prediction models for longitudinal phenotypes is limited in major crop species. The objective of this study is to demonstrate the utility of random regression (RR) models using Legendre polynomials for genomic prediction of shoot growth trajectories in rice (Oryza sativa). An estimate of shoot biomass, projected shoot area (PSA), was recored over a period of 20 days for a panel of 357 diverse rice accessions using an image-based greenhouse phenotyping platform. A RR that included a fixed second-order Legendre polynomial, a random second-order Legendre polynomial for the additive genetic effect, a first-order Legendre polynomial for the environmental effect, and heterogeneous residual variances was used to model PSA trajectories. The utility of the RR model over a single time point (TP) approach, where PSA is fit at each time point independently, is shown through four prediction scenarios. In the first scenario, the RR and TP approaches were used to predict PSA for a set of lines lacking phenotypic data. The RR approach showed a 11.6% increase in prediction accuracy over the TP approach. Much of this improvement could be attributed to the greater additive genetic variance captured by the RR approach. The remaining scenarios focused forecasting future phenotypes using a subset of early time points for known lines with phenotypic data, as well new lines lacking phenotypic data. In all cases, PSA could be predicted with high accuracy (r: 0.79 to 0.89 and 0.55 to 0.58 for known and unknown lines, respectively). This study provides the first application of RR models for genomic prediction of a longitudinal trait in rice, and demonstrates that RR models can be effectively used to improve the accuracy of genomic prediction for complex traits compared to a TP approach.
Isolation and Characterization of a Rhodobacter Capsulatus hemC Mutant.

Rhodobacter capsulatus, a purple, nonsulfur photosynthetic bacterium, uses the tetrapyrrole pathway to synthesize four end products: heme, bacteriochlorophyll, vitamin B12, and siroheme. This laboratory has focused on the regulation of the common pathway leading from aminolevulinate to protoporphyrin IX in R. capsulatus. The common portion of the pathway is regulated up to 100-fold by changes in oxygen tension. Research on the regulation of this pathway has been hampered due to a lack of mutants. Until now, the only mutants isolated which block heme production are hemA mutants, which lack aminolevulinate synthase. Since R. capsulatus lacks a cytochrome-independent growth mechanism, mutations later in the tetrapyrrole pathway would be lethal unless the mutant can use exogenous hemin or protoporphyrin. To overcome this lack of mutants, a method for isolating hem mutants has been devised. First, a growth medium was developed so that the hemA mutant, and presumably other hem mutants, grow well on exogenous hemin. We then took advantage of the recent cloning of several of the R. capsulatus hem genes to make a hem mutation in vitro and move it into R. capsulatus by conjugation. Thus, we were looking for a high probability recombination event rather than a much lower probability transposition event. This study describes the development of this medium as well as the isolation and characterization of a hemC mutant of R. capsulatus. This is the
Open‐top chambers for temperature manipulation in taller‐stature plant communities

Open‐top chambers simulate global warming by passively increasing air temperatures in field experiments. They are commonly used in low‐stature alpine and arctic ecosystems, but rarely in taller‐stature plant communities because of their limited height. We present a modified International Tundra Experiment (ITEX) chamber design for year‐round outdoor use in warming taller‐stature plant communities up to 1.5 m tall. We report a full year of results for the chambers' effects on air and soil temperature, relative humidity, and soil moisture in a northern hardwood forest clearing and a southern early successional grassland site located in Michigan, USA. Detailed construction plans are also provided. The chambers elevated daytime air temperatures at 1 m height by 1.8°C above ambient levels, on average over an entire year, at both the northern and southern site. The chambers did not affect relative humidity at either site. The chambers did not alter average soil temperature or moisture at the northern site and reduced soil temperatures and soil moisture at the southern site. The chambers increased variability in soil freeze/thaw cycles at both sites. The chambers achieved predicted levels of warming for mid‐century (2046–2065) scenarios consistent with the majority of representative concentration pathways in the International Panel on Climate Change Fifth Assessment Report, with minimal experimental artefact. This design is a valuable tool for examining the effects of in situ warming on understudied taller‐stature plant communities and creates the opportunity to expand future comparisons across a diversity of systems.
Blue Light Negatively Regulates Tolerance to Phosphate Deficiency in Arabidopsis

Plants have evolved mechanisms to improve utilization efficiency or acquisition of inorganic phosphate (Pi) in response to Pi deficiency, such as altering root architecture, secreting acid phosphatases, and activating the expression of genes related to Pi uptake and recycling. Although many genes responsive to Pi starvation have been identified, transcription factors that affect tolerance to Pi deficiency have not been well characterized. We show here that defect in the ELONGATED HYPOCOTYL 5 (HY5) transcription factor gene results in tolerance to Pi deficiency in Arabidopsis. The primary root length of hy5 was only slightly inhibited under Pi deficient condition and its fresh weight was significantly higher than that of wild type. The Pi deficiency-tolerant phenotype of hy5 was similarly observed when grown on the medium without Pi. In addition, a double mutant, hy5slr1, without lateral roots also showed tolerance to phosphate deficiency, indicating that the tolerance of hy5 does not result from increase of external Pi uptake and may be related to internal Pi utilization or recycling. Moreover, we found that blue light negatively regulates tolerance to Pi-deficiency and that hy5 exhibits tolerance to Pi deficiency due to blockage of blue-light responses. Collectively, this study points out light quality may play an important role in the regulation of internal Pi recycling and utilization efficiency. Also, it may contribute to reducing Pi fertilizer requirements in plants through a proper illumination.
Micropropagation of Adenia goetzei Harms, an attractive caudiciform from Central Africa

Summary: Adenia goetzei is a plant with a decorative prominent caudex. An efficient micropropagation system based on axillary shoot formation and subsequent rooting was developed. By alternating culture on a medium with 5µM BAP (a modified Murashige & Skoog (1962) medium) and a medium without BAP (Krogstrup et al., 1988), a multiplication factor of 3.93 +/- 1.16 (mean +/- SD) was achieved every 6 weeks. Approximately 61 % of the micro-cuttings rooted following a 24 day 5µM IBA treatment and 80–85% of the plants were successfully transplanted to soil. The juvenile twining growth- and leaf form reverted to a form with adult characteristics after 1–2 growth periods in soil. Using this micropropagation protocol for A. goetzei, it has been possible to produce several hundred vigorous and true-to-type plants, except for irregularly shaped caudices in contrast to the regular ones seen in seedlings.
Genetic variability, character association and path analysis for yield components in ginger ( Zingiber officinale Rosc.)

Twentynine collections of ginger ( Zingiber officinale ) were studied for variability, character association and path analysis for yield and its 10 component characters. Wide range of variability was observed for most of the characters studied. Rhizome yield per plant was positively associated with plant height, number of fingers per plant ,weight of fingers and weight of primary rhizome. Plant analysis revealed that weight of fingers, width of fingers and leaf width were the strongest forces influencing yield.
Fox transcription factors in adult neurogenesis

In this study, the role of Fox transcription factors in adult neurogenesis was investigated. The question was studied in conditional KO mice and via retroviral labeling and manipulation of newborn neurons. It was found that FoxO transcription factors are important for stem cell quiescence and neurogenesis, as well as for the maturation of newborn hippocampal neurons. Further it was shown that timing of FoxG1 expression is critical for survival and maturation of new neurons in the dentate gyrus.
Analysis of expressed sequence tags (ESTs) from sorghum bicolor germinating embryos

Sorghum is a major source of nutrition in developing countries. Additionally, among cereal grains sorghum has one of the smallest genomes, making it an excellent model system for cereal grains. In this study an Expressed Sequence Tag (EST) database from Sorghum bicolor embryos germinated for a period of 24 hr was constructed. Highthroughput sequencing produced a total of 5,405 and 5,126 ESTs from the 5′ and 3′ ends of the cDNA clones respectively. High-throughput bioinformatic analysis revealed that although a small percentage of contamination was observed most of the ESTs were derived from the cDNA library. Although expression analysis offered insight into the numerous processes taking place in the germinating embryo, a great majority of the ESTs were not able to be identified by BLAST searches. The results indicate that many of the embryo ESTs is not represented in the public database.
Flora Graeca Digitalis: Old Library Stock

Libraries have been digitizing old stock for several years now – mostly for a specific and restricted scientific user group. But what about the social obligation to preserve, and therefore call to mind digital cultural heritage in a contemporary manner? Flora Graeca is a large format masterpiece of printing, engraving, color and design of almost thousand plants of the Mediterranean area in the late 18th century comprising ten volumes. It was discovered in Darmstadt’s University and State Library three years ago. Encouraged by the overall good condition and the finely crafted, hand-colored illustrations, the library conducted a high-quality digitization of the whole work in order to make it digitally available to the public. The key question of the work presented here was how to reach a circle beyond scientific users, i.e. botanists and historians, and draw the general public’s interest to this wonderful masterpiece. The offer should address in particular young student library patrons, who use the library in hundreds as a place of work and communication. Why not making them curious in the libraries treasures while coming here every day? So, the idea was to enrich the illustrations by further information about the botanic illustrations by linked open data from the semantic web, such that entities could be linked semantically, and the digital copies could be connected to additional information. In combination with a presentation platform developed in a former project particularly for mobile usage, a virtual edition of Flora Graeca was formed, implemented as an edutainment application with responsive design and exploratory search for an intuitive and ludic handling. It breaks fresh ground by leaving the classic search and find paradigm towards digital strolling: just like a physical visit to a library or a museum, it allows strolling through a collection, discovering and comparing objects, and getting inspired.
Polca SARA – full polarization, direction-dependent calibration, and sparse imaging for radio interferometry

New generation of radio interferometers are envisaged to produce high quality, high dynamic range Stokes images of the observed sky from the corresponding undersampled Fourier domain measurements. In practice, these measurements are contaminated by the instrumental and atmospheric effects that are well represented by Jones matrices, and are most often varying with observation direction and time. These effects, usually unknown, act as a limiting factor in achieving the required imaging performance and thus, their calibration is crucial. To address this issue, we develop a global algorithm, named Polca SARA, aiming to perform full polarization, direction-dependent calibration, and sparse imaging by employing a non-convex optimization technique. In contrast with the existing approaches, the proposed method offers global convergence guarantees and flexibility to incorporate sophisticated priors to regularize the imaging as well as the calibration problem. Thus, we adapt a polarimetric imaging specific method, enforcing the physical polarization constraint along with a sparsity prior for the sought images. We perform extensive simulation studies of the proposed algorithm. The results indicate the superior performance of polarization constraint based imaging when combined with the calibration of the direction-dependent effects for full Jones matrices, including their off-diagonal terms (denoting polarization leakage). The chosen priors in the proposed approach are also shown to handle the unitary ambiguity problem to a good extent.
An arsenic hyperaccumulating fern, Pteris vittata L. (Pteridaceae) broadly affects terrestrial invertebrate abundance

1. The Chinese brake fern (Pteris vittata L.; Pteridaceae) can accumulate up to 27 000 mg kg−1 dry wt. of arsenic (As) from the soil into its above‐ground biomass. They may use this As to deter invertebrate threats.
Reniforma rhynchophori sp. nov. (Basidiomycota, Microbotryales) from guts of red palm weevil

During a survey of mycobiota inhabiting guts of red palm weevil (Rhynchophorus ferrugineus) in Assiut area of Egypt, two interesting yeast isolates were obtained from 2 different gut samples (out of 11 gut samples investigated). Two isolates were identified phenotypically and genotypically with 87% ITS sequencing similarities with the type strain Reniforma strues. The name Reniforma rhynchophori was assigned for the new species. The two strains were deposited in Assiut University Mycological Centre Culture Collection and AUMC numbers 10263 (as the type strain) and AUMC 10264 were given. The ITS gene sequences for AUMC 10263 & AUMC 10264 were also deposited at the National Center for Biotechnological Information (NCBI) and accession numbers are given as KX011609 and KX015891 respectively. Full description and photos of the new species are presented. This new species was recorded as the second species of the genus Reniforma.
Availability of potassium in biomass combustion ashes and gasification biochars after application to soils with variable pH and clay content

ABSTRACT The expansion of the bioenergy sector and adoption of novel thermal conversion technologies produce increasingly large amounts of biomass ashes and biochars. Before returning such products to agricultural soil, the plant availability of nutrients when mixing with soil should be assessed. The objective of this study was to evaluate the potassium (K) availability in various types of biomass ashes and gasification biochars (GBs) derived from straw, wood, sewage sludge and poultry manure when mixed with soil. A 16-week incubation study was conducted with three contrasting soils of variable pH (5.8–7.8) and clay contents (3–17%). Exchangeable K in the product-soil mixture was determined, and the K recovery rate from the applied products varied from 31 to 86%. The relative recovery compared to applied KCl was used to indicate K availability and was 50–86% across all soils, but lower for two sewage sludge-based GBs in the alkaline soil. Most of the K release occurred within the first week, with insignificant release thereafter. Wet storage of GB did not affect K availability. We conclude that the tested biochars and ashes can be used as K fertilisers with slightly lower short-term availability than KCl.
Scalable cytoarchitectonic characterization of large intact human neocortex samples

We describe MASH (Multiscale Architectonic Staining of Human cortex): a simple, fast and low-cost cytoarchitectonic labeling and optical clearing approach for human cortex samples, which can be applied to large formalin fixed adult brain samples. A suite of small-molecule fluorescent nuclear and cytoplasmic dyes in combination with new refractive index matching solutions allows deep volume imaging. This enables highly scalable human neocortical cytoarchitecture characterization with a large 3D scope.
RFLP-based genetic map of the homoeologous group 3 chromosomes of wheat and rye

Summary. Genetic maps of chromosomes 3A, 3B and 3D of wheat and 3R of rye were developed using 22 DNA probes and two isozyme marker systems. Analysis of the 49 loci mapped showed extreme clustering around the centromere in all four maps, with large 'gaps' in the distal chromosome regions, which is interpreted as being due to strong localisation of recombination towards the ends of the wheat and rye chromosomes. In the cen- tromeric regions gene orders are highly conserved be- tween the three wheat genomes and the rye genome. However, the unpredictable behaviour of the DNA clones that map in distal chromosome locations may indicate that the genomes are diverging most rapidly in the regions of higher recombination. A comparison of cDNA and genomic probes showed the latter to be much more efficient for revealing RFLP. Some classes of gDNA clones, i.e. chromosome-specific sequences and those hybridizing in a non-homoeologous manner, were seen to be most polymorphic. Correlations between map locations and RFLP levels showed no clear relationship. In addition to anonymous DNA clones, the locations of known function clones, sedoheptulose-l,7-bisphos- phatase
Large numbers of explanatory variables: an exploration

Data with a relatively small number of study individuals and a very large number of potential explanatory features arise particularly but by no means only in genomics. A powerful method of analysis, the lasso (Tibshirani, R. (1996), Regression shrinkage and selection via the lasso. J. R . Statist. Soc B. 58, 267–288), takes account of an assumed sparsity of effects, that is that most of the features are nugatory. Standard criteria for model fitting, such as the method of least squares, are modified by imposing a penalty for each explanatory variable used. There results a single model, leaving open the possibility that other sparse choices of explanatory features fit virtually equally well. The method suggested in the present paper aims to specify simple models that are essentially equally effective, leaving detailed interpretation to the specifics of the particular study. The method hinges on the ability to make initially a very large number of separate analyses allowing each explanatory feature to be assessed in combination with many other such features. Further stages allow the assessment of more complex patterns such as nonlinear and interactive dependences. The method has formal similarities with socalled partially balanced incomplete block designs introduced eighty years ago (Yates, F. (1936), A new method of arranging variety trials involving a large number of varieties. J. Agric. Sci. 26, 424–455) for the study of large-scale plant breeding trials. The emphasis in the present note is strongly on exploratory analysis; the more formal statistical properties obtained under idealized assumptions will be reported separately.