Miracle-dz/UniFAR-FTUs huggingface dataset:
GENE ACTION GOVERNING INHERITANCE OF ECONOMICALLY VALUED TRAITS AMONG F1HYBRIDS OF HEXAPLOID WHEAT DERIVED THROUGH DIALLEL MATTING SYSTEM

An experiment to investigate gene action for plant height, number of tillers per plant, spikes per plant, spike length, spikelets per spike, grains per spike, weight of grains per spike, 1000 grain weight, grain yield per plant was initiated by using 6X6 full diallel matting system among 15 F1 hybrids derived from 08 wheat varieties namely; TD-1, SKD-1, Imdad, Khirman, Moomal and H-68. The experimental design followed was Randomized Complete Block Design whereas replications were 04. The different trends recorded were over dominance due to maximization of genes of dominant nature in parents with negativity for the morphological characters like plant height, spike length, number of grains per spike, 1000 grain weight and grain yield per plant. In case of number of tillers per plant and spikes per plant, the traits were under partial dominance as per gene action, the parents had more number of recessive genes for tillers per plant, however, vice versa in case of spikes per plant. The gene action for number of spikelets per spike was observed as over dominant. Grain weight per spike was inherited as over dominant trait with equal amount of positive and negative gene effects.
Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon

Transposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation and nearby gene expression in additional plant species. Here we used the grass Brachypodium distachyon as a model and produced DNA methylation and transcriptome profiles for eleven natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated to a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon. Significance statement Transposable elements (TEs) are a major component of plant genomes and a source of genetic and epigenetic innovations underlying adaptation to changing environmental conditions. Yet molecular evidence linking TE silencing and nearby gene expression are lacking for many plant species. We show that in the model grass Brachypodium DNA methylation spreads over very short distances around TEs, with an influence on gene expression for a small subset of TE families.
Neural speech restoration at the cocktail party: Auditory cortex recovers masked speech of both attended and ignored speakers

Humans are remarkably skilled at listening to one speaker out of an acoustic mixture of several speech sources. Two speakers are easily segregated, even without binaural cues, but the neural mechanisms underlying this ability are not well understood. One possibility is that early cortical processing performs a spectro-temporal decomposition of the acoustic mixture, allowing the attended speech to be reconstructed via optimally weighted recombinations that discount spectro-temporal regions where sources heavily overlap. Using human magnetoencephalography (MEG) responses to a two-talker mixture, we show evidence for an alternative possibility, in which early, active segregation occurs even for strongly spectro-temporally overlapping regions. Early (∼70 ms) responses to non-overlapping spectro-temporal features are seen for both talkers. When competing talkers’ spectro-temporal features mask each other, the individual representations persist, but they occur with a ∼20 ms delay. This suggests that the auditory cortex recovers acoustic features that are masked in the mixture, even if they occurred in the ignored speech. The existence of such noise-robust cortical representations, of features present in attended as well as ignored speech, suggests an active cortical stream segregation process, which could explain a range of behavioral effects of ignored background speech.
The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2

To circumvent time-consuming clinical trials, testing whether existing drugs are effective inhibitors of SARS-CoV-2, has led to the discovery of Remdesivir. We decided to follow this path and screened approved medications “off-label” against SARS-CoV-2. In these screenings, Fluoxetine inhibited SARS-CoV-2 at a concentration of 0. 8µg/ml significantly, and the EC50 was determined with 387ng/ml. Fluoxetine is a racemate consisting of both stereoisomers, while the S-form is the dominant serotonin reuptake inhibitor. We found that both isomers show similar activity on the virus. Fluoxetine treatment resulted in a decrease in viral protein expression. Furthermore, Fluoxetine inhibited neither Rabies virus, human respiratory syncytial virus replication nor the Human Herpesvirus 8 or Herpes simplex virus type 1 gene expression, indicating that it acts virus-specific. We see the role of Fluoxetine in the early treatment of SARS-CoV-2 infected patients of risk groups.
Elevated air temperature alters an old‐field insect community in a multifactor climate change experiment

To address how multiple, interacting climate drivers may affect plant–insect community associations, we sampled insects that naturally colonized a constructed old‐field plant community grown for over 2 years under simultaneous CO2, temperature, and water manipulation. Insects were sampled using a combination of sticky traps and vacuum sampling, identified to morphospecies and the insect community with respect to abundance, richness, and evenness quantified. Individuals were assigned to four broad feeding guilds in order to examine potential trophic level effects. Although there were occasional effects of CO2 and water treatment, the effects of warming on the insect community were large and consistent. Warming significantly increased Order Thysanoptera abundance and reduced overall morphospecies richness and evenness. Nonmetric multidimensional scaling found that only temperature affected insect community composition, while a Sørensen similarity index showed less correspondence in the insect community between temperature treatments compared with CO2 or soil water treatments. Within the herbivore guild, elevated temperature significantly reduced richness and evenness. Corresponding reductions of diversity measures at higher trophic levels (i.e. parasitoids), along with the finding that herbivore richness was a significant predictor of parasitoid richness, suggest trophic‐level effects within the insect community. When the most abundant species were considered in temperature treatments, a small number of species increased in abundance at elevated temperature, while others declined compared with ambient temperature. Effects of temperature in the dominant insects demonstrated that treatment effects were limited to a relatively small number of morphospecies. Observed effects of elevated CO2 concentration on whole‐community foliar N concentration did not result in any effect on herbivores, which are probably the most susceptible guild to changes in plant nutritional quality. These results demonstrate that climatic warming may alter certain insect communities via effects on insect species most responsive to a higher temperature, contributing to a change in community structure.
Morphometric analysis of Rhynia and Asteroxylon: testing functional aspects of early land plant evolution

Abstract New morphometric data gathered from cross-sections of two Lower Devonian land plants (Rhynia gwynne-vaughanii and Asteroxylon mackiei) are interpreted in terms of the evolution of the function of vascular bundles in early land plants. The following conclusions can be drawn from these new data: (1) The ratio of the cross-sectional area of the xylem (representing the conducting volume supplying the axis with water) to the xylem perimeter (representing the “contact area” between xylem and parenchyma through which water leaves the xylem and enters the parenchyma) is not constant for Rhynia axes, almost constant for Asteroxylon axes, and different between Rhynia and Asteroxylon. Thus, Bower´s hypothesis that the ratio of cross-sectional area of the xylem to xylem perimeter is constant during ontogenetic development is true for Asteroxylon. That this ratio is constant during phylogeny, however, is not supported by our data. (2) The ratio between cross-sectional area of xylem to parenchyma is higher in Asteroxylon than in Rhynia. (3) As predicted by previous computer simulations, the ratio of the xylem perimeter to the axis perimeter plays a major role in determining water transport performance of the transpiring axis. This ratio is constant within ontogeny but is different in Asteroxylon and Rhynia. In Asteroxylon axes, this ratio is about twice as large as in Rhynia axes. (4) Contrary to the expectations, the distance between the outermost layer of the xylem and the transpiring surface, which represents the low-conductivity pathway through the parenchyma, appears not to be a limiting factor for the water transport in axes of Rhynia and Asteroxylon. (5) From the analysis of the geometric parameters, it is evident that Rhynia and Asteroxylon with their distinct stelar geometries represent two different constructional types for which no transitional stages are known.
Effects of frequency of fertilisation on production, foliar chemistry and nutrient leaching in young Norway spruce stands in Sweden.

There is a great need to increase the production in Swedish forests to meet future demand from the forest industry and the bio-energy sector. One option to increase the production is to supply nutrients to young stands of Norway spruce. For the practical application it is important to develop and optimise fertilisation regimes in terms of production, economy and leaching of nutrients. The frequency of fertilisation is one important variable in the fertilisation regime, and this study aimed to study effects of different fertilisation frequencies on production and leaching of nitrogen. In 2001, five field experiments were established in southern, central and northern Sweden. Young stands of Norway spruce were fertilised every year, every second year and every third year. In addition, fertilisation with sludge pellets and wood-ash combined with nitrogen was investigated. The current annual increment after five years of treatment was significantly larger in fertilised than in unfertilised treatments. The difference in production between fertilisation every year and every second year was insignificant, while fertilisation every third year resulted in lower production. Sludge pellets and wood-ash fertilisation gave significantly lower production than fertilisation every second year even though approximately the same amount of nitrogen was applied. There was relatively little leaching of nitrate to ground water in all treatments; 0.6–1 kg N ha–1 a–1 from plots with fertilisation every year or every second year; and 2.7 kg N ha–1 a–1 from plots with fertilisation every third year. Most of the leaching was after the first fertilisation, in all treatments at all sites.
INTENSIDADE DE QUEIMA DE DIFERENTES RETARDANTES DE FOGO

This research aimed to evaluate the effect of different types of fire retardants and dosages in the efficiency of fighting forest fires. The experiment was conducted in combustion table in the laboratory with 4 types of flame retardants (WD 881, RFC-88, F-500 and HMIS 1-0-0 DPnB) at 3 concentrations (0.5%, 1% and 1.5%) plus water as control. The dosage of the tail of the retardant mixture with water was 0.5 liter per square meter of area. For the analysis it was measured the time that it took to the fire to consume the area with the application of the product and the distance between the top of the parcel and the location where the fire was extinguished. During the firing of each plot (treatment / repeat) the following variables were evaluated: relative humidity, wind speed, time spent by the fire to burn the plot with and without the product and the distance advanced by the fire in the parcel with the product. Retardants with greater efficiency were F-500, HMIS 1-0-0 DPnB and WD 881, that showed significant differences by Tukey test at 5% probability, differentiating the control and the RFC-88. The most effective concentration was 1.5% with the lowest levels of flammability in all cases.
Niche characteristics of Danish woody species as derived from coenoclines

Abstract A main floristic coenocline is extracted from a Danish forest vegetation data set with Detrended Correspondence Analysis. Huisman-Olff-Fresco (HOF) modelling of 262 species occurrences relative to site scores along the coenocline is compared with Gaussian and Generalized Linear Modelling. HOF models allow for responses of variously skewed forms, which may result from interspecific interactions. Most species have symmetric (60%) or skewed (29%), and only few species have flat or monotone response curves. This provides evidence for the generality of unimodal plant species response curves, provided the gradient in question comprises a sufficient amount of compositional turnover. The Gaussian niche width is correlated with density of optima and probability of occurrence of the species. Detailed analysis of HOF estimates for 28 woody species indicates that early succession species such as Pinus sylvestris and Populus tremula have wider niches than middle to late successional canopy species such as Alnus glutinosa, Carpinus betulus, Fagus sylvatica, Fraxinus excelsior, Quercus robur and Tilia cordata. A marked overlap in niche range along the coenocline is interpreted in terms of species competition. Rubus idaeus intrudes into the niches of all other shrub species. Several canopy tree species, such as Fagus sylvatica, Fraxinus excelsior and Quercus robur overlap more than 60% of the ranges of all other species, while their internal overlaps are fairly equal, presenting evidence for their likely co-existence given more natural forest conditions. The combined analysis of coenoclines with HOF modelling of species behaviour is the most robust among the compared methods for estimating model parameters and niche characteristics of plant species. It is recommended for future ecological studies. Nomenclature: Lawesson et al. (1997).
Unsupervised neural network models of the ventral visual stream

Significance Primates show remarkable ability to recognize objects. This ability is achieved by their ventral visual stream, multiple hierarchically interconnected brain areas. The best quantitative models of these areas are deep neural networks trained with human annotations. However, they receive more annotations than infants, making them implausible models of the ventral stream development. Here, we report that recent progress in unsupervised learning has largely closed this gap. We find the networks learned with recent unsupervised methods achieve prediction accuracy in the ventral stream that equals or exceeds that of today’s best models. These results illustrate a use of unsupervised learning to model a brain system and present a strong candidate for a biologically plausible computational theory of sensory learning. Deep neural networks currently provide the best quantitative models of the response patterns of neurons throughout the primate ventral visual stream. However, such networks have remained implausible as a model of the development of the ventral stream, in part because they are trained with supervised methods requiring many more labels than are accessible to infants during development. Here, we report that recent rapid progress in unsupervised learning has largely closed this gap. We find that neural network models learned with deep unsupervised contrastive embedding methods achieve neural prediction accuracy in multiple ventral visual cortical areas that equals or exceeds that of models derived using today’s best supervised methods and that the mapping of these neural network models’ hidden layers is neuroanatomically consistent across the ventral stream. Strikingly, we find that these methods produce brain-like representations even when trained solely with real human child developmental data collected from head-mounted cameras, despite the fact that these datasets are noisy and limited. We also find that semisupervised deep contrastive embeddings can leverage small numbers of labeled examples to produce representations with substantially improved error-pattern consistency to human behavior. Taken together, these results illustrate a use of unsupervised learning to provide a quantitative model of a multiarea cortical brain system and present a strong candidate for a biologically plausible computational theory of primate sensory learning.
HABITAT, DOMINANCE, AND THE PHENOTYPIC QUALITY OF MALE BLACK-CAPPED CHICKADEES

Abstract ABSTRACT The provisioning of offspring is limited by resource abundance and is therefore likely to vary with habitat quality and the ability of parents to obtain food. Provisioning effort may also vary because males choose different life-history strategies depending on their rank and environment. Socially dominant males have higher costs of self-maintenance compared with subordinates, yet this is likely compensated for by their priority access to resources. It is unclear, however, whether this translates into benefits for females through male provisioning effort, and how this might vary with habitat suitability. We assessed patterns of body condition, blood hematocrit levels, and provisioning effort of dominant and subordinate male Black-capped Chickadees (Poecile atricapillus) breeding in two habitats known to differ in quality. Within ranks, males were similar in size and condition across habitats. Dominant males were not structurally larger than subordinates, but they were in better condition than subordinates in both habitats. There was an additive effect of habitat and dominance rank on hematocrit level; dominant males had higher hematocrit levels than subordinates regardless of habitat, and all males breeding in poor habitat had elevated hematocrits. A habitat-rank interaction revealed a greater disparity in provisioning rates among dominant and subordinate males in poor habitats. These results suggest that dominant males may be particularly good mates when resources are scarce.
A quantitative analysis of wing pattern in the Culicoides pulicaris species group (Diptera: Ceratopogonidae)

Wing pattern is very important in the taxonomy of the genus Culicoides. To date no quantitative method has been described permitting the inclusion of wing pattern characters with traditional morphometric characters in multivariate studies. Two alternative methods for quantifying wing pattern are developed here. The first superimposes a grid onto a wing and the 420 ‘characters’ generated are scanned for pigmentation. A second method recognizes 13 pattern elements from a sequentially arranged series of wings. The latter method was considered superior for several reasons: it uses logically acceptable characters, reduces character redundancy and allows easier and faster coding. Empirical multivariate studies show the pattern element method to be of taxonomic value in the difficult C. pulicaris group, and to have considerable potential for use in this and other groups of Diptera with patterned wings.
Promising early post-emergence herbicides for effective weed management in soybean

A field experiment was conducted during Kharif season of years 2011 and 2012 at Norman E. Borlaug crop research centre of Govind Ballabh Pant University of Agriculture & Technology, Pantnagar (U.S. Nagar), Uttarakhand. Fluazifop-p-butyl + fomesafen controlled grasses and non-grassy weeds effectively and recorded 29.3 weeds/m2 in 500 g/ha against (171.17/m2) in untreated check. However, the grain yield was highest (2.21 t/ha) in the treatment of weed free followed by fluazifop-p-butyl + fomesafen applied 313 g/ha as post-emergence (2–5 leaf stage of weeds). Biomass of weeds was also lowest in fluazifop-pbutyl + fomesafen 313 g/ha treated plots. However, total weed density was lowest in fluazifop-p-butyl + fomesafen 500 g/ha treated plot but this dose showed toxic effects on crop. Weed index was lowest (7.8%) in the treatment of fluazifop-p-butyl + fomesafen 313 g/ha and highest in untreated (63.5%).
Genome-wide CRISPR knockout screen reveals membrane tethering complexes EARP and GARP important for Bovine Herpes Virus Type 1 replication

We produced a genome wide CRISPR knockout library, btCRISPRko.v1, targeting all protein coding genes in the cattle genome and used it to identify host genes important for Bovine Herpes Virus Type 1 (BHV-1) replication. By infecting library transduced MDBK cells with a GFP tagged BHV-1 virus and FACS sorting them based on their GFP intensity, we identified a list of pro-viral and anti-viral candidate host genes that might affect various aspects of the virus biology, such as cell entry, RNA transcription and viral protein trafficking. Among them were VPS51, VPS52 and VPS53 that encode for subunits of two membrane tethering complexes EARP and GARP. Simultaneous loss of both complexes in MDBKs resulted in a significant reduction in the production of infectious cell free BHV-1 virions, suggesting the vital roles they play during capsid re-envelopment with endocytosed membrane tubules prior to endosomal recycling mediated cellular egress. We also observed potential capsid retention and aggregation in the nuclei of these cells, indicating that they might also indirectly affect capsid egress from the nucleus. The btCRISPRko.v1 library generated here greatly expanded our capability in BHV-1 related host gene discovery; we hope it will facilitate efforts intended to study interactions between the host and other pathogens in cattle and also basic host cell biology.