Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromosome‐scale genome assembly of Poa trivialis and population genomics reveal widespread gene flow in a cool‐season grass seed production system

Poa trivialis (L.) is a cool-season grass species found in various environments worldwide. In addition to being a desired turfgrass species, it is a common weed of agricultural systems and natural areas. As a weed, it is an important contaminant of commercial cool-season grass seed lots, resulting in widespread gene flow facilitated by human activities and causing significant economic losses to farmers. To better understand and manage infestations, we assembled and annotated a haploid genome of P. trivialis and studied troublesome field populations from Oregon, the largest cool-season grass seed producing region in the United States. The genome assembly resulted in 1.35 Gb of DNA sequence distributed among seven chromosome-scale scaffolds, revealing a high content of transposable elements, conserved synteny with P. annua, and a close relationship with other C3 grasses. A reduced-representation sequencing analysis of field populations revealed limited genetic diversity and suggested potential gene flow and human-assisted dispersal in the region. The genetic resources and insights into P. trivialis provided by this study will improve weed management strategies and enable the development of molecular detection tests for contaminated seed lots to limit seed-mediated gene flow. These resources should also be beneficial for turfgrass breeders seeking to improve desirable traits of commercial P. trivialis varieties and help to guide breeding efforts in other crops to enhance the resiliency of agricultural ecosystems under climate change. Significance statement The chromosome-scale assembly of Poa trivialis and population genomic analyses provide crucial insights into the gene flow of weedy populations and contribute a valuable genomic resource for the plant science community.
Predicting subject traits from brain spectral signatures: an application to brain ageing

The prediction of subject traits using brain data is an important goal in neuroscience, with relevant applications in clinical research, as well as in the study of differential psychology and cognition. While previous research has primarily focused on neuroimaging data, our focus is on the prediction of subject traits from electroencephalography (EEG), a relatively inexpensive, widely available and non-invasive data modality. However, EEG data is complex and needs some form of feature extraction for subsequent prediction. This process is almost always done manually, risking biases and suboptimal decisions. Here, we propose a largely data-driven use of the EEG spectrogram, which reflects macro-scale neural oscillations in the brain. Specifically, the key idea of this paper is to reinterpret the spectrogram as a probability distribution and then leverage advanced machine learning techniques that can handle probability distributions with mathematical rigour and without the need for manual feature extraction. The resulting technique, Kernel Mean Embedding Regression (KMER), shows superior performance to alternative methods thanks to its capacity to handle nonlinearities in the relation between the EEG spectrogram and the trait of interest. We leveraged this method to predict biological age in a multinational EEG data set, HarMNqEEG, showing the method’s capacity to generalise across experiments and acquisition setups.
Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression

Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations vs. pre-existing variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.
Interleukin-10-producing monocytes contribute to sex differences in pain resolution in mice and humans

Pain is closely associated with the immune system, which exhibits sexual dimorphism. For these reasons, neuro-immune interactions are suggested to drive sex differences in pain pathophysiology. However, our understanding of peripheral neuro-immune interactions on sex differences in pain resolution remains limited. Here, we have shown, in both a mouse model of inflammatory pain and in humans following traumatic pain, that males had higher levels of interleukin (IL)-10 than females, which were correlated with faster pain resolution. Following injury, we identified monocytes (CD11b+ Ly6C+ Ly6G-F4/80mid) as the primary source of IL-10, with IL-10-producing monocytes being more abundant in males than females. In a mouse model, neutralizing IL-10 signaling through antibodies, genetically ablating IL-10R1 in sensory neurons, or depleting monocytes with clodronate all impaired the resolution of pain hypersensitivity in both sexes. Furthermore, manipulating androgen levels in mice reversed the sexual dimorphism of pain resolution and the levels of IL-10-producing monocytes. These results highlight a novel role for androgen-driven peripheral IL-10-producing monocytes in the sexual dimorphism of pain resolution. These findings add to the growing concept that immune cells play a critical role in resolving pain and preventing the transition into chronic pain. Graphical abstract
JAGGER localization and function is dependent on GPI anchor addition

In flowering plants, successful double fertilization requires the correct delivery of two sperm cells to the female gametophyte inside the ovule. The delivery of a single pair of sperm cells is achieved by the entrance of a single pollen tube into one female gametophyte. To prevent polyspermy, Arabidopsis ovules avoid the attraction of multiples pollen tubes to one ovule – polytubey block. In Arabidopsis jagger mutants, a significant number of ovules attract more than one pollen tube to an ovule due to an impairment in synergid degeneration. JAGGER encodes a putative arabinogalactan protein (AGP) which is predicted to be anchored to the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor. Here, we show that JAGGER fused to citrine yellow fluorescent protein (JAGGER-cYFP) is functional and localizes mostly to the periphery of ovule integuments and transmitting tract cells. We further investigated the importance of GPI-anchor addition domains for JAGGER localization and function. Different JAGGER proteins with deletions in predicted ω-site regions and GAS (GPI attachment signal) domain, expected to compromise the addition of the GPI anchor, led to disruption of JAGGER localization in the cell periphery. All JAGGER proteins with disrupted localization were also not able to rescue the polytubey phenotype, pointing to the importance of GPI-anchor addition to in vivo function of the JAGGER protein.
Non-Poissonian bursts in the arrival of phenotypic variation can strongly affect the dynamics of adaptation

The introduction of novel phenotypic variation in a population through random mutations plays a crucial role in evolutionary dynamics. Here we show that, when the probability that a sequence has a particular phenotype in its 1-mutational neighbourhood is low, statistical fluctuations imply that in the weak-mutation or monomorphic regime, novel phenotypic variation is not introduced at a constant rate, but rather in non-Poissonian “bursts”. In other words, a novel phenotype appears multiple times in quick succession, or not at all for many generations. We use the RNA secondary-structure genotype-phenotype map to explore how increasing levels of heterogeneity in mutational neighbourhoods strengthen the bursts. Similar results are obtained for the HP model for protein tertiary structure and the Biomorphs model for morphological development. Burst can profoundly affect adaptive dynamics. Most notably, they imply that differences in arrival rates of novel variation can influence fixation rates more than fitness differences do.
A computational approach for deciphering the interactions between proximal and distal regulators in B cell differentiation

Delineating the intricate interplay between promoter-proximal and -distal regulators is crucial for understanding the function of transcriptional mediator complexes implicated in the regulation of gene expression. The aim of the present study was to develop a computational method for accurately modeling the spatial proximal and distal regulatory interactions. Our method combined regression-based models to identify key regulators through gene expression prediction and a graph- embedding approach to detect coregulated genes. This approach enabled a detailed investigation of the gene regulatory mechanisms underlying peripheral B cell differentiation, accompanied by dramatic rearrangements of the genome structure. We found that while the promoter-proximal elements were the principal regulators of gene expression, the distal regulators fine-tuned transcription. Moreover, our approach unveiled the presence of modular regulators, such as structural cofactors and proximal/distal transcriptional factors, which were co-expressed with their target genes. These findings imply that the dysregulation of interactions between transcriptional and structural factors is associated with chromatin reorganization failure and ultimately an increased risk of malignancy. We envisage that our computational approach will help crack the transcriptional cis-regulatory code of the three-dimensional network regulating gene expression.
Flood Inundation Hazard Modelling of the River Kaduna Using Remote Sensing and Geographic Information Systems

The hazard of and damage caused by flooding cannot be overemphasized in terms of loss of life, property, displacement of people and di sruption of Socio-economic activities as well as the loss of valuable agricultural land due to the attendant inundation of flood plains from floods. Urban flooding is gradually becoming a serious ecological problem in N igeria. Several areas along the coast of the Atlantic ocean and a long major river valleys are affected by floods every year. To g ain better understanding of the flood problem especially for planning purposes, flood risk maps are often required. A c ombination of recent data on flood plains such as land use/cover, river/flood stage, and digital elevation models are used to predict future flood stages and likely impacts. In addition, extreme val ue st atistical m odels s uch as the Gumbel's, distribution are used to determine flood frequencies and different return periods of flood hazards of certain m agnitudes. R emote sensing and GIS and results of an alysis of f lood stage data using Gumbel's Extreme distribution model an d a combination of Digital elevation model an d land use/land cover d ata were used to estimate t he ext ent of flood inundations in dif ferent flood return periods in K aduna Metropolis. Areas und er h igh risk d ue to flooding were a lso determined. The study reve aled that most of the areas lying cl ose t o the R iver Kaduna's flood plain are under severe t hreat to flooding i n dif ferent flood return periods.
Ethics: What is the Research Scenario in the Brazilian Symposium SBSC?

Ethics is a human construction, therefore historical, social and cultural. It is impossible to conceive Collaborative Systems without thinking about ethics, because this is manifested in the practices between us. The largest academic-scientific event dedicated to the field of CS in Brazil is the Brazilian Symposium on Collaborative Systems. Through a Systematic Literature Review, we aim to answer the question: what is the panorama of the explicit occurrence of ethical aspects in the publications of the main track of the SBSC? Considering the importance of ethics associated with free, conscious and intentional human practice in a collective and collaborative scope, how are ethical aspects considered, if any, in the communications of these researches? In this sense, what was initially proposed as an Systematic Literature Review became a stimulus to reflection, why are ethical aspects neglected? More than that, is there any way to improve ethical deliberation or is this neglect a symptom of the current political-scientific state of the event?
Middle‐ and low‐latitude ionosphere response to 2015 St. Patrick's Day geomagnetic storm

This paper presents a study of the St Patrick's Day storm of 2015, with its ionospheric response at middle and low latitudes. The effects of the storm in each longitudinal sector (Asian, African, American, and Pacific) are characterized using global and regional electron content. At the beginning of the storm, one or two ionospheric positive storm effects are observed depending on the longitudinal zones. After the main phase of the storm, a strong decrease in ionization is observed at all longitudes, lasting several days. The American region exhibits the most remarkable increase in vertical total electron content (vTEC), while in the Asian sector, the largest decrease in vTEC is observed. At low latitudes, using spectral analysis, we were able to separate the effects of the prompt penetration of the magnetospheric convection electric field (PPEF) and of the disturbance dynamo electric field (DDEF) on the basis of ground magnetic data. Concerning the PPEF, Earth's magnetic field oscillations occur simultaneously in the Asian, African, and American sectors, during southward magnetization of the Bz component of the interplanetary magnetic field. Concerning the DDEF, diurnal magnetic oscillations in the horizontal component H of the Earth's magnetic field exhibit a behavior that is opposed to the regular one. These diurnal oscillations are recognized to last several days in all longitudinal sectors. The observational data obtained by all sensors used in the present paper can be interpreted on the basis of existing theoretical models.
Magmatic Enclaves and Andesitic Lavas from Mt. Lamington, Papua New Guinea: Implications for Recycling of Earlier-fractionated Minerals through Magma Recharge

Mt. Lamington is a composite, dome-forming volcano in Papua New Guinea, sitting on the Papuan Ultramafic Belt (PUB) ophiolite. The 1951 eruption produced andesitic dome lavas with numerous basaltic–andesitic enclaves and a few PUB ultramafic xenoliths. To understand the nature of the 1951 eruption, and to assess the effect of assimilating ophiolitic crust in modifying the geochemistry of arc magmas, we carried out petrological, mineralogical and geochemical studies on andesitic lavas as well as magmatic enclaves and ultramafic inclusions. The mineralogy of the enclaves is dominated by amphibole and plagioclase, similar to the andesitic lava hosts. The textures of the enclaves vary from fine-grained diktytaxitic to coarser-grained plutonic textured. We interpret this variation to result from variable cooling rates in the enclave-forming magma body when it invades the overlying andesite. The diktytaxitic enclaves contain variable proportions of host-derived amph + plag antecrysts and xenocrysts of ol + sp ± cpx ± amph with disequilibrium textures, indicating interaction with host lava and assimilation of foreign materials, respectively. A previous study argued that the olivine xenocrysts with chromian spinel inclusions are derived from the PUB, and thus that the PUB contaminated the Mt. Lamington magmas. We demonstrate that this is highly unlikely on the basis of morphological and compositional discrepancies between PUB ol + sp, sampled in nodules, and the xenocrysts. Mass balance indicates that the high whole-rock Ni contents of enclaves and andesitic hosts can be explained by olivine incorporation and do not require any PUB involvement. The olivines are considered to represent crystal mush fractionated from precursor(s) of andesitic and/or pre-1951 shoshonitic lavas. Their presence in enclaves represents recycling of earlier-fractionated components through magma recharge. We argue that this recycling is an important and underestimated process in shaping arc magmas.
SNAKE ASSEMBLAGE STRUCTURES AND SEASONAL ACTIVITY PATTERNS ON A MILITARY BASE IN SOUTH-CENTRAL PENNSYLVANIA: LAND MANAGEMENT IMPLICATIONS FOR SNAKE CONSERVATION

We ascertained the assemblage structures of snakes occurring in a mixed habitat matrix of natural and disturbed habitats during 2008-2011 at Letterkenny Army Depot (LEAD), a 7200 ha U.S. Army base in south-central Pennsylvania, to understand the patterns of species abundance as they related to habitat type of managed lands. We detected eight species in 12 sites compris- ing natural and disturbed habitats of wetlands, forest, and thicket and open fields. The Common Gartersnake (Thamnophis sirtalis) occurred in the most sites, the Red-bellied Snake (Storeria oc- cipitomaculata) was the rarest species in the study. Two to six species occupied each site and were distributed unevenly. Dynamics of assemblages could be explained in part by habitat and also by the presence of the North American Racer (Coluber constrictor). All species for which data were available exhibited a unimodal pattern to their seasonal activity (mostly May and June); however, seasonal activity peaks differed between sexes. Sex ratios varied among species but were consis- tently female-biased in the Common Gartersnake and Ring-necked Snake (Diadophis punctatus) in Pennsylvania and surrounding areas. As elsewhere in Pennsylvania and the Northeast, body sizes of adults were larger for species syntopic with the North American Racer than for species not syntopic with this potential predator. We found a degree of predictability with respect to snake assemblage dynamics among habitats at LEAD, which in turn can prove useful in resource management of this large and protected human-impacted system.
How Magnet Hospital Status Affects Nurses, Patients, and Organizations:

Objective: As the number of Magnet hospitals continues to rise in the United States and abroad, the body of literature regarding various outcomes at Magnet hospitals is increasing also. A systematic review examining and compiling the most recent evidence would be invaluable to those seeking to pursue Magnet recognition for their facility. We conducted this systematic review to investigate how Magnet hospital status affects outcomes for nursing professionals, patients, and health care organizations. Methods: In January 2018, the databases CINAHL, ProQuest, PubMed, and La Biblioteca Cochrane Plus were searched for relevant studies. The reference lists of selected articles were also examined to identify additional studies. The PRISMA statement was followed, and established methods for systematic review were used to produce a narrative summary. The quality of the reviewed studies was assessed according to the 22-item Strength-ening the Reporting of Observational Studies in Epidemiology (STROBE) checklist for observational studies. Results: Of the 163 studies identified, 21 met the eligibility criteria and are included in this review. On the whole, lower rates of nursing shortages, burnout, job dissatisfaction, and turnover were observed at Magnet hospitals compared with non-Magnet hospitals. The rates of patient mortality, falls, hospital-acquired infections, and pressure ulcers were also lower. Nursing work environments were found to be safer and were associated with a higher quality of care in Magnet hospitals than in non-Magnet hospitals, and Magnet hospitals were found to provide more cost-effective care. Conclusion: This review provides nursing managers and administrators with the most recent evidence demonstrating that Magnet hospitals have better nursing work environments and are associated with better outcomes for nurses, patients, and organizations than non-Magnet hospitals. This evidence should inform future decision-making with regard to pursuing Magnet designation.
A test of granulometric control of desert dune geometry

I. G. Wilson's hypothesis of coarse-tail grain-size control of dune spacing was derived from three dunefields in the Sahara and, although it was supplemented by measurements of spacing from other parts of the world, the grain-size data come only from North Africa. In this paper the hypothesis is tested in the Australian dunefields. Australian dunes do not form separate categories on a P20/s (twentieth percentile/spacing) plot and, when placed on Wilson's diagram, the Australian data form a continuum between dunes and draas. Ripples maintain their identity, suggesting that the average saltation length of sand controls ripple wavelength while dunes and Wilson's draas are formed by secondary flow of some kind. In Australia the spread of data on the P20/s diagram indicates that grain-size is not the prime control on s. Data from Australia and the Sahara indicate that direct linear relationships between s and h (dune spacing and height means respectively for blocks of dunes) occur but they have different slopes in different areas. These differences possibly reflect variations in vegetation and substrate as well as differences in wind regime. The separation of dunes from draas in the Sahara reflects the greater role of grain-size in an area where coarse grains frequently occur in dune crests. The relative paucity of coarse grains in Australian dune crests may reflect the fine-grained alluvium from which the dunes are derived. These differences may be ascribed to differing topography in Australia and the Sahara.
Effect of Planting Date on Protein content of Wheat varieties

To study the effect of planting time on quality characteristics of wheat varieties, (MORVARID and N-85-5), an experiment was conducted at Wheat Research Institute, Faisalabad from 2012. The crop was sown from (Dec 21, Dec 30 and Jan 29). At harvest, samples were taken from each plot and analyzed qualitatively. Characters such as 1000-grain weight, test weight and flour yield declined progressively with delayed sowing. These had shown maximum value in first planting date i.e.21 Dec. and minimum value in the last planting date i.e. 29 Jan. Protein content and bread quality improved by delayed sowing. Best chapati quality was obtained in mid and late sowings, however in case of MORVARID, chapati quality was adversely affected in last sowing date. N-85-5 proved superior for protein content, chapati and bread quality while MORVARID was superior for rest of the characters. Year effects were non significant for all the characteristics.