Miracle-dz/UniFAR-FTUs huggingface dataset:
Inference of Selection from Genetic Time Series Using Various Parametric Approximations to the Wright-Fisher Model

Detecting genomic regions under selection is an important objective of population genetics. Typical analyses for this goal are based on exploiting genetic diversity patterns in present time data but rapid advances in DNA sequencing have increased the availability of time series genomic data. A common approach to analyze such data is to model the temporal evolution of an allele frequency as a Markov chain. Based on this principle, several methods have been proposed to infer selection intensity. One of their differences lies in how they model the transition probabilities of the Markov chain. Using the Wright-Fisher model is a natural choice but its computational cost is prohibitive for large population sizes so approximations to this model based on parametric distributions have been proposed. Here, we compared the performance of some of these approximations with respect to their power to detect selection and their estimation of the selection coefficient. We developped a new generic Hidden Markov Model likelihood calculator and applied it on genetic time series simulated under various evolutionary scenarios. The Beta with spikes approximation, which combines discrete fixation probabilities with a continuous Beta distribution, was found to perform consistently better than the others. This distribution provides an almost perfect fit to the Wright-Fisher model in terms of selection inference, for a computational cost that does not increase with population size. We further evaluated this model for population sizes not accessible to the Wright-Fisher model and illustrated its performance on a dataset of two divergently selected chicken populations.
Changes in Carbon Balance of Harvested Wood Products Resulting from Different Wood Utilization Scenarios

The bioeconomy focuses on the production of renewable biological resources and the utilisation of these resources and waste streams into value added products. One of the most important aims of the forest industry is the sustainable production of wood. Improved utilization of available industrial wood assortments generates profit for all in the supply chain. At the same time, it may ensure the production of long-life harvested wood products (HWP), and consequently, increase the volume of carbon stored. The objective of this study is to compare different scenarios of industrial wood utilization in Slovakia and the resulting impacts on the national carbon balance. In the proposed scenarios, we aimed to evaluate changes in the current utilization of domestic wood resources through optimizing harvested wood assortments. Two inventory stock methods were applied to determine the potential quality of domestic wood and its utilization through appropriate distribution of outputs. The model scenario assumes that the higher share of industrial roundwood utilised to produce long-life HWP (sawnwood, wood-based panels) will increase carbon sequestration in HWP. Other scenarios quantify the differences between the carbon volumes stored in HWP using the modelled wood assortment supplemented with alternatives with and without export. The results confirmed that increasing the level of carbon stored in HWP can be achieved by changing the wood assortment structure, while maintaining the same level of volume felled. The highest level of carbon stock was observed in the scenario assuming the optimal structure of wood assortments and no wood export. The scenario that optimized wood assortments and excluded wood exports resulted in the highest level of predicted carbon stock, estimated at 4.87 million tons (mil. tons).
Community Assembly and Climate Mismatch in Late Quaternary Eastern North American Pollen Assemblages

Plant community response to climate change ranges from synchronous tracking to strong mismatch. Explaining this variation in climate change response is critical for accurate global change modeling. Here we quantify how closely assemblages track changes in climate (match/mismatch) and how broadly climate niches are spread within assemblages (narrow/broad ecological tolerance, or “filtering”) using data for the past 21,000 years for 531 eastern North American fossil pollen assemblages. Although climate matching has been strong over the last 21 millennia, mismatch increased in 30% of assemblages during the rapid climate shifts between 14.5 and 10 ka. Assemblage matching rebounded toward the present day in 10%–20% of assemblages. Climate-assemblage mismatch was greater in tree-dominated and high-latitude assemblages, consistent with persisting populations, slower dispersal rates, and glacial retreat. In contrast, climate matching was greater for assemblages comprising taxa with higher median seed mass. More than half of the assemblages were climatically filtered at any given time, with peak filtering occurring at 8.5 ka for nearly 80% of assemblages. Thus, vegetation assemblages have highly variable rates of climate mismatch and filtering over millennial scales. These climate responses can be partially predicted by species’ traits and life histories. These findings help constrain predictions for plant community response to contemporary climate change.
Net reproductive rate and other population parameters of natural population of Anopheles sinensis in Zhengzhou

Compared with the corresponding parameters of the experimental population, the parametes gained inpresent studies were much lower except the percentage of survival adults after 12 days and mean length of generation. The natural factors and natural enemies have great effect in the composition of environmental resistance on An. sinensis. The parameters of natural population dynamics of An. sinensis will be of great importance in the establishment of the control program against malaria and its vectors. In addition, the mathematical model for calculating the last oviposition time is proved to be reasonable for the first time.
The complete mitochondrial genome of Chaetodon wiebeli (Chaetodontiformes, Chaetodontidae)

Abstract Chaetodon wiebeli is one of the most important genera of Chaetodontidae. However, the systemic classification and taxonomic studies have so far been limited. In this study, we report the complete mitochondrial genome sequence of C. wiebeli. The mitogenome has 16,523 bp (54.3% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs, and 2 ribosomal RNAs), and a putative control region. This study will provide useful genetic information for future phylogenetic and taxonomic classification of Chaetodontidae.
FBL17 targets CDT1a for degradation in early S-phase to prevent Arabidopsis genome instability

Maintenance of genome integrity depends on controlling the availability of DNA replication initiation proteins, e.g., CDT1, a component of the pre-replication complexes that regulates chromatin licensing for replication. To understand the evolutionary history of CDT1 regulation, we have identified the mechanisms involved in CDT1 dynamics. During cell cycle, CDT1a starts to be loaded early after mitotic exit and maintains high levels until the G1/S transition. Soon after the S-phase onset, CDT1a is rapidly degraded in a proteasome-dependent manner. Plant cells use a specific SCF-mediated pathway that relies on the FBL17 F-box protein for CDT1a degradation, which is independent of CUL4a-containing complexes. A similar oscillatory pattern occurs in endoreplicating cells, where CDT1a is loaded just after finishing the S-phase. CDT1a is necessary to maintain genome stability, an ancient strategy although unique proteins and mechanisms have evolved in different eukaryotic lineages to ensure its degradation during S-phase. Impact statement The DNA replication protein CDT1a is crucial for genome integrity and is targeted for proteasome degradation just after S-phase initiation by FBL17 in proliferating and endoreplicating cells of Arabidopsis
Elementary, Chemical and Energy Characterization of “Dendê” (Elaeis guineensis Jacq.) Waste in the State of Pará

This work aimed to chemically and energetically characterize palm waste in the municipality of Igarapé Açú-PA. The residue was crushed, sieved and acclimated up to 12% of humidity. Chemical analyses were performed in the fresh material, according to NBR standards. Part of the residue was transformed into charcoal at 450 °C, with heating rate of 1.67 °C.min-1 and residence time of 30 minutes. Elementary analysis (CHNS-O) was carried out in the fresh and carbonized material. For biomass, means of 32.67% of lignin and 2.58% of minerals were found. Means of 79.71% for volatile materials and 9.85% for fixed carbon were also found. In the elementary analysis, mean values of 53.79% for carbon and 0.7% for sulfur were found. Palm biomass residues presented high fixed carbon, structural carbon and lignin levels, thus presenting potential to be used in the direct production of energy, activated carbon and also biochar.
Dispersal behaviour of African wild dogs in Kenya

Dispersal behaviour plays a key role in social organisation, demography, and population genetics. We describe dispersal behaviour in a population of African wild dogs (Lycaon pictus) in Kenya. Almost all individuals, of both sexes, left their natal packs, with 45 of 46 reproductively-active “alpha” individuals acquiring their status through dispersal. Dispersal age, group size, and distance did not differ between males and females. However, only females embarked on secondary dispersal, probably reflecting stronger reproductive competition among females than males. When dispersing, GPS-collared wild dogs travelled further than when resident, both in daylight and by night, following routes an order of magnitude longer than the straight-line distance covered. Dispersers experienced a daily mortality risk three times that experienced by adults in resident packs. The detailed movement data provided by GPS-collars helped to reconcile differences between dispersal patterns reported previously from other wild dog populations. However, the dispersal patterns observed at this and other sites contrast with those assumed in published demographic models for this endangered species. Given the central role of dispersal in demography, models of wild dog population dynamics need to be updated to account for improved understanding of dispersal processes.
The Impacts of Flowering Time and Tillering on Grain Yield of Sorghum Hybrids across Diverse Environments

Sorghum in Australia is grown in water-limited environments of varying extent, generating substantial genotype × environment interactions (GEIs) for grain yield. Much of the yield variation and GEI results from variations in flowering time and tillering through their effects on canopy development. The confounding effects of flowering and tillering complicate the interpretation of breeding trials. In this study, we evaluated the impacts of both flowering time (DTF) and tillering capacity (FTN) on the yield of 1741 unique test hybrids derived from three common female testers in 21 yield testing trials (48 tester/trial combinations) across the major sorghum production regions in Australia in three seasons. Contributions of DTF and FTN to genetic variation in grain yield were significant in 14 and 12 tester/trial combinations, respectively. The proportion of genetic variance in grain yield explained by DTF and FTN ranged from 0.2% to 61.0% and from 1.4% to 56.9%, respectively, depending on trials and genetic background of female testers. The relationship of DTF or FTN with grain yield of hybrids was frequently positive but varied across the genetic background of testers. Accounting for the effects of DTF and FTN using linear models did not substantially increase the between-trial genetic correlations for grain yield. The results suggested that other factors affecting canopy development dynamics and grain yield might contribute GEI and/or the linear approach to account for DTF and FTN on grain yield did not capture the complex non-linear interactions.
Evaluating presence‐only species distribution models with discrimination accuracy is uninformative for many applications

Species distribution models are used across evolution, ecology, conservation and epidemiology to make critical decisions and study biological phenomena, often in cases where experimental approaches are intractable. Choices regarding optimal models, methods and data are typically made based on discrimination accuracy: a model's ability to predict subsets of species occurrence data that were withheld during model construction. However, empirical applications of these models often involve making biological inferences based on continuous estimates of relative habitat suitability as a function of environmental predictor variables. We term the reliability of these biological inferences ‘functional accuracy. ’ We explore the link between discrimination accuracy and functional accuracy.
Microbiological and Physicochemical Quality of Carp sausage Enriched With Propolis Natural Extract during Chilled Storage

ABSTRACT This study aimed to determine the effect of propolis extract on quality of liquid smoked carp (Cyprinus carpio) sausage stored at 2°C for 9 weeks. Carp sausages were separated into three groups: control group, without propolis extract; second group, with 1% (w/w) propolis extract added; and third group, with 2% (w/w) propolis extract added. Propolis extract added carp sausages showed lower total volatile basic nitrogen (TVB-N) value, peroxide value (PV), and free fatty acid (FFA) content compared to control during the storage period. During 9 weeks of storage, propolis extract added carp sausages showed significantly lower total aerobic mesophilic bacteria (TAMB) and psychrophilic bacteria count (PBC) than those of control samples (p < .05). Yeast and mold were not detected in all fish sausages throughout the storage period.
The mitochondrial genome of the gold-ringed cowry Monetaria annulus (Mollusca: Gastropoda: Cypraeidae) determined by whole-genome sequencing

Abstract The mitochondrial genome of the cowry snail Monetaria annulus (Caenogastropoda: Cypraeoidea: Cypraeidae) was determined by whole-genome next-generation sequencing. The mitogenome is composed of 13 protein-coding genes (PCGs), 2 ribosomal RNA (12S and 16S) genes, and 22 transfer RNA genes (tRNAs). This gene order is consistent with the previously published mitochondrial genomes of other species belonging to the order Littorinimorpha. The superfamily Cypraeoidea was recovered as a sister clade to the group of Tonnoidea and Neogastropoda.
Intensity of Sole-source Light-emitting Diodes Affects Growth, Yield, and Quality of Brassicaceae Microgreens

Indoor farming is an increasingly popular approach for growing leafy vegetables, and under this production system, artificial light provides the sole source (SS) of radiation for photosynthesis and light signaling. With newer horticultural light-emitting diodes (LEDs), growers have the ability to manipulate the lighting environment to achieve specific production goals. However, there is limited research on LED lighting specific to microgreen production, and available research shows that there is variability in how microgreens respond to their lighting environment. The present study examined the effects of SS light intensity (LI) on growth, yield, and quality of kale (Brassica napus L. ‘Red Russian’), cabbage (Brassica oleracea L.), arugula (Eruca sativa L.), and mustard (Brassica juncea L. ‘Ruby Streaks’) microgreens grown in a walk-in growth chamber. SS LEDs were used to provide six target photosynthetic photon flux density density (PPFD) treatments: 100, 200, 300, 400, 500, and 600 μmol·m−2·s−1 with a photon flux ratio of 15 blue: 85 red and a 16-hour photoperiod. As LI increased from 100 to 600 μmol·m−2· s−1, fresh weight (FW) increased by 0.59 kg·m−2 (36%), 0.70 kg·m−2 (56%), 0.71 kg·m−2 (76%), and 0.67 kg·m−2 (82%) for kale, cabbage, arugula, and mustard, respectively. Similarly, dry weight (DW) increased by 47 g·m−2 (65%), 45 g·m−2 (69%), 64 g·m−2 (122%), and 65 g·m−2 (145%) for kale, cabbage, arugula, and mustard, respectively, as LI increased from 100 to 600 μmol·m−2· s−1. Increasing LI decreased hypocotyl length and hue angle linearly in all genotypes. Saturation of cabbage and mustard decreased linearly by 18% and 36%, respectively, as LI increased from 100 to 600 μmol·m−2·s−1. Growers can use the results of this study to optimize SS LI for their production systems, genotypes, and production goals.
Effect of Nutrition and Temperature Humidity Index on The Performance of Lactating Holstein Cattle

Nine hundreds of lactating Holstein cows in three locations (300 cows at each location) were used to evaluate the effect of nutrition and temperature humidity index (THI) conditions on dairy cattle performance (milk production and composition, digestibility, rumination, rumen pH). Three rations (chemically varied in physical effective NDF (peNDF), neutral detergent fiber (NDF), starch, dietary cation anion difference (DCAD), forage to concentrate ratio (F:C), crude protein (CP), either extract (EE), acid detergent fiber (ADF) and non fiber carbohydrates (NFC) were used at the three locations (R1 in L1, R2 in L2 and R3 in L3). Reviewing the nutritional and THI conditions of dairy farming systems in three countries in the Middle East and provides an up-to-date description of farming systems in these countries. Due to the common dairy farming problems in the region, the study focuses on three countries: Sudan (L1), Lebanon (L2) and Kuwait (L3) for an in-depth evaluation of the nutritional and THI conditions of dairy farming systems. The results indicated that increasing the intake of peNDF increase rumination and ruminal pH, but did not affect intake of DM or NDF. So, the models of those predict rumen pH should include both peNDF and fermentable organic matter (OM) intake. Dietary particle size expressed as peNDF, was a reliable indicator of rumination activity. The digestibility of dry matter (DM), CP, EE and NDF increased as concentrations of CP and NFC increased in the ration. While, the digestibility of OM, NFC and ADF was decreased. Milk production and composition negatively affected by increasing of THI. As the THI increased from 63 to 76; the animal performance decreased either in dry matter intake (DMI) and milk production and composition.
Effect of AM fungus and oilcakes with different doses of fertilizers on root knot nematode (Meloidogyne incognita) infecting black gram

A replicated pot culture experiment was conducted for studying the effect of AM fungus and oilcakes with different doses of fertilizers on root knot nematode (Meloidogyne incognita) infecting black gram. All treatments significantly increased the plant growth parameters, uptake of phosphorus by plant, growth of AM fungus, extent of colonization of AM fungus in black gram roots and reduced root knot nematode population as well as number of galls over check. However, application of mustard cake @ 100g/m + AM fungus @ 5g/m along with 50% P and RDNK results more increase in growth parameters of both shoot and root, uptake of phosphorous by plants, colonization of AM fungus in roots and growth of AM fungus with corresponding decrease in number of root galls by and root knot nematode population over check. Thus application of mustard cake @ 100g/m and AM fungus @ 5g/m along with 50% P and RDNK could be the most promising management option against root knot nematode (Meloidogyne incognita) infecting black gram.
Feedback adaptation to unpredictable force fields in 250ms

Motor learning and adaptation are important functions of the nervous system. Classical studies have characterized how humans adapt to changes in the environment during tasks such as reaching, and have documented improvements in behavior across movements. Yet little is known about how quickly the nervous system adapts to such disturbances. In particular, recent work has suggested that adaptation could be sufficiently fast to alter the control strategies of an ongoing movement. To further address the possibility that learning occurred within a single movement, we designed a series of human reaching experiments to extract in muscles recordings the latency of feedback adaptation. Our results confirmed that participants adapted their feedback responses to unanticipated force fields applied randomly. In addition, our analyses revealed that the feedback response was specifically and finely tuned to the ongoing perturbation not only across trials with the same force field, but also across different kinds of force fields. Finally, changes in muscle activity consistent with feedback adaptation occurred in about 250ms following reach onset. We submit this estimate as the latency of motor adaptation in the nervous system.
Investigating the expression and function of the Steroid Receptor RNA Activator Protein (SRAP) in breast cancer

Seventeen years ago, the Steroid receptor RNA Activator (SRA) was identified as a functional non-coding RNA able to increase the activity of the estrogen receptor (ER), a critical player in mediating the mitogenic role of estradiol in breast cancer. Interestingly, four years later, SRA appeared to be the first ever discoved functional RNA also able to encode a corresponding protein (SRAP). As such, the products of the SRA1 gene delineate a fascinating bi-faceted system, involving both a functional RNA and a protein. Since its discovery, the non-coding aspect of this system has been widely investigated, with multiple groups contributing new information on the structure and related functions of SRA. Overall, the non-coding SRA transcript is thought to act as a broad co-regulator modulating the activity of different transcription factors. Conversely, limited information has been obtained on the coding aspect (SRAP) of this system,even though SRA/SRAP is currently believed to be involved in several mechanisms including tumourigenesis, tumour progression, myogenesis and adipogenesis. In this body of work, I have attempted to define the clinical relevance of SRAP to breast cancer and extend the understanding of the cellular processes potentially regulated by this protein. I first established that SRAP has the potential to become a new prognostic and predictive factor in specific groups of patients. Indeed, I have demonstrated, using tissue microarray analyses (TMAs), that SRAP expression was up-regulated in some breast tumours, with high levels associated with poor prognosis in estrogen receptor α (ER-α) positive breast cancer patients. Using the same technique, I have further identified a significant high correlation between a positive response to tamoxifen treatment and a high level of SRAP expression in a large cohort of ER-α negative cases. This observation highlights the potential for SRAP to become a new predictive factor of response to endocrine therapy in this specific group of patients. Using RNA-seq to define the