Miracle-dz/UniFAR-FTUs huggingface dataset:
A young age of subspecific divergence in the desert locust, Schistocerca gregaria

Dating population divergence within species from molecular data and relating such dating to climatic and biogeographic changes is not trivial. Yet it can help formulating evolutionary hypotheses regarding local adaptation and future responses to changing environments. Key issues include statistical selection of a demographic and historical scenario among a set of possible scenarios, and estimation of the parameter(s) of interest under the chosen scenario. Such inferences greatly benefit from new statistical approaches including Approximate Bayesian Computation - Random Forest (ABC-RF), the later providing reliable inference at a low computational cost, with the possibility to take into account prior knowledge on both biogeographical history and genetic markers. Here, we used ABC-RF, including independent information on evolutionary rate and pattern at microsatellite markers, to decipher the evolutionary history of the African arid-adapted pest locust, Schistocerca gregaria. We found that the evolutionary processes that have shaped the present geographical distribution of the species in two disjoint northern and southern regions of Africa were recent, dating back 2.6 Ky (90% CI: 0.9 – 6.6 Ky). ABC-RF inferences also supported a southern colonization of Africa from a low number of founders of northern origin. The inferred divergence history is better explained by the peculiar biology of S. gregaria, which involves a density-dependent swarming phase with some exceptional spectacular migrations, rather than a continuous colonization resulting from the continental expansion of open vegetation habitats during the past Quaternary glacial episodes.
Reproductive biology of Grey-breasted Wood-Wren (Henicorhina leucophrys): A comparative study of tropical and temperate wrens

ABSTRACT We provide a detailed breeding biology account for the Grey-breasted Wood-Wren (Henicorhina leucophrys) and a comparison of the reproductive life history of tropical and temperate wrens using literature data. We conducted this study at Yacambú National Park in Venezuela from 2002 to 2008. Clutch size was 1.99 (SE 0.01) and fresh egg mass was 2.35 g (0.02). Females incubated the eggs for 19.74 d (0.37), and nestlings left nests at 17.37 d (0.18). Nest attentiveness (percent time spent on the nest) increased across the incubation period while brooding attentiveness decreased as nestlings aged. Brooding effort began with similar attentiveness as at the end of incubation. Food provisioning rate and feeding rate per nestling increased as nestlings aged. Growth rates (K) based on mass, tarsus, and wing chord were relatively slow at 0.375, 0.246, and 0.257, respectively. The nesting season extended from mid-March to late June for 7 years and the average nesting season length was 64.5 d (3.68) with a median of May 4. Nest success was 22%. Nest predation was the cause of 77% of nest failures with a total daily predation rate of 0.030 (0.002). Results obtained from the literature demonstrated that tropical wrens averaged smaller clutch sizes and longer incubation periods than relatives in the temperate region.
Cell Cycle Control by Nuclear Sequestration of CDC20 and CDH1 mRNA in Plant Stem Cells

In eukaryotic cells, most RNA molecules are exported into the cytoplasm after being transcribed in the nucleus. Long noncoding RNAs (lncRNAs) have been found to reside and function primarily inside the nucleus, but nuclear localization of protein-coding messenger RNAs (mRNAs) has been considered rare in both animals and plants. Here we show that two mRNAs, transcribed from the CDC20 and CCS52B (plant orthologue of CDH1) genes, are specifically sequestered inside the nucleus during the cell cycle. CDC20 and CDH1 both function as coactivators of the anaphase-promoting complex or cyclosome (APC/C) E3 ligase to trigger cyclin B (C YCB) destruction. In the Arabidopsis thaliana shoot apical meristem (SAM), we find CDC20 and CCS52B are co-expressed with CYCBs in mitotic cells. CYCB transcripts can be exported and translated, whereas CDC20 and CCS52B mRNAs are strictly confined to the nucleus at prophase and the cognate proteins are not translated until the redistribution of the mRNAs to the cytoplasm after nuclear envelope breakdown (NEBD) at prometaphase. The 5’ untranslated region (UTR) is necessary and sufficient for CDC20 mRNA nuclear localization as well as protein translation. Mitotic enrichment of CDC20 and CCS52B transcripts enables the timely and rapid activation of APC/C, while their nuclear sequestration at prophase appears to protect cyclins from precocious degradation.
Nanoscale architecture of the axon initial segment reveals an organized and robust scaffold

The Axon Initial Segment [AIS], located within the first 30 μm of the axon, has two essential roles in generating action potentials and maintaining axonal identity. AIS assembly depends on a ßIV-spectrin / ankyrin G scaffold, but its macromolecular arrangement is not well understood. Here we quantitatively determined the AIS nanoscale architecture using STo-chastic Optical Reconstruction Microscopy [STORM]. First we directly demonstrate that the 190-nm periodicity of the AIS submembrane lattice results from longitudinal, head-to-head ßIV-spectrin molecules connecting actin rings. Using multicolor 3D-STORM, we resolve the nanoscale organization of ankyrin G: its aminoterminus associates with the submembrane lattice, whereas the carboxyterminus radially extends (~32 nm on average) toward the cytosol. This AIS nano-architecture is highly resistant to cytoskeletal perturbations, advocating its role in structural stabilization. Our findings provide a comprehensive view of the AIS molecular architecture, and will help understanding the crucial physiological functions of this compartment.
Educational simulation model for studying the impact of distributed generation on distribution networks using ATP-EMTP software

This work presents the use of the modern software tool Alternative Transients Program (ATP) in the teaching of power engineering, within the course Computer Aided Engineering. A simulation model is presented through which it is possible to analyse the effects of distributed generators (DG) on the operation of a distribution network in both a steady and a transient state, with the objective of fulfilling the conditions for connection. This problem was selected not only because it allows students to gain proper insight into the phenomena within a distribution network with a connected distributed generator, but also because it has been shown that the problem of educating engineers is often a constraining factor for implementing distributed generation (DG). It is shown that by using the software tool ATP-EMTP, very complex phenomena in large networks can be studied without great difficulty or the need for analytical methods. The problem-based learning (PBL) method was applied.
Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

Technological advancement has opened the door to systematic genetics in mammalian cells. Genome-scale loss-of-function screens can assay fitness defects induced by partial gene knockdown, using RNA interference, or complete gene knockout, using new CRISPR techniques. These screens can reveal the basic blueprint required for cellular proliferation. Moreover, comparing healthy to cancerous tissue can uncover genes that are essential only in the tumor; these genes are targets for the development of specific anticancer therapies. Unfortunately, progress in this field has been hampered by offtarget effects of perturbation reagents and poorly quantified error rates in large-scale screens. To improve the quality of information derived from these screens, and to provide a framework for understanding the capabilities and limitations of CRISPR technology, we derive gold-standard reference sets of essential and nonessential genes, and provide a Bayesian classifier of gene essentiality that outperforms current methods on both RNAi and CRISPR screens. Our results indicate that CRISPR technology is more sensitive than RNAi, and that both techniques have nontrivial false discovery rates that can be mitigated by rigorous analytical methods.
Experimental design, expert system and neural network approaches: comparison for the choice of parameters

The choice of the parameters in a system can be supported by several methods, which depend on the type of the available knowledge. In the experimental case of the parametrization of fuzzy dispatching rules in a scheduling software, three methods are tested: experimental design, fuzzy expert system and neural network. In an experimental design, combinations of different values of the parameters are tested in a way that allows to distinguish the respective influence of each parameter. If a deep knowledge on the influence of the parameters on the outputs of the system is available, and if this knowledge can be expressed through production rules, an expert system may be designed. If these conditions are not verified, but if examples of correct set-ups in various cases can be found, a neural network can give a satisfying answer to the problem. A possible implementation of each method is shortly described, and their fields of interest discussed. <<ETX>>
Plant community responses to environmentally friendly piste management in northeast Iran

Abstract It is well‐known that pistes have adverse effects on alpine ecosystems. Previous studies urged that pistes should be installed and managed in the ways to minimize negative impacts on natural habitats. However, the impacts of this type of management on the plant communities are not widely studied. The aim of this study was to examine species composition and biodiversity changes in an environmentally friendly managed piste in northeast Iran. This piste has been established in a previously degraded alpine landscape. For the vegetation survey, we sampled 44 within and 28 off‐piste plots. Except for the piste management, other environmental factors were similar between the piste and off‐piste plots. Dominant species were determined, and variation in community composition of the two areas was visualized. Also, native species, phylogenetic, and functional Hill diversity of the two areas were compared. The results showed that there was a moderate differentiation in the species composition of the piste and off‐piste. Two palatable species (i.e., Bupleurum falcatum and Melica persica) were dominant in the piste and were not recorded in the off‐piste. The diversity calculations results showed that the species diversity of the piste was higher than that of the off‐piste. Phylogenetic diversity at the level of frequent and dominant plants showed a similar result. The piste had a higher functional diversity in terms of functional richness, and functional diversity of frequent and dominant plants. Our findings imply, after 10 years, species, phylogenetic, and functional diversity of the piste is significantly improved. Environmentally friendly piste management (EFPM) induced species composition change that led to emerging species that were absent in the off‐piste. We can conclude that EFPM led to restoration of a degraded landscape. Long‐term impacts of EFPM are still unknown, therefore, caution should be undertaken regarding the installation of new environmentally friendly pistes in other areas.
New Hispanomeryx (Mammalia, Ruminantia, Moschidae) from Spain and a Reassessment of the Systematics and Paleobiology of the Genus Hispanomeryx Morales, Moyà-Solà, and Soria, 1981

ABSTRACT —We describe new specimens of the Miocene moschid Hispanomeryx, from the early Vallesian sites of Castell de Barberà (CB) and Ecoparc de Can Mata (ECM), Vallès-Penedès Basin, representing the first Iberian record of Hispanomeryx outside the inner Miocene basins. Fossils from ECM constitute Hispanomeryx lacetanus, sp. nov., the first Hispanomeryx to be described with a ‘Palaeomeryx fold (external postprotocristid). ’ Fossils from CB constitute the first unambiguous record of Hispanomeryx aragonensis outside its type locality (La Ciesma-1B, Ebro Basin, Spain) and allow us to describe for the first time the upper molars of this species. Our phylogenetic analysis of Hispanomeryx places H. andrewsi from China as the sister group of a clade containing two European lineages. One of the latter places H. daamsi in a clade with the sister species H. duriensis and H. lacetanus, sp. nov., and the other groups together the two forms of H. aragonensis (type series from La Ciesma-1B plus the new material from CB). Emended diagnoses for the genus Hispanomeryx and all previously described species are presented. The new Hispanomeryx material from the Vallès-Penedès Basin constitutes the first unambiguous forest-dwelling Hispanomeryx ever recorded in Iberia, demonstrating that the previous lack of Hispanomeryx fossils in the Vallès-Penedès Basin was due to insufficient sampling rather than to paleoecological absence. It is therefore apparent that Hispanomeryx was as environmentally plastic as its relative Micromeryx, inhabiting similar habitats that varied from dry and open to humid and forested.
Determination of Different Species of Animal from their Meats by Using PCR-RFLP Technique of Mitochondria Gene COI

Abstract: This study was conducted at Dr. Taleb A. Jaayad of Molecular Genetics, Department of Animal Production, College of Agriculture, University of Basrah. Samples of fresh and canned meat of cattle, buffalo, sheep, goats, chicken and turkey were collected randomly from different areas of Basrah province, as well as blood samples of camel. The aim was to determine different animal species from their meat (except camel). DNA was extracted from meat tissue (0.2 gm) and blood by using DNA kit (Invetrogen). DNA purity was estimated by using wavelength (260-280), to be 1.82. 0 ng. PCR was used to amplify mtco1 gene using a general primer and gave a band of 710 bp for all species used in this study. Different species were determined by using Taq restricted enzyme. Cattle, buffalo, chicken and turkey showed one band of 637 bp. Taq enzyme has recognized sheep and goat, while sheep did not show any band to the fragment 710 bp. However, goat showed a band at 650 bp. Furthermore, camel produced two bands of 303 and 403 bp.
A place in space - the horizontal vs vertical factors that influence zooplankton (Rotifera, Crustacea) communities in a mesotrophic lake

The factors that influence plankton distribution in lakes are currently widely debated. The primary objective of this study was to determine a combination of factors that influence the three-dimensional distribution patterns of both rotifer and crustacean communities in a pelagic ecosystem. We compared the abiotic (temperature, oxygen and nutrients) and biotic (phytoplankton) factors that affect the horizontal and vertical distribution of zooplankton in different habitat conditions in Lake Wigry. The results of our study indicate that the vertical gradient in a water profile is much more important for microcrustaceans than horizontal changes in environmental conditions, whereas Rotifera showed a strong spatial autocorrelation when connected with differences in trophic status. Generally, large zooplankton prefer cold, darker waters of the metalimnion-hypolimnion, while smaller zooplankton prefer the warm epilimnion. This niche segregation in water profiles promotes a large diversity of pelagic zooplankton. The vertical distribution of dominant Daphnia cucullata was strongly related to the phytoplankton distribution. Moreover, we found that the large-bodied Daphnia cucullata prefers the lower water layers, despite the presence of less optimal food resources, while smaller individuals clearly prefer the warm surface water with high quality resources.
Stomatal and non-stomatal limitations at different leaf temperatures to the photosynthetic process during the post-harvest period for Vitis vinifera cv. Chardonnay vines.

ABSTRACT Photosynthesis in Vitis vinifera cv. Chardonnay leaves was measured during the post-harvest period in relation to leaf temperatures and chloroplast CO2 concentrations to evaluate the limitations to photosynthesis once the fruit sink was removed. Photosynthesis was optimal at 30°C and rates were higher at high compared to low temperatures, consistent with the current climate. Stomatal limitation of photosynthesis ranged from 20% at low temperatures to 45% at high temperatures. RuBP carboxylation (Vcmax) and regeneration (Jmax) were optimal at 39 and 36°C, but their capacities were low below 25°C accounting for low assimilation rates. Chloroplast CO2 concentration transitioning between RuBP regeneration and RuBP carboxylation-limited assimilation, increased steeply with increasing temperature. Assimilation of Chardonnay leaves was limited by RuBP regeneration below 35°C and by RuBP carboxylation above 35°C, consistent with increased photorespiration at high temperatures. Results provide a quantitative explanation for the photosynthetic performance of Chardonnay vines in the post-harvest period.
ESTIMATED GENE EXPRESSION IN MEAT QUALITY TRAIT UNDER STRESS CONDITIONS FOR TWO BROILER STRAINS

The objective of this study was to estimated gene expression in breast muscles of two broiler strains with used to Myoustatin gene in marketing age (5 weeks of age) under heat stress and compared to control group for 1 hour daily for 7 days in Shalakan farm of Faculty of Agriculture, Ain Shams University, broiler chicks (150 chicks in each strains) of 1 day of age were used in this study. So, the measurements were taken (respiratory rate, rectal temperature and estimated gene expression). The results obtained the gene expression of Myostatin gene in muscle breast was observed highest in Ross strain compared with Indian River strain under heat stress, but no different between strains ( Ross and Indian River) in control group. However, respiratory rate of Ross and Indian River under heat at 5 week of age showed that the Indian River strain was high significant at 5 week of age compared to Ross ones. As shown that rectal temperature of Ross and Indian River were a high significant effect of treatment (heat group was higher from control group) and not a significant of strain.The present experiment was conducted to estimated gene expression on meat quality traits of different tropical stress conditions in different broiler strains during 7 days and 5 weeks of age. Introgressions some major genes likes myostatin gene in muscle breast into broiler improve under the heat stress.
Heuristic Problem Solving: The Next Advance in Operations Research

Address at the banquet of the Twelfth National Meeting of the Operations Research Society of America, Pittsburgh, Pennsylvania, November 14, 1957. Mr. Simon presented the paper; its content is a joint product of the authors. In this, they rely on the precedent of Genesis 27:22, “The voice is Jacob's voice, but the hands are the hands of Esau. ”
Phenoloxidase activity in hemolymph of naïve and HaNPV infected larvae of Helicoverpa armigera (HB), its characterization and inhibition

Helicoverpa armigera nucleo polyhedrosis virus (HaNPV) is the most promising bio-agent. However, as the age of the larvae increases, then susceptibility to HaNPV decreases. This becomes a bottleneck in its effectiveness. Present study deals with the reasons behind this decrease in efficacy. Role of phenoloxidase (PO) in age related resistance, characterization of PO was studied. Phenoloxidase activity was more in cellular fraction of hemolymph in normal larvae of H. armigera. Whereas it was high in plasma fraction of virosed larvae. Moreover its magnitude was more in 5 instar larvae as compared to 3 instar larvae. The Km of PO from virosed larvae decreased in respect to normal larvae, where as the Vmax in virosed larvae increased over that of normal larvae. Dopamine was found to be the best substrate than any other studied. Enzyme PO was optically active at 40C in normal larvae as well as virosed. The PO from normal and virosed larvae of H. armigera showed almost 100 % enzyme activity up to 30C, which decreased thereafter. Optimum pH for PO activity was found to be 9.0 for normal and virosed H. armigera larvae. Amongst all inhibitors of PO tested SDS was found to be the best followed by EGTA >PTU> EDTA > PMSF> DMSO > Garlic extract. Two PO isozymes were present in hemolymph of normal and virosed H armigera larvae.
Antibiotics can be used to contain drug-resistant bacteria by maintaining sufficiently large sensitive populations

Standard infectious disease practice calls for aggressive drug treatment that rapidly eliminates the pathogen population before resistance can emerge. When resistance is absent, this elimination strategy can lead to complete cure. However, when resistance is already present, removing drug-sensitive cells as quickly as possible removes competitive barriers that may slow the growth of resistant cells. In contrast to the elimination strategy, a containment strategy aims to maintain the maximum tolerable number of pathogens, exploiting competitive suppression to achieve chronic control. Here, we combine in vitro experiments in computer-controlled bioreactors with mathematical modeling to investigate whether containment strategies can delay failure of antibiotic treatment regimens. To do so, we measured the “escape time” required for drug-resistant Escherichia coli populations to eclipse a threshold density maintained by adaptive antibiotic dosing. Populations containing only resistant cells rapidly escape the threshold density, but we found that matched resistant populations that also contain the maximum possible number of sensitive cells could be contained for significantly longer. The increase in escape time occurs only when the threshold density—the acceptable bacterial burden—is sufficiently high, an effect that mathematical models attribute to increased competition. The findings provide decisive experimental confirmation that maintaining the maximum number of sensitive cells can be used to contain resistance when the size of the population is sufficiently large.
A rational theory of set size effects in working memory and attention

The precision with which items are encoded in working memory and attention decreases with the number of encoded items. Current theories typically account for this “set size effect” by postulating a hard constraint on the allocated amount of encoding resource. While these theories have produced models that are descriptively successful, they offer no principled explanation for the very existence of set size effects: given their detrimental consequences for behavioral performance, why have these effects not been weeded out by evolutionary pressure, by allocating resources proportionally to the number of encoded items? Here, we propose a theory that is based on an ecological notion of rationality: set size effects are the result of a near-optimal trade-off between behavioral performance and the neural costs associated with stimulus encoding. We derive models for four visual working memory and attention tasks and show that they account well for data from eleven previously published experiments. Moreover, our results suggest that the total amount of resource that subjects allocate for stimulus encoding varies non-monotonically with set size, which is consistent with our rational theory of set size effects but not with previous descriptive theories. Altogether, our findings suggest that set size effects may have a rational basis and highlight the importance of considering ecological costs in theories of human cognition.