Miracle-dz/UniFAR-FTUs huggingface dataset:
Nutrition Outweighs Defense: Myzus Persicae (Green Peach Aphid) Prefers and Performs Better on Young Leaves of Cabbage

Plant leaves of different ages differ in nutrition and toxic metabolites and thus exhibit various resistance levels against insect herbivores. However, little is known about the relationship between leaf ontogeny and plant resistance against phloem-feeding insects. In this study, we found that the green peach aphid, Myzus persicae Sulzer, preferred to settle on young cabbage leaves (Brassica oleracea L. var. capitata) rather than mature or old leaves, although young leaves contained the highest concentration of glucosinolates. Furthermore, aphids feeding on young leaves had higher levels of glucosinolates in their bodies, but aphids performed better on young leaves in terms of body weight and population growth. The concentration of glutamine in young leaves was the highest, which stimulated aphids feeding when added to the sucrose solution. Phloem sap of young leaves had higher amino acid:sucrose molar ratio than mature leaves, and aphids feeding on young leaves showed two times longer phloem feeding time and five times more dry honeydew excretion than on other leaves. These results indicate that aphids acquired the highest amount of nutrition and defensive metabolites when feeding on young cabbage leaves that are strong natural plant sinks. The higher phloem sap availability of young leaves likely contributes to the attractiveness and suitability for aphids and may compensate the negative effects of glucosinolates on aphids. According to these findings, we propose that phloem sap availability influenced by leaf ontogeny and source-sink status play a significant role in plant-aphid interaction, which desires more attention in future research.
Physiological and molecular studies on the akinete differentiation of filamentous cyanobacteria

2 | P a g e Abstract Akinetes are spore-like cells of filamentous cyanobacteria that allow these organisms to survive long periods of unfavourable conditions. The akinete differentiation and germination processes were studied in detail in two model species of cyanobacterial cell differentiation, the planktonic freshwater Anabaena variabilis ATCC 29413 and the terrestrial or symbiotic Nostoc punctiforme ATCC 29133. The best trigger of akinete differentiation of A. variabilis was low light, while of N. punctiforme was phosphate starvation. Akinetes differed from vegetative cells by their larger size, different cell morphology, and the presence of a large number of intracellular granules. The akinete envelopes of both strains were composed by the same glycolipids as heterocysts and by an exopolysaccharide layer. Also, an unknown and new lipid was detected in lipid extracts of A. variabilis akinetes. During akinete development the storage compounds cyanophycin, glycogen and lipid droplets transiently increased, and the photosynthesis and respiration activities decreased. In both strains, germination was an asynchronous process triggered by light. Fast cell divisions occurred inside of the akinetes envelope and did not need endogenous carbon or nitrogen resources but a functional photosystem to complete the process. Unusual fast heterocyst differentiation was observed during akinete germination in A. variabilis. Fast cell divisions and heterocysts differentiation during germination could have been supported by the high DNA content in akinetes. In the end of the germination process, the akinete envelope was opened (A. variabilis) or partially degraded (N. punctiforme) allowing the emergence of the short filament formed. At this point, the photosynthesis and respiration rates were similar to a vegetative cells culture. Focusing on the specific modulation of the cell wall and cell envelope, proteins were identified that are differentially expressed in akinetes or where shown to be involved in cell differentiation in N. punctiforme. One mutant was created in the ΔAva_2312 gene of A. variabilis encoding a protein with putative function associated to cell wall proteins and characterized. This mutant showed a severe filament dystrophy and it was not able to differentiate heterocysts and to grow without a combined nitrogen source. In addition, a thicker peptidoglycan with more noncrosslinked peptides residues was observed in the septum. Finally, this mutant differentiated akinete-like cells lacking a lipid envelope.
Piloting a polychotomous partial-credit scoring procedure in a multiple-choice test

Abstract Multiple-choice (MC) tests are frequently used to measure language competence because they are quick, economical and straightforward to score. While degrees of correctness have been investigated for partially correct responses in combined-response MC tests, degrees of incorrectness in distractors and the role they play in determining the test-taker's final score remain comparatively unexplored. This pilot study examines degrees of incorrectness in MC test items and their potential impact on the overall reliability of scoring procedures, test micro impact, and scoring performance of individual test-takers. Investigating the above properties as quality dimensions of language testing is crucial since decisions made on the basis of such tests influence the careers and lives of test-takers. Three scoring procedures were applied to an authentic test: dichotomous, which is straightforward – correct/incorrect; polychotomous, which offers partial credit to very plausible and plausible options; and negative, which includes negative scoring when a wholly incorrect answer is selected. While these three procedures proved to be equally reliable, the polychotomous scoring method offered more sensitive and precise results, while negative scoring was particularly disadvantageous for test-takers. The polychotomous method of scoring moves away from the absolute right or wrong view and enhances sensitivity in the field of individualised language testing.
Quality of experience and video services adaptation

With the network heterogeneity and increasing demand of multimedia services, Quality of Experience (QoE) becomes a crucial determinant of the success or failure of these services. In this thesis, we first propose to analyze the impact of quality metrics on user engagement, in order to understand the effects of video metrics (video startup time, average bitrate, buffering ratio) and content popularity on user engagement. Our results show that video buffering and content popularity are critical parameters which strongly impacts the end-user’s satisfaction and user engagement, while the video startup time appears as less significant. On other hand, we consider subjective approaches such as the Mean Opinion Score (MOS) for evaluating QoE, in which users are required to give their assessment according to contextual information. A detailed statistical analysis of our study shows the existence of non-trivial parameters impacting MOS (the type of device and the content type). We propose mathematical models to develop functional relationships between the QoE and the context information which in turn permits us to estimate the QoE. A video content optimization technique called MDASH (for MOS Dynamic Adaptive Streaming over HTTP) is proposed, which improves the perceived QoE for different video sessions sharing the same local network, while taking QoE fairness among users as a leitmotiv. We also propose a utility-based approach for video delivery optimization, in which a global utility function is computed based on different constraints (e.g. target strategies coming from the actors of the delivery chain)
Consideration of connection availability optimization in optical networks

Availability calculations of generalized span and path protected connections based on reference failure and repair times are performed. A case study analyzes the availability of a connection within a long haul network using three protection strategies: path protection, span protection and protection-cycles. A sensitivity analysis shows the dependency of the achieved connection availabilities on reliability data and the resulting improvement and optimization potential. Optimization aspects are completed by an estimation of spare parts provisioning and corrective maintenance actions.
Switching between different state representations in reinforcement learning

This paper proposes a reinforcement learning architecture containing multiple "experts", each of which is a specialist in a different region in the overall state space. The central idea is that the different experts use qualitatively different (but sufficiently Markov) state representations, each of which captures different information regarding the true underlying world state, and which for that reason is suitable for a different part of the state space. The experts themselves learn to switch to another state representation (other expert) by having switching actions. Value functions can be learned using standard reinforcement learning algorithms. This architecture has important advantages in RL problems that have large state spaces or where a sensor system must inherently choose between mutually exclusive state representations. Experiments in a small, proof-of-principle experiment as well as a larger, more realistic experiment illustrate the validity of this approach
Partitioning the Effects of Eco-Evolutionary Feedbacks on Community Stability

A fundamental challenge in ecology continues to be identifying mechanisms that stabilize community dynamics. In recent years, there has been growing empirical evidence highlighting that eco-evolutionary feedbacks can dramatically impact community-level properties, including stability. Moreover, there is evidence that evolution happens at rates ranging from slower than to commensurate to ecological rates, and this affects the impact of feedbacks. Theoretical work to mechanistically understand how eco-evolutionary feedbacks impact stability has focused on specific ecological modules with just one or two evolving species. Here, we provide a general framework for determining the effects of eco-evolutionary feedbacks on stability in communities with an arbitrary number of interacting species and evolving traits for when evolution is slow and fast. We characterize how these feedbacks lead to stable communities that would be unstable in the absence of the feedbacks, and vice versa. In addition, we show how this characterization provides a partitioning of the roles of direct and indirect feedbacks between ecological and evolutionary processes on community stability, and how this partitioning depends on the rate of evolution relative to ecology. Applying our methods to models of competing species and food chains, we demonstrate how the functional form of trade offs, genetic correlations between traits, and the rate of evolution determine whether eco-evolutionary feedbacks stabilize or destabilize community dynamics.
Review Article FUNDAMENTALS OF APPLIED RESEARCH AND SAMPLING TECHNIQUES

Research is an inseparable part of human knowledge activity. Fundamentals of research and sampling techniques plays important role in diverse problems of applied sciences, agricultural sciences, health sciences, environmentrelated studies and business research. Many researchers are conducted by survey research. The technique of research, sampling and determination of sample size has crucial role in field investigation as well as survey-based research problems in applied research. Specific sampling techniques are used for specific research problems because one technique and sample size may not be appropriate for all problems. The present paper based on basic knowledge of research and some commonly used techniques of sampling and determination of sample size for specific purposes.
Multilevel and sex-specific selection on competitive traits in North American red squirrels

Individuals often interact more closely with some members of the population (e.g. offspring, siblings or group members) than they do with other individuals. This structuring of interactions can lead to multilevel natural selection, where traits expressed at the group-level influence fitness alongside individual-level traits. Such multilevel selection can alter evolutionary trajectories, yet is rarely quantified in the wild, especially for species that do not interact in clearly demarcated groups. We quantified multilevel natural selection on two traits, postnatal growth rate and birth date, in a population of North American red squirrels (Tamiasciurus hudsonicus). The strongest level of selection was typically within-acoustic social neighbourhoods (within 130m of the nest), where growing faster and being born earlier than nearby litters was key, while selection on growth rate was also apparent both within-litters and within-study areas. Higher population densities increased the strength of selection for earlier breeding, but did not influence selection on growth rates. Females experienced especially strong selection on growth rate at the within-litter level, possibly linked to the biased bequeathal of the maternal territory to daughters. Our results demonstrate the importance of considering multilevel and sex-specific selection in wild species, including those that are territorial and sexually monomorphic. Data archival: the data set is archived on Dryad (info XXX), with a five-year embargo from the date of publication.
Phytase in diets with crude protein levels for commercial layers

The aim of this study was to evaluate the action of the phytase enzyme in diets formulated with variations in the crude protein content on performance and egg quality of commercial layers. A total of 336 commercial layers were housed at eight birds per cage in a 3 × 2 factorial arrangement with seven replicates. Treatments consisted of four crude-protein levels (17, 15, and 13%) and two enzyme levels (0 and 500 FTU kg -1 diet), distributed in a completely randomized design. Feed intake, egg production, feed conversion per dozen eggs and per kilogram, egg weight and mass, specific gravity, eggshell thickness, and Haugh unit were measured over five 28-day periods. The performance of commercial layers fed the diet containing 13% crude protein worsened, irrespective of phytase addition. However, at 15% crude protein, phytase inclusion did not affect feed conversion or egg weight. Inclusion of phytase leads to equal egg-quality and performance results at the dietary crude protein levels of 17 and 15%. The crude protein content of 13%, with or without phytase, is not recommended for the diet of brown-egg layers.
Dorsal anterior cingulate-midbrain ensemble as a reinforcement meta-learner

The dorsal anterior cingulate cortex (dACC) is central in higher-order cognition and behavioural flexibility. Reinforcement Learning, Bayesian decision-making, and cognitive control are currently the three main theoretical frameworks within which the elusive computational nature of this brain area is chased after–but with overall limited success. Here we propose a new model–the Reinforcement Meta Learner (RML)–in which we exploit core insights into the anatomical connections of the ACC with two midbrain catecholamine nuclei (VTA and LC). With its dual role of selecting and implementing optimal decisions (via VTA) and learning to control its own learning parameters (via LC), the RML generates an autonomous control system with the ability of learning to solve hierarchical decision problems without having an intrinsic hierarchical structure itself. We discuss how our model accounts for an unprecedented number of empirical findings across various cognitive domains, assimilates various previously proposed ACC computations while respecting biological constraints, and provides theoretical integration at various levels. The theoretical pillars of our work promise a generic template (i.e., recurrent connectivity between cortex and midbrain) with which meta-cognition can be computationally approached.
Trichoderma reesei complete genome sequence, repeat-induced point mutation and partitioning of CAZyme gene clusters

Trichoderma reesei (Ascomycota, Pezizomycotina) QM6a is a model fungus for a broad spectrum of physiological phenomena, including plant cell wall degradation, industrial production of enzymes, light responses, conidiation, sexual development, polyketide biosynthesis and plant-fungal interactions. The genomes of QM6a and its high-enzyme producing mutants have been sequenced by second-generation-sequencing methods and are publicly available from the Joint Genome Institute (JGI). While these genome sequences have offered useful information for genomic and transcriptomic studies, their limitations and especially their short read lengths make them poorly suited for some particular biological problems, including assembly, genome-wide determination of chromosome architecture and genetic modification or engineering. We integrated Pacific Biosciences and Illumina sequencing platforms for the highest-quality genome assembly yet achieved, revealing seven telomere-to-telomere chromosomes (34,922,528 bp; 10877 genes) with 1630 newly-predicted genes and >1.5 Mb of new sequences. Most new sequences are located on AT-rich blocks, including 7 centromeres, 14 subtelomeres and 2329 interspersed AT-rich blocks. The seven QM6a centromeres separately consist of 24 conserved repeats and 37 putative centromere-encoded genes. These findings open up a new perspective for future centromere and chromosome architecture studies. Next, we demonstrate that sexual crossing readily induced cytosine-to-thymine point mutations on both tandem and unlinked duplicated sequences. We also show by bioinformatic analysis that Trichoderma reesei has evolved a robust repeat-induced point mutation (RIP) system to accumulate AT-rich sequences, with longer AT-rich blocks having more RIP mutations. The widespread distribution of AT-rich blocks correlates genome-wide partitions with gene clusters, explaining why clustering of genes has been reported to not influence gene expression in Trichoderma reesei. Compartmentation of ancestral gene clusters by AT-rich blocks might promote flexibilities that are evolutionarily advantageous in this fungus’ soil habitats and other natural environments. Our analyses, together with the complete genome sequence, provide a better blueprint for biotechnological and industrial applications.
Prior expectations induce pre-stimulus sensory templates

Perception can be described as a process of inference, integrating bottom-up sensory inputs and top-down expectations. However, it is unclear how this process is neurally implemented. It has been proposed that expectations lead to pre-stimulus baseline increases in sensory neurons tuned to the expected stimulus, which in turn affects the processing of subsequent stimuli. Recent fMRI studies have revealed stimulus-specific patterns of activation in sensory cortex as a result of expectation, but this method lacks the temporal resolution necessary to distinguish pre- from post-stimulus processes. Here, we combined human MEG with multivariate decoding techniques to probe the representational content of neural signals in a time-resolved manner. We observed a representation of expected stimuli in the neural signal well before they were presented, demonstrating that expectations indeed induce a preactivation of stimulus templates. These results suggest a mechanism for how predictive perception can be neurally implemented.
Serotyping and Adaptation of Foot and Mouth Disease Virus in BHK-21 Cell Line towards the Development of Vaccine Candidate

This research work was conducted for isolation, identification and serotyping of Foot and Mouth Disease (FMD) virus from the field isolates of Gouripur Upazila of Mymensingh district, Bangladesh. Samples were collected from infected cattle in virus transportation medium and transported at the Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh with maintain proper cool chain duringOctober to April 2012. Inocula were prepared from the collected samples and treated with antibiotics-antimycotics, preserved at -20°C for isolation and serotyping of the virus by antigen detecting ELISA method. After serotyping, the prepared inoculum was inoculated into 24hours confluent BHK-21 cell culture separately and incubated at 37°C for 48hours for development of CPE. Within 48hours of post infection, complete development of cytopathic effects (CPE) in BHK-21 cell culture were observed under inverted microscope which included the rounding and flattening of the cells, breaking down of the intracellular bridges and finally cell death which indicated the presence of FMD virus. Clear BHK-21 cell culture fluid was collected and preserved at -80°C as seed. Of the 20 samples, 15(75%) samples were found positive for FMDV in cell culture of which 13 samples of tongue epithelia (86.67%) and 2 samples of foot tissues (40%) were positive on the basis of cytopathic effects (CPE). Again the prepared inoculum was taken for serotyping the virus by ELISA method. On the basis of the result of ELISA, it was concluded that the serotype of the FMD virus of the collected field isolate was serotype “O”.
A Study on the Incidental Development of English Competence in CMC, Focusing on Syntactic and Lexical Mastery

CMC has lent itself to a powerful motivator for authentic L2 interaction. Based on a corpus complied from a series of CMC interactions between college level native speakers and non-speakers of English at the graduate level, this paper explores incidental development in English, i.e, the by-products of asynchronous CMC interaction. Messages sampled to represent CMC discussion over a three-month period indicated an enhancement in syntactic and lexical development as well as in the overall proficiency. While syntactic enhancement as reflected in the human ratings was not significant, a reliable improvement was found in a quantitative investigation. Lexical development was apparent in the qualitative measures, but was not significant in the quantitative measures. Given a choice of syntactic and lexical competence, the judgment of written proficiency appeared to be slightly more inclined to lexical competence. The results in support of the efficacy of CMC for language learning suggest a curriculum that incorporates CMC into a content-based classroom.
DNA damage is a major cause of sequencing errors, directly confounding variant identification

Pervasive mutations in somatic cells generate a heterogeneous genomic population within an organism and may result in serious medical conditions. While cancer is the most studied disease associated with somatic variations, recent advances in single cell and ultra deep sequencing indicate that a number of phenotypes and pathologies are impacted by cell specific variants. Currently, the accurate identification of low allelic frequency somatic variants relies on a combination of deep sequencing coverage and multiple evidences of the presence of variants. However, in this study we show that false positive variants can account for more than 70% of identified somatic variations, rendering conventional detection methods inadequate for accurate determination of low allelic variants. Interestingly, these false positive variants primarily originate from mutagenic DNA damage which directly confounds determination of genuine somatic mutations. Furthermore, we developed and validated a simple metric to measure mutagenic DNA damage, and demonstrated that mutagenic DNA damage is the leading cause of sequencing errors in widely used resources including the 1000 Genomes Project and The Cancer Genome Atlas.