Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural selection interacts with recombination to shape the evolution of hybrid genomes

Selection, recombination, and hybrid evolution Hybridization is an important force in evolution. The effects of hybridization across the whole genome are not understood. Using a fine-scale genetic map, Schumer et al. examined local ancestry in replicate natural hybrid populations of swordtail fish. Each parental species contributes different proportions of genetic material to the genomes of their descendants. Genes from the “minor” (less well-represented) parent occur in regions of the genome that are subject to higher recombination rates and where there are fewer potentially deleterious genes. Neanderthal ancestry in human genomes shows similar patterns. Science, this issue p. 656 In hybrid fish, the “minor” parent species can be predicted from local recombination rates. To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the “minor” parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human and archaic admixture. These results support models in which ancestry from the minor parental species is more likely to persist when rapidly uncoupled from alleles that are deleterious in hybrids. Our analyses further indicate that selection on swordtail hybrids stems predominantly from deleterious combinations of epistatically interacting alleles.
Current evidence linking diet to gut microbiota and brain development and function

Abstract The gut:brain axis is emerging as an important information highway linking the foods we eat with neurophysiological development and functions. Some gut microorganisms have shown to alleviate anxiety and depression, improve cognitive performance and play a role in brain development in early life. However, most studies were conducted in laboratory animals and these findings await confirmation in carefully designed human interventions. Similarly, little attention has been given to how diet:microbe interactions within the gut can impact on neurotransmitter production or their subsequent biological effects within the nervous system. In this review, we discuss the possible influence of carbohydrates, polyphenols, lipids and proteins colonic fermentation on production, bioavailability and biological activity of metabolites linked to the gut-microbiota-brain axis. An increased understanding of how nervous system may be regulated by diet will greatly enhance our ability to design dietary strategies to improve healthy brain development and functions. Graphical Abstract
Universal patterns of inequality

Probability distributions of money, income and energy consumption per capita are studied for ensembles of economic agents. The principle of entropy maximization for partitioning of a limited resource gives exponential distributions for the investigated variables. A non-equilibrium difference of money temperatures between different systems generates net fluxes of money and population. To describe income distribution, a stochastic process with additive and multiplicative components is introduced. The resultant distribution interpolates between exponential at the low end and power law at the high end, in agreement with the empirical data for the USA. We show that the increase in income inequality in the USA originates primarily from the increase in the income fraction going to the upper tail, which now exceeds 20% of the total income. Analyzing the data from the World Resources Institute, we find that the distribution of energy consumption per capita around the world can be approximately described by the exponential function. Comparing the data for 1990, 2000 and 2005, we discuss the effect of globalization on the inequality of energy consumption.
Lossless video coding using variable block-size MC and 3D prediction optimized for each frame

This paper proposes an efficient lossless coding scheme for video signals. The coding scheme utilizes a novel block-adaptive 3D prediction method which predicts a video signal at each pel based on both the current frame and the motion-compensated previous frame. The resulting prediction errors are encoded using a kind of context-adaptive arithmetic coding. In order to improve coding efficiency, not only prediction coefficients of the 3D linear prediction but also motion vectors in all the blocks are iteratively optimized for each frame so that a coding rate of prediction errors can have a minimum. Moreover, a variable block-size motion compensation technique is employed for efficient representation of motion information. Experimental results show that coding rates of the proposed scheme are 18-55% lower than those of the JPEG-LS based intra-frame coding scheme.
Predicating Load Latencies Using Cache Profiling

cache profiling, simulation, cache management instructions, prefetching, memory system analysis, program characterization Due to increasing cache-miss latencies, cache control instructions are being implemented for future systems. In order to investigate the potential benefit of using these instructions in compiling a broad range of applications, we study the memory referencing behavior of individual machine-level instructions using simulations of fully-associative caches. Our objective is to obtain a deeper understanding of useful program behavior that can be eventually employed at optimizing programs and to motivate architectural features aimed at improving the efficacy of memory hierarchies. Our simulation results show that a small number of load instructions account for a majority of data cache misses in the SPEC89 benchmarks. Most load instructions rarely miss the data cache and a few instructions have miss rates much higher than the global miss ratio. We develop a model where the cost associated with scheduling loads with miss latencies is parameterized. Using this model, we explore the potential net benefit associated with profile-based scheduling of load instructions where some loads are selected for scheduling with miss latencies based on their behavior under profiling. Finally, we investigate the sensitivity of cache profiling information to input data sets. In many cases, the profile information obtained using one data set is quite effective in predicting the behavior of a program on other data sets, but in some cases the predicted caching behavior is quite different from the actual behavior.
Direct and indirect effects of an invasive planktonic predator on pelagic food webs

The relative importance of top‐down invader effects relative to environmental drivers was determined by sampling crustacean zooplankton, rotifer, and phytoplankton communities in a set of invaded and noninvaded reference lakes. The non‐native invertebrate predator Bythotrephes had significant effects on zooplankton community size structure, rotifers, and phytoplankton taxonomic composition, but no significant effects on crustacean zooplankton taxonomic and functional group composition. Part of the variation in phytoplankton communities was explained by the presence of the invader. Because Bythotrephes is generally known to be a carnivore and to not consume phytoplankton, this effect is likely mediated by the zooplankton community's response to environmental gradients. Although Bythotrephes appears to indirectly alter phytoplankton composition in invaded lakes, there was no evidence of a trophic cascade, and edible phytoplankton biovolume did not increase in invaded lakes. These complex direct and indirect interactions suggest that effects of invaders may be highly context‐dependent, and therefore pose a significant challenge for predicting wider community and ecosystem responses.
A general method to predict the amplitude of oscillation in nearly sinusoidal oscillators

In this paper, a general methodology for predicting the amplitude of oscillation in nearly sinusoidal oscillators is presented. The method relies on the recently proposed projection technique for the computation of the center manifold and on the Hopf normal form theory to approximate the corresponding limit cycle in state space. The Colpitts oscillator is selected as a case study and, for this circuit, a closed-form expression for the amplitude of oscillation is derived as a function of the circuit parameters.
Hybrid Carbon Nanotubes–TiO2 Photoanodes for High Efficiency Dye-Sensitized Solar Cells

We describe a fast and effective procedure for the preparation of high efficiency hybrid photoanodes for dye-sensitized solar cells (DSCs), based on nanocrystalline TiO2 with limited addition of multiwall carbon nanotubes (CNTs). The mixing process between CNTs and TiO2 nanoparticles is almost instantaneous, which makes it feasible for large-scale fabrication. Enhanced electron lifetime and reduced charge recombination lead to highly increased short circuit current density and overall photoconversion efficiency (from 13.6 mA cm–2 to 16.0 mA cm–2 and from 7.0% to 9.0%, respectively, considering the bare TiO2 and the optimum CNTs concentration, which is 0.010 wt %), while the small reduction in open circuit photovoltage does not significantly affect cell performances. This result is remarkable since a standard dye molecule (N719) was used and no chemical treatments of the photoanodes prior to cell fabrication were applied (i.e., soaking in TiCl4 to boost open circuit photovoltage).
Monkey Algorithm for Global Numerical Optimization

In this paper, monkey algorithm (MA) is designed to solve global numerical optimization problems with continuous variables. The algorithm mainly consists of climb process, watch-jump process, and somersault process in which the climb process is employed to search the local optimal solution, the watch-jump process to look for other points whose objective values exceed those of the current solutions so as to accelerate the monkeys’ search courses, and the somersault process to make the monkeys transfer to new search domains rapidly. The proposed algorithm is applied to efiectively solve the benchmark problems of global optimization with 30, 1000 or even 10000 dimensions. The computational results show that the MA can flnd optimal or near-optimal solutions to the problems with a large dimensions and very large numbers of local optima. c
Immobilization of Proteins in Silica Gel: Biochemical and Biophysical Properties

The development of silica-based sol-gel techniques compatible with the retention of protein structure and function started more than 20 years ago, mainly for the design of biotechnological devices or biomedical appli- cations. Silica gels are optically transparent, exhibit good mechanical stability, are manufactured with different geometries, and are easily separated from the reaction media. Biomolecules encapsulated in silica gel normally re- tain their structural and functional properties, are stabilized with respect to chemical and physical insults, and can sometimes exhibit enhanced activity in comparison to the soluble form. This review briefly describes the chemistry of protein encapsula- tion within the pores of a silica gel three-dimensional network, the mechanism of interaction between the protein and the gel matrix, and its effects on protein structure, function, stability and dynamics. The main applications in the field of biosensor design are described. Special emphasis is devoted to silica gel encapsulation as a tool to selectively stabilize subsets of protein conformations for biochemical and biophysical studies, an application where silica-based encapsulation demonstrated superior performance with respect to other immo- bilization techniques.
Telephone-quality pathological speech classification using empirical mode decomposition

This paper presents a computationally simple and effective methodology based on empirical mode decomposition (EMD) for classification of telephone quality normal and pathological speech signals. EMD is used to decompose continuous normal and pathological speech signals into intrinsic mode functions, which are analyzed to extract physically meaningful and unique temporal and spectral features. Using continuous speech samples from a database of 51 normal and 161 pathological speakers, which has been modified to simulate telephone quality speech under different levels of noise, a linear classifier is used with the feature vector thus obtained to obtain a high classification accuracy, thereby demonstrating the effectiveness of the methodology. The classification accuracy reported in this paper (89.7% for signal-to-noise ratio 30 dB) is a significant improvement over previously reported results for the same task, and demonstrates the utility of our methodology for cost-effective remote voice pathology assessment over telephone channels.
A New Design of Doherty Amplifiers Using Defected Ground Structure

In this letter, a new Doherty power amplifier having the ideal harmonic termination condition that has been usually ignored is proposed. A defected ground structure (DGS) is adopted on the ground pattern of the output lambda/4 impedance inverter of the carrier amplifier and output offset transmission line of the peaking amplifier that are essential for proper load modulation operation of a conventional Doherty amplifier. As a result of the second and third harmonic termination, excellent improvement in power added efficiency (PAE), gain, maximum output power as well as linearity is obtained. The acquired improvements in gain, maximum output power (P1 dB), PAE, and adjacent channel leakage ratio to wideband code division multiple access 2FA signal are 0.33 dB, 0.42 dB, 12.7%, and 5.1 dB, respectively. Moreover, physical length of microstrip line is shortened fairly by DGS, therefore the whole amplifier circuit size is considerably reduced
Huberine, a New Canthin-6-One Alkaloid from the Bark of Picrolemma huberi

A new alkaloid, Canthin-6-one, Huberine (1), together with three known compounds including 1-Hydroxy-canthin-6-one (2), Canthin-6-one (3) and stigma sterol (4), were isolated from the stem bark of Picrolemma huberi. The isolation was achieved by chromatographic techniques and the purification was performed on a C18 column using acetonitrile/water (90:10, v/v) with 0.1% formic acid as the mobile phase. The structural elucidation was performed via spectroscopic methods, notably 1D- and 2D-NMR, UV, IR, MS and HRMS. The antiplasmodial activity of the compounds was studied.
Evaluation of Workpiece Temperature during Drilling of GLARE Fiber Metal Laminates Using Infrared Techniques: Effect of Cutting Parameters, Fiber Orientation and Spray Mist Application

The rise in cutting temperatures during the machining process can influence the final quality of the machined part. The impact of cutting temperatures is more critical when machining composite-metal stacks and fiber metal laminates due to the stacking nature of those hybrids which subjects the composite to heat from direct contact with metallic part of the stack and the evacuated hot chips. In this paper, the workpiece surface temperature of two grades of fiber metal laminates commercially know as GLARE is investigated. An experimental study was carried out using thermocouples and infrared thermography to determine the emissivity of the upper, lower and side surfaces of GLARE laminates. In addition, infrared thermography was used to determine the maximum temperature of the bottom surface of machined holes during drilling GLARE under dry and minimum quantity lubrication (MQL) cooling conditions under different cutting parameters. The results showed that during the machining process, the workpiece surface temperature increased with the increase in feed rate and fiber orientation influenced the developed temperature in the laminate.
Preclinical development of HIvax: Human survivin highly immunogenic vaccines

Our previous work involved the development of a recombinant fowlpox virus encoding survivin (FP-surv) vaccine that was evaluated for efficacy in mesothelioma mouse models. Results showed that FP-surv vaccination generated significant immune responses, which led to delayed tumor growth and improved animal survival. We have extended those previous findings in the current study, which involves the pre-clinical development of an optimized version of FP-surv designed for human immunization (HIvax). Survivin-derived peptides for the most common haplotypes in the human population were identified and their immunogenicity confirmed in co-culture experiments using dendritic cells and T cells isolated from healthy donors. Peptides confirmed to induce CD8+ and CD4+ T cells activation in humans were then included in 2 transgenes optimized for presentation of processed peptides on MHC-I (HIvax1) and MHC-II (HIvax2). Fowlpox vectors expressing the HIvax transgenes were then generated and their efficacy was evaluated with subsequent co-culture experiments to measure interferon-γ and granzyme B secretion. In these experiments, both antigen specific CD4+ and CD8+ T cells were activated by HIvax vaccines with resultant cytotoxic activity against survivin-overexpressing mesothelioma cancer cells. These results provide a rationale for clinical testing of HIvax1 and HIvax2 vaccines in patients with survivin-expressing cancers.
Effects of impurities on membrane-protein crystallization in different systems

The effects of commonly encountered impurities on various membrane-protein crystallization regimes are investigated and it is found that the lipidic cubic phase crystallization methodology is the most robust, tolerating protein contamination levels of up to 50%, with little effect on crystal quality. If generally applicable, this tolerance may be exploited (i) in initial crystallization trials to determine the ‘crystallizability’ of a given membrane-protein and (ii) to subject partially pure membrane-protein samples to crystallization trials.
Scaling the propulsive performance of heaving flexible panels

Abstract We present an experimental investigation of flexible panels actuated with heave oscillations at their leading edge. Results are presented from kinematic video analysis, particle image velocimetry, and direct force measurements. Both the trailing edge amplitude and the mode shapes of the panel are found to scale with dimensionless parameters originating from the Euler–Bernoulli beam equation. The time-averaged net thrust increases with heaving frequency, but experiences localized boosts near resonant frequencies where the trailing edge amplitude is maximized. These boosts correspond to local maxima in the propulsive efficiency. For a constant heave amplitude, the time-averaged net thrust coefficient is shown to be a function of Strouhal number over a wide range of conditions. It appears, therefore, that self-propelled swimming (zero net thrust) only occurs over a small range of Strouhal numbers. Under these near-constant Strouhal number conditions, the propulsive economy increases with higher flexibilities and slower swimming speeds.
Effect of turbulence on the energetics of foraging in Atlantic cod Gadus morhua larvae

A net energy gain (NEG) model was used to assess the effects of turbulence on the energy budget of Atlantic cod Gadus morhua larvae, feeding on copepod nauplii at different concen- trations. The geometry of their prey search space was parameterised as either a sphere, hemisphere (the most commonly applied in analogous studies), or wedge. Observed distributions in behaviour (e.g. move duration, pause duration, turn angles) were used as model input, and 2 facets of this behaviour (move duration and move speed) were varied to examine how parameterised changes in foraging behaviour can affect the NEG of the predator. At a prey concentration of 100 l -1 , and in sta- tic water, NEG is an order of magnitude higher for a hemispherical shape relative to a wedge-shaped search volume. This difference decreases with increasing prey concentration (600 l -1 ), but always remains considerable. When parameterised turbulence was added, prey capture rates for a larva with a hemispherical search space increases 3 times as much as for a larva with a wedge-shaped search space (typically a 50% increase using the hemisphere vs 15% using a wedge). Thus, when this one key assumption (the search volume shape) of current turbulence-effects models is more realistically parameterised, the theorized advantage of turbulence is greatly reduced (at the level of the animal's prey capture and NEG). This result demonstrates the need to carefully reassess the underlying assumptions of current turbulence-effects models and, therefore, the conclusions that have been based upon those models. Our NEG model also demonstrates the energetic benefits of certain changes in larval behaviour — such as shorter move durations — which lead to a more thorough and cost-effective search of the surrounding water for larvae with a wedge-shaped search volume. This latter effect is not observed for predators with spherical or hemispherical search volumes. These results indicate that it would be prudent to reconsider the conclusions of any previous study that was based upon over-simplified search space geometries.
A Statistical Model to Identify Differentially Expressed Proteins in 2D PAGE Gels

Two dimensional polyacrylamide gel electrophoresis (2D PAGE) is used to identify differentially expressed proteins and may be applied to biomarker discovery. A limitation of this approach is the inability to detect a protein when its concentration falls below the limit of detection. Consequently, differential expression of proteins may be missed when the level of a protein in the cases or controls is below the limit of detection for 2D PAGE. Standard statistical techniques have difficulty dealing with undetected proteins. To address this issue, we propose a mixture model that takes into account both detected and non-detected proteins. Non-detected proteins are classified either as (a) proteins that are not expressed in at least one replicate, or (b) proteins that are expressed but are below the limit of detection. We obtain maximum likelihood estimates of the parameters of the mixture model, including the group-specific probability of expression and mean expression intensities. Differentially expressed proteins can be detected by using a Likelihood Ratio Test (LRT). Our simulation results, using data generated from biological experiments, show that the likelihood model has higher statistical power than standard statistical approaches to detect differentially expressed proteins. An R package, Slider (Statistical Likelihood model for Identifying Differential Expression in R), is freely available at http://www.cebl. auckland.ac. nz/slider.php.
Boundaries versus Onsets in Syllabic Segmentation

This study investigated the explicit syllabification of CVCV words in French. In a first syllable-reversal experiment, most responses corresponded to the expected canonical CV.CV segmentation, but a small proportion included the intervocalic consonant in both the first and second syllables, a result previously interpreted for English as indicating ambisyllabicity. Two further partial-repetition experiments showed that listeners systematically include the consonant in the onset of the second syllable, but also often include it in the offset of the first syllable. In addition, the assignment of the intervocalic consonant to the first and second syllables was differentially sensitive to the sonority of the consonant and to its spelling. We argue that the findings are inconsistent with the traditionally held boundary conception and instead support the view that distinct processes are involved in locating the onsets and the offsets of syllables. Onset determination is both more reliable and more dominant. Finally, we propose that syllable onsets serve as alignment points for the lexical search process in continuous spoken word recognition.