Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-lethal sampling for assessment of mitochondrial function does not affect metabolic rate and swimming performance

A fundamental issue in the metabolic field is whether it is possible to understand underlying mechanisms that characterize individual variation. Whole-animal performance relies on mitochondrial function as it produces energy for cellular processes. However, our lack of longitudinal measures to evaluate how mitochondrial function can change within and among individuals and with environmental context makes it difficult to assess individual variation in mitochondrial traits. The aims of this study were to test the repeatability of muscle mitochondrial metabolism by performing two biopsies of red muscle, and to evaluate the effects of biopsies on whole-animal performance in goldfish Carassius auratus. Our results show that basal mitochondrial respiration and net phosphorylation efficiency are repeatable at 14-day intervals. We also show that swimming performance (optimal cost of transport and critical swimming speed) was repeatable in biopsied fish, whereas the repeatability of individual oxygen consumption (standard and maximal metabolic rates) seemed unstable over time. However, we noted that the means of individual and mitochondrial traits did not change over time in biopsied fish. This study shows that muscle biopsies allow the measurement of mitochondrial metabolism without sacrificing animals and that two muscle biopsies 14 days apart affect the intraspecific variation in fish performance without affecting average performance of individuals. This article is part of the theme issue ‘The evolutionary significance of variation in metabolic rates’.
Tissue-specific metabolic enzyme levels covary with whole-animal metabolic rates and life-history loci via epistatic effects

Metabolic rates, including standard (SMR) and maximum (MMR) metabolic rate have often been linked with life-history strategies. Variation in context- and tissue-level metabolism underlying SMR and MMR may thus provide a physiological basis for life-history variation. This raises a hypothesis that tissue-specific metabolism covaries with whole-animal metabolic rates and is genetically linked to life history. In Atlantic salmon (Salmo salar), variation in two loci, vgll3 and six6, affects life history via age-at-maturity as well as MMR. Here, using individuals with known SMR and MMR with different vgll3 and six6 genotype combinations, we measured proxies of mitochondrial density and anaerobic metabolism, i.e. maximal activities of the mitochondrial citrate synthase (CS) and lactate dehydrogenase (LDH) enzymes, in four tissues (heart, intestine, liver, white muscle) across low- and high-food regimes. We found enzymatic activities were related to metabolic rates, mainly SMR, in the intestine and heart. Individual loci were not associated with the enzymatic activities, but we found epistatic effects and genotype-by-environment interactions in CS activity in the heart and epistasis in LDH activity in the intestine. These effects suggest that mitochondrial density and anaerobic capacity in the heart and intestine may partly mediate variation in metabolic rates and life history via age-at-maturity. This article is part of the theme issue ‘The evolutionary significance of variation in metabolic rates’.
Interactive effects of intrinsic and extrinsic factors on metabolic rate

Metabolism energizes all biological processes, and its tempo may importantly influence the ecological success and evolutionary fitness of organisms. Therefore, understanding the broad variation in metabolic rate that exists across the living world is a fundamental challenge in biology. To further the development of a more reliable and holistic picture of the causes of this variation, we review several examples of how various intrinsic (biological) and extrinsic (environmental) factors (including body size, cell size, activity level, temperature, predation and other diverse genetic, cellular, morphological, physiological, behavioural and ecological influences) can interactively affect metabolic rate in synergistic or antagonistic ways. Most of the interactive effects that have been documented involve body size, temperature or both, but future research may reveal additional ‘hub factors’. Our review highlights the complex, intimate inter-relationships between physiology and ecology, knowledge of which can shed light on various problems in both disciplines, including variation in physiological adaptations, life histories, ecological niches and various organism-environment interactions in ecosystems. We also discuss theoretical and practical implications of interactive effects on metabolic rate and provide suggestions for future research, including holistic system analyses at various hierarchical levels of organization that focus on interactive proximate (functional) and ultimate (evolutionary) causal networks. This article is part of the theme issue ‘The evolutionary significance of variation in metabolic rates’.
Evolutionary relationships between metabolism and behaviour require genetic correlations

As selection acts on multivariate phenotypes, the evolution of traits within populations not only depends on the genetic basis of each trait, but also on the genetic relationships among traits. As metabolic rate is often related to vital traits such as growth, physiology and behaviour, its variation and evolution is expected to have important repercussions on individual fitness. However, the majority of the correlations between metabolic rate and other traits has been based on phenotypic correlations, while genetic correlations, basis for indirect selection and evolution, have been overlooked. Using a case study, we explore the importance of properly estimating genetic correlations to understand and predict evolution of multivariate phenotypes. We show that selection on metabolic traits could result in indirect selection mainly on growth-related traits, owing to strong genetic correlations, but not on swimming or risk-taking and sociability behaviour even if they covary phenotypically. While phenotypic correlation can inform about genetic correlation direction, caution is needed in predicting the magnitude of genetic correlation. Therefore, even though phenotypic correlations among physiological and behavioural traits could be useful, deriving evolutionary conclusions based purely on them is not robust. In short, proper estimation of genetic correlations is needed when predicting evolutionary consequences. This article is part of the theme issue ‘The evolutionary significance of variation in metabolic rates’.
Estimating the relationship between fitness and metabolic rate: which rate should we use?

As physiologists seek to better understand how and why metabolism varies, they have focused on how metabolic rate covaries with fitness—that is, selection. Evolutionary biologists have developed a sophisticated framework for exploring selection, but there are particular challenges associated with estimating selection on metabolic rate owing to its allometric relationship with body mass. Most researchers estimate selection on mass and absolute metabolic rate; or selection on mass and mass-independent metabolic rate (MIMR)—the residuals generated from a nonlinear regression. These approaches are sometimes treated as synonymous: their coefficients are often interpreted in the same way. Here, we show that these approaches are not equivalent because absolute metabolic rate and MIMR are different traits. We also show that it is difficult to make sound biological inferences about selection on absolute metabolic rate because its causal relationship with mass is enigmatic. By contrast, MIMR requires less-desirable statistical practices (i.e. residuals as a predictor), but provides clearer causal pathways. Moreover, we argue that estimates of selection on MIMR have more meaningful interpretations for physiologists interested in the drivers of variation in metabolic allometry. This article is part of the theme issue ‘The evolutionary significance of variation in metabolic rates’.
MEG Weak Source Imaging Methods Based on Functional Connectivity

Beam former, as a class of Magnetoencephalography (MEG) source imaging methods, is widely used. However, it has difficulty in locating weak electromagnetic sources within brain. To solve this problem, this paper attempts to develop a method for MEG weak Source Imaging. Firstly classical beam former is used to extract the source intensities and waveforms. Secondly the strongest source is taken as the seed points and calculate correlation between seed points and other voxel points to obtain Functional Connectivity (FC) images. Finally, overlying the correlation on the anatomical image to get source imaging. Such method is successfully applied to imaging bilateral primary auditory sources in the case of classical beam former fails to locate weak source which is ipsilateral to the auditory stimulus. Such method is of significance in basic and clinical research. For example, it can be used to locate eloquent cortices of epilepsy patients. Identifying these cortices is critical for them to make preoperative planning. Introduction Magnetoencephalography (MEG) is a functional neuroimaging technique for mapping brain activity by recording magnetic fields produced by electrical currents occurring naturally in the brain, using very sensitive magnetometers. Brain electrical activity will produce a magnetic field perpendicular to the direction of currents, the relationship between them follows right-hand rule. Permeability in biological tissue and the vacuum is almost the same, so the scalp and skull can hardly lead to the distortion of the magnetic field [1], which is an advantage of MEG over Electroencephalogram(EEG). In addition, MEG can provide high spatial resolution. MEG as a non-invasive detection technology, can detect very weak magnetic field, in the order of between fT and pT (1pT = 10 -12 T) (1fT =10 -15 T), usually Brain electrical activities induce a few hundred fT. MEG imaging results can be superimposed on Magnetic Resonance Imaging(MRI) anatomical image of the subjects or patients, obtain neuromagnetic source imaging. MEG is currently approved for clinical use, mainly for epilepsy surgery, and preoperative brain imaging. In the United States, most MEG epilepsy centers uses it for preoperative imaging. Beamformer is a spatial filter, the equivalent of a virtual sensor, the time course of brain can be derived from any source, commonly used to make MEG imaging. However, Beamformer usually imaging energy source positions, so the energy source is often weak 517 This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/). Copyright © 2017, the Authors. Published by Atlantis Press. 2nd International Conference on Biomedical and Biological Engineering 2017 (BBE 2017) Advances in Biological Sciences Research (ABSR), volume 4
Slave labor productivity and wine output: Stellenbosch, 1680–1828

Abstract This paper examines wine output and slave labor productivity in the Dutch and British Cape Colony, leveraging annual tax censuses. We document a substantial increase in wine production, but, despite substantial institutional changes over more than a century, we find surprisingly stable median wine yields. Exploiting the farm-level nature of our data, we observe increasing heterogeneity in wine yields, suggesting that some farmers were able to realize productivity increases. We show that efficient slave labor utilization was a critical driver of productivity enhancement, largely unaffected by external factors.
High-throughput drug discovery on the Fujitsu A64FX architecture

High-performance computational kernels that optimally exploit modern vector-capable processors are critical in running large-scale drug discovery campaigns efficiently and promptly compatible with the constraints posed by urgent computing needs. Yet, state-of-the-art virtual screening workflows focus either on the broadness of features provided to the drug researcher or performance on high-throughput accelerators, leaving the task of deploying efficient CPU kernels to the compiler. We ported the key parts of the LiGen drug discovery pipeline, based on molecular docking, to the Fujitsu A64FX platform and leveraged its vector processing capabilities via an industry-proven retargetable SIMD programming model. By rethinking and optimizing key geometrical docking algorithms to leverage SVE instructions, we are able to provide efficient, high throughput execution on SVE-capable platforms.
An Overview on Mixing MPI and OpenMP Dependent Tasking on A64FX

The adoption of ARM processor architectures is on the rise in the HPC ecosystem. Fugaku supercomputer is a homogeneous ARM-based machine, and is one among the most powerful machine in the world. In the programming world, dependent task-based programming models are gaining tractions due to their many advantages: dynamic load balancing, implicit expression of communication/computation overlap, early-bird communication posting,. MPI and OpenMP are two widespreads programming standards that make possible task-based programming at a distributed memory level. Despite its many advantages, mixed-use of the standard programming models using dependent tasks is still under-evaluated on large-scale machines. In this paper, we provide an overview on mixing OpenMP dependent tasking model with MPI with the state-of-the-art software stack (GCC-13, Clang17, MPC-OMP). We provide the level of performances to expect by porting applications to such mixed-use of the standard on the Fugaku supercomputers, using two benchmarks (Cholesky, HPCCG) and a proxy-application (LULESH). We show that software stack, resource binding and communication progression mechanisms are factors that have a significant impact on performance. On distributed applications, performances reaches up to 80% of effiency for task-based applications like HPCCG. We also point-out a few areas of improvements in OpenMP runtimes.
The relationship between institutional quality, trust and private savings

Abstract This paper draws on macroeconomics, the economics of institutions and the economics of trust to explain private savings at the national level for 33 OECD (mostly European) countries from 2002 to 2012. More specifically, it raises two questions: (i) is it the quality of institutions or trust in institutions that drives private savings? (ii) if trust matters, what is the appropriate institutional level at which it operates? To answer these questions, we add to the usual explanatory variables of private savings three measures of institutional quality and six measures of institutional trust, distributed between the following institutional levels, presented in assumed hierarchical order: political, legal, financial and social. We find that trust in political institutions is the most significant driver of private savings. This contributes to the literature underlining the importance of subjectivity in social and economic phenomena and suggests, for private bank savings in countries having highly regulated banking systems, the existence of a hierarchy of trust in which trust in the highest-ranking institutions (political – and to a lesser extent legal – institutions) acts as a substitute for trust in every lower-ranking institution (financial institutions and social trust).
Exploring the positive factors supporting women's decisions to study undergraduate engineering

ABSTRACT This study, the second phase of a two-part investigation, employs the Reasoned Action Approach (Ajzen and Fishbein 2015) to analyse women's intentions to pursue undergraduate engineering—an approach not previously applied to address the gender disparity in engineering disciplines (Ajzen and Fishbein 2015). Through three focus groups comprising women at various stages and disciplines of undergraduate engineering studies at University College Dublin, the research identifies unique motivations and common themes. The primary findings reveal that two key factors influenced female participants' decisions to pursue undergraduate engineering: the presence of positive injunctive norms and a gender-based confidence gap in mathematics, identified in stage 1, impacting perceived behavioural control. Women with strong mathematical confidence were more likely to choose engineering. The role of mathematical confidence has been found in this study to impact the decision to study undergraduate engineering among women. As such, improving women's mathematical confidence should increase the number of women who choose to study undergraduate engineering. Furthermore, the impact of specific individual encouragement on the decision to choose to study undergraduate engineering among the group of young women who do hold high levels of perceived behavioural control is a new insight of research in this area.
Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment

Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic basis of Spt4/5 function in Archaea, we performed structure-function analyses using the archaeal transcriptional machinery of Pyrococcus furiosus (Pfu). We report single-particle cryo-electron microscopy reconstructions of apo RNAP and the archaeal elongation complex (EC) in the absence and presence of Spt4/5. Surprisingly, Pfu Spt4/5 also binds the RNAP in the absence of nucleic acids in a distinct super-contracted conformation. We show that the RNAP clamp/stalk module exhibits conformational flexibility in the apo state of RNAP and that the enzyme contracts upon EC formation or Spt4/5 engagement. We furthermore identified a contact of the Spt5-NGN domain with the DNA duplex that stabilizes the upstream boundary of the transcription bubble and impacts Spt4/5 activity in vitro. This study, therefore, provides the structural basis for Spt4/5 function in archaeal transcription and reveals a potential role beyond the well-described support of elongation.
The recombination landscape of introgression in yeast

Meiotic recombination is an important evolutionary force that acts by breaking up genomic linkage, thereby increasing the efficacy of selection. Meiotic recombination is initiated with a double-strand break which is resolved via a crossover, which involves the reciprocal exchange of genetic material between homologous chromosomes, or a non-crossover, which results in small tracts of non-reciprocal exchange of genetic material. While the meiotic process is largely conserved, crossover and non-crossover rates vary between species, populations, individuals, and across the genome. In recent years, recombination is observed to be positively associated with the distribution of ancestry derived from past interspecific hybridization (introgression) in a variety of species. This trend has been interpreted to signify that introgression carries genetic incompatibilities that are selected against, such that introgression is enriched in regions of high recombination. However, recombination is well known to be suppressed in divergent sequence to prevent non-homologous recombination. Since introgressed DNA is often divergent, we sought to explore this interaction of recombination and introgression by sequencing spores and detecting crossover and non-crossover events from two crosses of the budding yeast Saccharomyces uvarum. One cross is between strains isolated from natural environments, and the other cross is between strains from fermentation environments, in which each strain contains introgression from their sister species, S. eubayanus. We find that the recombination landscape is significantly different between S. uvarum crosses, and that most of these differences can be explained by the presence of heterozygous introgression in the fermentation cross. Crossovers are significantly reduced and non-crossovers are increased in heterozygous introgression compared to syntenic regions in the natural cross without introgression. This translates to reduced allele shuffling within introgressed regions, and an overall reduction of shuffling on most chromosomes with introgression compared to the syntenic regions and chromosomes without introgression. Our results indicate that recent hybridization can significantly influence the recombination landscape, and suggest that the reduction in allele shuffling contributes to the initial purging of introgressed ancestry in the generations following a hybridization event.
A limited concentration range of diaphorin, a polyketide produced by a bacterial symbiont of the Asian citrus psyllid, promotes the in vitro gene expression with bacterial ribosomes

Diaphorin is a polyketide produced by “Candidatus Profftella armatura” (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a devastating agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Physiological concentrations of diaphorin, which D. citri contains at levels as high as 2–20 mM, are inhibitory to various eukaryotes and Bacillus subtilis (Firmicutes: Bacilli) but promote the growth and metabolic activity of Escherichia coli (Gammaproteobacteria: Enterobacterales). Our previous study demonstrated that five-millimolar diaphorin, which exhibits significant inhibitory and promoting effects on cultured B. subtilis and E. coli, respectively, inhibits in vitro gene expression utilizing purified B. subtilis and E. coli ribosomes. This suggested that the adverse effects of diaphorin on B. subtilis are partly due to its influence on gene expression. However, the result appeared inconsistent with the positive effects on E. coli. Moreover, the diaphorin concentration in bacterial cells, where genes are expressed in vivo, may be lower than in culture media. Therefore, the present study analyzed the effects of 50 and 500 μM of diaphorin on bacterial gene expression using the same analytical method. The result revealed that this concentration range of diaphorin, in contrast to five-millimolar diaphorin, promotes the in vitro translation with the B. subtilis and E. coli ribosomes, suggesting that the positive effects of diaphorin on E. coli are due to its direct effects on translation. This study demonstrated for the first time that a pederin-type compound promotes gene expression, establishing a basis for utilizing its potential in pest management and industrial applications. Importance This study revealed that a limited concentration range of diaphorin, a secondary metabolite produced by a bacterial symbiont of an agricultural pest, promotes cell-free gene expression utilizing substrates and proteins purified from bacteria. The unique property of diaphorin, which is inhibitory to various eukaryotes and Bacillus subtilis but promotes the growth and metabolic activity of Escherichia coli, may affect the microbial flora of the pest insect, potentially influencing the transmission of devastating plant pathogens. Moreover, the activity may be exploited to improve the efficacy of industrial production by E. coli, which is often used to produce various important materials, including pharmaceuticals, enzymes, amino acids, and biofuels. This study elucidated a part of the mechanism by which the unique activity of diaphorin is expressed, constructing a foundation for applying the unique property to pest management and industrial use.