bluuebunny/crossref_metadata_2025 huggingface dataset:
The evolutionary implications of epigenetic inheritance
Authors: Jablonka Eva
Published: August 2017

The Modern Evolutionary Synthesis (MS) forged in the mid-twentieth century was built on a notion of heredity that excluded soft inheritance, the inheritance of the effects of developmental modifications. However, the discovery of molecular mechanisms that generate random and developmentally induced epigenetic variations is leading to a broadening of the notion of biological heredity that has consequences for ideas about evolution. After presenting some old challenges to the MS that were raised, among others, by Karl Popper, I discuss recent research on epigenetic inheritance, which provides experimental and theoretical support for these challenges. There is now good evidence that epigenetic inheritance is ubiquitous and is involved in adaptive evolution and macroevolution. I argue that the many evolutionary consequences of epigenetic inheritance open up new research areas and require the extension of the evolutionary synthesis beyond the current neo-Darwinian model.
A second inheritance system: the extension of biology through culture
Authors: Whiten Andrew
Published: August 2017

By the mid-twentieth century (thus following the ‘Modern Synthesis’ in evolutionary biology), the behavioural sciences offered only the sketchy beginnings of a scientific literature documenting evidence for cultural inheritance in animals—the transmission of traditional behaviours via learning from others (social learning). By contrast, recent decades have seen a massive growth in the documentation of such cultural phenomena, driven by long-term field studies and complementary laboratory experiments. Here, I review the burgeoning scope of discoveries in this field, which increasingly suggest that this ‘second inheritance system’, built on the shoulders of the primary genetic inheritance system, occurs widely among vertebrates and possibly in invertebrates too. Its novel characteristics suggest significant implications for our understanding of evolutionary biology. I assess the extent to which this second system extends the scope of evolution, both by echoing principal properties of the primary, organic evolutionary system, and going beyond it in significant ways. This is well established in human cultural evolution; here, I address animal cultures more generally. The further major, and related, question concerns the extent to which the consequences of widespread animal cultural transmission interact with the primary, genetically based inheritance systems, shaping organic evolution.
Genetic, epigenetic and exogenetic information in development and evolution
Authors: Griffiths Paul E.
Published: August 2017

The idea that development is the expression of information accumulated during evolution and that heredity is the transmission of this information is surprisingly hard to cash out in strict, scientific terms. This paper seeks to do so using the sense of information introduced by Francis Crick in his sequence hypothesis and central dogma of molecular biology. It focuses on Crick's idea of precise determination. This is analysed using an information-theoretic measure of causal specificity. This allows us to reconstruct some of Crick's claims about information in transcription and translation. Crick's approach to information has natural extensions to non-coding regions of DNA, to epigenetic marks, and to the genetic or environmental upstream causes of those epigenetic marks. Epigenetic information cannot be reduced to genetic information. The existence of biological information in epigenetic and exogenetic factors is relevant to evolution as well as to development.
Why developmental niche construction is not selective niche construction: and why it matters
Authors: Stotz Karola
Published: August 2017

In the last decade, niche construction has been heralded astheneglected process in evolution. But niche construction is just one way in which the organism's interaction with and construction of the environment can have potential evolutionary significance. The constructed environment does not justselect for, it alsoproduces newvariation. Nearly 3 decades ago, and in parallel with Odling-Smee's article ‘Niche-constructing phenotypes', West and King introduced the ‘ontogenetic niche’ to give the phenomena ofexogenetic inheritance a formal name. Since then, a range of fields in the life sciences and medicine has amassed evidence that parents influence their offspring by means other than DNA (parental effects), and proposed mechanisms for how heritable variation can be environmentally induced and developmentally regulated. The concept of ‘developmental niche construction’ (DNC) elucidates how a diverse range of mechanisms contributes to the transgenerational transfer of developmental resources. My most central of claims is that whereas the selective niche of niche construction theory is primarily used to explain the active role of the organism in its selective environment, DNC is meant to indicate the active role of the organism in its developmental environment. The paper highlights the differences between the construction of the selective and the developmental niche, and explores the overall significance of DNC for evolutionary theory.
Evolution viewed from physics, physiology and medicine
Authors: Noble Denis
Published: August 2017

Stochasticity is harnessed by organisms to generate functionality. Randomness does not, therefore, necessarily imply lack of function or ‘blind chance’ at higher levels. In this respect, biology must resemble physics in generating order from disorder. This fact is contrary to Schrödinger's idea of biology generating phenotypic order frommolecular-level order, which inspired the central dogma of molecular biology. The order originates at higher levels, which constrain the components at lower levels. We now know that this includes the genome, which is controlled by patterns of transcription factors and various epigenetic and reorganization mechanisms. These processes can occur in response to environmental stress, so that the genome becomes ‘a highly sensitive organ of the cell’ (McClintock). Organisms have evolved to be able to cope with many variations at the molecular level. Organisms also make use of physical processes in evolution and development when it is possible to arrive at functional development without the necessity to store all information in DNA sequences. This view of development and evolution differs radically from that of neo-Darwinism with its emphasis on blind chance as the origin of variation. Blind chance is necessary, but the origin of functional variation is not at the molecular level. These observations derive from and reinforce the principle of biological relativity, which holds that there is no privileged level of causation. They also have important implications for medical science.
EarlyHomo, plasticity and the extended evolutionary synthesis
Authors: Antón Susan C. , Kuzawa Christopher W.
Published: August 2017

The Modern Synthesis led to fundamental advances in understandings of human evolution. For human palaeontology, a science that works from ancestral phenotypes (i.e. the fossil record), particularly important have been perspectives used to help understand the heritable aspects of phenotypes and how fossil individuals might then be aggregated into species, and relationships among these groups understood. This focus, coupled with the fragmentary nature of the fossil record, however, means that individual phenotypic variation is often treated as unimportant ‘noise’, rather than as a source of insight into population adaptation and evolutionary process. The emphasis of the extended evolutionary synthesis on plasticity as a source of phenotypic novelty, and the related question of the role of such variation in long-term evolutionary trends, focuses welcome attention on non-genetic means by which novel phenotypes are generated and in so doing provides alternative approaches to interpreting the fossil record. We review evidence from contemporary human populations regarding some of the aspects of adult phenotypes preserved in the fossil record that might be most responsive to non-genetic drivers, and we consider how these perspectives lead to alternate hypotheses for interpreting the fossil record of early genusHomo.We conclude by arguing that paying closer attention to the causes and consequences of intraspecific phenotypic variation in its own right, as opposed to as noise around a species mean, may inspire a new generation of hypotheses regarding species diversity in the Early Pleistocene and the foundations for dispersal and regional diversification inHomo erectusand its descendants.
The purpose of adaptation
Authors: Gardner Andy
Published: August 2017

A central feature of Darwin's theory of natural selection is that it explains the purpose of biological adaptation. Here, I: emphasize the scientific importance of understanding what adaptations are for, in terms of facilitating the derivation of empirically testable predictions; discuss the population genetical basis for Darwin's theory of the purpose of adaptation, with reference to Fisher's ‘fundamental theorem of natural selection'; and show that a deeper understanding of the purpose of adaptation is achieved in the context of social evolution, with reference to inclusive fitness and superorganisms.
Why an extended evolutionary synthesis is necessary
Authors: Müller Gerd B.
Published: August 2017

Since the last major theoretical integration in evolutionary biology—the modern synthesis (MS) of the 1940s—the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance systems, the ‘-omics’ revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge about the factors responsible for evolutionary change. Some of these results are in agreement with the standard theory and others reveal different properties of the evolutionary process. A renewed and extended theoretical synthesis, advocated by several authors in this issue, aims to unite pertinent concepts that emerge from the novel fields with elements of the standard theory. The resulting theoretical framework differs from the latter in its core logic and predictive capacities. Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process. All these features stimulate research into new areas of evolutionary biology.
ICTV Virus Taxonomy Profile: Virgaviridae
Authors: Adams Michael J. , Adkins Scott , Bragard Claude , Gilmer David , Li Dawei , MacFarlane Stuart A. , Wong Sek-Man , Melcher Ulrich , Ratti Claudio , Ryu Ki Hyun ,   ICTV Report Consortium
Published: August 2017

The family Virgaviridae is a family of plant viruses with rod-shaped virions, a ssRNA genome with a 3′-terminal tRNA-like structure and a replication protein typical of alpha-like viruses. Differences in the number of genome components, genome organization and the mode of transmission provide the basis for genus demarcation. Tobacco mosaic virus (genus Tobamovirus) was the first virus to be discovered (in 1886); it is present in high concentrations in infected plants, is extremely stable and has been extensively studied. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Virgaviridae, which is available at www.ictv.global/report/virgaviridae.
On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data
Authors: Arredondo-Alonso Sergio , Willems Rob J. , van Schaik Willem , Schürch Anita C.
Published: August 2017

To benchmark algorithms for automated plasmid sequence reconstruction from short-read sequencing data, we selected 42 publicly available complete bacterial genome sequences spanning 12 genera, containing 148 plasmids. We predicted plasmids from short-read data with four programs (PlasmidSPAdes, Recycler, cBar and PlasmidFinder) and compared the outcome to the reference sequences. PlasmidSPAdes reconstructs plasmids based on coverage differences in the assembly graph. It reconstructed most of the reference plasmids (recall=0.82), but approximately a quarter of the predicted plasmid contigs were false positives (precision=0.75). PlasmidSPAdes merged 84 % of the predictions from genomes with multiple plasmids into a single bin. Recycler searches the assembly graph for sub-graphs corresponding to circular sequences and correctly predicted small plasmids, but failed with long plasmids (recall=0.12, precision=0.30). cBar, which applies pentamer frequency analysis to detect plasmid-derived contigs, showed a recall and precision of 0.76 and 0.62, respectively. However, cBar categorizes contigs as plasmid-derived and does not bin the different plasmids. PlasmidFinder, which searches for replicons, had the highest precision (1.0), but was restricted by the contents of its database and the contig length obtained from de novo assembly (recall=0.36). PlasmidSPAdes and Recycler detected putative small plasmids (<10 kbp), which were also predicted as plasmids by cBar, but were absent in the original assembly. This study shows that it is possible to automatically predict small plasmids. Prediction of large plasmids (>50 kbp) containing repeated sequences remains challenging and limits the high-throughput analysis of plasmids from short-read whole-genome sequencing data.
Modeling of dynamic cerebrovascular reactivity to spontaneous and externally induced CO2 fluctuations in the human brain using BOLD-fMRI
Authors: Prokopiou Prokopis C. , Pattinson Kyle T. S. , Wise Richard G. , Mitsis Georgios D.
Published: August 2017

In this work, we investigate the regional characteristics of the dynamic interactions between arterial CO2 and BOLD (dynamic cerebrovascular reactivity - dCVR) during normal breathing and hypercapnic, externally induced step CO2 challenges. To obtain CVR curves at each voxel, we use a custom set of basis functions based on the Laguerre and gamma basis sets. This allows us to obtain robust dCVR estimates both in larger regions of interest (ROIs) as well as in individual voxels. We also implement classification schemes to identify brain regions with similar dCVR characteristics. Our results reveal considerable variability of dCVR across different brain regions, as well as during different experimental conditions (normal breathing and hypercapnia), suggesting a differential response of cerebral vasculature to spontaneous CO2 fluctuations and larger, externally induced CO2 changes. The clustering results suggest that anatomically distinct brain regions exhibit different dCVR curves that do not exhibit the standard, positive valued curves that have been previously reported using measurements of global cerebral blood flow or using larger ROIs. They also revealed a consistent set of dCVR cluster shapes for resting and forcing conditions that exhibited different distribution patterns across brain voxels.
On the Stability Landscape of the Human Gut Microbiome: Implications for Microbiome-based Therapies
Authors: Gibson Travis E. , Carey Vincent , Bashan Amir , Hohmann Elizabeth L. , Weiss Scott T. , Liu Yang-Yu
Published: August 2017

Understanding how gut microbial species determine their abundances is crucial in developing any microbiome-based therapy. Towards that end, we show that the compositions of our gut microbiota have characteristic and attractive steady states, and hence respond to perturbations in predictable ways. This is achieved by developing a new method to analyze the stability landscape of the human gut microbiome. In order to illustrate the efficacy of our method and its ecological interpretation in terms of asymptotic stability, this novel method is applied to various human cohorts, including large cross-sectional studies, long longitudinal studies with frequent sampling, and perturbation studies via fecal microbiota transplantation, antibiotic and probiotic treatments. These findings will facilitate future ecological modeling efforts in human microbiome research. Moreover, the method allows for the prediction of the compositional shift of the gut microbiome during the fecal microbiota transplantation process. This result holds promise for translational applications, such as, personalized donor selection when performing fecal microbiota transplantations.

One Sentence Summary

A new method for analyzing the stability landscape of the human gut microbiome and predicting its steady-state composition is developed.
Desiccation plasticity and diapause in the Argentinian pearlfishAustrolebias bellottii
Authors: Van Dooren Tom J M , Varela-Lasheras Irma
Published: August 2017

Background

The annual life history strategy with diapauses evolved repeatedly in killifish. To understand their and to characterize their variation between species, patterns of desiccation plasticity seem central. Plasticity might have played a role in the origin of these developmental arrests, when annual fish evolved from non-annual ones. The consequences of desiccation on survival and developmental rates of embryos of annual fish are poorly known. Using detailed demographic modelling of embryonal life histories, we investigate plasticity for desiccation in the Argentinian pearlfishAustrolebias bellottii. The treatment protocol contains changing environmental conditions with successive phases of mild desiccation and rewetting.

Results

We observed no clear diapause II and thus no increased incidence caused by mild and prolonged desiccation. Embryos arrest development in the pre-hatching stage (DIII) or in the dispersed cell phase (DI) irrespective of environmental conditions. There are limited effects of desiccation on survival, limited developmental delays and an acceleration of development into the pre-hatching stage. We found significant parental variance components on developmental rates, but hardly any effect of parental age. Hatching probabilities increased with age, when embryos had been in air at 100% RH and increased further when embryos were rewetted a second time after a two month interval.

Conclusions

Mild desiccation and rewetting affect survival, rates of development and hatching probability, but not the fractions of embryos that arrest development in particular stages. We can conclude that the incidences of diapause have become relatively independent of the occurrence of mild desiccation, as if they have become assimilated. In contrast to the responses to mild desiccation observed in the non-annual rivulids,Austrolebiasaccelerates development into the pre-hatching stage.
When conflict cannot be avoided: executive control dominates early selective sensory modulations during cognitive conflict
Authors: Itthipuripat Sirawaj , Deering Sean , Serences John T.
Published: August 2017

When different sources of sensory information suggest competing behavioral responses, the efficiency of decision-making is impaired. Prior work suggests that at least two mechanisms may play a role in mitigating this interference: using early selective attention to extract the most relevant sensory inputs to avoid conflict or increasing the efficiency of the executive control network to resolve conflict during post-perceptual processing. To test these alternatives, we combined a stimulus-frequency tagging technique with a classic color-word Stroop paradigm, where color-bar targets and letter-string distractors were simultaneously flickered at different frequencies. Using electroencephalography (EEG), we measured the quality of early sensory processing by assessing the amplitude of steady-state visually evoked potentials (SSVEPs) elicited by the targets and distractors. We also measured the engagement of the executive control network by assessing changes in frontal theta (4-7Hz) and posterior alpha oscillations (8-14Hz). Counter to the ‘early selective sensory modulation’ account, the amplitude of the SSVEP response was not modulated by manipulations of color/word congruency, while the frontal theta activity increased and the posterior alpha activity decreased in response to conflict. Moreover, target-related SSVEP amplitude was not correlated with response times (RTs) and a higher (not lower) distractor-related SSVEP amplitude predicted faster RTs. On the other hand, the amplitude of the frontal theta and alpha activity was highly correlated with RTs, irrespective of conflict levels. Over all, these results highlight the dominant role of the executive control network in conflict resolution during post-perceptual processing.

Significance Statement

Conflicting information interferes with decision-making. However, this interference can be mitigated either by extracting the most relevant inputs during early sensory processing or by increasing the efficiency of the executive control processes to resolve conflict. By measuring electroencephalography (EEG) in humans performing a modified color-word Stroop task, we examined early sensory responses evoked by targets and distractors while simultaneously monitoring frontal theta and posterior alpha oscillations to index the activation of the executive control network. We found evidence that the executive control network played a more prominent role in resolving conflict.
Mapping Patient Trajectories using Longitudinal Extraction and Deep Learning in the MIMIC-III Critical Care Database
Authors: Beaulieu-Jones Brett K. , Orzechowski Patryk , Moore Jason H.
Published: August 2017

Electronic Health Records (EHRs) contain a wealth of patient data useful to biomedical researchers. At present, both the extraction of data and methods for analyses are frequently designed to work with a single snapshot of a patient’s record. Health care providers often perform and record actions in small batches over time. By extracting these care events, a sequence can be formed providing a trajectory for a patient’s interactions with the health care system. These care events also offer a basic heuristic for the level of attention a patient receives from health care providers. We show that is possible to learn meaningful embeddings from these care events using two deep learning techniques, unsupervised autoencoders and long short-term memory networks. We compare these methods to traditional machine learning methods which require a point in time snapshot to be extracted from an EHR.
CDX4 regulates the progression of neural maturation in the spinal cord
Authors: Joshi Piyush , Darr Andrew J. , Skromne Isaac
Published: August 2017

The progressive maturation of cells down differentiation lineages is controlled by collaborative interactions between networks of extracellular signals and intracellular transcription factors. In the vertebrate spinal cord, FGF, Wnt and Retinoic Acid signaling pathways regulate the progressive caudal-to-rostral maturation of neural progenitors by regulating a poorly understood gene regulatory network of transcription factors. We have mapped out this gene regulatory network in the chicken pre-neural tube, identifying CDX4 as a dual-function core component that simultaneously regulates gradual loss of cell potency and acquisition of differentiation states: in a caudal-to-rostral direction, CDX4 represses the early neural differentiation markerNkx1.2and promotes the late neural differentiation markerPax6.Significantly, CDX4 prevents premature PAX6-dependent neural differentiation by blockingNgn2activation. This regulation of CDX4 overPax6is restricted to the rostral pre-neural tube by Retinoic Acid signaling. Together, our results show that in the spinal cord, CDX4 is part of the gene regulatory network controlling the sequential and progressive transition of states from high to low potency during neural progenitor maturation. Given CDX well-known involvement inHoxgene regulation, we propose that CDX factors coordinate the maturation and axial specification of neural progenitor cells during spinal cord development.
Daytime eyeshine contributes to pupil camouflage in a cryptobenthic marine fish
Authors: Santon Matteo , Bitton Pierre-Paul , Harant Ulrike K. , Michiels Nico K.
Published: August 2017

Ocular reflectors enhance eye sensitivity in dim light, but can produce reflected eyeshine when illuminated. Most teleost fish occlude their reflectors during the day. The opposite is observed in cryptic sit-and-wait predators such as scorpionfish and toadfish, where reflectors are occluded at night and exposed during the day. This results in daytime eyeshine, proposed to enhance pupil camouflage by reducing the contrast between the otherwise black pupil and the surrounding tissue. In this study, we test this hypothesis in the scorpionfishScorpaena porcusand show that eyeshine is the result of two mechanisms: the previously describedStratum Argenteum Reflected(SAR) eyeshine, andPigment Epithelium Transmitted(PET) eyeshine, a newly described mechanism for this species. We confirm that the ocular reflector is exposed only when the eye is light-adapted, and present field measurements to show that eyeshine reduces pupil contrast against the iris. We then estimate the relative contribution of SAR and PET eyeshine to pupil brightness. Visual models for different light scenarios in the field show that daytime eyeshine enhances pupil camouflage from the perspective of a prey fish. We propose that the reversed occlusion mechanism of some cryptobenthic predators has evolved as a compromise between camouflage and vision.
Cortico-Cerebellar Networks Drive Sensorimotor Learning in Speech
Authors: Lametti Daniel R. , Smith Harriet J. , Freidin Phoebe , Watkins Kate E.
Published: August 2017

The motor cortex and cerebellum are thought to be critical for learning and maintaining motor behaviours. Here we use tDCS to test the role of the motor cortex and cerebellum in sensorimotor learning in speech. During productions of ‘head’, ‘bed’, and ‘dead’, the first formant of the vowel sound was altered in real-time towards the first formant of the vowel sound in ‘had’, ‘bad’, and ‘dad’. Compensatory changes in first and second formant production were used as a measure of motor adaptation. TDCS to either the motor cortex or the cerebellum improved sensorimotor learning in speech compared to sham stimulation. However, in the case of cerebellar tDCS, production changes were restricted to the source of the acoustical error (i.e. the first formant). Motor cortex tDCS drove production changes that offset errors in the first formant, but, unlike cerebellar tDCS, adaptive changes in the second formant also occurred. The results suggest that motor cortex and cerebellar tDCS have both shared and dissociable effects on motor adaptation. The study provides initial causal evidence in speech production that the motor cortex and the cerebellum support different aspects of sensorimotor learning. We propose that motor cortex tDCS drives sensorimotor learning towards previously learned patterns of movement, while cerebellar tDCS focuses sensorimotor learning on error correction.
Decoupling the roles of cell shape and mechanical stress in orienting and cueing epithelia mitosis
Authors: Nestor-Bergmann Alexander , Stooke-Vaughan Georgina A. , Goddard Georgina K. , Starborg Tobias , Jensen Oliver E. , Woolner Sarah
Published: August 2017

Distinct mechanisms involving cell shape and mechanical force are known to influence the rate and orientation of division in cultured cells. However, uncoupling the impact of shape and force in tissues remains challenging. Combining stretching ofXenopus laevistissue with a novel method of inferring relative mechanical stress, we find separate roles for cell shape in orientating division and mechanical stress in cueing division. We demonstrate that division orientation is best predicted by an axis of cell shape defined by the position of tricellular junctions (TCJs), which aligns exactly with the principal axis of local cell stress rather than the tissue-level stress. The alignment of division to cell shape requires functional cadherin and the localisation of the spindle orientation protein, LGN, to TCJs, but is not sensitive to relative cell stress magnitude. In contrast, cell proliferation rate is more directly regulated by mechanical stress, being correlated with relative isotropic stress, and can be decoupled from cell shape when myosin II is depleted.
Identification of universal and cell type specific p53 DNA binding
Authors: Hafner Antonina , Kublo Lyubov , Lahav Galit , Stewart-Ornstein Jacob
Published: August 2017

The tumor suppressor p53 is a major regulator of the DNA damage response and has been suggested to selectively bind and activate cell type specific gene expression programs, however recent studies and meta-analyses of genomic data propose largely uniform, and condition independent, p53 binding. To systematically assess the cell type specificity of p53, we measured its association with DNA in 12 p53 wild-type cell lines, from a range of epithelial linages, in response to ionizing radiation. We found that the majority of bound sites were occupied across all cell lines, however we also identified a subset of binding sites that were specific to one or a few cell lines. Unlike the shared p53-bound genome, which was not dependent on chromatin accessibility, the association of p53 with these atypical binding sites was well explained by chromatin accessibility and could be modulated by forcing cell state changes such as the epithelial-to-mesenchymal transition. These results position p53 as having both universal and cell type specific regulatory programs that have different regulators and dependence on chromatin state.
Effects of species invasion on population dynamics, vital rates, and life histories of the native species
Authors: Vincenzi Simone , Crivelli Alain J , Jesensek Dusan , Campbell Ellen , Garza John C
Published: August 2017

Invasions occurring in natural environments provide the opportunity to study how vital rates change and life histories evolve in the presence of a competing species. In this work, we estimate differences in reproductive traits, individual growth trajectories, survival, life histories, and population dynamics between a native species living in allopatry and in sympatry with an invasive species of the same taxonomic Family. We used as a model system marble troutSalmo marmoratus(native species) and rainbow troutOncorhynchus mykiss(non-native) living in the Idrijca River (Slovenia). An impassable waterfall separates the stream in two sectors only a few hundred meters apart: a downstream sector in which marble trout live in sympatry with rainbow trout and a upstream sector in which marble trout live in allopatry. We used an overarching modeling approach that uses tag-recapture and genetic data (> 2,500 unique marble and rainbow trout were sampled and SNP-genotyped) to reconstruct pedigrees, test for synchrony of population dynamics, and model survival and growth while accounting for individual heterogeneity in performance. The population dynamics of the two marble trout populations and of rainbow trout were overall synchronous. We found higher prevalence of younger parents, higher mortality, and lower population density in marble trout living in sympatry with rainbow trout than in marble trout living in allopatry. There were no differences in the average individual growth trajectories between the two marble trout populations. Faster life histories of marble trout living in sympatry with rainbow trout are consistent with predictions of life-history theory.
Case report: intermittent fasting and probiotic yogurt consumption are associated with reduction of serum alpha-N-acetylgalactosaminidase and increased urinary excretion of lipophilic toxicants
Authors: Blythe Jerry , Ruggiero Marco , Pacini Stefania
Published: August 2017

In this study, we describe the changes associated with three months of intermittent fasting and probiotic yogurt consumption in a 72-year-old marathon runner with chronic lymphocytic leukemia for a number of years. Serum alpha-N-acetylgalactosaminidase (nagalase), a marker of inflammation and cancer cell proliferation, was significantly decreased at the end of a three-month observation. These results are consistent with immune modulating properties of certain probiotics based on the fermentation of milk and colostrum. Urinary excretion of non-metal toxicants that accumulate in adipose tissue such as Perchlorate, N-acetyl(2-hydroxypropyl)cysteine (NAHP), 2,4-Dichlorophenoxyacetic acid, 3-Phenoxybenzoic acid (3PBA), N-acetyl phenyl cysteine (NAP), Phenylglycoxylic acid (PGO), Monoethylphthalate (MEP) and 2-Hydroxyisobutyric Acid (2HIB) was significantly increased. These results are consistent with the weight loss (5 Kg) associated with intermittent fasting and with the known features of probiotics as detoxification tools. Consistent with certain toxicants acting as endocrine disruptors, we observed an increased elimination of toxicants and a 33% decrease of serum Thyroid Stimulating Hormone (TSH), suggesting a trend toward normalization of thyroid function. These results support the hypothesis that a combination of intermittent fasting with the consumption of specific probiotic yogurts may lead to immune modulation, detoxification and other improvements.

Abbreviations

(NAHP)

N-acetyl(2-hydroxypropyl)cysteine

(3PBA)

3-Phenoxybenzoic acid

(NAP)

Nacetyl phenyl cysteine

(PGO)

Phenylglycoxylic acid

(MEP)

Monoethylphthalate

(2HIB)

2-Hydroxyisobutyric Acid

(TSH)

Thyroid Stimulating Hormone

(Dr. JB)

Dr. Jerry Blythe

(CLL)

chronic lymphocytic leukemia

(IRB)

Institutional Review Board

(GcMAF)

Gc protein-derived Macrophage Activating Factor
The evolution of nesting behaviour inPeromyscusmice
Authors: Lewarch Caitlin L. , Hoekstra Hopi E.
Published: August 2017

Structures built by animals, such as nests, often can be considered extended phenotypes that facilitate the study of animal behaviour. For rodents, nest building is both an important form of behavioural thermoregulation and a critical component of parental care. Changes in nest structure or the prioritization of nesting behaviour are therefore likely to have consequences for survival and reproduction, and both biotic and abiotic environmental factors are likely to influence the adaptive value of such differences. Here we first develop a novel assay to investigate interspecific variation in the nesting behaviour of deer mice (genusPeromyscus). Using this assay, we find that, while there is some variation in the complexity of the nests built byPeromyscusmice, differences in the latency to begin nest construction are more striking. Four of the seven taxa examined here build nests within an hour of being given nesting material, but this latency to nest is not related to ultimate differences in nest structure, suggesting that the ability to nest is relatively conserved within the genus, but species differ in their prioritization of nesting behaviour. We also find that latency to nest is not correlated with body size, climate, or the construction of burrows that create microclimates. However, the four taxa with short nesting latencies all have monogamous mating systems, suggesting that differences in nesting latency may be related to social environment. This detailed characterization of nesting behaviour within the genus provides an important foundation for future studies of the genetic and neurobiological mechanisms that contribute to the evolution of behaviour.
Characteristics of a Block to Entry via an HIV-2 Envelope, MCR
Authors: Gray Eleanor R.
Published: August 2017

Successful viral infection depends not only on targeting the correct cell type, but also on the route taken into the cell. After entry, a retrovirus must reverse transcribe its genome and access the nucleus. Blocks to infection can arise at many different stages of the cycle; if they occur only in some cell types it can reveal hitherto unknown aspects of viral or cellular biology. A block to infection of a primary isolate of HIV-2 was previously identified in specific cell types. In this study, parameters of route of entry of the envelope protein from this primary isolate, MCR, were investigated. A critical component of the block acts at a pre-reverse transcription stage, as virions pseudotyped with MCR envelope did not undergo fusion and entry rates commensurate with productive infection. Furthermore, expression of p56lck, which regulates CD4 surface expression, partially rescued infection of MCR envelope-pseudotyped virus in restrictive cell types. Based on these findings, we propose that a part of this block results from poor cell-surface expression of CD4.
Determination of active layer morphology in all-polymer photovoltaic cells
Authors: Mulderig Andrew J. , Jin Yan , Yu Fei , Keum Jong , Hong Kunlun , Browning James F. , Beaucage Gregory , Smith Gregory S. , Kuppa Vikram K.
Published: August 2017

This study investigates the structure of films spin-coated from blends of the semiconducting polymers poly(3-hexylthiophene-2,5-diyl) (P3HT) and poly{2,6-[4,4-bis-(2-ethylhexyl)-4H-cyclopenta[2,1-b;3,4-b′]dithiophene]-alt-4,7(2,1,3-benzothiadiazole)} (PCPDTBT). Such blends are of potential use in all-polymer solar cells in which both the acceptor and the donor material generate excitons to contribute to the photocurrent. Prompted by threefold performance gains seen in polymer/fullerene and polymer blend solar cells upon addition of pristine graphene, devices are prepared from P3HT/PCPDTBT blends both with and without graphene. This report focuses on the morphology of the active layer since this is of critical importance in determining performance. Small-angle neutron scattering (SANS) is utilized to study this polymer blend with deuterated P3HT to provide contrast and permit the investigation of buried structure in neat and graphene-doped films. SANS reveals the presence of P3HT crystallites dispersed in an amorphous blend matrix of P3HT and PCPDTBT. The crystallites are approximately disc shaped and do not show any evidence of higher-order structure or aggregation. While the structure of the films does not change with the addition of graphene, there is a perceptible effect on the electronic properties and energy conversion efficiency in solar cells made from such films. Determination of the active layer morphology yields crucial insight into structure–property relationships in organic photovoltaic devices.
A simple device for transferring an oriented crystal from an X-ray Laue diffractometer to a cutting machine
Authors: Stishov S. M.
Published: August 2017

A simple transfer device is described that enables cutting of an oriented single crystal.
A tool for automatic recognition of [110] tilt grain boundaries in zincblende-type crystals
Authors: Kozak Roksolana , Kurdzesau Fiodar , Prieto Ivan , Skibitzki Oliver , Schroeder Thomas , Arroyo Rojas Dasilva Yadira , Erni Rolf , von Känel Hans , Rossell Marta D.
Published: August 2017

The local atomic structure of [110] tilt grain boundaries (GBs) formed in ∼100 nm-sized GaAs nanocrystals, which crystallize in the non-centrosymmetric zincblende-type structure with face-centred cubic lattice symmetry, was imaged and analysed by means of high-resolution high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). The nanocrystals were grown by metal–organic vapour phase epitaxy on top of (001) Si nanotips embedded in an oxide matrix. This paper introduces an automatic analysis method and corresponding processing tool for the identification of the GBs. The method comprises (i) extraction of crystallographic parameters,i.e.misorientation angles and transformation matrices for the different crystal parts (grains/twins) observed by HAADF-STEM, and (ii) determination of their common plane(s) by modelling all possible intersections of the corresponding three-dimensional reciprocal lattices. The structural unit model is also used to characterize the GB structures and to validate the data obtained by the developed algorithm.
Characterization of enamel caries lesions in rat molars using synchrotron X-ray microtomography
Authors: Free R. D. , DeRocher K. , Stock S. R. , Keane D. , Scott-Anne K. , Bowen W. H. , Joester D.
Published: August 2017

Dental caries is a ubiquitous infectious disease with a nearly 100% lifetime prevalence. Rodent caries models are widely used to investigate the etiology, progression and potential prevention or treatment of the disease. To explore the suitability of these models for deeper investigations of intact surface zones during enamel caries, the structures of early-stage carious lesions in rats were characterized and compared with previous reports on white spot enamel lesions in humans. Synchrotron X-ray microcomputed tomography non-destructively mapped demineralization in carious rat molar specimens across a range of caries severity, identifying 52 lesions across the 30 teeth imaged. Of these lesions, 13 were shown to have intact surface zones. Depth profiles of fractional mineral density were qualitatively similar to lesions in human teeth. However, the thickness of the surface zone in the rat model ranges from 10 to 58 µm, and is therefore significantly thinner than in human enamel. These results indicate that a fraction of lesions in rat caries possess an intact surface zone and are qualitatively similar to human lesions at the micrometer scale. This suggests that rat caries models may be a suitable analog through which to investigate the structure of surface zone enamel and its role during dental caries.
Making visible the invisible through the analysis of acknowledgements in the humanities
Authors: A. Díaz-Faes Adrian , Bordons María
Published: August 2017

Purpose

Science is subject to a normative structure that includes how the contributions and interactions between scientists are rewarded. Authorship and citations have been the key elements within the reward system of science, whereas acknowledgements, despite being a well-established element in scholarly communication, have not received the same attention. The purpose of this paper is to put forward the bearing of acknowledgements in the humanities to bring to the foreground contributions and interactions that, otherwise, would remain invisible through traditional indicators of research performance.

Design/methodology/approach

The study provides a comprehensive framework to understanding acknowledgements as part of the reward system with a special focus on their value in the humanities as a reflection of intellectual indebtedness. The distinctive features of research in the humanities are outlined and the role of acknowledgements as a source of contributorship information is reviewed to support these assumptions.

Findings

“Peer interactive communication” is the prevailing support thanked in the acknowledgements of humanities, so the notion of acknowledgements as “super-citations” can make special sense in this area. Since single-authored papers still predominate as publishing pattern in this domain, the study of acknowledgements might help to understand social interactions and intellectual influences that lie behind a piece of research and are not visible through authorship.

Originality/value

Previous works have proposed and explored the prevailing acknowledgement types by domain. This paper focusses on the humanities to show the role of acknowledgements within the reward system and highlight publication patterns and inherent research features which make acknowledgements particularly interesting in the area as a reflection of the socio-cognitive structure of research.
Why do you publish? On the tensions between generating scientific knowledge and publication pressure
Authors: Hangel Nora , Schmidt-Pfister Diana
Published: August 2017

Purpose

The purpose of this paper is to examine researchers’ motivations to publish by comparing different career stages (PhD students; temporarily employed postdocs/new professors; scholars with permanent employment) with regard to epistemic, pragmatic, and personal motives.

Design/methodology/approach

This qualitative analysis is mainly based on semi-structured narrative interviews with 91 researchers in the humanities, social, and natural sciences, based at six renowned (anonymous) universities in Germany, the UK, and the USA. These narratives contain answers to the direct question “why do you publish?” as well as remarks on motivations to publish in relation to other questions and themes. The interdisciplinary interpretation is based on both sociological science studies and philosophy of science in practice.

Findings

At each career stage, epistemic, pragmatic, and personal motivations to publish are weighed differently. Confirming earlier studies, the authors find that PhD students and postdoctoral researchers in temporary positions mainly feel pressured to publish for career-related reasons. However, across status groups, researchers also want to publish in order to support collective knowledge generation.

Research limitations/implications

The sample of interviewees may be biased toward those interested in reflecting on their day-to-day work.

Social implications

Continuous and collective reflection is imperative for preventing uncritical internalization of pragmatic reasons to publish. Creating occasions for reflection is a task not only of researchers themselves, but also of administrators, funders, and other stakeholders.

Originality/value

Most studies have illuminated how researchers publish while adapting to or growing into the contemporary publish-or-perish culture. This paper addresses the rarely asked question why researchers publish at all.
Foreign subsidiaries’ competitive strategy: the impact of corporate support and local competition
Authors: Pehrsson Anders
Published: August 2017

Purpose

The study draws on the resource-based view and the contingency view of strategy. The purpose of this paper is to contribute to international strategy literature by extending the current understanding of foreign subsidiary’s competitive strategy in terms of cost leadership and product differentiation.

Design/methodology/approach

Hypotheses concern associations between corporate support building on product and skills relatedness and subsidiary strategies. Also, it is hypothesized that strategies are due to the type of local competitive intensity. The hypotheses were tested on wholly owned subsidiaries of Swedish industrial firms in Germany, the UK and the USA.

Findings

Product and skills relatedness between the subsidiary and the corporate core unit are positively associated with the subsidiary’s emphasis on cost leadership. Also, a positive association was found between skills relatedness and product differentiation, and extensive competitive intensity strengthens the relationship.

Research limitations/implications

The study specifies what business relatedness is needed for a subsidiary’s competitive strategy; skills relatedness is more important than product relatedness; the type of local competitive intensity is important; corporate support and local strategy operate simultaneously.

Practical implications

Management is advised to implement a foreign subsidiary’s competitive strategy by recognizing the mechanisms identified in this study.

Originality/value

In a unique way, the study captures the role of corporate support of a foreign subsidiary’s competitive strategy relying on business relatedness and the importance of aligning the strategy with competitive intensity.