bluuebunny/crossref_metadata_2025 huggingface dataset:
Causality re-established
Authors: D’Ariano Giacomo Mauro
Published: May 2018

Causality has never gained the status of a ‘law’ or ‘principle’ in physics. Some recent literature has even popularized the false idea that causality is a notion that should be banned from theory. Such misconception relies on an alleged universality of the reversibility of the laws of physics, based either on the determinism of classical theory, or on the multiverse interpretation of quantum theory, in both cases motivated by mere interpretational requirements for realism of the theory. Here, I will show that a properly defined unambiguous notion of causality is a theorem of quantum theory, which is also a falsifiable proposition of the theory. Such a notion of causality appeared in the literature within the framework of operational probabilistic theories. It is a genuinely theoretical notion, corresponding to establishing a definite partial order among events, in the same way as we do by using the future causal cone on Minkowski space. The notion of causality is logically completely independent of the misidentified concept of ‘determinism’, and, being a consequence of quantum theory, is ubiquitous in physics. In addition, as classical theory can be regarded as a restriction of quantum theory, causality holds also in the classical case, although the determinism of the theory trivializes it. I then conclude by arguing that causality naturally establishes an arrow of time. This implies that the scenario of the ‘block Universe’ and the connected ‘past hypothesis’ are incompatible with causality, and thus with quantum theory: they are both doomed to remain mere interpretations and, as such, are not falsifiable, similar to the hypothesis of ‘super-determinism’.

This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
Transforming graph states using single-qubit operations
Authors: Dahlberg Axel , Wehner Stephanie
Published: May 2018

Stabilizer states form an important class of states in quantum information, and are of central importance in quantum error correction. Here, we provide an algorithm for deciding whether one stabilizer (target) state can be obtained from another stabilizer (source) state by single-qubit Clifford operations (LC), single-qubit Pauli measurements (LPM) and classical communication (CC) between sites holding the individual qubits. What is more, we provide a recipe to obtain the sequence of LC+LPM+CC operations which prepare the desired target state from the source state, and show how these operations can be applied in parallel to reach the target state in constant time. Our algorithm has applications in quantum networks, quantum computing, and can also serve as a design tool—for example, to find transformations between quantum error correcting codes. We provide a software implementation of our algorithm that makes this tool easier to apply. A key insight leading to our algorithm is to show that the problem is equivalent to one in graph theory, which is to decide whether some graphG′ is avertex-minorof another graphG. The vertex-minor problem is, in general,-Complete, but can be solved efficiently on graphs which are not too complex. A measure of the complexity of a graph is therank-widthwhich equals theSchmidt-rank widthof a subclass of stabilizer states called graph states, and thus intuitively is a measure of entanglement. Here, we show that the vertex-minor problem can be solved in timeO(|G|3), where |G| is the size of the graphG, whenever the rank-width ofGand the size ofG′ are bounded. Our algorithm is based on techniques by Courcelle for solving fixed parameter tractable problems, where here the relevant fixed parameter is the rank width. The second half of this paper serves as an accessible but far from exhausting introduction to these concepts, that could be useful for many other problems in quantum information.

This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
From quantum foundations to applications and back
Authors: Gisin Nicolas , Fröwis Florian
Published: May 2018

Quantum non-locality has been an extremely fruitful subject of research, leading the scientific revolution towards quantum information science, in particular, to device-independent quantum information processing. We argue that the time is ripe to work on another basic problem in the foundations of quantum physics, the quantum measurement problem, which should produce good physics in theoretical, mathematical, experimental and applied physics. We briefly review how quantum non-locality contributed to physics (including some outstanding open problems) and suggest ways in which questions around macroscopic quantumness could equally contribute to all aspects of physics.

This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
Thermosiphospp. immune system differences affect variation in genome size and geographical distributions
Authors: Haverkamp Thomas H.A. , Geslin Claire , Lossouarn Julien , Podosokorskaya Olga A. , Kublanov Ilya , Nesbø Camilla L.
Published: May 2018

Thermosiphospecies inhabit thermal environments such as marine hydrothermal vents, petroleum reservoirs and terrestrial hot springs. A 16S rRNA phylogeny of availableThermosiphospp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents and hotsprings. Comparative genomics of 15Thermosiphogenomes separated them into three distinct species with different habitat distributions: the widely distributedT. africanusand the more specialized,T. melanesiensisandT. affectus. Moreover, the species can be differentiated on the basis of genome size, genome content and immune system composition. For instance, theT. africanusgenomes are largest and contained the most carbohydrate metabolism genes, which could explain why these isolates were obtained from ecologically more divergent habitats. Nonetheless, all theThermosiphogenomes, like other Thermotogae genomes, show evidence of genome streamlining. Genome size differences between the species could further be correlated to differences in defense capacities against foreign DNA, which influence recombination via HGT. The smallest genomes are found inT. affectusthat contain both CRISPR-cas Type I and III systems, but no RM system genes. We suggest that this has caused these genomes to be almost devoid of mobile elements, contrasting the two other species genomes that contain a higher abundance of mobile elements combined with different immune system configurations. Taken together, the comparative genomic analyses ofThermosiphospp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA.
MD-AD: Multi-task deep learning for Alzheimer’s disease neuropathology
Authors: Beebe-Wang Nicasia , Celik Safiye , Lee Su-In
Published: May 2018

Systematic modeling of Alzheimer’s Disease (AD) neuropathology based on brain gene expression would provide valuable insights into the disease. However, relative scarcity and regional heterogeneity of brain gene expression and neuropathology datasets obscure the ability to robustly identify expression markers. We propose MD-AD (Multi-task Deep learning for AD) to effectively combine heterogeneous AD datasets by simultaneously modeling multiple phenotypes with shared layers. MD-AD leads to an 8% and 5% reduction in mean squared error over MLP for predicting counts of two AD hallmarks: plaques and tangles. It also leads to a 40% and 30% reduction in classification error over MLP for two common staging systems for AD: CERAD score and Braak stage. Additionally, MD-AD’s network representation tends to better capture known metabolic pathways, including some AD-related pathways. Together, these results indicate that MD-AD is particularly useful for learning expressive network representations from heterogeneous and sparsely labeled AD data.
Contribution of rare and common variants to intellectual disability in a high-risk population sub-isolate of Northern Finland
Authors: Kurki Mitja I , Saarentaus Elmo , Pietiläinen Olli , Gormley Padhraig , Lal Dennis , Kerminen Sini , Torniainen-Holm Minna , Hämäläinen Eija , Rahikkala Elisa , Keski-Filppula Riikka , Rauhala Merja , Korpi-Heikkilä Satu , Komulainen-Ebrahim Jonna , Helander Heli , Vieira Päivi , Salomaa Veikko , Pirinen Matti , Suvisaari Jaana , Moilanen Jukka S , Körkkö Jarmo , Kuismin Outi , Daly Mark J , Palotie Aarno
Published: May 2018

The contribution of de novo and ultra-rare genetic variants in severe and moderate intellectual disability (ID) has been extensively studied whereas the genetic architecture of mild ID has been less well characterized. To elucidate the genetic background of milder ID we studied a regional cohort of 442 ID patients enriched for mild ID (>50%) from a population isolate of Finland. We analyzed rare variants using exome sequencing and CNV genotyping and common variants using common variant polygenic risk scores. As controls we used a Finnish collection of exome sequenced (n=11311) and GWAS chip genotyped (n=11699) individuals.

We show that rare damaging variants in genes known to be associated with cognitive defects are observed more often in severe (27%) than in mild ID (13%) patients (p-value: 7.0e-4). We further observed a significant enrichment of protein truncating variants in loss-of-function intolerant genes, as well as damaging missense variants in genes not yet associated with cognitive defects (OR: 2.1, p-value: 3e-8). For the first time to our knowledge, we show that a common variant polygenic load significantly contributes to all severity forms of ID. The heritability explained was the highest for educational attainment (EDU) in mild ID explaining 2.2% of the heritability on liability scale. For more severe ID it was lower at 0.6%. Finally, we identified a homozygote variant in the CRADD gene to be a cause of a specific syndrome with ID and pachygyria. The frequency of this variant is 50x higher in the Finnish population than in non-Finnish Europeans, demonstrating the benefits of utilizing population isolates in rare variant analysis of diseases under negative selection.
Genetic characterization of invasive house mouse populations on small islands
Authors: Morgan Andrew P , Didion John P , Hughes Jonathan J , Searle Jeremy B , Jolley Wesley J , Campbell Karl J , Threadgill David W , de Villena Fernando Pardo-Manuel
Published: May 2018

House mice (Mus musculus) have dispersed to nearly every major landmass around the globe as a result of human activity. They are a highly successful invasive species, but their presence can be devastating for native ecosystems. This is particularly true on small offshore islands where mouse populations may grow unchecked by predators. Here we use genome-wide SNP genotypes to examine ancestry and population structure on two islands of ecological interest - Southeast Farallon Island, near San Francisco, CA; and Floreana Island in the Galápagos - in the context of a total cohort of 520 mice with diverse geographic origins, as a first step towards genetically-based eradication campaigns. We show that Farallon and Floreana mice, like those from previously-studied islands in both the Atlantic and Pacific Oceans, are of admixed European ancestry. We find that these populations are on average more inbred than mainland ones and passed through a strong colonization bottleneck with little subsequent genetic exchange. Finally we show that rodenticide resistance alleles present in parts of Europe are absent from all island populations studied. Our results add nuance to previous studies of island populations based on mitochondrial sequences or small numbers of microsatellites and will be useful for future eradication and monitoring efforts.
A metastable contact and structural disorder in the estrogen receptor transactivation domain
Authors: Peng Yi , Cao Shufen , Kiselar Jana , Xiao Xiangzhu , Du Zhanwen , Hsien An , Ko Soobin , Chen Yinghua , Agrawal Prashansa , Zheng Wenwei , Shi Wuxian , Jiang Wei , Yang Lin , Chance Mark , Surewicz Witold , Buck Matthias , Yang Sichun
Published: May 2018

The N-terminal transactivation domain (NTD) of estrogen receptor alpha, a well-known member of the family of intrinsically disordered proteins (IDPs), mediates the receptor's transactivation function to regulate gene expression. However, an accurate molecular dissection of NTD's structure-function relationships remains elusive. Here, using small-angle X-ray scattering (SAXS), nuclear magnetic resonance (NMR), circular dichroism, and hydrogen exchange mass spectrometry, we show that NTD adopts a mostly disordered, unexpectedly compact conformation that undergoes structural expansion upon chemical denaturation. By combining SAXS, hydroxyl radical protein footprinting and computational modeling, we derive the ensemble-structures of the NTD and determine its ensemble-contact map that reveals metastable regional and long-range contacts, including interactions between residues I33 and S118. We show that mutation at S118, a known phosphorylation site, promotes conformational changes and increases coactivator binding. We further demonstrate via fluorine-19 (19F) NMR that mutations near residue I33 alter 19F chemical shifts at residue S118, confirming the proposed I33-S118 contact in the ensemble of structural disorder. These findings extend our understanding of IDPs' structure-function relationship, and how specific metastable contacts mediate critical functions of disordered proteins.
Abnormal microstructural development of the cerebral cortex in neonates with congenital heart disease is associated with impaired cerebral oxygen delivery
Authors: Kelly Christopher J. , Christiaens Daan , Batalle Dafnis , Makropoulos Antonios , Cordero-Grande Lucilio , Steinweg Johannes K. , O’Muircheartaigh Jonathan , Khan Hammad , Lee Geraint , Victor Suresh , Alexander Daniel C. , Zhang Hui , Simpson John , Hajnal Joseph V. , Edwards A. David , Rutherford Mary A. , Counsell Serena J.
Published: May 2018

Background

Abnormal macrostructural development of the cerebral cortex has been associated with hypoxia in infants with congenital heart disease (CHD). Animal studies have suggested that hypoxia results in cortical dysmaturation at the cellular level. New magnetic resonance imaging (MRI) techniques offer the potential to investigate the relationship between cerebral oxygen delivery and microstructural development of the cortex in newborn infants with CHD.

Methods

We measured macrostructural and microstructural properties of the cortex in 48 newborn infants with complex CHD and 48 age-matched healthy controls. Cortical volume and gyrification index were calculated from high resolution structural MRI. Neurite density and orientation dispersion indices were modelled using high angular resolution diffusion MRI. Cerebral oxygen delivery was estimated in infants with CHD using phase contrast MRI and pre-ductal pulse oximetry. We used tract-based spatial statistics to examine voxel-wise group differences in cortical microstructure.

Results

Microstructural development of the cortex was abnormal in 48 infants with CHD, with regions of increased fractional anisotropy (FA) and reduced orientation dispersion index (ODI) compared to 48 healthy controls, correcting for gestational age at birth and scan (FWE-corrected for multiple comparisons at P<0.05). Regions of reduced cortical ODI in infants with CHD were related to impaired cerebral oxygen delivery (R2=0.637, n=39). Cortical ODI was associated with gyrification index (R2=0.589, P<0.0001, n=48).

Conclusions

This study suggests that the primary component of cerebral cortex dysmaturation in CHD is impaired dendritic arborisation, which may underlie abnormal macrostructural findings reported in this population. The degree of impairment was related to cerebral oxygen delivery, supporting the hypothesis that maternal oxygen therapy may be beneficial in this population.
DNA metabarcoding diet analysis reveals dynamic feeding behaviour and biological control potential of carabid farmland communities
Authors: Kamenova Stefaniya , Bretagnolle Vincent , Plantegenest Manuel , Canard Elsa
Published: May 2018

Maximizing the delivery of key ecosystem services such as biological control through the management of natural enemy communities is one of the major challenges for modern agriculture. The main obstacle lies in our yet limited capacity of identifying the factors that drive the dynamics of trophic interactions within multi-species assemblages. Invertebrate generalist predators like carabid beetles are known for their dynamic feeding behaviour. Yet, at what extent different carabid species contribute to the regulation of animal and plant pests within agroecosystems is currently unknown. Here, we developed a DNA metabarcoding approach for characterizing the full diet spectrum of a community of fourteen very common carabid species inhabiting an intensively managed Western-European agroecosystem. We then investigated how diet and biological control potential within the carabid community varies with the sampling field location and the crop type (wheatvsoilseed rape). DNA metabarcoding diet analysis allowed to detect a wide variety of animal and plant taxa from carabid gut contents thus confirming their generalist feeding behaviour. The most common prey categories detected were arachnids, insects, earthworms and several plant families potentially including many weed species. Our results also show that the field location and the crop type are much stronger determinants then the species regarding carabid dietary choice: significantly more trophic links involving dipteran prey were observed in wheat, whereas more collembolan and plant prey was consumed in oilseed rape by the same carabid community. We speculate that structural differences in the habitats provided by these two crop types drive differences in resource availability cascading up the trophic chain, and we assume that specific carabid taxa could hardly be used to infer levels of ecosystem services (biological control) or disservices (e.g. intraguild predation). However, as this is the first study to report the use of DNA metabarcoding diet analysis in predatory carabid beetles we urge caution over the interpretation of our results. For instance, overall detection rates were rather low (31% of the individuals analysed tested positive for at least one prey category) most likely due to the overwhelming amplification of the carabid host DNA. Therefore, we acknowledge that more studies are required in order to confirm our observations and conclude with few recommendations for further improvements of the community-level DNA metabarcoding analysis of carabid diet.
Utilising the boundary layer to help restore the connectivity of fish habitats and populations
Authors: Watson Jabin R. , Goodrich Harriet R. , Cramp Rebecca L. , Gordos Matthew A. , Franklin Craig E.
Published: May 2018

Significance

Habitat fragmentation is a significant contributor to the worldwide decline of freshwater ecosystem health, the most pervasive cause of which is culverts. Culverts act as a barrier to fish movement, impacting feeding, predator avoidance, spawning, and community structures. Here we show that a common remediation strategy that involves baffles, is detrimental to the successful passage of small bodied and juvenile fish at high velocities. To remedy this widespread problem, we present a novel remediation design that benefits a range of small-bodied species and juvenile fish at the same high velocities, regardless of morphology or ecological niche. The application of this remediation design may be expanded to any smooth surfaced anthropogenic structure, to improve fish passage and restore ecosystem functionality.

Culverts are a major cause of habitat fragmentation in freshwater ecosystems, are a barrier to fish movement, and are regarded as a significant contributor in the decline of freshwater fish populations globally. To try to address this, various culvert remediation designs have been implemented, including the installation of vertical baffles and the provision of naturalistic (rock) substrates. While remediation strategies generally aim to reduce the velocity of water flowing through the structure, there is often resistance to their use because the resultant reduction in culvert discharge can negatively impact upstream flooding while also resulting in debris clogging and increased culvert maintenance costs. In addition, baffles markedly increase water turbulence that may be detrimental to passage by some fish species or size classes. Here we present some novel remediation designs that exploit the reduced water velocity in boundary layers along the culvert wall to enhance fish passage without significantly compromising discharge capacity. These longitudinal designs produce an expanded reduced velocity zone along the culvert margins that generate minimal turbulence. We show that these novel designs are significantly advantageous to the swimming endurance and traversability for six small-bodied Australian fish species. We also provide data on how and why some culvert baffle designs may impede small-bodied fish passage. This data scales with increasing water velocity, encompassing inter-specific differences in swimming capacity. These results have broad implications for fish community structure and the requirement of juvenile cohort of large-bodied commercially important species where baffles have been implemented to facilitate fish passage.
From apparent competition to facilitation, impacts of consumer niche construction on the coexistence and stability of consumer-resource communities
Authors: Picot Aurore , Monnin Thibaud , Loeuille Nicolas
Published: May 2018

In addition to their direct trophic effects, some consumers have a positive indirect effect on their resource, due to niche construction. A predator can facilitate its prey resource acquisition, through prey transport, or through modifications of nutrient cycling. Other predators defend their prey against other predators, or actively manage it, as in agriculture, which is found in numerous taxa such as humans, but also ants, beetles, fishes and microbes.

Here we investigate the ecological consequences of considering such positive effects in a simple two resource–one predator module, in which the consumer has a positive effect on one of the resources.

We consider several scenarios, in which the positive effect of the resource is either non costly, ie resulting from a by-product of the consumer phenotype such as nutrient cycling, or costly. The cost either decreases the exploitation of the helped resource or the opportunity to forage the alternative resource.

We show that by modifying the trophic interactions in the module, niche construction alters the apparent competition between the resources, thereby impacting their coexistence.

We investigate how the intensity of niche construction impacts species coexistence, the distribution of biomass among the three species, and the stability of the community. When niche construction has little or no cost, it leads to higher consumer and helped resource densities, while decreasing the alternative resource density. Alternatively, when niche construction has a strong cost, the alternative resource can increase in density, niche construction thereby leading to the emergence of facilitative interactions among resource species.
Single-molecule imaging of mRNA localization and regulation during the integrated stress response
Authors: Wilbertz Johannes H. , Voigt Franka , Horvathova Ivana , Roth Gregory , Zhan Yinxiu , Chao Jeffrey A.
Published: May 2018

Biological phase transitions form membrane-less organelles that generate distinct cellular environments. How molecules are partitioned between these compartments and the surrounding cellular space and the functional consequence of this localization is not well understood. Here, we report the localization of mRNA to stress granules(SGs) and processing bodies(PBs), which are distinct biomolecular condensates, and its effect on translation and mRNA degradation during the integrated stress response. Using single mRNA imaging in living human cells, we find that the interactions of mRNAs with SGs and PBs have different dynamics and that specific RNA binding proteins can anchor mRNAs within these compartments. During recovery from stress, mRNAs that were within SGs and PBs are translated and degraded at similar rates as their cytosolic counterparts.
In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation
Authors: Wu Chi-Chih , Klaesson Axel , Buskas Julia , Ranefall Petter , Mirzazadeh Reza , Söderberg Ola , Wolf Jochen B. W.
Published: May 2018

Functional validation of candidate genes for adaptation and speciation remains challenging. We here exemplify the utility of a method quantifying individual mRNA transcripts in revealing the molecular basis of divergence in feather pigment synthesis during early-stage speciation in crows. Using a padlock probe assay combined with rolling circle amplification we quantified cell-type specific gene expression in the native, histological context of growing feather follicles. Expression of Tyrosinase related protein 1 (TYRP1), Solute carrier family 45 member 2 (SLC45A2) and Hematopoietic prostaglandin D synthase (HPGDS) was melanocyte-limited and significantly reduced in follicles from hooded crow explaining the substantially lower melanin content in grey vs. black feathers. The central upstream transcription factor Microphthalmia-associated transcription factor (MITF) only showed differential expression specific to melanocytes - a feature not captured by bulk RNA-seq. Overall, this study provides insight into the molecular basis of an evolutionary young transition in pigment synthesis, and demonstrates the power of histologically explicit, statistically substantiated single-cell gene expression quantification for functional genetic inference in natural populations.
Physiological predictors of reproductive performance in the European Starling (Sturnus vulgaris): I. Univariate analysis
Authors: Fowler M.A. , Cohen A. , Paquet M. , Williams T.D.
Published: May 2018

Costs of reproduction are assumed to be widespread, and to have a physiological basis, but the mechanisms driving decreased survival and future fecundity remain elusive. Our overall goals were to assess whether physiological variables are related to workload ability or immediate fitness consequences and if they mediate future survival or reproductive success. We investigated individual variation in physiological state at two breeding stages (incubation, chick-rearing) in female European starlings (Sturnus vulgaris), for first-and second-broods over two years. Specifically, we measured a suite of 13 physiological traits related to aerobic/metabolic capacity, oxidative stress and muscle damage, intermediary metabolism and energy supply, and immune function. We tested for relationships to traits for workload (e.g. nest visit rate) and fitness (current reproduction, survival and future reproduction).

There was little co-variation among the 13 physiological traits, either in incubating or chick-rearing birds. There were some systematic differences in incubation versus chick-rearing physiology. Chick-rearing birds had lower hematocrit and plasma creatine kinase but higher hemoglobin, triglyceride and uric acid levels. Only plasma corticosterone was repeatable between incubation and chick-rearing. We assessed relationships in a univariate manner, and found very few significant relationships between incubation or chick-rearing physiology and measures of workload, current productivity, future fecundity or survival. Variability in ecological context may complicate the relationship between physiology and behavior. Additionally, individuals may regulate different aspects of their physiology independently, making detection of physiological mediators of cost of reproduction difficult. In a companion paper (Cohen et al. submitted) we explore the utility of multivariate analysis (Principal Components Analysis, Mahalanobis distance) of the same data to account for potentially complex physiological integration.
Actomyosin dynamics, Bmp and Notch signaling pathways drive apical extrusion of proepicardial cells
Authors: Andrés-Delgado Laura , Ernst Alexander , Galardi-Castilla María , Bazaga David , Peralta Marina , Münch Juliane , González-Rosa Juan Manuel , Tessadori Federico , Bakkers Jeroen , de la Pompa José Luis , Vermot Julien , Mercader Nadia
Published: May 2018

The epicardium, the outer mesothelial layer enclosing the myocardium, plays key roles in heart development and regeneration. During embryogenesis it arises from the proepicardium (PE), a cell cluster that appears in the dorsal pericardium close to the venous pole of the heart. Little is known about how the PE emerges from the pericardial mesothelium. Using the zebrafish model and a combination of genetic tools, pharmacological agents and quantitativein vivoimaging we reveal that a coordinated collective movement of the dorsal pericardium drives PE formation. We found that PE cells are apically extruded in response to actomyosin activity. Our results reveal that the coordinated action of Notch/Bmp pathways is critically needed for apical extrusion of PE cells. More generally, by comparison to cell extrusion for the elimination of unfit cells from epithelia, our results describe a unique mechanism where extruded cell viability is maintained.
Intraspecific variation alters ecosystem and next-generation performance as much as temperature
Authors: Raffard Allan , Cucherousset Julien , Santoul Frédéric , Di Gesu Lucie , Blanchet Simon
Published: May 2018

Phenotypic or genotypic variation within species affects ecological processes, from populations to ecosystems. However, whether the ecological imprint of intraspecific variation is substantial compared to key environmental drivers, and persistent enough to carry over to next generations is still questioned. Here, we experimentally showed that intraspecific variation manipulated in a freshwater fish (the European minnow,Phoxinus phoxinus) led to ecological and transgenerational carry-over effects that were as strong as those of varying temperature by 2°C. Specifically, variation in fish body mass, growth rate and activity altered the size and abundance of prey, which ultimately affected traits and survival of the next fish generation. Temperature variation modulated other ecosystem functions (e.g. litter decomposition) that were also associated to transgenerational carry-over effects. Our results demonstrate that shifting genotypes or phenotypes in wild populations can have substantial and persistent consequences on ecosystems with a similar intensity than climatic variation.
Osmolality controls the expression of cathelicidin antimicrobial peptide in human macrophages
Authors: Li Youxian , Johnsen Ingvild B.
Published: May 2018

An imbalance between extracellular and intracellular fluid osmolality causes osmotic stress and affects cellular homeostasis. Recent research suggests that osmotic stress is also associated with various innate and adaptive immune responses. Here we present the surprising finding that osmolality tightly controls the expression of cathelicidin antimicrobial peptide (CAMP) in human macrophages. CAMP expression is strongly upregulated under hyperosmotic conditions and downregulated under hypoosmotic conditions. We also provide evidence that this osmolality-mediated antimicrobial response is dependent on nuclear factor of activated T-cells 5 (NFAT5) and mitogen-activated protein kinase (MAPK) p38. Finally, Toll-like receptor (TLR) activation inhibits osmolality-mediated expression of CAMP in human macrophages, suggesting that this osmolality-dependent regulation of CAMP is more relevant under homeostatic conditions, rather than during acute infections. This study expands our knowledge of the regulation of human antimicrobial peptides and highlights osmolality as an important and independent factor shaping host innate immune homeostasis.
Low fidelity assembly of influenza A virus promotes escape from host cells
Authors: Vahey Michael D. , Fletcher Daniel A.
Published: May 2018

Influenza viruses inhabit a wide range of host environments using a limited repertoire of protein components. Unlike viruses with stereotyped shapes, influenza produces virions with significant morphological variability even within clonal populations. Whether this tendency to form pleiomorphic virions is coupled to compositional heterogeneity and whether it affects replicative fitness remains unclear. Here we address these questions by developing live strains of influenza A virus amenable to rapid compositional characterization through quantitative, site-specific labeling of viral proteins. Using these strains, we find that influenza A produces virions with broad variations in size and composition from even single infected cells. The virus leverages this phenotypic variability to survive environmental challenges including temperature changes and anti-virals. Complimenting genetic adaptations that act over larger populations and longer times, this ‘low fidelity’ assembly of influenza A virus allows small populations to survive environments that fluctuate over individual replication cycles.
Imaging of single mRNA translation repression reveals diverse interactions with mRNP granules
Authors: Moon Stephanie L. , Morisaki Tatsuya , Khong Anthony , Lyon Kenneth , Parker Roy , Stasevich Timothy J.
Published: May 2018

During cellular stress mRNAs exit translation and accumulate in stress granules and P-bodies, although the dynamics of these interactions remain unclear. We imaged in real-time single mRNAs, their translational output, and mRNA-granule interactions during stress. We observed single mRNAs interacting with stress granules and P-bodies, with mRNAs moving bidirectionality between them. While translating mRNAs only interact with RNP granules dynamically, non-translating mRNAs can form stable associations that rigidly immobilize the mRNA within the granule. Imaging thousands of individual mRNA-granule interactions showed the probability of stable association increases with both mRNA length and granule size. Therefore, the recruitment of mRNAs to RNP granules involves both highly dynamic and stable interactions, influenced by several parameters, demonstrating a new layer of complexity in mRNA regulation during stress.

One Sentence Summary

mRNAs interact with stress granules and P-bodies in stable and dynamic manners influenced by ribosome association, mRNA length, and granule size.
Sibling rivalry: Males with more brothers develop larger testes
Authors: Fisher Heidi S. , Hook Kristin A. , Weber W. David , Hoekstra Hopi E.
Published: May 2018

When females mate with multiple partners in a reproductive cycle, the relative number of competing sperm from rival males is often the most critical factor in determining paternity. Gamete production is directly related to testis size in most species, and is associated with both mating behavior within a system and perceived risk of competition.Peromyscus maniculatusis naturally promiscuous and males invest significantly more in sperm production than males ofP. polionotus, their monogamous sister-species. Here we show that the relatively larger testes inP. maniculatusare retained, even after decades of enforced monogamy in captivity. While these results suggest that differences in sperm production between species with divergent evolutionary histories can be maintained, we also show that the early rearing environment of males can strongly influence their testis size as adults. Using a second-generation hybrid population to increase variation in testis size, we show that males reared in litters with more brothers develop larger testes as adults. Importantly, this difference in testis size is also associated with increased fertility. Together, our findings suggest that sperm production may be both broadly shaped by natural selection over evolutionary timescales and also finely tuned during early development.
The Wright-Fisher Site Frequency Spectrum as a Perturbation of the Coalescent’s
Authors: Melfi Andrew , Viswanath Divakar
Published: May 2018

The first terms of the Wright-Fisher (WF) site frequency spectrum that follow the coalescent approximation are determined precisely, with a view to understanding the accuracy of the coalescent approximation for large samples. The perturbing terms show that the probability of a single mutant in the sample (singleton probability) is elevated in WF but the rest of the frequency spectrum is lowered. A part of the perturbation can be attributed to a mismatch in rates of merger between WF and the coalescent. The rest of it can be attributed to the difference in the way WF and the coalescent partition children between parents. In particular, the number of children of a parent is approximately Poisson under WF and approximately geometric under the coalescent. Whereas the mismatch in rates raises the probability of singletons under WF, its offspring distribution being approximately Poisson lowers it. The two effects are of opposite sense everywhere except at the tail of the frequency spectrum. The WF frequency spectrum begins to depart from that of the coalescent only for sample sizes that are comparable to the population size. These conclusions are confirmed by a separate analysis that assumes the sample sizento be equal to the population sizeN. Partly thanks to the canceling effects, the total variation distance of WF minus coalescent is 0.12/logNfor a population sized sample withn=N, which is only 1% forN= 2×104.
Characteristics and origins of non-functional Pm21 alleles in Dasypyrum villosum and wheat genetic stocks
Authors: Zhu Shanying , He Huagang
Published: May 2018

Most Dasypyrum villosum resources are highly resistant to wheat powdery mildew that carries Pm21 alleles. However, in the previous studies, four D. villosum lines (DvSus-1 ∼ DvSus-4) and two wheat-D. villosum addition lines (DA6V#1 and DA6V#3) were reported to be susceptible to powdery mildew. In the present study, the characteristics of non-functional Pm21 alleles in the above resources were analyzed after Sanger sequencing. The results showed that loss-of-functions of Pm21 alleles Pm21-NF1 ∼ Pm21-NF3 isolated from DvSus-1, DvSus-2/DvSus-3 and DvSus-4 were caused by two potential point mutations, a 1-bp deletion and a 1281-bp insertion, respectively. The non-functional Pm21 alleles in DA6V#1 and DA6V#3 were same to that in DvSus-4 and DvSus-2/DvSus-3, respectively, indicating that the susceptibilities of the two wheat genetic stocks came from their D. villosum donors. The origins of non-functional Pm21 alleles were also investigated in this study. Except the target variants involved, the sequences of Pm21-NF2 and Pm21-NF3 were identical to that of Pm21-F2 and Pm21-F3 in the resistant D. villosum lines DvRes-2 and DvRes-3, derived from the accessions GRA961 and GRA1114, respectively. It was suggested that the non-functional alleles Pm21-NF2 and Pm21-NF3 originated from the wild-type alleles Pm21-F2 and Pm21-F3. In summary, this study gives an insight into the sequence characteristics of non-functional Pm21 alleles and their origins in natural population of D. villosum.
Direct shape determination of intermediates in evolving macromolecular solutions from small-angle scattering data
Authors: Konarev Petr V. , Svergun Dmitri I.
Published: May 2018

Many important biological processes like amyloid formation, viral assembly etc. can be monitored in vitro. Small-angle X-ray scattering (SAXS) is one of the most effective techniques to structurally characterize these processes in solution. For monodisperse systems and some oligomeric mixtures, low-resolution shapes can be determined ab initio from the SAXS data, but for evolving systems, such analysis is hampered by the presence of multiple species and no direct reconstruction procedures are available. The authors consider a frequently occurring case where the scattering from the initial and final states of the process are known but there exists a major (unknown) intermediate component. A method is presented to directly reconstruct the low-resolution shape of this transient component together with its volume fractions from multiple scattering patterns recorded from an evolving system. The method is implemented in the computer program DAMMIX freely available to academic users and its effectiveness is illustrated in several synthetic and experimental examples.
Implementation of the surgical safety checklist in hospitals of Iran; operating room personnel’s attitude, awareness and acceptance
Authors: Sokhanvar Mobin , Kakemam Edris , Goodarzi Narges
Published: May 2018

Purpose

The WHO Surgical Safety Checklist (SSC) has improved patient safety effectively. Despite the known benefits of applying the checklist before surgery, its implementation is less than universal in practice. The purpose of this paper is to determine the operating room personnel’s attitude, their awareness and knowledge of the SSC, and to evaluate staff acceptance of the SSC (including personal beliefs).

Design/methodology/approach

This cross-sectional study was conducted in eight tertiary general hospitals in Tehran, Iran. Some 145 operating room personnel (surgeons, anaesthetists and nurses) were selected for the study. Data collection was carried out via a validated questionnaire in three parts which included socio-demographic, attitude, awareness and acceptance. Data were then analysed using the Kruskal–Wallis and χ2 statistical test.

Findings

Out of the 145 participants in the study, 92 per cent were aware of the existence of the SSC and 73.9 per cent of them were aware of the objectives of SSC. Overall, the attitude to SSC was positive. The attitude of surgeons was positive towards the impact of the SSC on safety and teamwork. Surgeons were significantly more sensitive to the barriers of SSC application compared to nurses and anaesthetists (p=0.046). Among the three groups, nurses had the highest level of support for SSC (p=0.001).

Practical implications

Despite high acceptance of the checklist among staff, there is still a gap in knowledge about when exactly the checklist should be used. Therefore, involvement of all surgical team members to complete the checklist process, support of senior managers, on-going education and training and consideration of the barriers to its implementation are all key areas that need to be taken into account.

Originality/value

This is the first research to examine the operating room personnel’s attitude, awareness and acceptance about SSC in Iranian hospitals. The outcomes of this study provide documentation and possible justification for effective establishment of SSC in Iran and other countries.
Structural quality of healthcare facilities in India
Authors: Armenta Bianca , Rathi Naveen , Assasnik Nushean , Kamimura Akiko
Published: May 2018

Purpose

Although India has a number of health issues, the healthcare facilities in India are insufficient due to poor quality of care. The purpose of this paper is to examine the factors affecting the structural quality of healthcare facilities in India.

Design/methodology/approach

This study used the medical facility data from the India Human Development Survey-II, 2011–2012 (ICPSR 36151) (n=4,218). Logistic regression was conducted to predict structural quality of healthcare facilities.

Findings

The results suggest that it is difficult to have all standard resources available at health care facilities in India. Surprisingly, having a drinking water source inside the health facility appears to be an indicator of poor structural quality of health care facilities. Having a water source inside a health care facility is associated with not having a separate exam room and not having a sink to wash hands. A higher registration fee was associated with good structural quality and with having a separate exam room and having a sink to wash hands.

Originality/value

This study shows the complexity of providing quality health care to the poor, particularly in developing countries. Research on quality of healthcare facilities in India is needed to improve the health of the population. Little research has been done on the factors influencing the structural quality of the healthcare facilities in India. This study is an important contribution to the current knowledge of structural healthcare facility standards and its influences in India.
Towards Islamic Accounting Anthropology
Authors: Mulawarman Aji Dedi , Kamayanti Ari
Published: May 2018

Purpose

The purpose of this study is to shed light on how accounting, which has been recognised as a contributor to the modernity problem, has been influenced by secular anthropology, which hinges on the concept of “self”. Based on Akbar S. Ahmed’s concept of Islamic Anthropology, Islamic Accounting Anthropology (IAA) is proposed as an answer to shift the accounting paradigm.

Design/methodology/approach

A case study in Indonesia was conducted by studying the development of the nation’s Shariah accounting from the perspective of diffusionism as an approach to anthropology. Following the constructivist tradition, IAA, which rejects the Social Darwinism notion of the superiority of the West over the East as the basis of the evolution of civilisation, is used as tool to realise Islamic norms through synchronic-diachronic study, constructing an accounting concept and invoking accounting transformation through accounting education.

Findings

This study finds that accounting has been greatly affected by secular Western culture through education and educators as agents that find their legitimation in country policies. Standard setters have also taken the same stance by siding with the capital market. By proposing IAA, it is hoped that Islam will replace the concept of “self-interest” as the faith of accounting and promote welfare for the ummah.

Research limitations/implications

The problem of modernisation lies in the newfound faith of self-interest. In accounting, self-interest is ingrained in accounting theories such as Positive Accounting Theory, Entity Theory and Agency Theory, and thus accounting has become a tool to support neoliberal society. IAA will help produce accounting that is rooted in local wisdom and necessity yet very much embedded in Islamic values.

Practical implications

IAA suggests that accounting education must be geared towards anthropology detached from the Orientalism-secularism concept. This shift can be accomplished by integrating IAA into the accounting education curriculum.

Social implications

Based on IAA, accounting practices can be designed under the guidance of the Quran and result using a synchronic-diachronic approach. By changing the ontological view through accounting education, accounting can drive societal consciousness towards the welfare of society instead of self-happiness.

Originality/value

Islamic accounting and anthropology are two subjects that are rarely discussed concurrently.