bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThermosiphospecies 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

AbstractSystematic 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

AbstractThe 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

AbstractHouse 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.
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

AbstractBackgroundAbnormal 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.MethodsWe 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.ResultsMicrostructural 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).ConclusionsThis 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

AbstractMaximizing 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

SignificanceHabitat 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.AbstractCulverts 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

SummaryIn 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

AbstractBiological 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

AbstractFunctional 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.