bluuebunny/crossref_metadata_2025 huggingface dataset:
Lost at sea: ocean acidification undermines larval fish orientation via altered hearing and marine soundscape modification
Authors: Rossi Tullio , Nagelkerken Ivan , Pistevos Jennifer C. A. , Connell Sean D.
Published: January 2016

The dispersal of larvae and their settlement to suitable habitat is fundamental to the replenishment of marine populations and the communities in which they live. Sound plays an important role in this process because for larvae of various species, it acts as an orientational cue towards suitable settlement habitat. Because marine sounds are largely of biological origin, they not only carry information about the location of potential habitat, but also information about the quality of habitat. While ocean acidification is known to affect a wide range of marine organisms and processes, its effect on marine soundscapes and its reception by navigating oceanic larvae remains unknown. Here, we show that ocean acidification causes a switch in role of present-day soundscapes from attractor to repellent in the auditory preferences in a temperate larval fish. Using natural CO
2
vents as analogues of future ocean conditions, we further reveal that ocean acidification can impact marine soundscapes by profoundly diminishing their biological sound production. An altered soundscape poorer in biological cues indirectly penalizes oceanic larvae at settlement stage because both control and CO
2
-treated fish larvae showed lack of any response to such future soundscapes. These indirect and direct effects of ocean acidification put at risk the complex processes of larval dispersal and settlement.
Dissecting the self-assembly kinetics of multimeric pore-forming toxins
Authors: Lee A. A. , Senior M. J. , Wallace M. I. , Woolley T. E. , Griffiths I. M.
Published: January 2016

Pore-forming toxins are ubiquitous cytotoxins that are exploited by both bacteria and the immune response of eukaryotes. These toxins kill cells by assembling large multimeric pores on the cell membrane. However, a quantitative understanding of the mechanism and kinetics of this self-assembly process is lacking. We propose an analytically solvable kinetic model for stepwise, reversible oligomerization. In biologically relevant limits, we obtain simple algebraic expressions for the rate of pore formation, as well as for the concentration of pores as a function of time. Quantitative agreement is obtained between our model and time-resolved kinetic experiments of
Bacillus thuringiensis
Cry1Ac (tetrameric pore), aerolysin,
Staphylococcus aureus
α
-haemolysin (heptameric pores) and
Escherichia coli
cytolysin A (dodecameric pore). Furthermore, our model explains how rapid self-assembly can take place with low concentrations of oligomeric intermediates, as observed in recent single-molecule fluorescence experiments of α-haemolysin self-assembly. We propose that suppressing the concentration of oligomeric intermediates may be the key to reliable, error-free, self-assembly of pores.
Simultaneous DNA-based diet analysis of breeding, non-breeding and chick Adélie penguins
Authors: McInnes Julie C. , Emmerson Louise , Southwell Colin , Faux Cassandra , Jarman Simon N.
Published: January 2016

As central place foragers, breeding penguins are restricted in foraging range by the need to return to the colony to feed chicks. Furthermore, breeding birds must balance energetic gain from self-feeding with the costs of returning to provision young. Non-breeding birds, however, are likely to be less restricted in foraging range and lack the high energy demands of provisioning, therefore may consume different prey to breeders. We used DNA dietary analysis to determine whether there was a difference in provisioning and self-feeding diet by identifying prey DNA in scat samples from breeding and chick Adélie penguins at two locations in East Antarctica. We also investigated diet differences between breeders and non-breeders at one site. Although previous work shows changing foraging behaviour between chick provisioning and self-feeding, our results suggest no significant differences in the main prey groups consumed by chicks and breeders at either site or between breeding stages. This may reflect the inability of penguins to selectively forage when provisioning, or resources were sufficient for all foraging needs. Conversely, non-breeders were found to consume different prey groups to breeders, which may reflect less restricted foraging ranges, breeders actively selecting particular prey during breeding or reduced foraging experience of non-breeders.
The Peer Reviewers' Openness Initiative: incentivizing open research practices through peer review
Authors: Morey Richard D. , Chambers Christopher D. , Etchells Peter J. , Harris Christine R. , Hoekstra Rink , Lakens Daniël , Lewandowsky Stephan , Morey Candice Coker , Newman Daniel P. , Schönbrodt Felix D. , Vanpaemel Wolf , Wagenmakers Eric-Jan , Zwaan Rolf A.
Published: January 2016

Openness is one of the central values of science. Open scientific practices such as sharing data, materials and analysis scripts alongside published articles have many benefits, including easier replication and extension studies, increased availability of data for theory-building and meta-analysis, and increased possibility of review and collaboration even after a paper has been published. Although modern information technology makes sharing easier than ever before, uptake of open practices had been slow. We suggest this might be in part due to a social dilemma arising from misaligned incentives and propose a specific, concrete mechanism—reviewers withholding comprehensive review—to achieve the goal of creating the expectation of open practices as a matter of scientific principle.
Formation of wave packets in the Ostrovsky equation for both normal and anomalous dispersion
Authors: Grimshaw Roger , Stepanyants Yury , Alias Azwani
Published: January 2016

It is well known that the Ostrovsky equation with normal dispersion does not support steady solitary waves. An initial Korteweg–de Vries solitary wave decays adiabatically through the radiation of long waves and is eventually replaced by an envelope solitary wave whose carrier wave and envelope move with different velocities (phase and group velocities correspondingly). Here, we examine the same initial condition for the Ostrovsky equation with anomalous dispersion, when the wave frequency increases with wavenumber in the limit of very short waves. The essential difference is that now there exists a steady solitary wave solution (Ostrovsky soliton), which in the small-amplitude limit can be described asymptotically through the solitary wave solution of a nonlinear Schrödinger equation, based at that wavenumber where the phase and group velocities coincide. Long-time numerical simulations show that the emergence of this steady envelope solitary wave is a very robust feature. The initial Korteweg–de Vries solitary wave transforms rapidly to this envelope solitary wave in a seemingly non-adiabatic manner. The amplitude of the Ostrovsky soliton strongly correlates with the initial Korteweg–de Vries solitary wave.
One-dimensional hydrogen atom
Authors: Loudon Rodney
Published: January 2016

The theory of the one-dimensional (1D) hydrogen atom was initiated by a 1952 paper but, after more than 60 years, it remains a topic of debate and controversy. The aim here is a critique of the current status of the theory and its relation to relevant experiments. A 1959 solution of the Schrödinger equation by the use of a cut-off at
x
=
a
to remove the singularity at the origin in the 1/|
x
| form of the potential is clarified and a mistaken approximation is identified. The singular atom is not found in the real world but the theory with cut-off has been applied successfully to a range of four practical three-dimensional systems confined towards one dimension, particularly their observed large increases in ground state binding energy. The true 1D atom is in principle restored when the short distance
a
tends to zero but it is sometimes claimed that the solutions obtained by the limiting procedure differ from those obtained by solution of the basic Schrödinger equation without any cut-off in the potential. The treatment of the singularity by a limiting procedure for applications to practical systems is endorsed.
Bright solitons in non-equilibrium coherent quantum matter
Authors: Pinsker F. , Flayac H.
Published: January 2016

We theoretically demonstrate a mechanism for bright soliton generation in spinor non-equilibrium Bose–Einstein condensates made of atoms or quasi-particles such as polaritons in semiconductor microcavities. We give analytical expressions for bright (half) solitons as minimizing functions of a generalized non-conservative Lagrangian elucidating the unique features of inter and intra-competition in non-equilibrium systems. The analytical results are supported by a detailed numerical analysis that further shows the rich soliton dynamics inferred by their instability and mutual cross-interactions.
Deformation of a micro-torque swimmer
Authors: Ishikawa Takuji , Tanaka Tomoyuki , Imai Yohsuke , Omori Toshihiro , Matsunaga Daiki
Published: January 2016

The membrane tension of some kinds of ciliates has been suggested to regulate upward and downward swimming velocities under gravity. Despite its biological importance, deformation and membrane tension of a ciliate have not been clarified fully. In this study, we numerically investigated the deformation of a ciliate swimming freely in a fluid otherwise at rest. The cell body was modelled as a capsule with a hyperelastic membrane enclosing a Newtonian fluid. Thrust forces due to the ciliary beat were modelled as torques distributed above the cell body. The effects of membrane elasticity, the aspect ratio of the cell's reference shape, and the density difference between the cell and the surrounding fluid were investigated. The results showed that the cell deformed like a heart shape, when the capillary number was sufficiently large. Under the influence of gravity, the membrane tension at the anterior end decreased in the upward swimming while it increased in the downward swimming. Moreover, gravity-induced deformation caused the cells to move gravitationally downwards or upwards, which resulted in a positive or negative geotaxis-like behaviour with a physical origin. These results are important in understanding the physiology of a ciliate's biological responses to mechanical stimuli.
Deformation compatibility in a single crystalline Ni superalloy
Authors: Jiang Jun , Zhang Tiantian , Dunne Fionn P. E. , Britton T. Ben
Published: January 2016

Deformation in materials is often complex and requires rigorous understanding to predict engineering component lifetime. Experimental understanding of deformation requires utilization of advanced characterization techniques, such as high spatial resolution digital image correlation (HR-DIC) and high angular resolution electron backscatter diffraction (HR-EBSD), combined with clear interpretation of their results to understand how a material has deformed. In this study, we use HR-DIC and HR-EBSD to explore the mechanical behaviour of a single-crystal nickel alloy and to highlight opportunities to understand the complete deformations state in materials. Coupling of HR-DIC and HR-EBSD enables us to precisely focus on the extent which we can access the deformation gradient,F, in its entirety and uncouple contributions from elastic deformation gradients, slip and rigid body rotations. Our results show a clear demonstration of the capabilities of these techniques, found within our experimental toolbox, to underpin fundamental mechanistic studies of deformation in polycrystalline materials and the role of microstructure.
On firework blasts and qualitative parameter dependency
Authors: Zohdi T. I.
Published: January 2016

In this paper, a mathematical model is developed to qualitatively simulate the progressive time-evolution of a blast from a simple firework. Estimates are made for the blast radius that one can expect for a given amount of detonation energy and pyrotechnic display material. The model balances the released energy from the initial blast pulse with the subsequent kinetic energy and then computes the trajectory of the material under the influence of the drag from the surrounding air, gravity and possible buoyancy. Under certain simplifying assumptions, the model can be solved for analytically. The solution serves as a guide to identifying key parameters that control the evolving blast envelope. Three-dimensional examples are given.
Irrational time allocation in decision-making
Authors: Oud Bastiaan , Krajbich Ian , Miller Kevin , Cheong Jin Hyun , Botvinick Matthew , Fehr Ernst
Published: January 2016

Time is an extremely valuable resource but little is known about the efficiency of time allocation in decision-making. Empirical evidence suggests that in many ecologically relevant situations, decision difficulty and the relative reward from making a correct choice, compared to an incorrect one, are inversely linked, implying that it is optimal to use relatively less time for difficult choice problems. This applies, in particular, to value-based choices, in which the relative reward from choosing the higher valued item shrinks as the values of the other options get closer to the best option and are thus more difficult to discriminate. Here, we experimentally show that people behave sub-optimally in such contexts. They do not respond to incentives that favour the allocation of time to choice problems in which the relative reward for choosing the best option is high; instead they spend too much time on problems in which the reward difference between the options is low. We demonstrate this by showing that it is possible to improve subjects' time allocation with a simple intervention that cuts them off when their decisions take too long. Thus, we provide a novel form of evidence that organisms systematically spend their valuable time in an inefficient way, and simultaneously offer a potential solution to the problem.
Resilience and stability of a pelagic marine ecosystem
Authors: Lindegren Martin , Checkley David M. , Ohman Mark D. , Koslow J. Anthony , Goericke Ralf
Published: January 2016

The accelerating loss of biodiversity and ecosystem services worldwide has accentuated a long-standing debate on the role of diversity in stabilizing ecological communities and has given rise to a field of research on biodiversity and ecosystem functioning (BEF). Although broad consensus has been reached regarding the positive BEF relationship, a number of important challenges remain unanswered. These primarily concern the underlying mechanisms by which diversity increases resilience and community stability, particularly the relative importance of statistical averaging and functional complementarity. Our understanding of these mechanisms relies heavily on theoretical and experimental studies, yet the degree to which theory adequately explains the dynamics and stability of natural ecosystems is largely unknown, especially in marine ecosystems. Using modelling and a unique 60-year dataset covering multiple trophic levels, we show that the pronounced multi-decadal variability of the Southern California Current System (SCCS) does not represent fundamental changes in ecosystem functioning, but a linear response to key environmental drivers channelled through bottom-up and physical control. Furthermore, we show strong temporal asynchrony between key species or functional groups within multiple trophic levels caused by opposite responses to these drivers. We argue that functional complementarity is the primary mechanism reducing community variability and promoting resilience and stability in the SCCS.
Tracking and forecasting ecosystem interactions in real time
Authors: Deyle Ethan R. , May Robert M. , Munch Stephan B. , Sugihara George
Published: January 2016

Evidence shows that species interactions are not constant but change as the ecosystem shifts to new states. Although controlled experiments and model investigations demonstrate how nonlinear interactions can arise in principle, empirical tools to track and predict them in nature are lacking. Here we present a practical method, using available time-series data, to measure and forecast changing interactions in real systems, and identify the underlying mechanisms. The method is illustrated with model data from a marine mesocosm experiment and limnologic field data from Sparkling Lake, WI, USA. From simple to complex, these examples demonstrate the feasibility of quantifying, predicting and understanding state-dependent, nonlinear interactions as they occur
in situ
and in real time—a requirement for managing resources in a nonlinear, non-equilibrium world.
The pertussis enigma: reconciling epidemiology, immunology and evolution
Authors: Domenech de Cellès Matthieu , Magpantay Felicia M. G. , King Aaron A. , Rohani Pejman
Published: January 2016

Pertussis, a highly contagious respiratory infection, remains a public health priority despite the availability of vaccines for 70 years. Still a leading cause of mortality in developing countries, pertussis has re-emerged in several developed countries with high vaccination coverage. Resurgence of pertussis in these countries has routinely been attributed to increased awareness of the disease, imperfect vaccinal protection or high infection rates in adults. In this review, we first present 1980–2012 incidence data from 63 countries and show that pertussis resurgence is not universal. We further argue that the large geographical variation in trends probably precludes a simple explanation, such as the transition from whole-cell to acellular pertussis vaccines. Reviewing available evidence, we then propose that prevailing views on pertussis epidemiology are inconsistent with both historical and contemporary data. Indeed, we summarize epidemiological evidence showing that natural infection and vaccination both appear to provide long-term protection against transmission and disease, so that previously infected or vaccinated adults contribute little to overall transmission at a population level. Finally, we identify several promising avenues that may lead to a consistent explanation of global pertussis epidemiology and to more effective control strategies.
Ambient temperature influences tolerance to plant secondary compounds in a mammalian herbivore
Authors: Kurnath P. , Merz N. D. , Dearing M. D.
Published: January 2016

Growing evidence suggests that plant secondary compounds (PSCs) ingested by mammals become more toxic at elevated ambient temperatures, a phenomenon known as temperature-dependent toxicity. We investigated temperature-dependent toxicity in the desert woodrat (Neotoma lepida), a herbivorous rodent that naturally encounters PSCs in creosote bush (Larrea tridentata), which is a major component of its diet. First, we determined the maximum dose of creosote resin ingested by woodrats at warm (28–29°C) or cool (21–22°C) temperatures. Second, we controlled the daily dose of creosote resin ingested at warm, cool and room (25°C) temperatures, and measured persistence in feeding trials. At the warm temperature, woodrats ingested significantly less creosote resin; their maximum dose was two-thirds that of animals at the cool temperature. Moreover, woodrats at warm and room temperatures could not persist on the same dose of creosote resin as woodrats at the cool temperature. Our findings demonstrate that warmer temperatures reduce PSC intake and tolerance in herbivorous rodents, highlighting the potentially adverse consequences of temperature-dependent toxicity. These results will advance the field of herbivore ecology and may hone predictions of mammalian responses to climate change.
The genomic basis of adaptation to the fitness cost of rifampicin resistance inPseudomonas aeruginosa
Authors: Qi Qin , Toll-Riera Macarena , Heilbron Karl , Preston Gail M. , MacLean R. Craig
Published: January 2016

Antibiotic resistance carries a fitness cost that must be overcome in order for resistance to persist over the long term. Compensatory mutations that recover the functional defects associated with resistance mutations have been argued to play a key role in overcoming the cost of resistance, but compensatory mutations are expected to be rare relative to generally beneficial mutations that increase fitness, irrespective of antibiotic resistance. Given this asymmetry, population genetics theory predicts that populations should adapt by compensatory mutations when the cost of resistance is large, whereas generally beneficial mutations should drive adaptation when the cost of resistance is small. We tested this prediction by determining the genomic mechanisms underpinning adaptation to antibiotic-free conditions in populations of the pathogenic bacteriumPseudomonas aeruginosathat carry costly antibiotic resistance mutations. Whole-genome sequencing revealed that populations founded by high-cost rifampicin-resistant mutants adapted via compensatory mutations in three genes of the RNA polymerase core enzyme, whereas populations founded by low-cost mutants adapted by generally beneficial mutations, predominantly in the quorum-sensing transcriptional regulator genelasR. Even though the importance of compensatory evolution in maintaining resistance has been widely recognized, our study shows that the roles of general adaptation in maintaining resistance should not be underestimated and highlights the need to understand how selection at other sites in the genome influences the dynamics of resistance alleles in clinical settings.
Comparative Analysis of Single-Cell RNA Sequencing Methods
Authors: Ziegenhain Christoph , Vieth Beate , Parekh Swati , Reinius Björn , Smets Martha , Leonhardt Heinrich , Hellmann Ines , Enard Wolfgang
Published: January 2016

Background

Single-cell RNA sequencing (scRNA-seq) offers exciting possibilities to address biological and medical questions, but a systematic comparison of recently developed protocols is still lacking.

Results

We generated data from 447 mouse embryonic stem cells using Drop-seq, SCRB-seq, Smart-seq (on Fluidigm C1) and Smart-seq2 and analyzed existing data from 35 mouse embryonic stem cells prepared with CEL-seq. We find that Smart-seq2 is the most sensitive method as it detects the most genes per cell and across cells. However, it shows more amplification noise than CEL-seq, Drop-seq and SCRB-seq as it cannot use unique molecular identifiers (UMIs). We use simulations to model how the observed combinations of sensitivity and amplification noise affects detection of differentially expressed genes and find that SCRB-seq reaches 80% power with the fewest number of cells. When considering cost-efficiency at different sequencing depths at 80% power, we find that Drop-seq is preferable when quantifying transcriptomes of a large numbers of cells with low sequencing depth, SCRB-seq is preferable when quantifying transcriptomes of fewer cells and Smart-seq2 is preferable when annotating and/or quantifying transcriptomes of fewer cells as long one can use in-house produced transposase.

Conclusions

Our analyses allows an informed choice among five prominent scRNA-seq protocols and provides a solid framework for benchmarking future improvements in scRNA-seq methodologies.
Beyond comparisons of means: understanding changes in gene expression at the single-cell level
Authors: Vallejos Catalina A , Richardson Sylvia , Marioni John C
Published: January 2016

Single-cell RNA sequencing (scRNA-seq) can be used to characterise differences in gene expression patterns between pre-specified populations of cells. Traditionally, differential expression tools are restricted to the study of changes in overall expression between cell populations. However, such analyses do not take full advantage of the rich information provided by scRNA-seq. In this article, we present a Bayesian hierarchical model which can be used to study changes in expression that lie beyond comparisons of means. In particular, our method can highlight genes that undergo changes in cell-to-cell heterogeneity between the populations but whose overall expression is preserved. Evidence supporting these changes is quantified using a probabilistic approach based on tail posterior probabilities, where a probability cut-off is calibrated through the expected false discovery rate. Our method incorporates a built-in normalisation strategy and quantifies technical artefacts by borrowing information from technical spike-in genes. Control experiments validate the performance of our approach. Finally, we compare expression patterns of mouse embryonic stem cells between different stages of the cell cycle, revealing substantial differences in cellular heterogeneity.
Identification of physical interactions between genomic regions by enChIP-Seq
Authors: Fujita Toshitsugu , Yuno Miyuki , Suzuki Yutaka , Sugano Sumio , Fujii Hodaka
Published: January 2016

Physical interactions between genomic regions play critical roles in the regulation of genome functions, including gene expression. However, the methods for confidently detecting physical interactions between genomic regions remain limited. Here, we demonstrate the feasibility of using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) in combination with next-generation sequencing (NGS) (enChIP-Seq) to detect such interactions. In enChIP-Seq, the target genomic region is captured by an engineered DNA-binding complex, such as a CRISPR system consisting of a catalytically inactive form of Cas9 (dCas9) and a single guide RNA (sgRNA). Subsequently, the genomic regions that physically interact with the target genomic region in the captured complex are sequenced by NGS. Using enChIP-Seq, we found that the 5’HS5 locus, which regulates expression of theβ-globingenes, interacts with multiple genomic regions upon erythroid differentiation in the human erythroleukemia cell line K562. Genes near the genomic regions inducibly associated with the 5’HS5 locus were transcriptionally up-regulated in the differentiated state, suggesting the existence of a coordinated transcription mechanism directly or indirectly mediated by physical interactions between these loci. Our data suggest that enChIP-Seq is a potentially useful tool for detecting physical interactions between genomic regions in a non-biased manner, which would facilitate elucidation of the molecular mechanisms underlying regulation of genome functions.
Inferring population size history from large samples of genome wide molecular data - an approximate Bayesian computation approach
Authors: Boitard Simon , Rodríguez Willy , Jay Flora , Mona Stefano , Austerlitz Frédéric
Published: January 2016

Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.
Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana
Authors: Bouche Frederic , D'Aloia Maria , Tocquin Pierre , Lobet Guillaume , Detry Nathalie , Perilleux Claire
Published: January 2016

Molecular data concerning the involvement of the roots in the genetic pathways regulating floral transition are lacking. In this study, we performed global analyses of root transcriptome in Arabidopsis in order to identify flowering time genes that are expressed in the roots and genes that are differentially expressed in the roots during the induction of flowering. Data mining of public microarray experiments uncovered that about 200 genes whose mutation was reported to alter flowering time are expressed in the roots but only few flowering integrators were found. Transcriptomic analysis of the roots during synchronized induction of flowering by a single 22-h long day revealed that 595 genes were differentially expressed. A delay in clock gene expression was observed upon extension of the photoperiod. Enrichment analyses of differentially expressed genes in root tissues, gene ontology categories and cis-regulatory elements converged towards sugar signaling. We inferred that roots are integrated in systemic signaling whereby carbon supply coordinates growth at the whole plant level during the induction of flowering.
De novoGenome Assembly ofGeosmithia morbida, the Causal Agent of Thousand Cankers Disease
Authors: Aggarwal Taruna , Westbrook Anthony , Broders Kirk , Woeste Keith , MacManes Matthew D
Published: January 2016

Background: Geosmithia morbida is a filamentous ascomycete that causes Thousand Cankers Disease in the eastern black walnut tree. This pathogen is commonly found in the western U.S.; however, recently the disease was also detected in several eastern states where the black walnut lumber industry is concentrated. G. morbida is one of two known phytopathogens within the genus Geosmithia, and it is vectored into the host tree via the walnut twig beetle.

Results: We present the first de novo draft genome of G. morbida. It is 26.5 Mbp in length and contains less than 1% repetitive elements. The genome possesses an estimated 6,273 genes, 277 of which are predicted to encode proteins with unknown functions. Approximately 31.5% of the proteins in G. morbida are homologous to proteins involved in pathogenicity, and 5.6% of the proteins contain signal peptides that indicate these proteins are secreted.

Conclusions: Several studies have investigated the evolution of pathogenicity in pathogens of agricultural crops; forest fungal pathogens are often neglected because research efforts are focused on food crops. G. morbida is one of the few tree phytopathogens to be sequenced, assembled and annotated. The first draft genome of G. morbida serves as a valuable tool for comprehending the underlying molecular and evolutionary mechanisms behind pathogenesis within the Geosmithia genus.
Rare loss-of-function variants inKMT2Fare associated with schizophrenia and developmental disorders
Authors: Singh Tarjinder , Kurki Mitja I. , Curtis David , Purcell Shaun M. , Crooks Lucy , McRae Jeremy , Suvisaari Jaana , Chheda Himanshu , Blackwood Douglas , Breen Gerome , Pietiläinen Olli , Gerety Sebastian S. , Ayub Muhammad , Blyth Moira , Cole Trevor , Collier David , Coomber Eve L. , Craddock Nick , Daly Mark J. , Danesh John , DiForti Marta , Foster Alison , Freimer Nelson B. , Geschwind Daniel , Johnstone Mandy , Joss Shelagh , Kirov Georg , Körkkö Jarmo , Kuismin Outi , Holmans Peter , Hultman Christina M. , Iyegbe Conrad , Lönnqvist Jouko , Männikkö Minna , McCarroll Steve A. , McGuffin Peter , McIntosh Andrew M. , McQuillin Andrew , Moilanen Jukka S. , Moore Carmel , Murray Robin M. , Newbury-Ecob Ruth , Ouwehand Willem , Paunio Tiina , Prigmore Elena , Rees Elliott , Roberts David , Sambrook Jennifer , Sklar Pamela , St. Clair David , Veijola Juha , Walters James T. R. , Williams Hywel ,   Swedish Schizophrenia Study,   INTERVAL Study,   DDD Study,   UK10K Consortium, Sullivan Patrick F. , Hurles Matthew E. , O'Donovan Michael C. , Palotie Aarno , Owen Michael J. , Barrett Jeffrey C.
Published: January 2016

Schizophrenia is a common, debilitating psychiatric disorder with a substantial genetic component. By analysing the whole-exome sequences of 4,264 schizophrenia cases, 9,343 controls, and 1,077 parent-proband trios, we identified a genome-wide significant association between rare loss-of-function (LoF) variants inKMT2Fand risk for schizophrenia. In this dataset, we observed threede novoLoF mutations, seven LoF variants in cases, and none in controls (P = 3.3x10−9). To search for LoF variants inKMT2Fin individuals without a known neuropsychiatric diagnosis, we examined the exomes of 45,376 individuals in the ExAC database and found only two heterozygous LoF variants, showing thatKMT2Fis significantly depleted of LoF variants in the general population. Seven of the ten individuals with schizophrenia carryingKMT2FLoF variants also had varying degrees of learning difficulties. We further identified fourKMT2FLoF carriers among 4,281 children with diverse, severe, undiagnosed developmental disorders, and two additional carriers in an independent sample of 5,720 Finnish exomes, both with notable neuropsychiatric phenotypes. Together, our observations show that LoF variants inKMT2Fcause a range of neurodevelopmental disorders, including schizophrenia. Combined with previous common variant evidence, we more generally implicate epigenetic dysregulation, specifically in the histone H3K4 methylation pathway, as an important mechanism in the pathogenesis of schizophrenia.
Variation in the molecular clock of primates
Authors: Moorjani Priya , Amorim Carlos Eduardo G. , Arndt Peter F. , Przeworski Molly
Published: January 2016

Events in primate evolution are often dated by assuming a “molecular clock”, i.e., a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life-history traits, suggesting that it should also be found among primates. Motivated by these considerations, we analyze whole genomes from ten primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs) and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are ˜65% higher in lineages leading from the hominoid-NWM ancestor to NWMs than to apes. Within apes, rates are ˜2% higher in chimpanzees and ˜7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however: in particular, transitions at CpG sites exhibit a more clock-like behavior than do other types, presumably due to their non-replicative origin. Thus, not only the total rate, but also the mutational spectrum varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate that the average time to the most recent common ancestor of human and chimpanzee is 12.1 million years and their split time 7.9 million years.

Significance statement

Much of our understanding of the chronology of human evolution relies on the “molecular clock”, i.e., a constant rate of substitutions per unit time. To evaluate the validity of this assumption, we analyze whole genome sequences from ten primate species. We find that there is substantial variation in the molecular clock between apes and monkeys, and rates even differ within hominoids. Importantly, not all mutation types behave similarly: notably, transitions at CpG sites exhibit a more clock-like behavior than other substitutions, presumably due to their non-replicative origin. Thus, the mutation spectra, and not just the overall substitution rates, are changing across primates. This finding further suggests that events in primate evolution are most reliably dated using CpG transitions.
Comparing the Citation Performance of PNAS Papers by Submission Track
Authors: Davis Philip M.
Published: January 2016

Purpose:To determine whether papers contributed by National Academy of Sciences (NAS) members perform differently than direct submissions.

Data/Methods:55,889 original papers published inPNASfrom 1997 through 2014. Regression analysis measuring total citations, controlling for editorial track (Contributed, Direct, Communicated), date of publication, and paper topic.

Main findings:Contributed papers consistently underperformed against Direct submissions, receiving 9% fewer citations,ceteris paribus. The effect was greatest for Social Sciences papers (12% fewer citations). Nonetheless, the main effect has attenuated over the past decade, from 13.6% fewer citations in 2005 to just 2.2% fewer citations in 2014.

Significance:Successive editorial policies placing limits, restrictions, and other qualifications on the publication privileges of NAS members may be responsible for the submission of better performing Contributed papers.
Advances in two photon scanning and scanless microscopy technologies for functional neural circuit imaging
Authors: Schultz Simon R. , Copeland Caroline S. , Foust Amanda J. , Quicke Peter , Schuck Renaud
Published: January 2016

Recent years have seen substantial developments in technology for imaging neural circuits, raising the prospect of large scale imaging studies of neural populations involved in information processing, with the potential to lead to step changes in our understanding of brain function and dysfunction. In this article we will review some key recent advances: improved fluorophores for single cell resolution functional neuroimaging using a two photon microscope; improved approaches to the problem ofscanningactive circuits; and the prospect ofscanlessmicroscopes which overcome some of the bandwidth limitations of current imaging techniques. These advances in technology for experimental neuroscience have in themselves led to technical challenges, such as the need for the development of novel signal processing and data analysis tools in order to make the most of the new experimental tools. We review recent work in some active topics, such as region of interest segmentation algorithms capable of demixing overlapping signals, and new highly accurate algorithms for calcium transient detection. These advances motivate the development of new data analysis tools capable of dealing with spatial or spatiotem-poral patterns of neural activity, that scale well with pattern size.
Reaction-path calculations and crystal structures of 1,1′-(ethylene-1,2-diyl)dipyridinium dichloride dihydrate and 1,1′-(ethylene-1,2-diyl)dipyridinium dibromide
Authors: Rukiah Mwaffak , Al-Ktaifani Mahmoud M. , Sabra Mohammad K.
Published: January 2016

The design of new organic–inorganic hybrid ionic materials is of interest for various applications, particularly in the areas of crystal engineering, supramolecular chemistry and materials science. The monohalogenated intermediates 1-(2-chloroethyl)pyridinium chloride, C5H5NCH2CH2Cl+·Cl−, (I′), and 1-(2-bromoethyl)pyridinium bromide, C5H5NCH2CH2Br+·Br−, (II′), and the ionic disubstituted products 1,1′-(ethylene-1,2-diyl)dipyridinium dichloride dihydrate, C12H14N22+·2Cl−·2H2O, (I), and 1,1′-(ethylene-1,2-diyl)dipyridinium dibromide, C12H14N22+·2Br−, (II), have been isolated as powders from the reactions of pyridine with the appropriate 1,2-dihaloethanes. The monohalogenated intermediates (I′) and (II′) were characterized by multinuclear NMR spectroscopy, while (I) and (II) were structurally characterized using powder X-ray diffraction. Both (I) and (II) crystallize with half the empirical formula in the asymmetric unit in the triclinic space groupP\overline{1}. The organic 1,1′-(ethylene-1,2-diyl)dipyridinium dications, which display approximateC2hsymmetry in both structures, are situated on inversion centres. The components in (I) are linkedviaintermolecular O—H...Cl, C—H...Cl and C—H...O hydrogen bonds into a three-dimensional framework, while for (II), they are connectedviaweak intermolecular C—H...Br hydrogen bonds into one-dimensional chains in the [110] direction. The nucleophilic substitution reactions of 1,2-dichloroethane and 1,2-dibromoethane with pyridine have been investigated byab initioquantum chemical calculations using the 6–31G** basis. In both cases, the reactions occur in two exothermic stages involving consecutive SN2 nucleophilic substitutions. The isolation of the monosubstituted intermediate in each case is strong evidence that the second step is not fast relative to the first.
Linking apple farmers to markets
Authors: Ma Wanglin , Abdulai Awudu
Published: January 2016

Purpose

– The purpose of this paper is to investigate the determinants of marketing contract choices including written contracts, oral contracts and no contracts, as well as to examine the impact of marketing contracts on net returns from apple production in China.

Design/methodology/approach

– A two-stage selection correction approach (Bourguignon, Fournier, and Gurgand (BFG)) for the multinomial logit model is employed to estimate the impact of marketing contracts on net returns from apple production. On the basis of the BFG estimation, the authors also use an endogenous switching regression model and a propensity score matching technique to estimate the causal effects of marketing contract choices on net returns from apple production.

Findings

– The results reveal significant selectivity correction terms in the choices of both written contracts and no contracts and insignificant selectivity correction terms in the choice of oral contract, indicating that accounting for selection bias is a prerequisite for unbiased and consistent estimation. The findings also indicate written contracts increase apple farmers’ net returns, while oral contracts exert the opposite effect.

Originality/value

– To the best of the authors’ knowledge, this study is the first to examine the impact of marketing contract choices on net returns from apple production, accounting for selectivity effects.
An economic analysis on intergenerational lock-in effects of belief in rural China
Authors: Ruan Rongping , Xiuhua Wang , Zheng Fengtian
Published: January 2016

Purpose

– Rural China has been undergoing the “religion fever” since the Reform and Opening-up. By comparing the intergenerational lock-in effects of religious belief with that of non-religious belief, the purpose of this paper is to explain why more and more peasants convert to religion especially Christianity in China.

Design/methodology/approach

– Data used in this paper comes from a field survey conducted in villages, Funan county. The samples were obtained by the two-stage cluster probability proportional sampling method. Based on the collected survey data, econometric model on the intergenerational lock-in effects of belief was constructed and used for analysis.

Findings

– Compared with non-religious believers, religious believers can transmit their beliefs more successfully. In addition, the intergenerational lock-in effects of religious beliefs is weakened by oblique socialization in contemporary rural China.

Originality/value

– This is the first paper focussing on intergenerational transmission of belief in rural China; although many researchers did careful analyses on effects of parents’ belief or religiosity on children’s belief or religiosity in the West, few of them compared the success of intergenerational transmission between different beliefs. This paper fills this gap; as an interdisciplinary study, this paper tries to study religion in economics analysis approaches. This attempt extends research field in Economics and at the same time enriches analysis tools in Religion.
Can poor farmers afford higher micro-credit interest rates than the un-poor?
Authors: Tan Xiaoping , lin Wanlong
Published: January 2016

Purpose

– The purpose of this paper is to test whether there is higher return rate of investment for poor farmers than for un-poor farmers and to discuss its implication for poverty reduction microcredit rate policy.

Design/methodology/approach

– By using the household-level data of six provinces of China, farmer household production function is used in this paper to estimate the investment return rate of farmer.

Findings

– The paper indicates that regardless which kind of grouping standard is adopted, the investment return rates of poor farmer households in general are far lower than the non-poor. In general, the richer a farmer household, the higher is the return rate of his household productive operations.

Practical implications

– The study of this paper reminds policy makers that poverty reduction microcredit rate should really take endurance capacity of poor farmers for credit rate into accounting because of the low return rate of their family investment. Exorbitant credit rate should be avoided to protect the credit right of poor farmers.

Originality/value

– There is seldom study on the comparison of return rates of family operation investment between poor and un-poor farmers; there is also unenough empirical study on the rationality of high interest rate on poor households from the return rate of investment point of view. The authors expect this paper will have some contribution on these two points.
A fresh look at calorie-income elasticities in China
Authors: Nie Peng , Sousa-Poza Alfonso
Published: January 2016

Purpose

– The purpose of this paper is to use data from the 1991 to 2009 China Health and Nutrition Survey (CHNS) to analyze how income in China is related to calorie intake.

Design/methodology/approach

– The paper employs a variety of parametric, nonparametric, and semiparametric methods for cross-sectional and panel data, and estimates calorie-income elasticities for adults aged 18-60.

Findings

– The calorie-income elasticities are generally small, ranging from −0.031 to 0.022. In addition, the results show no clear nonlinearity, regardless of whether parametric, nonparametric, or semiparametric approaches are used.

Originality/value

– Using a wealth of estimation techniques, including parametric, nonparametric, and semiparametric approaches, this paper addresses some of the main methodological challenges encountered in estimating calorie-income elasticities. The magnitudes of calorie-income elasticities have policy implications especially with regards to the effectiveness of income-mediated policies aimed at combating food insecurity in China.