bluuebunny/crossref_metadata_2025 huggingface dataset:
Probing quantum state space: does one have to learn everything to learn something?
Authors: Carmeli Claudio , Heinosaari Teiko , Schultz Jussi , Toigo Alessandro
Published: May 2017

Determining the state of a quantum system is a consuming procedure. For this reason, whenever one is interested only in some particular property of a state, it would be desirable to design a measurement set-up that reveals this property with as little effort as possible. Here, we investigate whether, in order to successfully complete a given task of this kind, one needs an informationally complete measurement, or if something less demanding would suffice. The first alternative means that in order to complete the task, one needs a measurement which fully determines the state. We formulate the task as a membership problem related to a partitioning of the quantum state space and, in doing so, connect it to the geometry of the state space. For a general membership problem, we prove various sufficient criteria that force informational completeness, and we explicitly treat several physically relevant examples. For the specific cases that do not require informational completeness, we also determine bounds on the minimal number of measurement outcomes needed to ensure success in the task.
Exact semi-separation of variables in waveguides with non-planar boundaries
Authors: Athanassoulis G. A. , Papoutsellis Ch. E.
Published: May 2017

Series expansions of unknown fieldsΦ=∑φnZnin elongated waveguides are commonly used in acoustics, optics, geophysics, water waves and other applications, in the context of coupled-mode theories (CMTs). The transverse functionsZnare determined by solving local Sturm–Liouville problems (reference waveguides). In most cases, the boundary conditions assigned toZncannot be compatible with the physical boundary conditions ofΦ, leading to slowly convergent series, and rendering CMTs mild-slope approximations. In the present paper, the heuristic approach introduced in Athanassoulis & Belibassakis (Athanassoulis & Belibassakis 1999J. Fluid Mech.389, 275–301) is generalized and justified. It is proved that an appropriately enhanced series expansion becomes an exact, rapidly convergent representation of the fieldΦ, valid for any smooth, non-planar boundaries and any smooth enoughΦ. This series expansion can be differentiated termwise everywhere in the domain, including the boundaries, implementing an exact semi-separation of variables for non-separable domains. The efficiency of the method is illustrated by solving a boundary value problem for the Laplace equation, and computing the corresponding Dirichlet-to-Neumann operator, involved in Hamiltonian equations for nonlinear water waves. The present method provides accurate results with only a few modes for quite general domains. Extensions to general waveguides are also discussed.
How important is thermal history? Evidence for lasting effects of developmental temperature on upper thermal limits inDrosophila melanogaster
Authors: Kellermann Vanessa , van Heerwaarden Belinda , Sgrò Carla M.
Published: May 2017

A common practice in thermal biology is to take individuals directly from the field and estimate a range of thermal traits. These estimates are then used in studies aiming to understand broad scale distributional patterns, understanding and predicting the evolution of phenotypic plasticity, and generating predictions for climate change risk. However, the use of field-caught individuals in such studies ignores the fact that many traits are phenotypically plastic and will be influenced by the thermal history of the focal individuals. The current study aims to determine the extent to which estimates of upper thermal limits (CTmax), a frequently used measure for climate change risk, are sensitive to developmental and adult acclimation temperatures and whether these two forms of plasticity are reversible. Examining a temperate and tropical population ofDrosophila melanogasterwe show that developmental acclimation has a larger and more lasting effect on CTmax than adult acclimation. We also find evidence for an interaction between developmental and adult acclimation, particularly when flies are acclimated for a longer period, and that these effects can be population specific. These results suggest that thermal history can have lasting effects on estimates of CTmax. In addition, we provide evidence that developmental and/or adult acclimation are unlikely to contribute to substantial shifts in CTmax and that acclimation capacity may be constrained at higher temperatures.
Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics
Authors: Slater Graham J. , Goldbogen Jeremy A. , Pyenson Nicholas D.
Published: May 2017

Vertebrates have evolved to gigantic sizes repeatedly over the past 250 Myr, reaching their extreme in today's baleen whales (Mysticeti). Hypotheses for the evolution of exceptionally large size in mysticetes range from niche partitioning to predator avoidance, but there has been no quantitative examination of body size evolutionary dynamics in this clade and it remains unclear when, why or how gigantism evolved. By fitting phylogenetic macroevolutionary models to a dataset consisting of living and extinct species, we show that mysticetes underwent a clade-wide shift in their mode of body size evolution during the Plio-Pleistocene. This transition, from Brownian motion-like dynamics to a trended random walk towards larger size, is temporally linked to the onset of seasonally intensified upwelling along coastal ecosystems. High prey densities resulting from wind-driven upwelling, rather than abundant resources alone, are the primary determinant of efficient foraging in extant mysticetes and Late Pliocene changes in ocean dynamics may have provided an ecological pathway to gigantism in multiple independent lineages.
Harvest and group effects on pup survival in a cooperative breeder
Authors: Ausband David E. , Mitchell Michael S. , Stansbury Carisa R. , Stenglein Jennifer L. , Waits Lisette P.
Published: May 2017

Recruitment in cooperative breeders can be negatively affected by changes in group size and composition. The majority of cooperative breeding studies have not evaluated human harvest; therefore, the effects of recurring annual harvest and group characteristics on survival of young are poorly understood. We evaluated how harvest and groups affect pup survival using genetic sampling and pedigrees for grey wolves in North America. We hypothesized that harvest reduces pup survival because of (i) reduced group size, (ii) increased breeder turnover and/or (iii) reduced number of female helpers. Alternatively, harvest may increase pup survival possibly due to increasedper capitafood availability or it could be compensatory with other forms of mortality. Harvest appeared to be additive because it reduced both pup survival and group size. In addition to harvest, turnover of breeding males and the presence of older, non-breeding males also reduced pup survival. Large groups and breeder stability increased pup survival when there was harvest, however. Inferences about the effect of harvest on recruitment require knowledge of harvest rate of young as well as the indirect effects associated with changes in group size and composition, as we show. The number of young harvested is a poor measure of the effect of harvest on recruitment in cooperative breeders.
How are species interactions structured in species-rich communities? A new method for analysing time-series data
Authors: Ovaskainen Otso , Tikhonov Gleb , Dunson David , Grøtan Vidar , Engen Steinar , Sæther Bernt-Erik , Abrego Nerea
Published: May 2017

Estimation of intra- and interspecific interactions from time-series on species-rich communities is challenging due to the high number of potentially interacting species pairs. The previously proposed sparse interactions model overcomes this challenge by assuming that most species pairs do not interact. We propose an alternative model that does not assume that any of the interactions are necessarily zero, but summarizes the influences of individual species by a small number of community-level drivers. The community-level drivers are defined as linear combinations of species abundances, and they may thus represent e.g. the total abundance of all species or the relative proportions of different functional groups. We show with simulated and real data how our approach can be used to compare different hypotheses on community structure. In an empirical example using aquatic microorganisms, the community-level drivers model clearly outperformed the sparse interactions model in predicting independent validation data.
Spatial organization of the mouse auditory cortex to sound dynamics revealed using automated image segmentation
Authors: Liu Ji , Whiteway Matthew R. , Butts Daniel A. , Kanold Patrick O.
Published: May 2017

Sound stimuli are characterized by their rich spectral and temporal dynamic properties. Individual neurons in auditory cortex (ACX) encode both spectral and temporal aspects of sounds e.g. sound onset and/or offset. While the different fields of the ACX show gradients of frequency selectivity the large-scale organization of sound dynamics is unknown. We used widefield imaging of GCaMP6s in awake mouse ACX combined with a novel unsupervised image segmentation technique to investigate the spatiotemporal representation of sound onset and offset. Using this technique, we identified known auditory fields but also detected novel ACX areas. Furthermore, we found that ACX areas differed in their responses to tone onset and offset. Multiple areas were preferentially activated by tone offset, and on-response areas were more spatially localized than off-response areas. We also found tonotopy in off-responses. Together our results demonstrate a different spatial distribution of neurons across ACX for processing sound onsets versus offsets.
Sequence Specific Modeling ofE. coliCell-Free Protein Synthesis
Authors: Vilkhovoy Michael , Horvath Nicholas , Shih Che-Hsiao , Wayman Joseph A. , Calhoun Kara , Swartz James , Varner Jeffrey D.
Published: May 2017

Cell-free protein synthesis (CFPS) is a widely used research tool in systems and synthetic biology. However, if CFPS is to become a mainstream technology for applications such as point of care manufacturing, we must understand the performance limits and costs of these systems. Toward this question, we used sequence specific constraint based modeling to evaluate the performance ofE. colicell-free protein synthesis. A coreE. colimetabolic network, describing glycolysis, the pentose phosphate pathway, energy metabolism, amino acid biosynthesis and degradation was augmented with sequence specific descriptions of transcription and translation and effective models of promoter function. Model parameters were largely taken from literature, thus the constraint based approach coupled the transcription and translation of the protein product, and the regulation of gene expression, with the availability of metabolic resources using only a limited number of adjustable model parameters. We tested this approach by simulating the expression of two model proteins: chloramphenicol acetyltransferase and dual emission green fluorescent protein, for which we have training data sets; we then expanded the simulations to a range of additional proteins. Protein expression simulations were consistent with measurements for a variety of cases. The constraint based simulations confirmed that oxidative phosphorylation was active in the CAT cell-free extract, as without it there was no feasible solution within the experimental constraints of the system. We then compared the metabolism of theoretically optimal and experimentally constrained CFPS reactions, and developed parameter free correlations which could be used to estimate productivity as a function of protein length and promoter type. Lastly, global sensitivity analysis identified the key metabolic processes that controlled CFPS productivity and energy efficiency. In summary, sequence specific constraint based modeling of CFPS offered a novel means toa prioriestimate the performance of a cell-free system, using only a limited number of adjustable parameters. While we modeled the production of a single protein in this study, the approach could easily be extended to multi-protein synthetic circuits, RNA circuits or the cell free production of small molecule products.
Leg length, skull circumference, and the incidence of dementia in Latin America and China; a 10/66 population-based cohort study
Authors: Prince Martin J. , Acosta Daisy , Guerra Mariella , Huang Yueqin , Jimenez-Velazquez Ivonne Z , Llibre Rodriguez Juan J. , Salas Aquiles , Sosa Ana Luisa , Dewey Michael E. , Guerchet Maelenn M. , Liu Zhaorui , Llibre-Guerra Jorge J. , Prina Matthew A.
Published: May 2017

Background

Adult leg length is influenced by nutrition in the first few years of life. Adult head circumference is an indicator of brain growth. Cross-sectional studies indicate inverse associations with dementia risk, but there have been few prospective studies.

Methods

Population-based cohort studies in urban sites in Cuba, Dominican Republic Puerto Rico and Venezuela, and rural and urban sites in Peru, Mexico and China. Sociodemographic and risk factor questionnaires were administered to all participants, and anthropometric measures taken, with ascertainment of incident 10/66 dementia, and mortality, three to five years later.

Results

Of the original at risk cohort of 13,587 persons aged 65 years and over, 2,443 (18.0%) were lost to follow-up; 10,540 persons with skull circumference assessments were followed up for 40,466 person years, and 10,400 with leg length assessments were followed up for 39,954 person years. There were 1,009 cases of incident dementia, and 1,605 dementia free deaths. The fixed effect pooled meta-analysed adjusted subhazard ratio (ASHR) for leg length (highest vs. lowest quarter) was 0.80 (95% CI, 0.66-0.97) and for skull circumference was 1.02 (95% CI, 0.84-1.25), with no heterogeneity of effect between sites (I2=0%). Leg length measurements tended to be shorter at follow-up, particularly for those with baseline cognitive impairment and dementia. However, leg length change was not associated with dementia incidence (ASHR, per cm 1.006, 95% CI 0.992-1.020), and the effect of leg length was little altered after adjusting for baseline frailty (ASHT 0.82, 95% CI 0.67-0.99). A priori hypotheses regarding effect modification by gender or educational level were not supported.

Conclusions

Consistent findings across settings provide quite strong support for an association between adult leg length and dementia incidence in late-life. Leg length is a relatively stable marker of early life nutritional programming, which may confer brain reserve and protect against neurodegeneration in later life through mitigation of cardiometabolic risk. Further clarification of these associations could inform predictive models for future dementia incidence in the context of secular trends in adult height, and invigorate global efforts to improve childhood nutrition, growth and development.
Loss oflrrk2impairs dopamine catabolism, cell proliferation, and neuronal regeneration in the zebrafish brain
Authors: Suzzi Stefano , Ahrendt Reiner , Hans Stefan , Semenova Svetlana A. , Bilican Saygın , Sayed Shady , Winkler Sylke , Spieß Sandra , Kaslin Jan , Panula Pertti , Brand Michael
Published: May 2017

LRRK2mutations are a major cause of Parkinson’s disease. Pathogenicity of LRRK2 loss-of-function is controversial, as knockout in rodents reportedly induces no brain-specific effects and knockdown studies in zebrafish are conflicting. Here we show that CRISPR/Cas9-engineered deletion of the ~60-kbp-long zebrafishlrrk2locus elicits a pleomorphic, albeit transient brain phenotype in maternal-zygotic mutants (mzLrrk2). Intriguingly, 11-month-old mzLrrk2 adults display increased dopamine and serotonin catabolism. Additionally, we find decreased mitosis in the larval brain and reduced stab injury-induced neuronal regeneration in the adult telencephalon. Finally, hypokinesia associates with loss oflrrk2in larvae. Our results demonstrate thatlrrk2knockout has an early neurodevelopmental effect, and leads to perturbed dopamine and serotonin catabolism in aLRRK2knockout. We propose mzLrrk2 zebrafish as a valuable tool to study LRRK2 loss-of-functionin vivo, and provide a link between LRRK2 and the control of basal cell proliferation in the brain that may become potentially critical upon challenges like brain injury.
Dynamic blue light-inducible T7 RNA polymerases (Opto-T7RNAPs) for precise spatiotemporal gene expression control
Authors: Baumschlager Armin , Aoki Stephanie K. , Khammash Mustafa
Published: May 2017

Light has emerged as control input for biological systems due to its precise spatiotemporal resolution. The limited toolset for light control in bacteria motivated us to develop a light-inducible transcription system that is independent from cellular regulation through the use of an orthogonal RNA polymerase. Here, we present our engineered blue light-responsive T7 RNA polymerases (Opto-T7RNAPs) that show properties such as low leakiness of gene expression in the dark-state, high expression strength when induced with blue light, or an inducible range of more than 300-fold. Following optimization of the system to reduce expression variability, we have created a variant, which returns to the inactive dark-state within minutes, once blue light is turned off. This allows for precise dynamic control of gene expression, which is a key aspect for most applications using optogenetic regulation. The regulators were developed and tested in the bacteriumEscherichia coli, which is a crucial cell factory for biotechnology due to its fast and inexpensive cultivation and well understood physiology and genetics. However, minor alterations should be sufficient to allow their use in other species in which the T7 RNAP polymerase and the light-inducible Vivid regulator were shown to be functional, which comprises other bacterial species and eukaryotes such as mammalian cells or yeast. We anticipate that our approach will expand the applicability of using light as an inducer for gene expression independent from cellular regulation, and allow for a more reliable dynamic control of synthetic and natural gene networks.
SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements
Authors: Liang Jason , Li Bin-zhong , Tan Alexander P. , Kolodner Richard D. , Putnam Christopher D. , Zhou Huilin
Published: May 2017

Mms21, a subunit of the Smc5/6 complex, possesses an E3 ligase activity for the Small Ubiquitin-like MOdifier (SUMO), which has a major, but poorly understood role in genome maintenance. Here we show mutations that inactivate the E3 ligase activity of Mms21 cause Rad52- and Pol32-dependent break-induced replication (BIR), which specifically requires the Rrm3 DNA helicase. Interestingly, mutations affecting both Mms21 and the Sgs1 helicase, but not sumoylation of Sgs1, cause further accumulation of genome rearrangements, indicating the distinct roles of Mms21 and Sgs1 in suppressing genome rearrangements. Whole genome sequencing further revealed that the Mre11 endonuclease prevents microhomology-mediated translocations and hairpin-mediated inverted duplications in themms21mutant. Consistent with the accumulation of endogenous DNA lesions,mms21cells accumulate spontaneous Ddc2 foci and display a hyper-activated DNA damage checkpoint. Together, these findings support a new paradigm that Mms21 prevents the accumulation of spontaneous DNA lesions that cause diverse genome rearrangements.
Realizing ‘integral control’ in living cells: How to overcome leaky integration due to dilution?
Authors: Qian Yili , Del Vecchio Domitilla
Published: May 2017

A major problem in the design of synthetic genetic circuits is robustness to perturbations and uncertainty. Because of this, there have been significant efforts in recent years in finding approaches to implement integral control in genetic circuits. Integral controllers have the unique ability to make the output of a process adapt perfectly to disturbances. However, implementing an integral controller is challenging in living cells. This is because a key aspect of any integral controller is a “memory” element that stores the accumulation (integral) of the error between the output and its desired set-point. The ability to realize such a memory element in living cells is fundamentally challenged by the fact that all biomolecules dilute as cells grow, resulting in a “leaky” memory that gradually fades away. As a consequence, the adaptation property is lost. Here, we propose a general principle for designing integral controllers such that the performance is practically unaffected by dilution. In particular, we mathematically prove that if the reactions implementing the integral controller are all much faster than dilution, then the adaptation error due to integration leakiness becomes negligible. We exemplify this design principle with two synthetic genetic circuits aimed at reaching adaptation of gene expression to fluctuations in cellular resources. Our results provide concrete guidance on the biomolecular processes that are most appropriate for implementing integral controllers in living cells.
Defining marine microbial biomes from environmental and dispersal filtered metapopulations
Authors: Lindh Markus V.
Published: May 2017

Energy and matter fluxes essential for all life1are modulated by spatial and temporal shifts in microbial community structure resulting from environmental and dispersal filtering2,3, emphasizing the continued need to characterize microbial biogeography4,5. Yet, application of metapopulation theory, traditionally used in general ecology for understanding shifts in biogeographical patterns among macroorganisms, has not been tested extensively for defining marine microbial populations filtered by environmental conditions and dispersal limitation at global ocean scales. Here we show, from applying metapopulation theory on two major global ocean datasets6,7, that microbial populations exhibit core- and satellite distributions with cosmopolitan compared to geographically restricted distributions of populations. We found significant bimodal occupancy-frequency patterns (the different number of species occupying different number of patches) at varying spatial scales, where shifts from bimodal to unimodal patterns indicated environmental and dispersal filtering. Such bimodal occupancy-frequency patterns were validated in Longhurst’s classical biogeographical framework andin silicowhere observed bimodal patterns often aligned with specific biomes and provinces described by Longhurst and where found to be non-random in randomized datasets and mock communities. Taken together, our results show that application of metapopulation theory provides a framework for determining distinct microbial biomes maintained by environmental and dispersal filtering.
On growth and form of the distal air exchange surfaces within the lung
Authors: Warburton David , Wigfall Clarence , Pollack Harvey , Koos David , AlAlam Denise , Turcatel Gianluca , Shi Wei , Fraser Scott , Moats Rex
Published: May 2017

Herein we show, using several novel imaging and computational approaches, how the air exchange units (AEUs) of the lung develop from the tips and sides of distinct families of tortuous ducts, that themselves ramify as distinct families distal to the bronchoalveolar duct junctions (BADJs), prenatally in humans but postnatally in mice. The mature AEUs thus consist of indented spheroids tightly packed between quite regularly spaced distal ducts. Since the diameter of the BADJs and the distal ducts increases rather than decreasing during the formation of AEUs, we further deduce that the AEUs must form by circular epithelial precursor buckling at their mouths with resulting extrusion of their lumen into the surrounding mesenchyme, stabilized firstly by interlocking rings of elastin and later by rings of elastin and collagen fibers surrounding the mouth of each of the prospective AEUs. Furthermore, we show that the surface of each of the AEUs is highly rugose, being indented by the capillary network that lies close beneath the AES membranes. We propose that, the kissing theorem proposed of Newton that expresses the number of times billiard balls may touch within their frame is a parsimonious solution to achieving optimum packing of the distal AES unit spaces, while allowing sufficient space between them to allow for conducting airways, closely applied pulsatile capillary blood vessels, lymphatics, nerves and other key components of the interstitial mesenchyme.

Summary statement

Employing novel imaging and computational approaches we here deduce some new concepts as to how the distal shaping of airway lineage stem and progenitor cells may contribute to the growth and form of the air exchange surface (AES) of the lung, distal to the bronchoalveolar duct junction (BADJ). We then propose that the AES extrudes from the sides and tips of distinct families of small ducts, apparently by buckling of the thinning luminal epithelium into the surrounding mesenchyme, stabilized firstly by rings of elastin and later by rings of collagen and elastin fibers, that surround the mouth of each distal unit of the AES. We propose this mechanism as a parsimonious solution to achieving the optimum form, packing density and functional efficiency of the AES, while allowing sufficient space between for the plumbing of conducting airways, pulsatile capillary blood vessels, lymphatics, nerves and other key matrix and cellular components within the interstitial mesenchyme.
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes
Authors: Pericard Pierre , Dufresne Yoann , Blanquart Samuel , Touzet Hélène
Published: May 2017

Motivation

Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution

Results

We designed MATAM, a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. The method implements a stepwise process based on construction and analysis of a read overlap graph. It is applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes. We show that MATAM outperforms other available methods in terms of low error rates and recovered genome fractions and is suitable to provide improved assemblies for precise taxonomic assignments.

Availability

https://github.com/bonsai-team/matam

Contact

pierre.pericard@gmail.com,helene.touzet@univ-lille1.fr
High-content protein localization screeningin vivoreveals novel regulators of multiciliated cell development and function
Authors: Tu Fan , Sedzinski Jakub , Ma Yun , Marcotte Edward M. , Wallingford John B.
Published: May 2017

Multiciliated cells (MCCs) drive fluid flow in diverse tubular organs and are essential for development and homeostasis of the vertebrate central nervous system, airway, and reproductive tracts. These cells are characterized by dozens or hundreds of long, motile cilia that beat in a coordinated and polarized manner (Brooks and Wallingford, 2014). In recent years, genomic studies have not only elucidated the transcriptional hierarchy for MCC specification, but also identified myriad new proteins that govern MCC ciliogenesis, cilia beating, or cilia polarization (e.g. (Choksi et al., 2014b; Chung et al., 2014; Hoh et al., 2012; Ma et al., 2014; Treutlein et al., 2014)). Interestingly, this burst of genomic data has also highlighted the obvious importance of the “ignorome,” that large fraction of vertebrate genes that remain only poorly characterized (Pandey et al., 2014). Understanding the function of novel proteins with little prior history of study presents a special challenge, especially when faced with large numbers of such proteins. Here, we explored the MCC ignorome by defining the subcellular localization of 260 poorly defined proteins in vertebrate MCCsin vivo. Moreover, functional analyses that arose from results of the screen provide novel insights into the mechanisms by which the actin cytoskeleton simultaneously influences diverse aspects of MCC biology, including basal body docking, and ciliogenesis.
Stratified time-course gene preselection shows a pre-diagnostic transcriptomic signal for metastasis in blood cells: a proof of concept from the NOWAC study
Authors: Holsbø Einar , Perduca Vittorio , Bongo Lars Ailo , Lund Eiliv , Birmelé Etienne
Published: May 2017

We investigate whether there is information in gene expression levels in blood that predicts breast cancer metastasis. Our data comes from the NOWAC epidemiological cohort study where blood samples were provided at enrollment. This could be anywhere from years to weeks before any cancer diagnosis. When and if a cancer is diagnosed, it could be so in different ways: at a screening, between screenings, or in the clinic, outside of the screening program. To build predictive models we propose that variable selection should include followup time and stratify by detection method. We show by simulations that this improves the probability of selecting relevant predictor genes. We also demonstrate that it leads to improved predictions and more stable gene signatures in our data. There is some indication that blood gene expression levels hold predictive information about metastasis. With further development such information could be used for early detection of metastatic potential and as such aid in cancer treatment.
A receptor-like protein acts as a specificity switch for the regulation of stomatal development
Authors: Lin Guangzhong , Zhang Liang , Han Zhifu , Yang Xinru , Liu Weijia , Li Ertong , Chang Junbiao , Qi Yijun , Shpak Elena D. , Chai Jijie
Published: May 2017

Stomata are microscopic openings that allow for the exchange of gases between plants and the environment. In Arabidopsis, stomatal patterning is specified by the ERECTA family (ERf) receptor kinases (RKs), the receptor-like protein (RLP) TOO MANY MOUTHS (TMM), and EPIDERMAL PATTERNING FACTOR (EPF) peptides. Here we show that TMM and ER or ER-LIKE1 (ERL1) form constitutive complexes, which recognize EPF1 and EPF2, but the single ERfs do not. TMM interaction with ERL1 creates a binding pocket for recognition of EPF1 and EPF2, indicating that the constitutive TMM–ERf complexes function as the receptors of EPF1 and EPF2. EPFL9 competes with EPF1 and EPF2 for binding to the ERf–TMM complex. EPFL4 and EPFL6, however, are recognized by the single ERfs without the requirement of TMM. In contrast to EPF1,2, the interaction of EPFL4,6 with an ERf is greatly reduced in the presence of TMM. Taken together, our data demonstrate that TMM dictates the specificity of ERfs for the perception of different EPFs, thus functioning as a specificity switch for the regulation of the activities of ERfs.
Healing X-ray scattering images
Authors: Liu Jiliang , Lhermitte Julien , Tian Ye , Zhang Zheng , Yu Dantong , Yager Kevin G.
Published: May 2017

X-ray scattering images contain numerous gaps and defects arising from detector limitations and experimental configuration. We present a method to heal X-ray scattering images, filling gaps in the data and removing defects in a physically meaningful manner. Unlike generic inpainting methods, this method is closely tuned to the expected structure of reciprocal-space data. In particular, we exploit statistical tests and symmetry analysis to identify the structure of an image; we then copy, average and interpolate measured data into gaps in a way that respects the identified structure and symmetry. Importantly, the underlying analysis methods provide useful characterization of structures present in the image, including the identification of diffuseversussharp features, anisotropy and symmetry. The presented method leverages known characteristics of reciprocal space, enabling physically reasonable reconstruction even with large image gaps. The method will correspondingly fail for images that violate these underlying assumptions. The method assumes point symmetry and is thus applicable to small-angle X-ray scattering (SAXS) data, but only to a subset of wide-angle data. Our method succeeds in filling gaps and healing defects in experimental images, including extending data beyond the original detector borders.
What macromolecular crystallogenesis tells us – what is needed in the future
Authors: Giegé Richard
Published: May 2017

Crystallogenesis is a longstanding topic that has transformed into a discipline that is mainly focused on the preparation of crystals for practising crystallographers. Although the idiosyncratic features of proteins have to be taken into account, the crystallization of proteins is governed by the same physics as the crystallization of inorganic materials. At present, a diversified panel of crystallization methods adapted to proteins has been validated, and although only a few methods are in current practice, the success rate of crystallization has increased constantly, leading to the determination of ∼105X-ray structures. These structures reveal a huge repertoire of protein folds, but they only cover a restricted part of macromolecular diversity across the tree of life. In the future, crystals representative of missing structures or that will better document the structural dynamics and functional steps underlying biological processes need to be grown. For the pertinent choice of biologically relevant targets, computer-guided analysis of structural databases is needed. From another perspective, crystallization is a self-assembly process that can occur in the bulk of crowded fluids, with crystals being supramolecular assemblies. Life also uses self-assembly and supramolecular processes leading to transient, or less often stable, complexes. An integrated view of supramolecularity implies that proteins crystallizing eitherin vitroorin vivoor participating in cellular processes share common attributes, notably determinants and antideterminants that favour or disfavour their correct or incorrect associations. As a result, underin vivoconditions proteins show a balance between features that favour or disfavour association. If this balance is broken, disorders/diseases occur. Understanding crystallization underin vivoconditions is a challenge for the future. In this quest, the analysis of packing contacts and contacts within oligomers will be crucial in order to decipher the rules governing protein self-assembly and will guide the engineering of novel biomaterials. In a wider perspective, understanding such contacts will open the route towards supramolecular biology and generalized crystallogenesis.
Stochastic polarity formation in molecular crystals, composite materials and natural tissues
Authors: Hulliger Jürg , Burgener Matthias , Hesterberg Rolf , Sommer Martin , Brahimi Khadidja , Aboulfadl Hanane
Published: May 2017

This topical review summarizes the theoretical and experimental findings obtained over the last 20 years on the subject of growth-induced polarity formation driven by a Markov chain process. When entering the growing surface of a molecular crystal, an inorganic–organic composite or a natural tissue, the building blocks may undergo 180° orientational disorder. Driven by configurational entropy, faulted orientations can promote the conversion of a growing non-polar seed into an object showing polar domains. Similarly, orientational disorder at the interface may change a polar seed into a two-domain state. Analytical theory and Monte Carlo simulations were used to model polarity formation. Scanning pyroelectric, piezoresponse force and phase-sensitive second-harmonic microscopies are methods for investigating the spatial distribution of polarity. Summarizing results from different types of materials, a general principle is provided for obtaining growth-induced polar domains: a non-zero difference in the probabilities for 180° orientational misalignments of building blocks, together with uni-directional growth, along with Markov chain theory, can produce objects showing polar domains.
Modeling heterogeneous risk preferences
Authors: Guan Zhengfei , Wu Feng
Published: May 2017

Purpose

The purpose of this paper is to propose a general framework for modeling heterogeneous risk preferences of agricultural producers and identifying the underlying factors that affect risk preferences.

Design/methodology/approach

This paper nests the risk preference function in a general production decision framework to test and model producers’ risk preferences. The framework allows for both production and price risk, and accommodates potential inefficient behavior. Panel data and the GMM method are used in the empirical estimation.

Findings

The results in this study confirmed the hypothesis of heterogeneous risk preferences. Farmers are found to have decreasing absolute risk aversion. Both farmer characteristics and socioeconomic factors have significant impact on producers’ risk preferences. The results suggest that ignoring heterogeneity in risk preferences across individuals and how non-wealth variables could affect farmers’ risk preferences could result in biased economic behavior analysis.

Originality/value

It is generally assumed in the literature that risk preferences are homogeneous among farmers at given wealth. This is a strong assumption and there are abundant evidences that suggest otherwise. This paper makes contributions to the literature by proposing an approach to modeling heterogeneous risk preferences and identifying the factors that affect preferences.
Credit constraints and labour allocation decisions in rural Burkina Faso
Authors: Porgo Mohamed , Kuwornu John K.M. , Zahonogo Pam , Jatoe John Baptist D. , Egyir Irene S.
Published: May 2017

Purpose

Credit is central in labour allocation decisions in smallholder agriculture in developing countries. The purpose of this paper is to analyse the effect of credit constraints on farm households’ labour allocation decisions in rural Burkina Faso.

Design/methodology/approach

The study used a direct elicitation approach of credit constraints and applied a farm household model to categorize households into four labour market participation regimes. A joint estimation of both the multinomial logit model and probit model was applied on survey data from Burkina Faso to assess the effect of credit constraint on the probability of choosing one of the four alternatives.

Findings

The results of the probit model showed that households’ endowment of livestock, access to news, and membership to an farmer-based organization were factors lowering the probability of being credit constrained in rural Burkina Faso. The multinomial logit model results showed that credit constraints negatively influenced the likelihood of a farm household to use hired labour in agricultural production and perhaps more importantly it induces farm households to hire out labour off farm. The results also showed that the other components of household characteristics and farm attributes are important factors determining the relative probability of selecting a particular labour market participation regime.

Social implications

Facilitating access to credit in rural Burkina Faso can encourage farm households to use hired labour in agricultural production and thereby positively impacting farm productivity and relieving unemployment pressures.

Originality/value

In order to identify the effect of credit constraints on farm households’ labour decisions, this study examined farm households’ decisions of hiring on-farm labour, supplying labour off-farm or simultaneously hiring on-farm labour and supplying family labour off-farm under credit constraints using the direct elicitation approach of credit constraints. To the best of the authors’ knowledge, this study is the first to examine this problem in Burkina Faso.
The economics and productivity of US dairy farms that use crossbred vs non-crossbred breeding technology (production systems)
Authors: Nehring Richard , Barton Richard , Hallahan Charles
Published: May 2017

Purpose

The purpose of this paper is to examine the rise in crossbred cow numbers in the US dairy herd. Methods used look at well managed herds to see if crossbreeding provides a management tool that producers are using to maintain profitability.

Design/methodology/approach

The authors estimate a Translog stochastic production frontier (SPF) for US dairy farms to examine the competitiveness of crossbred and non-crossbred dairy herds by system and region.

Findings

The bottom-line conclusion is that WM or highly efficient crossbred herds solidly compete on a financial basis with larger WM Western Holstein herds, the most technically efficient managed group, based on the SPF results in the authors’ study. The study finds that net return on assets for crossbred herds are not different from Western Holstein herds and that there is no significant difference in amount of milk per cow produced annually.

Research limitations/implications

Because of a need to unmask the advantages of crossbreeding as a technology it was necessary to separate WM herds from poorly managed herds. That was done by frontier estimates that robustly ranked operation and corrected for endogeneity, tested for selectivity bias, and incorporated the NASS survey design.

Originality/value

For the first time, the 2010 Dairy Cost and Returns questionnaire version of the Agricultural Resource Management Survey (Dairy CAR) design allows researchers to expand survey observations to represent the vast majority of the US dairy farm population and to sort dairy farms into crossbred/non-crossbred herds.
A phenomenological research study on writer’s block: causes, processes, and results
Authors: Bastug Muhammet , Ertem Ihsan Seyit , Keskin Hasan Kagan
Published: May 2017

Purpose

The purpose of this paper is to investigate the causes, processes of writer’s block experienced by a group of classroom teacher candidates and its impact on them.

Design/methodology/approach

The phenomenological design, which is a qualitative research design, was preferred in the research since it was aimed to investigate the causes, processes of writer’s block experienced by a group of classroom teacher candidates and its effects on the students.

Findings

As a result of the data analysis, it is possible to suggest the limitations of subject and time, problems in the process of writing teaching since primary school, anxiety of being controlled and assessed by grades, fear of being criticized, negativity of classroom settings, lack of information about writing, not being able to read and shortcomings in the vocabulary as the causes of writer’s block.

Research limitations/implications

The research has some limitations. First, the research is only in the phenomenology design. Quantitative research is needed to determine the more common effects of outcomes. The other one is a limitation on the participants. A group of adult teacher candidates constitute the participants of this research. Writer’s block of students at different age levels can be examined longitudinally. Nevertheless, the results of the research have the theoretical implications for teaching writing. It specifically guides to understand and eliminate negative affective factors related to writing.

Practical implications

The results of this research have practical implications in terms of classroom practices. The results of the study show that there are practical implications for what should be considered in classroom writing teaching and to prevent the writer’s block.

Originality/value

Writer’s block is an affective state and the examination of it is important in terms of writing instruction. Many students suffer from writer’s block. However, this subject is neglected by writing researchers and educators. The authors expect the results to guide teachers and writing education researchers. Because of these reasons, this study is important and gives good contribution to literature.
Tightroping between APT and BCI in small enterprises
Authors: Kaukola Jesse , Ruohonen Jukka , Tuomisto Antti , Hyrynsalmi Sami , Leppänen Ville
Published: May 2017

Purpose

The contemporary internet provisions increasingly sophisticated security attacks. Besides underlining the advanced nature of these attacks, the concept of an advanced persistent threat (APT) catalyzes the important perspective of longitudinal persistence; attacks are not only carefully planned and targeted but the subsequent exploitation period covers long periods of time. If an APT successfully realizes into such exploitation, information assets may be continuously monitored for harvesting business-critical information (BCI). These threats are relevant for the security of small enterprises, and this study aims to examine the qualitative factors that shape the security mindsets among these.

Design/methodology/approach

The data are collected with semi-structured interviews of six enterprises in a small regional market segment. The analysis is based on a fourfold taxonomy that delivers three mindset profiles, while particular emphasis is placed on the subjective security notions that shape the typical strategizing among enterprises.

Findings

APT is poorly understood among the observed segment, which tends to often also explicitly downplay the strategic relevance of the concept, but a more pressing challenge relates to the observation that business data is often perceived to have no value. The delivered results can be used to improve the situation.

Originality/value

This study is among the firsts to explore perceptions of small enterprises toward APT and BCI. The results reveal problematic mindsets and offers new avenues for practitioners as well as academics to study and improve the situation.
Understanding virtual community members’ relationships from individual, group, and social influence perspectives
Authors: Chih Wen-Hai , Hsu Li-Chun , Liou Dah-Kwei
Published: May 2017

Purpose

The purpose of this paper is to explore a model of how people are influenced from the perspectives of individuals (cognitive trust and affective trust), group (sense of virtual community), and social influence (normative influence and information influence) factors.

Design/methodology/approach

This research adopts structural equation modeling to test the proposed model and the structural model shows a good fit. This research sample consists of 312 members who have used Facebook for at least six months.

Findings

The results indicate the following. Both cognitive trust and affective trust have effects on members’ sense of virtual community. Cognitive trust, affective trust, and sense of virtual community have effects on both normative influence and informative influence, respectively. Members in a virtual community could create a sense of virtual community via affective trust. Members’ sense of virtual community partially mediates between cognitive/affective trust and normative/informative influence.

Originality/value

This study investigates the multiple perspectives of the interpersonal interaction between individual, community, and social influence.