bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative analysis of 3D alignment quality: its impact on soft-validation, particle pruning and homogeneity analysis
Authors: Vargas J. , Melero R. , Gómez-Blanco J. , Carazo J. M. , Sorzano C. O. S. 
Published: November 2016

AbstractSingle Particle Analysis using cryo-electron microscopy is a structural biology technique to capture the three-dimensional conformation of biological macromolecules. The projection images used to construct the 3D density map are characterized by a very low signal-to-noise ratio to minimize radiation damage in the samples. As a consequence, the 3D alignment process is a challenging and error prone task and this job usually determines the success or failure of the macromolecule reconstruction. In this work, we present a soft-alignment validation approach, which can quantify the alignment precision and accuracy as well as the data homogeneity of the single particles when they are confronted with the resultant reconstructed 3DEM map. We have also applied this method to data homogeneity analysis and particle pruning, improving the data quality and as a consequence the final map resolution.
Chimeras Link to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish
Authors: Ye Lihai , Tang Xiaojun , Chen Yiyi , Ren Li , Hu Fangzhou , Wang Shi , Wen Ming , Zhang Chun , Tao Ming , Zhao Rurong , Yao Zhanzhou , Liu Shaojun 
Published: November 2016

AbstractThe formation of the allotetraploid hybrid lineage (4nAT) encompasses both distant hybridization and polyploidization processes. The allotetraploid offspring have two sets of sub-genomes inherited from both parental species and therefore it is important to explore its genetic structure. Herein, we construct a bacterial artificial chromosome library of allotetraploids, and then sequence and analyze the full-length sequences of 19 bacterial artificial chromosomes. Sixty-eight DNA chimeras are identified, which are divided into four models according to the distribution of the genomic DNA derived from the parents. Among the 68 genetic chimeras, 44 (64.71%) are linked to tandem repeats (TRs) and 23 (33.82%) are linked to transposable elements (TEs). The chimeras linked to TRs are related to slipped-strand mispairing and double-strand break repair while the chimeras linked to TEs are benefit from the intervention of recombinases. In addition, TRs and TEs are linked not only with the recombinations, but also with the insertions/deletions of DNA segments. We conclude that DNA chimeras accompanied by TRs and TEs coordinate a balance between the sub-genomes derived from the parents which reduces the genomic shock effects and favors the evolutionary and adaptive capacity of the allotetraploidization. It is the first report on the relationship between formation of the DNA chimeras and TRs and TEs in the polyploid animals.
Upstream trophic structure modulates downstream community dynamics via resource subsidies
Authors: Harvey Eric , Gounand Isabelle , Little Chelsea , Fronhofer Emanuel A. , Altermatt Florian 
Published: November 2016

AbstractIn many natural systems, the physical structure of the landscape dictates the flow of resources. Despite mounting evidence that communities’ dynamics can be indirectly coupled by reciprocal among-ecosystem resource flows, our understanding of how directional resource flows might indirectly link biological communities is limited. We here propose that differences in community structure upstream should lead to different downstream dynamics, even in the absence of dispersal. We report an experimental test of the effect of upstream community structure on downstream community dynamics in a simplified but highly controlled setting, using protist microcosms. We implemented directional flows of resources, without dispersal, from a standard resource pool into upstream communities of contrasting interaction structure and then to further downstream communities of either one or two trophic levels. Our results demonstrate that different types of species interactions in upstream habitats may lead to different population sizes and levels of biomass in these upstream habitats. This, in turn, leads to varying levels of detritus transfer (dead biomass) to the downstream communities, thus influencing their population densities and trophic interactions in predictable ways. Our results suggest that the structure of species interactions in directionally structured ecosystems can be a key mediator of alterations to downstream habitats. Alterations to upstream habitats can thus cascade down to downstream communities, even without dispersal.
Visualizing adenosine to inosine RNA editing in single mammalian cells
Authors: Mellis Ian A. , Gupte Rohit K. , Raj Arjun , Rouhanifard Sara H. 
Published: November 2016

AbstractConversion of adenosine bases to inosine in RNA is a frequent type of RNA editing, but important details about its biology, including subcellular localization, remain unknown due to a lack of imaging tools. We developed an RNA FISH strategy we called inoFISH that enables us to directly visualize and quantify adenosine-to-inosine edited transcriptsin situ. Applying this tool to three edited transcripts (GRIA2, EIF2AK2 and NUP43), we found that editing of these transcripts is not correlated with nuclear localization nor paraspeckle association, and that NUP43 exhibits constant editing rates between single cells while the rates for GRIA2 vary.
Shared characteristics underpinning C4leaf maturation derived from analysis of multiple C3and C4species ofFlaveria
Authors: Kümpers Britta M.C. , Burgess Steven J. , Reyna-Llorens Ivan , Smith-Unna Richard , Boursnell Chris , Hibberd Julian M. 
Published: November 2016

AbstractMost terrestrial plants use C3photosynthesis to fix carbon. In multiple plant lineages a modified system known as C4photosynthesis has evolved. To better understand the molecular patterns associated with induction of C4photosynthesis the genusFlaveriathat contains C3and C4species was used. A base to tip maturation gradient of leaf anatomy was defined, and RNA sequencing was undertaken along this gradient for two C3and two C4Flaveriaspecies. Key C4traits including vein density, mesophyll and bundle sheath cross-sectional area, chloroplast ultrastructure, and abundance of transcripts encoding proteins of C4photosynthesis were quantified. Candidate genes underlying each of these C4characteristics were identified. Principal Components Analysis indicated that leaf maturation and then photosynthetic pathway were responsible for the greatest amount of variation in transcript abundance. Photosynthesis genes were over-represented for a prolonged period in the C4species. Through comparison with publically available datasets we identify a small number of transcriptional regulators that have been up-regulated in diverse C4species. The analysis identifies similar patterns of expression in independent C4lineages and so indicates that the complex C4pathway is associated with parallel as well as convergent evolution.HighlightWe identify transcription factors that show conserved patterns of expression in multiple 29 C4species, both within the Flaveria genus, but also in more distantly related C4plants.
Shade tolerance and the functional trait: demography relationship in temperate and boreal forests
Authors: Ameztegui Aitor , Paquette Alain , Shipley Bill , Heym Michael , Messier Christian , Gravel Dominique 
Published: November 2016

Summary

Despite being instrumental in forest ecology, the definition and nature of shade tolerance are complex and not beyond controversy. Moreover, the role it plays in the trait–demography relationship remains unclear.

Here, we hypothesize that shade tolerance can be achieved by alternative combinations of traits depending on the species' functional group (evergreen vs. deciduous species) and that its ability to explain the array of traits involved in demography will also vary between these two groups.

We used dimension reduction to identify the main trait spectra for 48 tree species, including 23 evergreens and 25 deciduous – dispersed across 21 genera and 13 families. We assessed the relationship between functional traits, shade tolerance, and demographic performance at high and low light using structural equation modelling.

The dimensions found corresponded to the trait spectra previously observed in the literature and were significantly related to measures of demography. However, our results support the existence of a divergence between evergreen and deciduous species in the way shade tolerance relates to the demography of species along light gradients.

We show that shade tolerance can be attained through different combination of traits depending on the functional and geographical context, and thus, its utilization as a predictor of forest dynamics and species coexistence requires previous knowledge on the role it plays in the demographic performance of the species under study.

A lay summary is available for this article.
Does movement behaviour predict population densities? A test with 25 butterfly species
Authors: Schultz Cheryl B. , Pe'er B. Guy , Damiani Christine , Brown Leone , Crone Elizabeth E. 
Published: November 2016

SummaryDiffusion, which approximates a correlated random walk, has been used by ecologists to describe movement, and forms the basis for many theoretical models. However, it is often criticized as too simple a model to describe animal movement in real populations.We test a key prediction of diffusion models, namely, that animals should be more abundant in land cover classes through which they move more slowly. This relationship between density and diffusion has rarely been tested across multiple species within a given landscape.We estimated diffusion rates and corresponding densities of 25 Israeli butterfly species from flight path data and visual surveys. The data were collected across 19 sites in heterogeneous landscapes with four land cover classes: semi‐natural habitat, olive groves, wheat fields and field margins.As expected from theory, species tended to have higher densities in land cover classes through which they moved more slowly and lower densities in land cover classes through which they moved more quickly. Two components of movement (move length and turning angle) were not associated with density, nor was expected net squared displacement. Move time, however, was associated with density, and animals spent more time per move step in areas with higher density.The broad association we document between movement behaviour and density suggests that diffusion is a good first approximation of movement in butterflies. Moreover, our analyses demonstrate that dispersal is not a species‐invariant trait, but rather one that depends on landscape context. Thus, land cover classes with high diffusion rates are likely to have low densities and be effective conduits for movement.
Co‐parenting conversation process: a qualitative study of Chinese Singaporean parents
Authors: Sim Charles T. K. 
Published: November 2016

Although co‐parenting in two‐parent families has been an increasingly important area of research, little is known about the co‐parenting conversation as a crucial aspect of co‐parenting. This study used grounded theory methodology to explore how Chinese Singaporean parents perceive their co‐parenting conversations in light of the influence of their families of origin. Interviews were conducted with mothers and fathers in sixteen families. Findings revealed a central category, ‘conversations along the co‐parenting journey’, and two main categories, ‘conversations that connect and collaborate in co‐parenting’, and ‘conversations on family heritage and practices’. A substantive theory of co‐parenting conversation process was generated from the synthesis of the findings. This study serves as the foundation for future research in co‐parenting conversation, and its implications for clinicians and researchers are presented and discussed.Practitioner Points

The typology of co‐parenting conversation can serve as a common language of communication for family practitioners, clinicians, and researchers working with parents of young children
The scheme of co‐parenting conversation process, and the classification for decision‐making conversations, can provide a working framework to consider how, when, and where to intervene in therapy for parents dealing with co‐parenting issues
Co‐parenting intentionality is potentially important in addressing family‐of‐origin issues in co‐parenting therapy sessions
Trait Anger, Physical Aggression, and Violent Offending in Antisocial and Borderline Personality Disorders
Authors: Kolla Nathan J. , Meyer Jeffrey H. , Bagby R. Michael , Brijmohan Amanda 
Published: November 2016

AbstractAntisocial personality disorder (ASPD) and borderline personality disorder (BPD) are common conditions in forensic settings that present high rates of violence. Personality traits related to the five‐factor model personality domains of neuroticism and agreeableness have shown a relationship with physical aggression in nonclinical and general psychiatric samples. The aim of the present investigation was to examine the association of these personality traits with violence and aggression in ASPD and BPD. Results revealed that trait anger/hostility predicted self‐reported physical aggression in 47 ASPD and BPD subjects (β = 0.5, p = 0.03) and number of violent convictions in a subsample of the ASPD participants (β = 0.2, p = 0.009). These preliminary results suggest that high anger and hostility are associated with physical aggression in BPD and ASPD. Application of validated, self‐report personality measures could provide useful and easily accessible information to supplement clinical risk assessment of violence in these conditions.
Self‐Strangulation Through A Sphygmomanometer: An Uncommon Suicide
Authors: Lo Pinto Sara , Tacchella Tiziana , Fossati Francesca , Bonsignore Alessandro , Ventura Francesco 
Published: November 2016

AbstractSuicide by asphyxia is quite a common event in forensic practice and may be implemented in different ways. The authors report a unique case of a 16‐year‐old youth who committed suicide by means of a standard mercury sphygmomanometer. This manner of suicide has never been described in the literature reviewed. A complete forensic investigation led to the conclusion that the cause of death was mechanical asphyxia, ascribed to self‐strangulation by means of an atypical item. The victim suffered from attention‐deficit/hyperactivity disorder (ADHD) syndrome and was assisted by support teachers. He had a solitary and depressive personality. The exceptional nature of this case suggests that sphygmomanometers may be regarded as possible means of self‐strangulation. The case also highlights the importance of managing patients with psychiatric or cognitive disorders; indeed, particular caution is required to keep them away from objects that, although apparently harmless, can become lethal.
Engineering Mycobacterium smegmatis for testosterone production
Authors: Fernández‐Cabezón Lorena , Galán Beatriz , García José L. 
Published: November 2016

SummaryA new biotechnological process for the production of testosterone (TS) has been developed to turn the model strain Mycobacterium smegmatis suitable for TS production to compete with the current chemical synthesis procedures. We have cloned and overexpressed two genes encoding microbial 17β‐hydroxysteroid: NADP 17‐oxidoreductase, from the bacterium Comamonas testosteroni and from the fungus Cochliobolus lunatus. The host strains were M. smegmatis wild type and a genetic engineered androst‐4‐ene‐3,17‐dione (AD) producing mutant. The performances of the four recombinant bacterial strains have been tested both in growing and resting‐cell conditions using natural sterols and AD as substrates respectively. These strains were able to produce TS from sterols or AD with high yields. This work represents a proof of concept of the possibilities that offers this model bacterium for the production of pharmaceutical steroids using metabolic engineering approaches.
Microbial synthesis of a novel terpolyester P(LA‐co‐3HB‐co‐3HP) from low‐cost substrates
Authors: Ren Yilin , Meng Dechuan , Wu Linping , Chen Jinchun , Wu Qiong , Chen Guo‐Qiang 
Published: November 2016

SummaryPolylactide (PLA) is a bio‐based plastic commonly synthesized by chemical catalytic reaction using lactic acid (LA) as a substrate. Here, novel LA‐containing terpolyesters, namely, P[LA‐co‐3‐hydroxybutyrate (3HB)‐co‐3‐hydroxypropionate (3HP)], short as PLBP, were successfully synthesized for the first time by a recombinant Escherichia coli harbouring polyhydroxyalkanoate (PHA) synthase from Pseudomonas stutzeri (PhaC1Ps) with 4‐point mutations at E130D, S325T, S477G and Q481K, and 3‐hydroxypropionyl‐CoA (3HP‐CoA) synthesis pathway from glycerol, 3‐hydroxybutyryl‐CoA (3HB‐CoA) as well as lactyl‐CoA (LA‐CoA) pathways from glucose. Combining these pathways with the PHA synthase mutant phaC1Ps (E130D S325T S477G Q481K), the random terpolyester P(LA‐co‐3HB‐co‐3HP), or PLBP, was structurally confirmed by nuclear magnetic resonance to consist of 2 mol% LA, 90 mol% 3HB, and 8 mol% 3HP respectively. Remarkably, the PLBP terpolyester was produced from low‐cost sustainable glycerol and glucose. Monomer ratios of PLBP could be regulated by ratios of glycerol to glucose. Other terpolyester thermal and mechanical properties can be manipulated by adjusting the monomer ratios. More PLBP applications are to be expected.
Depositional Controls on the Ichnology of Ordovician Wave‐dominated Marine Facies: New Evidence from the Shirgesht Formation, Central Iran
Authors: BAYET‐GOLL Aram , MYROW Paul M. , ACEÑOLAZA Guillermo F. , MOUSSAVI‐HARAMI Reza , MAHBOUBI Asadollah 
Published: November 2016

AbstractThe Lower Ordovician Shirgesht Formation in central Iran is composed of siliciclastic and carbonate rocks deposited in diverse coastal and marine shelfal environments (tidal flat, lagoon, shoreface, offshore‐shelf and carbonate ramp). Five facies associations contain diverse ichnofossil assemblages that show distinct proximal to distal trends formed in a wide range of physical‐chemical conditions. The ethological groups of trace fossils in the Shirgesht Formation reflect a gradient of depositional stress conditions across a wave‐influenced shoreline and shelf. Deposits of wave‐influenced environments make up a significant component of the geological record of shallow marine settings, and the ability to determine paleoenvironments in detail in such successions is critical for reconstruction of depositional histories and sequence‐stratigraphic interpretation.The Cruziana ichnofacies of the study shows highly diverse suites that record the establishment of a benthic community under stable conditions and a long‐term colonization window. The Skolithos ichnofacies recognized is a low diversity opportunistic ichnocommunity suite that resulted from colonization after tempestite deposition in a stressed environment. The strata record an onshore to offshore replacement of the Cruziana ichnofacies (with abundant feeding traces of deposit‐feeders) by the Skolithos ichnofacies (dominated by suspension‐feeders and predators). A transitional zone between the two ichnofacies coincides with the offshore‐transition/distal lower‐surface deposits. The distribution of ichnofacies, the diversity and range of ethological characteristics reflected by the ichnogenera, and the wide range of wave‐dominated coastal facies demonstrate the potential to use individual trace fossils and ichnofacies for significantly refined palaeoenvironmental analysis of wave‐dominated coastal settings, particularly in Ordovician successions.
Uneven Distribution ofPseudotormentusDe Wever et Caridroit (Radiolaria, Protozoa): Provincialism of a Permian Planktonic Microorganism
Authors: ITO Tsuyoshi , FENG Qinglai , MATSUOKA Atsushi 
Published: November 2016

AbstractThe Permian planktonic distribution is not well known, in contrast to other fossil distributions of nekton and benthos. Radiolaria are representative microfossils of plankton in the Permian palaeocean. This study compares both correlated radiolarian occurrences (PseudotormentusDe Wever et Caridroit andQuadriremisNazarov et Ormiston) in literature data from the Pacific Rim and quantitative data from the Liuhuang and Gujingling sections in South China.Pseudotormentusdistributions are concentrated in the Panthalassa, whereasQuadriremisoccurrences are distributed over both the Panthalassa and the Palaeotethys. The uneven distribution ofPseudotormentusseems to have been controlled by a difference in the oceanic basins, indicating the presence of faunal differences in Permian planktonic microorganisms between the Panthalassa and the Palaeotethys. In other words, this study infers the provincialism of Permian planktonic microorganisms. The uneven distribution is explainable by a hypothesis thatPseudotormentuswas strongly affected by a Panthalassan equatorial current.
Structure of the Upper Mantle and Transition Zone Beneath the South China Block Imaged by Finite Frequency Tomography
Authors: SUN Ya , LIU Jianxin , TANG Youcai , CHEN Jiawei , ZHOU Keping , CHEN Bo 
Published: November 2016

AbstractWe applied the finite frequency tomography method to S wave data recorded by 350 broadband stations beneath the South China Block (SCB) and its surroundings from earthquakes occurring between July 2007 and July 2010, to better understand upper mantle deformation. Differential travel‐times in the pair of stations with appropriate weighting for each station are used in the inversion. Our results are consistent with previous tomography that show a high velocity anomaly beneath the Sichuan basin and a high velocity anomaly in the transition zone beneath the Yangtze Craton. However, the resolution of mantle heterogeneity provides new insight into the tectonic framework of subduction of Burmese lithosphere in the west part of the study region and subduction of oceanic lithosphere in the east. In the subduction realm, west of 107°E, a significant fast S‐wave anomaly is located on the southeast of Sichuan Basin. East of 107°E, and two narrow and discontinuous fast S‐wave anomalies occur at a depth of 400–600 km beneath the middle of the South China block overlain by the pronounced low S‐wave anomalies at a depth of 100 and 400 km. If the fast anomalies located in the mantle transition zone represent stagnant slabs, their fragmented nature may suggest that they could be produced by different episodes of subduction beneath western Pacific island and the above slow velocity anomaly may associated with the back‐arc regions of ongoing subduction. In addition, tomography also reveals an anomalously high S‐wave velocity continental root extends eastward to a depth 400 km beneath the eastern Sichuan Basin. This anomaly may be related to eastern extrusion of Indian lithosphere associated with the collision of India and Eurasia. Moreover, our results also show large slow anomalies beneath the Red River fault region connected to deeper anomalies beneath the South China Fold Belt and South China Sea. All these observations are consistent with the scenario that the South China block has been built by both of subduction of Paleo‐pacific plate and eastward subduction of Burma microplate.