bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconstituting the genome of a young allopolyploid crop, Brassica napus, with its related species
Authors: Hu Dandan , Zhang Wenshan , Zhang Yikai , Chang Shihao , Chen Lunlin , Chen Yingying , Shi Yongdi , Shen Jinxiong , Meng Jinling , Zou Jun
Published: November 2018

Brassica napus (AnAnCnCn) is an important worldwide oilseed crop, but it is a young allotetraploid with a short evolutionary history and limited genetic diversity. To significantly broaden its genetic diversity and create a novel heterotic population for sustainable rapeseed breeding, this study reconstituted the genome of B. napus by replacing it with the subgenomes from 122 accessions of Brassica rapa (ArAr) and 74 accessions of Brassica carinata (BcBcCcCc) and developing a novel gene pool of B. napus through five rounds of extensive recurrent selection. When compared with traditional B. napus using SSR markers and high‐throughput SNP/Indel markers through genotyping by sequencing, the newly developed gene pool and its homozygous progenies exhibited a large genetic distance, rich allelic diversity, new alleles and exotic allelic introgression across all 19 AC chromosomes. In addition to the abundant genomic variation detected in the AC genome, we also detected considerable introgression from the eight chromosomes of the B genome. Extensive trait variation and some genetic improvements were present from the early recurrent selection to later generations. This novel gene pool produced equally rich phenotypic variation and should be valuable for rapeseed genetic improvement. By reconstituting the genome of B. napus by introducing subgenomic variation within and between the related species using intense selection and recombination, the whole genome could be substantially reorganized. These results serve as an example of the manipulation of the genome of a young allopolyploid and provide insights into its rapid genome evolution affected by interspecific and intraspecific crosses.
Effects of instantaneous and growth CO2 levels and abscisic acid on stomatal and mesophyll conductances
Authors: Mizokami Yusuke , Noguchi Ko , Kojima Mikiko , Sakakibara Hitoshi , Terashima Ichiro
Published: November 2018

C3 photosynthesis is often limited by CO2 diffusivity or stomatal (gs) and mesophyll (gm) conductances. To characterize effects of stomatal closure induced by either high CO2 or abscisic acid (ABA) application on gm, we examined gs and gm in the wild type (Col‐0) and ost1 and slac1‐2 mutants of Arabidopsis thaliana grown at 390 or 780 μmol mol−1 CO2. Stomata of these mutants were reported to be insensitive to both high CO2 and ABA. When the ambient CO2 increased instantaneously, gm decreased in all these plants, whereas gs in ost1 and slac1‐2 was unchanged. Therefore, the decrease in gm in response to high CO2 occurred irrespective of the responses of gs. gm was mainly determined by the instantaneous CO2 concentration during the measurement and not markedly by the CO2 concentration during the growth. Exogenous application of ABA to Col‐0 caused the decrease in the intercellular CO2 concentration (Ci). With the decrease in Ci, gm did not increase but decreased, indicating that the response of gm to CO2 and that to ABA are differently regulated and that ABA content in the leaves plays an important role in the regulation of gm.
Understanding tailored PHN interventions and outcomes of Latina mothers
Authors: Park Young Shin , McNaughton Diane B. , Mathiason Michelle A. , Monsen Karen A.
Published: November 2018

Objective

To examine associations of data‐driven intervention approaches (IAs) with the outcomes of adolescent or adult Latina mothers with or without the Mental health problem.

Design and Sample

Retrospective observational study using public health nurse (PHN)‐generated data for 676 Latina mothers aged 14–52.

Measures

Mothers’ age, having the Mental health problem, number of problems and interventions, and Knowledge, Behavior, and Status scores using the Omaha System. Mother‐specific percentages of interventions to the total number received were calculated. Visualizations and statistical tests were used to analyze the association of IAs relating mothers’ characteristics, problems, interventions, and outcomes.

Results

Four IAs were discovered. Sample characteristics differed significantly among IAs by age and having the Mental health problems. There was a small effect of age on outcomes (<0.10). PHNs differentially addressed problems in IA1–IA4 compared with IA2–IA3 (p < 0.001). Mothers who received IA3 had the most improvement and highest scores in Knowledge and Behavior (all p < 0.001). Mothers who received IA2 had the most improvement and highest scores in Status (both p < 0.001).

Conclusions

The IAs were associated with outcomes differentially among Latina mothers, depending on multiple complex factors. These methods may be useful in understanding intervention tailoring and should be replicated with other populations and datasets.
Change in nuclear DNA content and pollen size with polyploidisation in the sweet potato (Ipomoea batatas, Convolvulaceae) complex
Authors: Srisuwan S. , Sihachakr D. , Martín J. , Vallès J. , Ressayre A. , Brown S. C. , Siljak‐Yakovlev S.
Published: November 2018

Genome size evolution and its relationship with pollen grain size has been investigated in sweet potato (Ipomoea batatas), an economically important crop which is closely related to diploid and tetraploid species, assessing the nuclear DNA content of 22 accessions from five Ipomoea species, ten sweet potato varieties and two outgroup taxa.

Nuclear DNA amounts were determined using flow cytometry. Pollen grains were studied using scanning and transmission electron microscopy.

2C DNA content of hexaploid I. batatas ranged between 3.12–3.29 pg; the mean monoploid genome size being 0.539 pg (527 Mbp), similar to the related diploid accessions. In tetraploid species I. trifida and I. tabascana, 2C DNA content was, respectively, 2.07 and 2.03 pg. In the diploid species closely related to sweet potato e.g. I. ×leucantha, I. tiliacea, I. trifida and I. triloba, 2C DNA content was 1.01–1.12 pg. However, two diploid outgroup species, I. setosa and I. purpurea, were clearly different from the other diploid species, with 2C of 1.47–1.49 pg; they also have larger chromosomes. The I. batatas genome presents 60.0% AT bases.

DNA content and ploidy level were positively correlated within this complex. In I. batatas and the more closely related species I. trifida, the genome size and ploidy levels were correlated with pollen size. Our results allow us to propose alternative or complementary hypotheses to that currently proposed for the formation of hexaploid Ipomoea batatas.
A metabolomic strategy revealed the role of JA and SA balance in Clematis terniflora DC. Response to UVB radiation and dark
Authors: Yang Bingxian , Chen Meng , Wang Tantan , Chen Xi , Li Yaohan , Wang Xin , Zhu Wei , Xia Li'an , Hu Xingjiang , Tian Jingkui
Published: November 2018

Clematis terniflora DC. is a valuable resource with potential high pharmaceutical value. Proteomic, transcriptomic and metabolomic analyses of C. terniflora that has been exposed to high levels of UVB irradiation and dark conditions (HUVB + D) have revealed the mechanisms underlying its medicinal potential. However, the signal transduction pathways and the mechanisms of regulation for the accumulation of secondary metabolites remain unclear. In this study, we show that the jasmonic acid (JA) and salicylic acid (SA) signals were activated in C. terniflora in response to HUVB + D. Metabolomic analysis demonstrated that the perturbation in JA and SA balance led to additional reallocation of carbon and nitrogen resources. Evaluating the fold change ratios of differentially changed metabolites proved that JA signal enhanced the transformation of nitrogen to carbon through the 4‐aminobutyric acid (GABA) shunt pathway, which increased the carbon reserve to be utilized in the production of secondary metabolites. However, SA signal induced the synthesis of proline, while avoiding the accumulation of secondary metabolites. Over all, the results indicate that the co‐increase of JA and SA reconstructed the dynamic stability of transformation from nitrogen to carbon, which effectively enhanced the oxidative defense to HUVB + D in C. terniflora by increasing the secondary metabolites.
Income Distribution and Aggregate Saving: A Non‐Monotonic Relationship
Authors: Bofinger Peter , Scheuermeyer Philipp
Published: November 2018

Drawing on a panel of advanced economies, this paper documents a concave and non‐monotonic link between inequality and the aggregate household saving rate. We find that, at a low level of inequality, more inequality is associated with higher saving; but we also show that a negative relationship between inequality and saving prevails where inequality is high. Using different empirical approaches, we locate the turning point, where the marginal effect of inequality turns from positive to negative, at a net income Gini coefficient of around 30. Moreover, we show that the relationship between inequality and saving also depends on financial market conditions. While inequality increases saving, when credit is scarce it tends to reduce saving at high levels of credit. This paper primarily focuses on household saving, yet we also find some evidence for a non‐monotonic effect of inequality on private saving, national saving, and the current account balance.
Sticky Consumption and Wealth Effects in Switzerland
Authors: Galli Alain
Published: November 2018

When assessing the effect of changes in wealth on household expenditures, most empirical studies have used cointegration‐based approaches. These approaches rely on the existence of a stable long‐run relationship among consumption, wealth, and income. However, in Switzerland no such relationship seems to be present after 2001. Motivated by this issue, this paper applies a recently suggested approach to estimating long‐run wealth effects on consumption that does not rely on cointegration. This new approach relies on sticky consumption growth, which can be motivated by consumption habits or sticky expectations. In both cases, long‐run wealth effects are the result of short‐run reactions of households to changes in wealth which become long‐lasting. Using this methodology, the estimated wealth effects on consumption in Switzerland are larger than suggested by cointegration‐based estimates. Furthermore, the results show that there seems to be a remarkably high degree of consumption stickiness in Switzerland.
An official nomenclature for the major histocompatibility complex allele sequences from the domestic goat (Capra hircus)
Authors: Ballingall Keith T. , Todd Helen
Published: November 2018

Official allelic nomenclature and corresponding databases of validated major histocompatibility complex (MHC) alleles from most of the major species of farmed livestock are now represented on the IPD‐MHC Database. The major exception is the domestic goat (Capra hircus) which can lead to confusion in the research community. Here, we propose to start the process of developing such a resource which will support the research community's interests in livestock population genetics, infectious disease research, vaccine development and comparative studies. In this manuscript, we assign the official nomenclature for the major transcribed and highly polymorphic MHC class II DRB1 locus. Additional class II loci including DRA and DQ and MHC class I loci will be added in the future.
The complexity and diversity of major histocompatibility complex challenge disease association studies
Authors: Lokki Marja‐Liisa , Paakkanen Riitta
Published: November 2018

The major histocompatibility complex (MHC; 6p21.3) contains the most polymorphic genes, the most gene dense parts, and the highest diversity of functional gene clusters of the human genome. The clusters form haplotypes, which differ in linkage disequilibrium and show large variations in strength and extent between populations. Haplotype cis‐ and trans‐expression quantitative trait loci have increased the knowledge of regulatory interactions between multiple MHC genes. The detailed haplotype data offer a reference for future studies in immune‐mediated diseases and may unravel disease associations in conditions traditionally considered not to be immunologic. This article aims to describe the structural and functional variations of the MHC genes and haplotypes and their role on selected immune‐mediated diseases. In immune‐/inflammation‐mediated complex diseases, hundreds of common variants influence the development of the disease trait, but the individual variants have small effects on the disease phenotypes as seen in genome‐wide association studies. The genetic influence may still be significant on the cellular or molecular level. Nonetheless, the HLA alone is not sufficient as a susceptible genetic background to deduce the disease. For a comprehensive insight of the disease mechanisms, both immunological and genome assays methods are required.
Examining political connections to study institutional change: Evidence from two unexpected election outcomes in South Korea
Authors: Jäger Kai , Kim Seungjun
Published: November 2018

We argue that the analysis of multiple political connections in an event study framework can improve the study of institutional change. Based on a unique data set of multiple political relationships of 4,936 South Korean board of director members, we show that the large business conglomerates, the chaebol, did not benefit from the unexpected conservative election victories in the 2012 South Korean parliamentary and presidential elections. Personal connections to the presidential candidates and to the opposition party were relevant for the stock returns of small firms. Our findings suggest that Korea's political economy has evolved into a hybrid regime in which the political power of large multinational corporations is limited, but political connections still matter for smaller firms. The corruption scandal that led to the impeachment of President Park in 2017 and the long‐term development of market capitalisation appear to be congruent with the results of our study.
Artificial cells gain communication skills
Authors: Leslie Mitch
Published: November 2018

Cell mimics make and pass on proteins that influence their neighbors.
ESCRT-dependent membrane repair negatively regulates pyroptosis downstream of GSDMD activation
Authors: Rühl Sebastian , Shkarina Kateryna , Demarco Benjamin , Heilig Rosalie , Santos José Carlos , Broz Petr
Published: November 2018

Fine-tuning pyroptosis with ESCRT-III

Pyroptosis is an inflammatory form of cell death induced by select caspases downstream of inflammasome complexes. These caspases cleave gasdermin D (GSDMD), whose N-terminal fragments quickly form large permeability pores that induce cell death. However, a large percentage of cells with active inflammasomes are resistant to pyroptosis. Rühl
et al.
found that the membrane-remodeling ESCRT-III machinery was recruited to the plasma membrane upon GSDMD activation. ESCRT-III–dependent membrane repair limited proinflammatory cytokine secretion and pyroptosis after activation of inflammasomes.

Science
, this issue p.
956
Social network plasticity decreases disease transmission in a eusocial insect
Authors: Stroeymeyt Nathalie , Grasse Anna V. , Crespi Alessandro , Mersch Danielle P. , Cremer Sylvia , Keller Laurent
Published: November 2018

Protecting the colony

When we get a cold and then stay home from work, we are not only taking care of ourselves but also protecting others. Such changes in behavior after infection are predicted in social animals but are difficult to quantify. Stroeymeytet al.looked for such changes in the black garden ant and found that infected workers did alter their behavior—and healthy workers altered their behavior toward the sick. The changed behavior was especially valuable for protecting the most important and vulnerable members of the colony.

Science, this issue p.941
Molecular to organismal chirality is induced by the conserved myosin 1D
Authors: Lebreton G. , Géminard C. , Lapraz F. , Pyrpassopoulos S. , Cerezo D. , Spéder P. , Ostap E. M. , Noselli S.
Published: November 2018

A single myosin sets chirality at all scales

When viewed externally, most organisms appear symmetric between the left and right sides. However, many organs are left-right asymmetric. Whether macroscopic asymmetries are directly related to molecular-level chirality remains an open question. Working in
Drosophila
, Lebreton
et al.
found that the conserved molecular motor myosin 1D induced stereotyped chirality at all biological scales—from F-actin turning in vitro to the organ level and even organismal behavior. Thus, a single conserved myosin can generate de novo nano-to-macroscopic changes in form and direction through chiral interaction with the actin cytoskeleton.

Science
, this issue p.
949
Egocentric coding of external items in the lateral entorhinal cortex
Authors: Wang Cheng , Chen Xiaojing , Lee Heekyung , Deshmukh Sachin S. , Yoganarasimha D. , Savelli Francesco , Knierim James J.
Published: November 2018

Egocentric representation of objects

The lateral entorhinal cortex (LEC) and medial entorhinal cortex (MEC) are the two major cortical projections to the hippocampus. The discovery of a variety of functional cell types in MEC has greatly advanced our understanding of the functional anatomy of entorhinal-hippocampal circuits. However, the function of LEC and the behavioral correlates of LEC cells are still not fully understood. Wang
et al.
analyzed the firing properties of LEC and MEC neurons. They found that LEC and MEC used different reference frames, with LEC encoding objects egocentrically.

Science
, this issue p.
945
Structures and gating mechanism of human TRPM2
Authors: Wang Longfei , Fu Tian-Min , Zhou Yiming , Xia Shiyu , Greka Anna , Wu Hao
Published: November 2018

Architecture of the human TRPM2 channel

Adenosine diphosphate–ribose (ADPR) mediates calcium (Ca
2+
) release by activating the transient receptor potential melastatin 2 (TRPM2) channel. Three structures now elucidate the conformational regulation mechanism of TRPM2 gating. Wang
et al.
describe cryo–electron microscopy structures of human TRPM2 in the apo, ADPR-bound, and ADPR- and Ca
2+
-bound states. In the apo state, both intra- and intersubunit interactions appeared to lock TRPM2 into a closed and autoinhibited state. ADPR binding disrupted some interactions and dramatically altered the TRPM2 conformation. Binding of Ca
2+
further primed the opening of the channel.

Science
, this issue p.
eaav4809
Microbiome dynamics in obesity
Authors: Thaiss Christoph A.
Published: November 2018

The microbiome influences central features of metabolic disease
The ecology of an olfactory trap
Authors: Savoca Matthew
Published: November 2018

Chemical cues lead marine organisms to consume plastic debris
Patterns of moderate and severe injury in children after the introduction of major trauma networks
Authors: Jones Samantha , Tyson Sarah , Young Michael , Gittins Matthew , Davis Naomi
Published: November 2018

Objective

To describe the demographics, mechanisms, presentation, injury patterns and outcomes for children with traumatic injuries.

Setting

Data collected from the UK’s Trauma and Audit Research Network.

Design and patients

The demographics, mechanisms of injury and outcomes were described for children with moderate and severe injuries admitted to the Major Trauma Network in England between 2012 and 2017.

Results

Data regarding 9851 children were collected. Most (69%) were male. The median age was 6.4 (SD 5.2) years, but infants aged 0.1 year (36.5 days) were the most frequently injured of all ages (0–15 years); 447 (36.0%) of injuries in infants aged <1 year were from suspected child abuse. Most injuries occurred in the home, from falls <2 m, after school hours, at weekends and during the summer. The majority of injuries were of moderate severity (median Injury Severity Score 9.0, SD 8.7). The limbs and pelvis, followed by the head, were the most frequently and most severely injured body parts. Ninety-two per cent were discharged home and 72.8% made a ‘good recovery’ according to the Glasgow Outcome Scale. 3.1% of children died, their median age was 7.0 years (SD 5.8), but infants were the most commonly fatally injured group.

Conclusions

A common age of injury and mortality was infants aged <1 year. Accident prevention strategies need to focus on the prevention of non-accidental injuries in infants. Trauma services need to be organised to accommodate peak presentation times, which are after school, weekends and the summer.
Language in 2-year-old children born preterm and term: a cohort study
Authors: Sanchez Katherine , Spittle Alicia J , Cheong Jeanie LY , Thompson Deanne K , Doyle Lex W , Anderson Peter J , Morgan Angela T
Published: November 2018

Purpose

Language skills are critical. Children born very preterm are vulnerable to language problems, but further work is needed to determine characteristics and specific predictors of language problems in this population. We aimed to compare language outcomes between 2-year-old children born <30 weeks and their term-born peers; and to explore risk factors for language difficulties in this cohort.

Design

Language at 2 years was examined in 134 children born <30 weeks and 133 children born at term using the Bayley Scales of Infant and Toddler Development – 3rd Edition (Bayley-3) and the Communication and Symbolic Behaviour Scale: Developmental Profile (Infant Toddler Checklist) (CSBS:DP). Outcomes were compared between groups. Factors hypothesised to predict language outcome were examined in the preterm group: gestational age at birth, birth weight z-score, sex, hearing loss, multilingualism, maternal education, brain abnormality on MRI, medical risk and oromotor concerns at 12 months.

Results

Children born <30 weeks performed more poorly on the CSBS:DP (particularly the social and symbolic composites) and the language scale of the Bayley-3 at 2 years than term-born peers. Lower gestational age at birth, male sex, hearing loss and multilingualism predicted poorer language scores.

Conclusions

Despite improvements in medical management, children born very preterm exhibit language delays at 2 years of age, with specific deficits in social communication and symbolic skills. Significant predictors of poorer language outcomes were similar to those in the general population (male sex, hearing loss, multilingualism), suggesting that further work is needed to establish which specific factors place preterm-born children at heightened risk.
Evaluating effects of recent changes in NHS resource allocation policy on inequalities in amenable mortality in England, 2007–2014: time-series analysis
Authors: Currie Jonny , Guzman Castillo Maria , Adekanmbi Victor , Barr Ben , O’Flaherty Martin
Published: November 2018

Background

Health investment in England post-2010 has increased at lower rates than previously, with proportionally less being allocated to deprived areas. This study seeks to explore the impact of this on inequalities in amenable mortality between local areas.

Methods

We undertook a time-series analysis across 324 lower-tier local authorities in England, evaluating the impact of changes in funding allocations to health commissioners from 2007 to 2014 on spatial inequalities in age-standardised under-75 mortality rates for conditions amenable to healthcare for men and women, adjusting for trends in household income, unemployment and time-trends.

Results

More deprived areas received proportionally more funding between 2007 and 2014, though the reorganisation of commissioning in 2012 stalled this. Funding increases to more deprived local areas accounted for a statistically significant reduction in inequalities in male amenable mortality between local areas of 13 deaths per 100 000 (95% CI 2.5 to 25.9). Funding changes were associated with a reduction in inequalities in female amenable mortality of 7.0 per 100,000, though this finding did not reach significance (p=0.09).

Conclusion

Current National Health Service (NHS) resource allocation policy in England appears to be contributing to a convergence in health outcomes between affluent and deprived areas. However, careful surveillance is needed to evaluate whether diminished allocations to more deprived areas in recent years and reduced NHS investment as a whole is impacting adversely on inequalities between groups.
Eco-friendly recycled crushed glass for cushioning boulder impacts
Authors: Su Y. , Choi C.E. , Ng C.W.W. , Lam C. , Kwan J.S.H. , Wu G. , Huang J. , Zhang Z.
Published: November 2018

A large amount of waste glass is generated every year and contributes significantly to landfills. Large-scale physical model tests were carried out to study the dynamic response of recycled crushed glass (RCG) contained in gabion baskets and its performance against successive boulder impacts at energy levels of up to 70 kJ. The cushioning performance of RCG is compared with that of more conventional cushioning materials, including rock fragments and cellular glass aggregates. Results reveal that for the first impact, RCG can provide up to 144% and 128% reduction in the transmitted wall loads and boulder impact loads, respectively, when compared with cushion layers comprising rock fragments. It follows that by adopting RCG, practitioners could potentially reduce the recommended design load for impact by a single boulder by up to three times. Furthermore, the load-diffusion angle of RCG is three times larger than that of cellular glass aggregates. The observed trend in the diffusion angle implies that the transmitted load for RCG is distributed more uniformly on the barrier wall compared to cellular glass aggregates.
A newly discovered ageing-repair bacterium,Pseudomonas geniculata, isolated from rescuegrass (Bromus cartharticusVahl) promotes the germination and seedling growth of aged seeds
Authors: Liu Xv , Chen Zhao , Gao Yani , Liu Qian , Zhou Wennan , Zhao Tian , Jiang Wenbo , Cui Xuewen , Cui Jian , Wang Quanzhen
Published: November 2018

Plant-growth-promoting rhizobacteria (PGPR) have been shown to relieve various biotic and abiotic stresses, but little information is available regarding their influence on germination and seedling growth of aged seeds. We isolated a promising PGPR from rescuegrass (Bromus cartharticus Vahl) roots and investigated the effect of PGPR biopriming combined with another seed priming treatment on aged rescuegrass seeds using an orthogonal matrix design with four factors. A potential ageing-repair bacterium, BCR5 (Pseudomonas geniculata), was selected from the screening trials and was identified. The reintroduction of strain BCR5 into the aged seeds pre-primed with different approaches had positive effects on germination and seedling growth. The results indicated that the bacterial cell density was the most effective factor for seed germination and vigour. Four factors were optimized for this study, including an artificial ageing duration of 54.21 h, bacterial cell density of 527.50 × 106CFU·mL−1, and priming with H2O2for 14.50 h, after analyzing the range and variance, and using binary quadratic regressions. Furthermore, the treatment also affected the content of malondialdehyde and the activities of superoxide dismutase and peroxidase. Bio-priming of the PGPR with another seed priming approach could be exploited as a promising technique for reinvigorating aged seeds. Moreover, we unexpectedly found that an appropriate artificial ageing treatment could break seed dormancy.
What’s in a name? On fibroblast phenotype and nomenclature
Authors: Nagalingam Raghu S. , Al-Hattab Danah S. , Czubryt Michael P.
Published: November 2018

Fibroblasts have long been recognized as important stromal cells, playing key roles in synthesizing and maintaining the extracellular matrix, but historically were treated as a relatively uniform cell type. Studies in recent years have revealed a surprising level of heterogeneity of fibroblasts across tissues, and even within organs such as the skin and heart. This heterogeneity may have functional consequences, including during stress and disease. While the field has moved forward quickly to begin to address the scientific import of this heterogeneity, the descriptive language used for these cells has not kept pace, particularly when considering the phenotype changes that occur as fibroblasts convert to myofibroblasts in response to injury. We discuss here the nature and sources of the heterogeneity of fibroblasts, and review how our understanding of the complexity of the fibroblast to myofibroblast phenotype conversion has changed with increasing scrutiny. We propose that the time is opportune to reevaluate how we name and describe these cells, particularly as they transition to myofibroblasts through discrete stages. A standardized nomenclature is essential to address the confusion that currently exists in the literature as to the usage of terms like myofibroblast and the description of fibroblast phenotype changes in disease.
Lie algebroids, gauge theories, and compatible geometrical structures
Authors: Kotov Alexei , Strobl Thomas
Published: November 2018

The construction of gauge theories beyond the realm of Lie groups and algebras leads one to consider Lie groupoids and algebroids equipped with additional geometrical structures which, for gauge invariance of the construction, need to satisfy particular compatibility conditions. This paper is supposed to analyze these compatibilities from a mathematical perspective.

In particular, we show that the compatibility of a connection with a Lie algebroid that one finds is the Cartan condition, introduced previously by A. Blaom. For the metric on the base [Formula: see text] of a Lie algebroid equipped with any connection, we show that the compatibility suggested from gauge theories implies that the foliation induced by the Lie algebroid becomes a Riemannian foliation. Building upon a result of del Hoyo and Fernandes, we prove, furthermore, that every Lie algebroid integrating to a proper Lie groupoid admits a compatible Riemannian base. We also consider the case where the base is equipped with a compatible symplectic or generalized Riemannian structure.
Primordial fluctuations of scale factor in closed Universe in Einstein–Cartan gravity
Authors: Popławski Nikodem
Published: November 2018

We consider a homogeneous and isotropic Universe, described by the minisuperspace Lagrangian with the scale factor as a generalized coordinate. We show that the energy of a closed Universe is zero. We apply the uncertainty principle to this Lagrangian and propose that the quantum uncertainty of the scale factor causes the primordial fluctuations of the matter density. We use the dynamics of the early Universe in the Einstein–Cartan theory of gravity with spin and torsion, which eliminates the big-bang singularity and replaces it with a nonsingular bounce. Quantum particle production in highly curved spacetime generates a finite period of cosmic inflation that is consistent with the Planck satellite data. From the inflated primordial fluctuations we determine the magnitude of the temperature fluctuations in the cosmic microwave background, as a function of the numbers of the thermal degrees of freedom of elementary particles and the particle production coefficient which is the only unknown parameter.
Coherence resonance in a modified FHN neuron with autapse and phase noise
Authors: Liu Xiaoqiang , Yang Xiaoli
Published: November 2018

The influences of phase noise together with autapse on the resonance dynamics in a modified FitzHugh–Nagumo (FHN) neuron are investigated by numerical simulation, where the neuronal model is in the environment of electromagnetic induction. First, it is found that phase noise can induce double coherence resonances, which is further confirmed to be robust to the feedback gain of induction current. Surprisingly, by individually changing the period of phase noise and the feedback gain, a resonance-like behavior also appears. Subsequently, the significant phenomenon of autapse-induced multiple coherence resonances is discovered. Moreover, the phenomenon of multiple coherence resonances can emerge at a broad parameter range of autaptic strength and autaptic delay.
Many-objective flexible job shop scheduling using NSGA-III combined with multi-attribute decision making
Authors: Wang Chun , Ji Zhicheng , Wang Yan
Published: November 2018

This paper considers many-objective flexible job shop scheduling problem (MaOFJSP) in which the number of optimization problems is larger than three. An integrated multi-objective optimization method is proposed which contains both optimization and decision making. The non-dominated sorting genetic algorithm III (NSGA-III) is utilized to find a trade-off solution set by simultaneously optimizing six objectives including makespan, workload balance, mean of earliness and tardiness, cost, quality, and energy consumption. Then, an integrated multi-attribute decision-making method is introduced to select one solution that fits into the decision maker’s preference. NSGA-III is compared with three multi-objective evolutionary algorithms (MOEAs)-based scheduling methods, and the simulation results show that NSGA-III performs better in generating the Pareto solutions. In addition, the impacts of using different reference points and decoding methods are investigated.
YaNoC: Yet Another Network-on-Chip Simulation Acceleration Engine Supporting Congestion-Aware Adaptive Routing Using FPGAs
Authors: Parane Khyamling , Prabhu Prasad B. M. , Talawar Basavaraj
Published: November 2018

Many-core systems employ the Network on Chip (NoC) as the underlying communication architecture. To achieve an optimized design for an application under consideration, there is a need for fast and flexible NoC simulator. This paper presents an FPGA-based NoC simulation acceleration framework supporting design space exploration of standard and custom NoC topologies considering a full set of microarchitectural parameters. The framework is capable of designing custom routing algorithms, various traffic patterns such as uniform random, transpose, bit complement and random permutation are supported. For conventional NoCs, the standard minimal routing algorithms are supported. For designing the custom topologies, the table-based routing has been implemented. A custom topology called diagonal mesh has been evaluated using table-based and novel shortest path routing algorithm. A congestion-aware adaptive routing has been proposed to route the packets along the minimally congested path. The congestion-aware adaptive routing algorithm has negligible FPGA area overhead compared to the conventional XY routing. Employing the congestion-aware adaptive routing, network latency is reduced by 55% compared to the XY routing algorithm. The microarchitectural parameters such as buffer depth, traffic pattern and flit width have been varied to observe the effect on NoC behavior. For the [Formula: see text] mesh topology, the LUT and FF usages will be increased from 32.23% to 34.45% and from 12.62% to 15% considering the buffer depth of 4 and flit widths of 16 bits, and 32 bits, respectively. Similar behavior has been observed for other configurations of buffer depth and flit width. The torus topology consumes 24% more resources than the mesh topology. The 56-node fat tree topology consumes 27% and 2.2% more FPGA resources than the [Formula: see text] mesh and torus topologies. The 56-node fat tree topology with buffer depth of 8 and 16 flits saturates at the injection rates of 40% and 45%, respectively.
Free Gelfand–Dorfman–Novikov superalgebras and a Poincaré–Birkhoff–Witt type theorem
Authors: Zhang Zerui , Chen Yuqun , Bokut Leonid A.
Published: November 2018

We construct linear bases of free Gelfand–Dorfman–Novikov (GDN) superalgebras. As applications, we prove a Poincaré–Birkhoff–Witt (PBW) type theorem, that is, every GDN superalgebra can be embedded into its universal enveloping associative differential supercommuative algebra. An Engel theorem is given.
A SCANNING TUNNELING MICROSCOPY STUDY OF MONOLAYER AND BILAYER TRANSITION-METAL DICHALCOGENIDES GROWN BY MOLECULAR-BEAM EPITAXY
Authors: XIE MAOHAI , CHEN JINGLEI
Published: November 2018

This review presents an account of some recent scanning tunneling microscopy and spectroscopy (STM/S) studies of monolayer and bilayer transition-metal dichalcogenide (TMD) films grown by molecular-beam epitaxy (MBE). In addition to some intrinsic properties revealed by STM/S, defects such as inversion domain boundaries and point defects, their properties and induced effects, are presented. More specifically, the quantum confinement and moiré potential effects, charge state transition, quasi-particle interference and structural phase transition as revealed by STM/S are described.
STM STUDIES ON MOLECULAR ROTORS AND MOTORS
Authors: NI CHEN , WANG JUN-ZHONG
Published: November 2018

Molecular motor is a nanoscale machine that consumes energy to produce work via the unidirectional and controlled movement. They are universal in nature and essential to numerous processes of life. When mounted onto solid surfaces, scanning tunneling microscopy (STM) is a powerful technique to characterize the molecular rotors and motors due to the atomic-scale resolution coupled with its ability to track the motion of molecular rotor and motor over time. Moreover, the molecular rotors and motors can be powered by STM tip through injecting tunneling electrons. This review addresses recent advances in the STM studies of the structure, motion, and manipulation of molecular rotors and motors. The developments of surface-mounted azimuthal and altitudinal rotor and motors, large-scale array of molecular rotors, as well as the molecular motors with translational motion will be addressed.
Wavelet shrinkage generalized Bayes estimation for elliptical distribution parameter’s under LINEX loss
Authors: Karamikabir Hamid , Afshari Mahmoud
Published: November 2018

In this paper, the generalized Bayes estimator of elliptical distribution parameter’s under asymmetric Linex error loss function is considered. The new shrinkage generalized Bayes estimator by applying wavelet transformation is investigated. We develop admissibility and minimaxity of shrinkage estimator on multivariate normal distribution.We present the simulation in order to test validity of purpose estimator.
Cyclic codes over R3,m
Authors: Mahmoodi Hamidreza
Published: November 2018

Let [Formula: see text] be the ring [Formula: see text]. We study cyclic codes of arbitrary length [Formula: see text] over the ring [Formula: see text] and obtain a complete characterization for them by presenting a unique set of generators for these codes. For example, we try to determine all distinct cyclic codes of length [Formula: see text] over the ring [Formula: see text] by a practical algorithm.
Sedimentary architecture during Carboniferous rift initiation – the arid Billefjorden Trough, Svalbard
Authors: Smyrak-Sikora Aleksandra , Johannessen Erik P. , Olaussen Snorre , Sandal Geir , Braathen Alvar
Published: November 2018

Analysis of the sedimentary architecture of the early Billefjorden Trough, an exceptionally well-exposed Carboniferous half-graben located in Svalbard, Arctic Norway, allows detailed reconstruction of fault development and basin geometry. Sedimentary facies distribution reveals facies variability in an early synrift fill, when an array of meso-scale intra-basinal faults segmented the basin into rotated blocks with differential subsidence. Growth of these faults into larger systems impacted the distribution of accommodation space and the drainage pattern expressed in fluvial and deltaic sandstone-dominated units. An axially back-stepping character of the early synrift facies associations (Stages 1–3) is reflected in aggrading homogenous facies types of continental depositional Stage 1, which evolved into back-stepping facies belts of deltaic to nearshore depositional environment, Stages 2 and 3, due to the opening of a connection to the sea. The drainage pattern and accommodation distribution in the early synrift deposits reflect a relatively symmetrical basin that predates a later prominent half-graben configuration of the basin.

Supplementary material:
Figures presenting lithostratigraphic columns of the well data (Supplementary material 1), location of logs in Ragnardalen (Supplementary material 2) and geological map used in Figure 2b (Supplementary material 3) are available at
https://doi.org/10.6084/m9.figshare.c.4293077
Variants in APOA5 and ADIPOQ Moderate Improvements in Metabolic Syndrome during a One-Year Lifestyle Intervention
Authors: Lowry Dana E. , Fenwick Peri H. , Roke Kaitlin , Jeejeebhoy Khursheed , Dhaliwal Rupinder , Brauer Paula , Royall Dawna , Tremblay Angelo , Klein Doug , Mutch David M.
Published: November 2018

Background: Metabolic syndrome (MetS) comprises a cluster of risk factors including central obesity, hypertension, dyslipidemia, and impaired glucose homeostasis. Lifestyle interventions that promote improvements in diet quality and physical activity represent a first line of therapy for MetS. However, varying responses to lifestyle interventions are well documented and may be partially explained by underlying genetic differences. The aim of this study was to investigate if variants in genes previously associated with MetS influence the magnitude of change in MetS risk during a 1-year lifestyle intervention. Methods: The present study used data collected from the Canadian Health Advanced by Nutrition and Graded Exercise study cohort (n = 159 men and women) to investigate the effect of 17 candidate single nucleotide polymorphisms (SNPs) on response to a 1-year lifestyle intervention. Associations between SNPs and the continuous MetS (cMetS) score, as well as individual MetS components, were examined. Results: Reductions in cMetS score at both 3 months and 1 year were significantly associated with 2 variants: rs662799 (A/G) in apolipoprotein A5 (APOA5) and rs1501299 (G/T) in adiponectin (ADIPOQ). Individuals carrying a minor T allele in rs1501299 experienced a greater reduction in cMetS score at both 3 months and 1 year, whereas major allele AA homozygotes in rs662799 experienced greater reductions in cMetS score during the intervention. No associations were identified between the aforementioned SNPs and individual components of MetS. Both un-weighted and weighted genetic risk scores (GRS) using these 2 SNPs revealed that individuals carrying none of the risk alleles experienced significantly greater reductions in cMetS score after 1 year. Conclusions: The findings from the current study suggest that individuals with certain genotypes may benefit more from a lifestyle intervention for MetS and that specific variants, either independently or as part of a GRS, could be used as a nutrigenomic tool to tailor the intervention to reduce the risk of MetS.
Trends in the Causes of Death among Kidney Transplant Recipients in the United States (1996–2014)
Authors: Awan Ahmed A. , Niu Jingbo , Pan Jenny S. , Erickson Kevin F. , Mandayam Sreedhar , Winkelmayer Wolfgang C. , Navaneethan Sankar D. , Ramanathan Venkat
Published: November 2018

Background: Death with graft function remains an important cause of graft loss among kidney transplant recipients (KTRs). Little is known about the trend of specific causes of death in KTRs in recent years. Methods: We analyzed United States Renal Data System data (1996–2014) to determine 1- and 10-year all-cause and cause-specific mortality in adult KTRs who died with a functioning allograft. We also studied 1- and 10-year trends in the various causes of mortality. Results: Of 210,327 KTRs who received their first kidney transplant from 1996 to 2014, 3.2% died within 1 year after transplant. Cardiovascular deaths constituted the majority (24.7%), followed by infectious (15.2%) and malignant (2.9%) causes; 40.1% of deaths had no reported cause. Using 1996 as the referent year, all-cause as well as cardiovascular mortality declined, whereas mortality due to malignancy did not. For analyses of 10-year mortality, we studied 94,384 patients who received a first kidney transplant from 1996 to 2005. Of those, 22.1% died over 10 years and the causative patterns of their causes of death were similar to those associated with 1-year mortality. Conclusions: Despite the downtrend in mortality over the last 2 decades, a significant percentage of KTRs die in 10-years with a functioning graft, and cardiovascular mortality remains the leading cause of death. These data also highlight the need for diligent collection of mortality data in KTRs.
Early Start Peritoneal Dialysis: Technique Survival in Long-Term Follow-Up
Authors: Silva Bruno C. , Adelina Erica , Pereira Benedito J. , Cordeiro Lilian , Rodrigues Camila E. , Duarte Ricardo J. , Abensur Hugo , Elias Rosilene M.
Published: November 2018

Background/Aims: Peritoneal dialysis (PD) has gained interest over the last decade as a viable option for early start dialysis. It is still unknown if shorter break-in periods and less time for proper patient evaluation and training could influence technique survival in comparison to planned-start PD. Methods: A prospective and observational study that compared technique survival in a cohort of patients who started either early or planned PD. Early start PD was defined as break-in period from 3 to 14 days with no previous nephrologist follow-up or patient training. Results: A total of 154 patients were included (40 as early start PD), followed by a median time of 381 days. Comparing early vs. planned-start PD, groups were similar concerning age 56 (40; 70) vs. 48 (32; 63) years, p=0.071, body mass index (BMI) 23.3 ± 4.2 vs. 23.8 ± 4.0 kg/m2, p=0.567 and male gender (60 vs. 48%, p=0.201), respectively. Comparing early vs. planned-start groups, there were no differences regarding PD dropout for peritonitis (7.5 vs. 11.4%, p=0.764), catheter dysfunction (12.5 vs. 17.5%, p=0.619) and patient burnout (0 vs. 4.4%, p=0.328), respectively. Less patients in early start group quit PD for peritoneal membrane failure in comparison to planned-start group (2.5 vs. 16.7%, p=0.026). In multivariate cox-regression analysis, the only factors independently associated with technique failure were BMI> 25 kg/m² (p=0.033) and Diabetes Mellitus (p=0.013), whereas no differences regarding early vs. planned-PD start were observed (p=0.184). Conclusion: Despite the adverse scenario for initiating dialysis, early start PD had similar outcomes in comparison to planned-start PD in long-term follow-up.
Sequential Nano-Patterning Using Electron and Laser Beams: A Numerical Methodology
Authors: Wong Basil T. , Mengüç M. Pinar , Vallance R. Ryan
Published: November 2018

A methodology is presented for nanometer-size patterning of a workpiece using both an electron-beam and a laser. A Monte Carlo/Ray Tracing technique is used in modeling the electron-beam propagation inside a thin gold film. This approach is identical to that of a typical Monte Carlo
simulation in radiative transfer except that proper electron scattering properties are employed. The laser propagation within the one-dimensional, non-scattering film on top of a quartz substrate is modeled using a ray-tracing approach and reflections at the boundaries are accounted for with
the Fresnel-expressions. The temperature distribution inside a gold film is then predicted using the Fourier law of heat conduction, after evaluating the accuracy of the model for the range considered. A sequential nano-pattern is created using these coupled numerical simulations. The procedure
we present here is the first to outline the sequential nano-machining processes and likely to guide the experimental studies to success with less trial-and-error attempts.