bluuebunny/crossref_metadata_2025_split huggingface dataset:
Export dynamics as an optimal growth problem in the network of global economy
Authors: Caraglio Michele , Baldovin Fulvio , Stella Attilio L. 
Published: August 2016

AbstractWe analyze export data aggregated at world global level of 219 classes of products over a period of 39 years. Our main goal is to set up a dynamical model to identify and quantify plausible mechanisms by which the evolutions of the various exports affect each other. This is pursued through a stochastic differential description, partly inspired by approaches used in population dynamics or directed polymers in random media. We outline a complex network of transfer rates which describes how resources are shifted between different product classes and determines how casual favorable conditions for one export can spread to the other ones. A calibration procedure allows to fit four free model-parameters such that the dynamical evolution becomes consistent with the average growth, the fluctuations and the ranking of the export values observed in real data. Growth crucially depends on the balance between maintaining and shifting resources to different exports, like in an explore-exploit problem. Remarkably, the calibrated parameters warrant a close-to-maximum growth rate under the transient conditions realized in the period covered by data, implying an optimal self organization of the global export. According to the model, major structural changes in the global economy take tens of years.
Spatially governed climate factors dominate management in determining the quantity and distribution of soil organic carbon in dryland agricultural systems
Authors: Hoyle Frances C. , O’Leary Rebecca A. , Murphy Daniel V. 
Published: August 2016

AbstractFew studies describe the primary drivers influencing soil organic carbon (SOC) stocks and the distribution of carbon (C) fractions in agricultural systems from semi-arid regions; yet these soils comprise one fifth of the global land area. Here we identified the primary drivers for changes in total SOC and associated particulate (POC), humus (HOC) and resistant (ROC) organic C fractions for 1347 sample points in the semi-arid agricultural region of Western Australia. Total SOC stock (0–0.3 m) varied from 4 to 209 t C ha−1 with 79% of variation explained by measured variables. The proportion of C in POC, HOC and ROC fractions averaged 28%, 45% and 27% respectively. Climate (43%) and land management practices (32%) had the largest relative influence on variation in total SOC. Carbon accumulation was constrained where average daily temperature was above 17.2 °C and annual rainfall below 450 mm, representing approximately 42% of the 197,300 km2 agricultural region. As such large proportions of this region are not suited to C sequestration strategies. For the remainder of the region a strong influence of management practices on SOC indicate opportunities for C sequestration strategies associated with incorporation of longer pasture phases and adequate fertilisation.
Identifying the genetic diversity, genetic structure and a core collection of Ziziphus jujuba Mill. var. jujuba accessions using microsatellite markers
Authors: Xu Chaoqun , Gao Jiao , Du Zengfeng , Li Dengke , Wang Zhe , Li Yingyue , Pang Xiaoming 
Published: August 2016

AbstractZiziphus is a genus of spiny shrubs and small trees in the Rhamnaceae family. This group has a controversial taxonomy, with more than 200 species described, including Chinese jujube (Ziziphus jujuba Mill. var. jujuba) and Indian jujube (Z. mauritiana), as well as several other important cultivated fruit crops. Using 24 SSR markers distributed across the Chinese jujube genome, 962 jujube accessions from the two largest germplasm repositories were genotyped with the aim of analyzing the genetic diversity and structure and constructing a core collection that retain high genetic diversity. A molecular profile comparison revealed 622 unique genotypes, among which 123 genotypes were genetically identical to at least one other accessions. STRUCTURE analysis and multivariate analyses (Cluster and PCoA) roughly divided the accessions into three major groups, with some admixture among groups. A simulated annealing algorithm and a heuristic algorithm were chosen to construct the core collection. A final core of 150 accessions was selected, comprising 15.6% of the analyzed accessions and retaining more than 99.5% of the total alleles detected. We found no significant differences in allele frequency distributions or in genetic diversity parameters between the chosen core accessions and the 622 genetically unique accessions. This work contributes to the understanding of Chinese jujube diversification and the protection of important germplasm resources.
The tetrameric MotA complex as the core of the flagellar motor stator from hyperthermophilic bacterium
Authors: Takekawa Norihiro , Terahara Naoya , Kato Takayuki , Gohara Mizuki , Mayanagi Kouta , Hijikata Atsushi , Onoue Yasuhiro , Kojima Seiji , Shirai Tsuyoshi , Namba Keiichi , Homma Michio 
Published: August 2016

AbstractRotation of bacterial flagellar motor is driven by the interaction between the stator and rotor and the driving energy is supplied by ion influx through the stator channel. The stator is composed of the MotA and MotB proteins, which form a hetero-hexameric complex with a stoichiometry of four MotA and two MotB molecules. MotA and MotB are four- and single-transmembrane proteins, respectively. To generate torque, the MotA/MotB stator unit changes its conformation in response to the ion influx and interacts with the rotor protein FliG. Here, we overproduced and purified MotA of the hyperthermophilic bacterium Aquifex aeolicus. A chemical crosslinking experiment revealed that MotA formed a multimeric complex, most likely a tetramer. The three-dimensional structure of the purified MotA, reconstructed by electron microscopy single particle imaging, consisted of a slightly elongated globular domain and a pair of arch-like domains with spiky projections, likely to correspond to the transmembrane and cytoplasmic domains, respectively. We show that MotA molecules can form a stable tetrameric complex without MotB and for the first time, demonstrate the cytoplasmic structure of the stator.
Structural Investigation of Park’s Nucleotide on Bacterial Translocase MraY: Discovery of Unexpected MraY Inhibitors
Authors: Chen Kuo-Ting , Chen Po-Ting , Lin Cheng-Kun , Huang Lin-Ya , Hu Chia-Ming , Chang Yi-Fan , Hsu Hua-Ting , Cheng Ting-Jen R. , Wu Ying-Ta , Cheng Wei-Chieh 
Published: August 2016

AbstractSystematic structural modifications of the muramic acid, peptide and nucleotide moieties of Park’s nucleotide were performed to investigate the substrate specificity of B. subtilis MraY (MraYBS). It was found that the simplest analogue of Park’s nucleotide only bearing the first two amino acids, l-alanine-iso-d-glutamic acid, could function as a MraYBS substrate. Also, the acid group attached to the Cα of iso-d-glutamic acid was found to play an important role for substrate activity. Epimerization of the C4-hydroxyl group of muramic acid and modification at the 5-position of the uracil in Park’s nucleotide were both found to dramatically impair their substrate activity. Unexpectedly, structural modifications on the uracil moiety changed the parent molecule from a substrate to an inhibitor, blocking the MraYBS translocation. One unoptimized inhibitor was found to have a Ki value of 4 ± 1 μM against MraYBS, more potent than tunicamycins.
Queens become workers: pesticides alter caste differentiation in bees
Authors: dos Santos Charles F. , Acosta André L. , Dorneles Andressa L. , dos Santos Patrick D. S. , Blochtein Betina 
Published: August 2016

AbstractBees are important for the world biodiversity and economy because they provide key pollination services in forests and crops. However, pesticide use in crops has adversely affected (decreased) queen production because of increased mortality among larvae. Here, we demonstrated thatin vitro-reared queens of a neotropical social bee species (Plebeia droryana) also showed high larval mortality after exposure to an organophosphate pesticide (chlorpyrifos) via larval food. Moreover, most of the surviving larvae that were destined to develop into queens became workers more likely because they ate less food than expected without pesticide skewing thus caste differentiation in this bee species. This adverse effect has not been previously reported for any other social insects, such as honeybees or bumblebees. Queens are essential for breeding and colony growth. Therefore, if our data are applicable to other pantropical social bee species across the globe, it is likely that these bees are at a serious risk of failure to form new colonies.
Integrated live imaging and molecular profiling of embryoid bodies reveals a synchronized progression of early differentiation
Authors: Boxman Jonathan , Sagy Naor , Achanta Sirisha , Vadigepalli Rajanikanth , Nachman Iftach 
Published: August 2016

AbstractEmbryonic stem cells can spontaneously differentiate into cell types of all germ layers within embryoid bodies (EBs) in a highly variable manner. Whether there exists an intrinsic differentiation program common to all EBs is unknown. Here, we present a novel combination of high-throughput live two-photon imaging and gene expression profiling to study early differentiation dynamics spontaneously occurring within developing EBs. Onset timing of Brachyury-GFP was highly variable across EBs, while the spatial patterns as well as the dynamics of mesendodermal progression following onset were remarkably similar. We therefore defined a ‘developmental clock’ using the Brachyury-GFP signal onset timing. Mapping snapshot gene expression measurements to this clock revealed their temporal trends, indicating that loss of pluripotency, formation of primitive streak and mesodermal lineage progression are synchronized in EBs. Exogenous activation of Wnt or BMP signaling accelerated the intrinsic clock. CHIR down-regulated Wnt3, allowing insights into dependency mechanisms between canonical Wnt signaling and multiple genes. Our findings reveal a developmental clock characteristic of an early differentiation program common to all EBs, further establishing them as an in vitro developmental model.
Up- regulation of miR-328-3p sensitizes non-small cell lung cancer to radiotherapy
Authors: Ma Wei , Ma Chao-nan , Zhou Nan-nan , Li Xian-dong , Zhang Yi-jie 
Published: August 2016

AbstractMicroRNAs (miRNAs) are believed to be resistant against radiotherapy in certain types of cancers. The aim of our study was to determine the clinical application of miRNAs in non-small cell lung cancer (NSCLC). Sixty NSCLC tissue samples and adjacent histologically normal tissues were obtained for miRNAs microarray analysis and validated by RT-qPCR. Correlation between miRNA expression level and clinicopathological features was evaluated. Our study examined the influence of changed miRNA expression on the damaged DNA and its associated radio sensitivity. Luciferase assay was performed to determine potential effects on the targeted gene. Our study identified fifteen altered miRNAs in which miR-328-3p was down regulated in NSCLC tumour tissue as compared to normal tissues. Down-expression of miR-328-3p was positively associated with an enhanced lymph node metastasis, advanced clinical stage and a shortened survival rate. miR-328-3p expression was decreased in A549 cells compared to other NSCLC cell lines. Up-regulation of miR-328-3p demonstrated a survival inhibition effect in A549 and restored NSCLC cells’ sensitivity to radio therapy. An increased miR-328-3p expression promoted irradiation-induced DNA damage in cells. γ-H2AX was identified as the direct target of miR-328-3p. Over-expressed miR-328-3p can improve the radiosensitvity of cells by altering the DNA damage/repair signalling pathways in NSCLC.
Green bean biofortification for Si through soilless cultivation: plant response and Si bioaccessibility in pods
Authors: Montesano Francesco Fabiano , D’Imperio Massimiliano , Parente Angelo , Cardinali Angela , Renna Massimiliano , Serio Francesco 
Published: August 2016

AbstractFood plants biofortification for micronutrients is a tool for the nutritional value improvement of food. Soilless cultivation systems, with the optimal control of plant nutrition, represent a potential effective technique to increase the beneficial element content in plant tissues. Silicon (Si), which proper intake is recently recommended for its beneficial effects on bone health, presents good absorption in intestinal tract from green bean, a high-value vegetable crop. In this study we aimed to obtain Si biofortified green bean pods by using a Si-enriched nutrient solution in soilless system conditions, and to assess the influence of boiling and steaming cooking methods on Si content, color parameters and Si bioaccessibility (by using an in vitro digestion process) of pods. The Si concentration of pods was almost tripled as a result of the biofortification process, while the overall crop performance was not negatively influenced. The Si content of biofortified pods was higher than unbiofortified also after cooking, despite the cooking method used. Silicon bioaccessibility in cooked pods was more than tripled as a result of biofortification, while the process did not affect the visual quality of the product. Our results demonstrated that soilless cultivation can be successfully used for green bean Si biofortification.
The γ-Protocadherin-C3 isoform inhibits canonical Wnt signalling by binding to and stabilizing Axin1 at the membrane
Authors: Mah Kar Men , Houston Douglas W. , Weiner Joshua A. 
Published: August 2016

AbstractThe 22 γ-Protocadherin (γ-Pcdh) adhesion molecules encoded by the Pcdhg gene cluster play critical roles in nervous system development, including regulation of dendrite arborisation, neuronal survival, and synaptogenesis. Recently, they have been implicated in suppression of tumour cell growth by inhibition of canonical Wnt signalling, though the mechanisms through which this occurs remain unknown. Here, we show differential regulation of Wnt signalling by individual γ-Pcdhs: The C3 isoform uniquely inhibits the pathway, whilst 13 other isoforms upregulate signalling. Focusing on the C3 isoform, we show that its unique variable cytoplasmic domain (VCD) is the critical one for Wnt pathway inhibition. γ-Pcdh-C3, but not other isoforms, physically interacts with Axin1, a key component of the canonical Wnt pathway. The C3 VCD competes with Dishevelled for binding to the DIX domain of Axin1, which stabilizes Axin1 at the membrane and leads to reduced phosphorylation of Wnt co-receptor Lrp6. Finally, we present evidence that Wnt pathway activity can be modulated up (by γ-Pcdh-A1) or down (by γ-Pcdh-C3) in the cerebral cortex in vivo, using conditional transgenic alleles. Together, these data delineate opposing roles for γ-Pcdh isoforms in regulating Wnt signalling and identify Axin1 as a novel protein interactor of the widely-expressed γ-Pcdh-C3 isoform.
Light-Driven Reversible Shaping of Individual Azopolymeric Micro-Pillars
Authors: Pirani Federica , Angelini Angelo , Frascella Francesca , Rizzo Riccardo , Ricciardi Serena , Descrovi Emiliano 
Published: August 2016

AbstractAzopolymers are known to exhibit a strong light responsivity known as athermal photofluidization. Although the underlying physics is still under debate, athermal photofluidization has been demonstrated to trigger mass-migration according to the polarization of a proper illumination light. Here, a polymer blend is proposed wherein a commercial azo-polyelectrolyte is mixed with a passive polymer. The blend is patterned as an array of micro-pillars that are individually exposed to visible laser illumination. Thanks to the interplay between the two blend components, a reversible and controlled deformation of the micro-pillars by periodically tuning the laser polarization in time is demonstrated. A reduced mobility of the azo-compound allows to repeatibly elongate and rotate micro-pillars along specific directions, with no significant material flow outisde the initial volume and no significant degradation of the structure morphology over several cycles. The proposed work suggests new degrees of freedom in controlling the mechanical features of micro-patterned light-responsive materials that can be usefully exploited in many application fields.
Cellular adhesome screen identifies critical modulators of focal adhesion dynamics, cellular traction forces and cell migration behaviour
Authors: Fokkelman Michiel , Balcıoğlu Hayri E. , Klip Janna E. , Yan Kuan , Verbeek Fons J. , Danen Erik H. J. , van de Water Bob 
Published: August 2016

AbstractCancer cells migrate from the primary tumour into surrounding tissue in order to form metastasis. Cell migration is a highly complex process, which requires continuous remodelling and re-organization of the cytoskeleton and cell-matrix adhesions. Here, we aimed to identify genes controlling aspects of tumour cell migration, including the dynamic organization of cell-matrix adhesions and cellular traction forces. In a siRNA screen targeting most cell adhesion-related genes we identified 200+ genes that regulate size and/or dynamics of cell-matrix adhesions in MCF7 breast cancer cells. In a subsequent secondary screen, the 64 most effective genes were evaluated for growth factor-induced cell migration and validated by tertiary RNAi pool deconvolution experiments. Four validated hits showed significantly enlarged adhesions accompanied by reduced cell migration upon siRNA-mediated knockdown. Furthermore, loss of PPP1R12B, HIPK3 or RAC2 caused cells to exert higher traction forces, as determined by traction force microscopy with elastomeric micropillar post arrays, and led to considerably reduced force turnover. Altogether, we identified genes that co-regulate cell-matrix adhesion dynamics and traction force turnover, thereby modulating overall motility behaviour.
Immune tolerance to an intestine-adapted bacteria, Chryseobacterium sp., injected into the hemocoel of Protaetia brevitarsis seulensis
Authors: Lee Jiae , Hwang Sejung , Cho Saeyoull 
Published: August 2016

AbstractTo explore the interaction of gut microbes and the host immune system, bacteria were isolated from the gut of Protaetia brevitarsis seulensis larvae. Chryseobacterium sp., Bacillus subtilis, Arthrobacter arilaitensis, Bacillus amyloliquefaciens, Bacillus megaterium, and Lysinibacillus xylanilyticus were cultured in vitro, identified, and injected in the hemocoel of P. brevitarsis seulensis larvae, respectively. There were no significant changes in phagocytosis-associated lysosomal formation or pathogen-related autophagosome in immune cells (granulocytes) from Chryseobacterium sp.-challenged larvae. Next, we examined changes in the transcription of innate immune genes such as peptidoglycan recognition proteins and antimicrobial peptides following infection with Chryseobacterium sp. PGRP-1 and -2 transcripts, which may be associated with melanization generated by prophenoloxidase (PPO), were either highly or moderately expressed at 24 h post-infection with Chryseobacterium sp. However, PGRP-SC2 transcripts, which code for bactericidal amidases, were expressed at low levels. With respect to antimicrobial peptides, only coleoptericin was moderately expressed in Chryseobacterium sp.-challenged larvae, suggesting maintenance of an optimum number of Chryseobacterium sp. All examined genes were expressed at significantly higher levels in larvae challenged with a pathogenic bacterium. Our data demonstrated that gut-inhabiting bacteria, the Chryseobacterium sp., induced a weaker immune response than other pathogenic bacteria, E. coli K12.
SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley
Authors: Ren Xifeng , Wang Jibin , Liu Lipan , Sun Genlou , Li Chengdao , Luo Hong , Sun Dongfa 
Published: August 2016

AbstractA high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley.
Clinical features and management of multifocal hepatic hemangiomas in children: a retrospective study
Authors: Ji Yi , Chen Siyuan , Xiang Bo , Xu Zhicheng , Jiang Xiaoping , Liu Xingtao , Wang Qi , Lu Guoyan , Yang Li 
Published: August 2016

AbstractMultifocal hepatic hemangioma (MHH) is a benign hepatic tumor that is commonly diagnosed in children with multiple cutaneous infantile hemangiomas (IHs). We present a review of all children with MHH at our institutions. Of the 42 patients, the median age at presentation of MHH was 2.5 months. Thirty-six (85.7%) patients had cutaneous IHs. Twelve (28.6%) patients were symptomatic at presentation. There was no significant association between the number of hepatic hemangiomas and the number of cutaneous IHs. Fourteen (33.3%) patients received some form of treatment for hepatic hemangiomas. The most common type of treatment was oral prednisone in 8 patients, followed by oral propranolol in 6 patients. Two patients were totally resistant to prednisone treatment. They died from congestive heart failure or respiratory distress and coagulopathy. Two patients with problematic facial IH were treated with intralesional triamcinolone injection. The remaining 26 patients were managed with imaging surveillance. On follow-up, all of the survivors had a favorable outcome. Our study suggests that the clinical features of MHH are variable. Our data emphasize the treatment strategy that aggressive treatment is indicated in symptomatic or progressive MHHs, whereas observation management of asymptomatic patients with a few small lesions is safe and appropriate.