bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thresholds of change in a multi-use conservation landscape of South Africa: historical land-cover, future transformation and consequences for environmental decision-making
Authors: COETZER-HANACK KAERA L. , WITKOWSKI E.T.F. , ERASMUS BAREND F.N. 
Published: May 2016

SUMMARYAs multi-use conservation landscapes, biosphere reserves (BRs) exemplify the landscape mosaic approach to environmental decision-making. In this study, time-series remotely-sensed data (1993–2006–2012) were used to monitor vegetation transformation in the Kruger to Canyons Biosphere Reserve (K2C) of South Africa, updating previous land-cover research. We identified changes in spatial extent, rate and intensity of land-cover change and extrapolated observed trends to 2018. The increased rate of change in the recent observation period (2.3 vs. 5.7%) was driven by more intensive gains in impacted vegetation and settlement since 2006 (>210 km2and >120 km2), with resultant transformation of intact habitat undermining regional connectivity. By 2012, intact vegetation had suffered losses of 6.3% (>350 km2) since 2006 and >14% (>750 km2) since 1993. A further 9.5% loss of intact habitat may represent a critical threshold, establishing K2C above the 50% threshold of landscape transformation, whereafter a rapid decline in landscape resilience is likely. Given the BR's spatial zonation, such a loss across the full extent of K2C is unlikely, at least in the short-term (i.e., by 2018). Yet, based on past trends of transformation in the unprotected transition zone, anticipating such losses in the longer term, is not unfounded (i.e., 2024).
Positive influences of home food environment on primary-school children’s diet and weight status: a structural equation model approach
Authors: Ong Jia Xin , Ullah Shahid , Magarey Anthea , Leslie Eva 
Published: May 2016

AbstractObjectivesThe mechanism by which the home food environment (HFE) influences childhood obesity is unclear. The present study aimed to investigate the relationship between HFE and childhood obesity as mediated by diet in primary-school children.DesignCross-sectional data collected from parents and primary-school children participating in the Obesity Prevention and Lifestyle Evaluation Project. Only children aged 9–11 years participated in the study. Matched parent/child data (n3323) were analysed. Exploratory factor analysis underlined components of twenty-one HFE items; these were linked to child diet (meeting guidelines for fruit, vegetable and non-core food intakes) and measured child BMI, in structural equation modelling, adjusting for confounders.SettingTwenty geographically bounded metropolitan and regional South Australian communities.SubjectsSchool children and their parents from primary schools in selected communities.ResultsIn the initial exploratory factor analysis, nineteen items remaining extracted eight factors with eigenvalues >1·0 (72·4 % of total variance). A five-factor structure incorporating ten items described HFE. After adjusting for age, gender, socio-economic status and physical activity all associations in the model were significant (P<0·05), explaining 9·3 % and 4·5 % of the variance in child diet and BMI, respectively. A more positive HFE was directly and indirectly associated with a lower BMI in children through child diet.ConclusionsThe robust statistical methodology used in the present study provides support for a model of direct and indirect dynamics between the HFE and childhood obesity. The model can be tested in future longitudinal and intervention studies to identify the most effective components of the HFE to target in childhood obesity prevention efforts.
A novel type II collagen gene mutation in a family with spondyloepiphyseal dysplasia and extensive intrafamilial phenotypic diversity
Authors: Nakashima Yasuharu , Sakamoto Yuma , Nishimura Gen , Ikegawa Shiro , Iwamoto Yukihide 
Published: May 2016

AbstractThe purpose of this study was to describe a family with spondyloepiphyseal dysplasia caused by a novel type II collagen gene (COL2A1) mutation and the family’s phenotypic diversity. Clinical and radiographic examinations of skeletal dysplasia were conducted on seven affected family members across two generations. The entire coding region of COL2A1, including the flanking intron regions, was analyzed with PCR and direct sequencing. The stature of the subjects ranged from extremely short to within normal height range. Hip deformity and advanced osteoarthritis were noted in all the subjects, ranging from severe coxa plana to mild acetabular dysplasia. Atlantoaxial subluxation combined with a hypoplastic odontoid process was found in three of the subjects. Various degrees of platyspondyly were confirmed in all subjects. Genetically, a novel COL2A1 mutation (c.1349G>C, p.Gly450Ala) was identified in all the affected family members; however, it was not present in the one unaffected family member tested. We described a family with spondyloepiphyseal dysplasia and a novel COL2A1 mutation (c.1349G>C, p.Gly450Ala). Phenotypes were diverse even among individuals with the same mutation and within the same family.
A curated and standardized adverse drug event resource to accelerate drug safety research
Authors: Banda Juan M. , Evans Lee , Vanguri Rami S. , Tatonetti Nicholas P. , Ryan Patrick B. , Shah Nigam H. 
Published: May 2016

AbstractIdentification of adverse drug reactions (ADRs) during the post-marketing phase is one of the most important goals of drug safety surveillance. Spontaneous reporting systems (SRS) data, which are the mainstay of traditional drug safety surveillance, are used for hypothesis generation and to validate the newer approaches. The publicly available US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) data requires substantial curation before they can be used appropriately, and applying different strategies for data cleaning and normalization can have material impact on analysis results. We provide a curated and standardized version of FAERS removing duplicate case records, applying standardized vocabularies with drug names mapped to RxNorm concepts and outcomes mapped to SNOMED-CT concepts, and pre-computed summary statistics about drug-outcome relationships for general consumption. This publicly available resource, along with the source code, will accelerate drug safety research by reducing the amount of time spent performing data management on the source FAERS reports, improving the quality of the underlying data, and enabling standardized analyses using common vocabularies.
Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions
Authors: Law Yingyu , Kirkegaard Rasmus Hansen , Cokro Angel Anisa , Liu Xianghui , Arumugam Krithika , Xie Chao , Stokholm-Bjerregaard Mikkel , Drautz-Moses Daniela I. , Nielsen Per Halkjær , Wuertz Stefan , Williams Rohan B. H. 
Published: May 2016

AbstractManagement of phosphorus discharge from human waste is essential for the control of eutrophication in surface waters. Enhanced biological phosphorus removal (EBPR) is a sustainable, efficient way of removing phosphorus from waste water without employing chemical precipitation, but is assumed unachievable in tropical temperatures due to conditions that favour glycogen accumulating organisms (GAOs) over polyphosphate accumulating organisms (PAOs). Here, we show these assumptions are unfounded by studying comparative community dynamics in a full-scale plant following systematic perturbation of operational conditions, which modified community abundance, function and physicochemical state. A statistically significant increase in the relative abundance of the PAO Accumulibacter was associated with improved EBPR activity. GAO relative abundance also increased, challenging the assumption of competition. An Accumulibacter bin-genome was identified from a whole community metagenomic survey, and comparative analysis against extant Accumulibacter genomes suggests a close relationship to Type II. Analysis of the associated metatranscriptome data revealed that genes encoding proteins involved in the tricarboxylic acid cycle and glycolysis pathways were highly expressed, consistent with metabolic modelling results. Our findings show that tropical EBPR is indeed possible, highlight the translational potential of studying competition dynamics in full-scale waste water communities and carry implications for plant design in tropical regions.
DgcA, a diguanylate cyclase from Xanthomonas oryzae pv. oryzae regulates bacterial pathogenicity on rice
Authors: Su Jianmei , Zou Xia , Huang Liangbo , Bai Tenglong , Liu Shu , Yuan Meng , Chou Shan-Ho , He Ya-Wen , Wang Haihong , He Jin 
Published: May 2016

AbstractXanthomonas oryzae pv. oryzae (Xoo) is the causal agent of rice blight disease as well as a serious phytopathogen worldwide. It is also one of the model organisms for studying bacteria-plant interactions. Current progress in bacterial signal transduction pathways has identified cyclic di-GMP as a major second messenger molecule in controlling Xanthomonas pathogenicity. However, it still remains largely unclear how c-di-GMP regulates the secretion of bacterial virulence factors in Xoo. In this study, we focused on the important roles played by DgcA (XOO3988), one of our previously identified diguanylate cyclases in Xoo, through further investigating the phenotypes of several dgcA-related mutants, namely, the dgcA-knockout mutant ΔdgcA, the dgcA overexpression strain OdgcA, the dgcA complemented strain CdgcA and the wild-type strain. The results showed that dgcA negatively affected virulence, EPS production, bacterial autoaggregation and motility, but positively triggered biofilm formation via modulating the intracellular c-di-GMP levels. RNA-seq data further identified 349 differentially expressed genes controlled by DgcA, providing a foundation for a more solid understanding of the signal transduction pathways in Xoo. Collectively, the present study highlights DgcA as a major regulator of Xoo virulence and can serve as a potential target for preventing rice blight diseases.
Long-distance temporal quantum ghost imaging over optical fibers
Authors: Dong Shuai , Zhang Wei , Huang Yidong , Peng Jiangde 
Published: May 2016

AbstractSince the first quantum ghost imaging (QGI) experiment in 1995, many QGI schemes have been put forward. However, the position-position or momentum-momentum correlation required in these QGI schemes cannot be distributed over optical fibers, which limits their large-scale geographical applications. In this paper, we propose and demonstrate a scheme for long-distance QGI utilizing frequency correlated photon pairs. In this scheme, the frequency correlation is transformed to the correlation between the illuminating position of one photon and the arrival time of the other photon, by which QGI can be realized in the time domain. Since frequency correlation can be preserved when the photon pairs are distributed over optical fibers, this scheme provides a way to realize long-distance QGI over large geographical scale. In the experiment, long-distance QGI over 50 km optical fibers has been demonstrated.
Strain-induced growth instability and nanoscale surface patterning in perovskite thin films
Authors: Pandya Shishir , Damodaran Anoop R. , Xu Ruijuan , Hsu Shang-Lin , Agar Joshua C. , Martin Lane W. 
Published: May 2016

AbstractDespite extensive studies on the effects of epitaxial strain on the evolution of the lattice and properties of materials, considerably less work has explored the impact of strain on growth dynamics. In this work, we demonstrate a growth-mode transition from 2D-step flow to self-organized, nanoscale 3D-island formation in PbZr0.2Ti0.8O3/SrRuO3/SrTiO3 (001) heterostructures as the kinetics of the growth process respond to the evolution of strain. With increasing heterostructure thickness and misfit dislocation formation at the buried interface, a periodic, modulated strain field is generated that alters the adatom binding energy and, in turn, leads to a kinetic instability that drives a transition from 2D growth to ordered, 3D-island formation. The results suggest that the periodically varying binding energy can lead to inhomogeneous adsorption kinetics causing preferential growth at certain sites. This, in conjunction with the presence of an Ehrlich-Schwoebel barrier, gives rise to long-range, periodically-ordered arrays of so-called “wedding cake” 3D nanostructures which self-assemble along the [100] and [010].
Limited value of pro-inflammatory oxylipins and cytokines as circulating biomarkers in endometriosis – a targeted ‘omics study
Authors: Lee Yie Hou , Cui Liang , Fang Jinling , Chern Bernard Su Min , Tan Heng Hao , Chan Jerry K. Y. 
Published: May 2016

AbstractEndometriosis is a common, complex gynecologic disorder characterized by the presence of endometrial-like tissues at extrauterine sites. Elevation in protein and lipid mediators of inflammation including oxylipins and cytokines within the peritoneum characterize the inflamed pelvic region and may contribute to the survival and growth of displaced endometrial tissues. The presence of a clinically silent but molecularly detectable systemic inflammation in endometriosis has been proposed. Thus, we examined serum oxylipin and immunomodulatory protein levels in 103 women undergoing laparoscopy to evaluate systematically any involvement in systemic pathophysiological inflammation in endometriosis. Oxylipin levels were similar between women with and without endometriosis. Stratification by menstrual phase or severity did not offer any difference. Women with ovarian endometriosis had significantly lower 12-HETE relative to peritoneal endometriosis (−50.7%). Serum oxylipin levels were not associated with pre-operative pain symptoms. Changes to immunomodulatory proteins were minimal, with IL-12(p70), IL-13 and VEGF significantly lower in mild endometriotic women compared to non-endometriotic women (−39%, −54% and −76% respectively). Verification using C-reactive protein as a non-specific marker of inflammation further showed similar levels between groups. The implications of our work suggest pro-inflammatory mediators in the classes studied may have potentially limited value as circulating biomarkers for endometriosis, suggesting of potentially tenuous systemic inflammation in endometriosis.
On the Variability and Increasing Trends of Heat Waves over India
Authors: Rohini P. , Rajeevan M. , Srivastava A. K. 
Published: May 2016

AbstractOver India, heat waves occur during the summer months of April to June. A gridded daily temperature data set for the period, 1961–2013 has been analyzed to examine the variability and trends in heat waves over India. For identifying heat waves, the Excess Heat Factor (EHF) and 90th percentile of maximum temperatures were used. Over central and northwestern parts of the country, frequency, total duration and maximum duration of heat waves are increasing. Anomalous persistent high with anti-cyclonic flow, supplemented with clear skies and depleted soil moisture are primarily responsible for the occurrence of heat waves over India. Variability of heat waves over India is influenced by both the tropical Indian Ocean and central Pacific SST anomalies. The warming of the tropical Indian Ocean and more frequent El Nino events in future may further lead to more frequent and longer lasting heat waves over India.
Black perithecial pigmentation in Fusarium species is due to the accumulation of 5-deoxybostrycoidin-based melanin
Authors: Frandsen Rasmus J. N. , Rasmussen Silas A. , Knudsen Peter B. , Uhlig Silvio , Petersen Dirk , Lysøe Erik , Gotfredsen Charlotte H. , Giese Henriette , Larsen Thomas O. 
Published: May 2016

AbstractBiosynthesis of the black perithecial pigment in the filamentous fungus Fusarium graminearum is dependent on the polyketide synthase PGL1 (oPKS3). A seven-membered PGL1 gene cluster was identified by over-expression of the cluster specific transcription factor pglR. Targeted gene replacement showed that PGL1, pglJ, pglM and pglV were essential for the production of the perithecial pigment. Over-expression of PGL1 resulted in the production of 6-O-demethyl-5-deoxybostrycoidin (1), 5-deoxybostrycoidin (2), and three novel compounds 5-deoxybostrycoidin anthrone (3), 6-O-demethyl-5-deoxybostrycoidin anthrone (4) and purpurfusarin (5). The novel dimeric bostrycoidin purpurfusarin (5) was found to inhibit the growth of Candida albicans with an IC50 of 8.0 +/− 1.9 μM. The results show that Fusarium species with black perithecia have a previously undescribed form of 5-deoxybostrycoidin based melanin in their fruiting bodies.
Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family
Authors: Uhart Marina , Flores Gabriel , Bustos Diego M. 
Published: May 2016

AbstractPosttranslational regulation of protein function is an ubiquitous mechanism in eukaryotic cells. Here, we analyzed biological properties of nodes and edges of a human protein-protein interaction phosphorylation-based network, especially of those nodes critical for the network controllability. We found that the minimal number of critical nodes needed to control the whole network is 29%, which is considerably lower compared to other real networks. These critical nodes are more regulated by posttranslational modifications and contain more binding domains to these modifications than other kinds of nodes in the network, suggesting an intra-group fast regulation. Also, when we analyzed the edges characteristics that connect critical and non-critical nodes, we found that the former are enriched in domain-to-eukaryotic linear motif interactions, whereas the later are enriched in domain-domain interactions. Our findings suggest a possible structure for protein-protein interaction networks with a densely interconnected and self-regulated central core, composed of critical nodes with a high participation in the controllability of the full network and less regulated peripheral nodes. Our study offers a deeper understanding of complex network control and bridges the controllability theorems for complex networks and biological protein-protein interaction phosphorylation-based networked systems.
An efficient algorithm to identify the optimal one-bit perturbation based on the basin-of-state size of Boolean networks
Authors: Hu Mingxiao , Shen Liangzhong , Zan Xiangzhen , Shang Xuequn , Liu Wenbin 
Published: May 2016

AbstractBoolean networks are widely used to model gene regulatory networks and to design therapeutic intervention strategies to affect the long-term behavior of systems. In this paper, we investigate the less-studied one-bit perturbation, which falls under the category of structural intervention. Previous works focused on finding the optimal one-bit perturbation to maximally alter the steady-state distribution (SSD) of undesirable states through matrix perturbation theory. However, the application of the SSD is limited to Boolean networks with about ten genes. In 2007, Xiao et al. proposed to search the optimal one-bit perturbation by altering the sizes of the basin of attractions (BOAs). However, their algorithm requires close observation of the state-transition diagram. In this paper, we propose an algorithm that efficiently determines the BOA size after a perturbation. Our idea is that, if we construct the basin of states for all states, then the size of the BOA of perturbed networks can be obtained just by updating the paths of the states whose transitions have been affected. Results from both synthetic and real biological networks show that the proposed algorithm performs better than the exhaustive SSD-based algorithm and can be applied to networks with about 25 genes.
Local anesthetic bupivacaine induced ovarian and prostate cancer apoptotic cell death and underlying mechanisms in vitro
Authors: Xuan Wei , Zhao Hailin , Hankin James , Chen Lin , Yao Shanglong , Ma Daqing 
Published: May 2016

AbstractRetrospective studies indicate that the use of regional anesthesia can reduce cancer recurrence after surgery which could be due to ranging from immune function preservation to direct molecular mechanisms. This study was to investigate the effects of bupivacaine on ovarian and prostate cancer cell biology and the underlying molecular mechanisms. Cell viability, proliferation and migration of ovarian carcinoma (SKOV-3) and prostate carcinoma (PC-3) were examined following treatment with bupivacaine. Cleaved caspase 3, 8 and 9 and GSK-3β, pGSK-3βtyr216 and pGSK-3βser9 expression were assessed by immunofluorescence. FAS ligand neutralization, caspase and GSK-3 inhibitors and GSK-3β siRNA were applied to further explore underlying mechanisms. Clinically relevant concentrations of bupivacaine reduced cell viability and inhibited cellular proliferation and migration in both cell lines. Caspase 8 and 9 inhibition generated partial cell death reversal in SKOV-3, whilst only caspase 9 was effective in PC-3. Bupivacaine increased the phosphorylation of GSK-3βTyr216 in SKOV-3 but without measurable effect in PC3. GSK-3β inhibition and siRNA gene knockdown decreased bupivacaine induced cell death in SKOV-3 but not in PC3. Our data suggests that bupivacaine has direct ‘anti-cancer’ properties through the activation of intrinsic and extrinsic apoptotic pathways in ovarian cancer but only the intrinsic pathway in prostate cancer.
TNFα promotes CAR-dependent migration of leukocytes across epithelial monolayers
Authors: Morton Penny E. , Hicks Alexander , Ortiz-Zapater Elena , Raghavan Swetavalli , Pike Rosemary , Noble Alistair , Woodfin Abigail , Jenkins Gisli , Rayner Emma , Santis George , Parsons Maddy 
Published: May 2016

AbstractTrans-epithelial migration (TEpM) of leukocytes during inflammation requires engagement with receptors expressed on the basolateral surface of the epithelium. One such receptor is Coxsackie and Adenovirus Receptor (CAR) that binds to Junctional Adhesion Molecule-like (JAM-L) expressed on leukocytes. Here we provide the first evidence that efficient TEpM of monocyte-derived THP-1 cells requires and is controlled by phosphorylation of CAR. We show that TNFα acts in a paracrine manner on epithelial cells via a TNFR1-PI3K-PKCδ pathway leading to CAR phosphorylation and subsequent transmigration across cell junctions. Moreover, we show that CAR is hyper-phosphorylated in vivo in acute and chronic lung inflammation models and this response is required to facilitate immune cell recruitment. This represents a novel mechanism of feedback between leukocytes and epithelial cells during TEpM and may be important in controlling responses to pro-inflammatory cytokines in pathological settings.
Irc3 is a mitochondrial DNA branch migration enzyme
Authors: Gaidutšik Ilja , Sedman Tiina , Sillamaa Sirelin , Sedman Juhan 
Published: May 2016

AbstractIntegrity of mitochondrial DNA (mtDNA) is essential for cellular energy metabolism. In the budding yeast Saccharomyces cerevisiae, a large number of nuclear genes influence the stability of mitochondrial genome; however, most corresponding gene products act indirectly and the actual molecular mechanisms of mtDNA inheritance remain poorly characterized. Recently, we found that a Superfamily II helicase Irc3 is required for the maintenance of mitochondrial genome integrity. Here we show that Irc3 is a mitochondrial DNA branch migration enzyme. Irc3 modulates mtDNA metabolic intermediates by preferential binding and unwinding Holliday junctions and replication fork structures. Furthermore, we demonstrate that the loss of Irc3 can be complemented with mitochondrially targeted RecG of Escherichia coli. We suggest that Irc3 could support the stability of mtDNA by stimulating fork regression and branch migration or by inhibiting the formation of irregular branched molecules.