bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spatial and temporal analysis of paediatric central nervous system infections from 2005 to 2015 in Ho Chi Minh City, Vietnam
Authors: HO N. T. , HOANG V. M. T. , LE N. N. T. , NGUYEN D. T. , TRAN A. , KAKI D. , TRAN P. M. , THOMPSON C. N. , NGO M. N. Q. , TRUONG K. H. , NGUYEN H. T. , HA T. M. , NGUYEN C. V. V. , THWAITES G. E. , THAKUR K. T. , HESDORFFER D. , BAKER S. 
Published: October 2017

SUMMARYCentral nervous system infections (CNSI) are a leading cause of death and long-term disability in children. Using ICD-10 data from 2005 to 2015 from three central hospitals in Ho Chi Minh City (HCMC), Vietnam, we exploited generalized additive mixed models (GAMM) to examine the spatial-temporal distribution and spatial and climatic risk factors of paediatric CNSI, excluding tuberculous meningitis, in this setting. From 2005 to 2015, there were 9469 cases of paediatric CNSI; 33% were ⩽1 year old at admission and were mainly diagnosed with presumed bacterial CNSI (BI) (79%), the remainder were >1 year old and mainly diagnosed with presumed non-bacterial CNSI (non-BI) (59%). The urban districts of HCMC in proximity to the hospitals as well as some outer districts had the highest incidences of BI and non-BI; BI incidence was higher in the dry season. Monthly BI incidence exhibited a significant decreasing trend over the study. Both BI and non-BI were significantly associated with lags in monthly average temperature, rainfall, and river water level. Our findings add new insights into this important group of infections in Vietnam, and highlight where resources for the prevention and control of paediatric CNSI should be allocated.
Households' responses to climate change: contingent behavior evidence from rural South Africa
Authors: Dassanayake Wijaya , Mohapatra Sandeep , Luckert Martin K. , Adamowicz Wiktor 
Published: October 2017

AbstractWe investigate households' decisions regarding livelihood activities in response to future climate change in the Eastern Cape, South Africa. We use the contingent behavior method and account for unobserved heterogeneity in order to overcome problems associated with limited data, collinearity and endogeneity. We characterize the climate change with two types of climate change scenarios: dry-spells and wet-spells. Results show that moderate and extreme increases in dry-spells increase adoption of off-farm activities such as casual labor and small business, and decrease adoption of on-farm activities such as gardening. We find opposite cases for mild or moderate wet-spells. Our results also show that households tend to diversify their livelihood portfolios in response to a moderate increase in dry-spells and a mild increase in wet-spells. Some household characteristics are also important in influencing some types of activities, including household's health status, gender of the household head, and household's prior experience.
Exploring perceptions of the Mexican sugar-sweetened beverage tax among adolescents in north-west Mexico: a qualitative study
Authors: Ortega-Avila Ana G , Papadaki Angeliki , Jago Russell 
Published: October 2017

AbstractObjectiveTo explore awareness and perceptions of the sugar-sweetened beverage (SSB) tax implemented in Mexico in 2014 among a sample of Mexican adolescents, and to investigate how the tax has affected their purchases and intake of SSB.DesignQualitative.SettingSemi-structured interviews were conducted in April–May 2016. The data were analysed using thematic analysis.SubjectsAdolescents residing in north-west Mexico (n29, 55·2 % females), aged 15–19 years.ResultsFour main themes emerged: awareness of taxation; perceptions of how the tax has affected SSB intake; reasons why the tax was not perceived to have affected SSB intake; and preferences for substitution of the taxed SSB. Participants were mostly unaware of the tax and perceived that it would not cause reductions in their intake of SSB; they felt that the price increase was low and insufficient to affect intake. Taste preferences and ‘addiction’ to SSB were highlighted as the main reasons why participants perceived taxation would not affect intake. If SSB prices were to increase further via a higher tax, participants would consider substituting SSB with other beverages, namely home-made drinks (e.g. 100 % fruit juices), non-caloric, instant-flavoured drinks and water.ConclusionsThese findings provide important insights into the views of this sample of Mexican adolescents regarding the taxation of SSB, by pointing out several possible limitations of the tax policy in Mexico. These results could inform the design of future interventions directed at Mexican youth that would complement and strengthen the current SSB taxation.
Complex fault interaction controls continental rifting
Authors: Naliboff John B. , Buiter Susanne J. H. , Péron-Pinvidic Gwenn , Osmundsen Per Terje , Tetreault Joya 
Published: October 2017

AbstractRifted margins mark a transition from continents to oceans and contain in their architecture a record of their rift history. Recent investigations of rift architecture have suggested that multiphase deformation of the crust and mantle lithosphere leads to the formation of distinct margin domains. The processes that control transitions between these domains, however, are not fully understood. Here we use high-resolution numerical simulations to show how structural inheritance and variations in extension velocity control the architecture of rifted margins and their temporal evolution. Distinct domains form as extension velocities increase over time and deformation focuses along lithosphere-scale detachment faults, which migrate oceanwards through re-activation and complex linkages of prior fault networks. Our models demonstrate, in unprecedented detail, how faults formed in the earliest phases of continental extension control the subsequent structural evolution and complex architecture of rifted margins through fault interaction processes, hereby creating the widely observed distinct margin domains.
Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq
Authors: Bottini Silvia , Hamouda-Tekaya Nedra , Mategot Raphael , Zaragosi Laure-Emmanuelle , Audebert Stephane , Pisano Sabrina , Grandjean Valerie , Mauduit Claire , Benahmed Mohamed , Barbry Pascal , Repetto Emanuela , Trabucchi Michele 
Published: October 2017

AbstractThere is a growing body of evidence about the presence and the activity of the miRISC in the nucleus of mammalian cells. Here, we show by quantitative proteomic analysis that Ago2 interacts with the nucleoplasmic protein Sfpq in an RNA-dependent fashion. By a combination of HITS-CLIP and transcriptomic analyses, we demonstrate that Sfpq directly controls the miRNA targeting of a subset of binding sites by local binding. Sfpq modulates miRNA targeting in both nucleoplasm and cytoplasm, indicating a nucleoplasmic commitment of Sfpq-target mRNAs that globally influences miRNA modes of action. Mechanistically, Sfpq binds to a sizeable set of long 3′UTRs forming aggregates to optimize miRNA positioning/recruitment at selected binding sites, including let-7a binding to Lin28A 3′UTR. Our results extend the miRNA-mediated post-transcriptional gene silencing into the nucleoplasm and indicate that an Sfpq-dependent strategy for controlling miRNA activity takes place in cells, contributing to the complexity of miRNA-dependent gene expression control.
Multi-dimensional genomic analysis of myoepithelial carcinoma identifies prevalent oncogenic gene fusions
Authors: Dalin Martin G. , Katabi Nora , Persson Marta , Lee Ken-Wing , Makarov Vladimir , Desrichard Alexis , Walsh Logan A. , West Lyndsay , Nadeem Zaineb , Ramaswami Deepa , Havel Jonathan J. , Kuo Fengshen , Chadalavada Kalyani , Nanjangud Gouri J. , Ganly Ian , Riaz Nadeem , Ho Alan L. , Antonescu Cristina R. , Ghossein Ronald , Stenman Göran , Chan Timothy A. , Morris Luc G. T. 
Published: October 2017

AbstractMyoepithelial carcinoma (MECA) is an aggressive salivary gland cancer with largely unknown genetic features. Here we comprehensively analyze molecular alterations in 40 MECAs using integrated genomic analyses. We identify a low mutational load, and high prevalence (70%) of oncogenic gene fusions. Most fusions involve the PLAG1 oncogene, which is associated with PLAG1 overexpression. We find FGFR1-PLAG1 in seven (18%) cases, and the novel TGFBR3-PLAG1 fusion in six (15%) cases. TGFBR3-PLAG1 promotes a tumorigenic phenotype in vitro, and is absent in 723 other salivary gland tumors. Other novel PLAG1 fusions include ND4-PLAG1; a fusion between mitochondrial and nuclear DNA. We also identify higher number of copy number alterations as a risk factor for recurrence, independent of tumor stage at diagnosis. Our findings indicate that MECA is a fusion-driven disease, nominate TGFBR3-PLAG1 as a hallmark of MECA, and provide a framework for future diagnostic and therapeutic research in this lethal cancer.
Drug-tunable multidimensional synthetic gene control using inducible degron-tagged dCas9 effectors
Authors: Kleinjan Dirk A. , Wardrope Caroline , Nga Sou Si , Rosser Susan J. 
Published: October 2017

AbstractThe nuclease-deactivated variant of CRISPR-Cas9 proteins (dCas9) fused to heterologous transactivation domains can act as a potent guide RNA sequence-directed inducer or repressor of gene expression in mammalian cells. In such a system the long-term presence of a stable dCas9 effector can be a draw-back precluding the ability to switch rapidly between repressed and activated target gene expression states, imposing a static environment on the synthetic regulatory circuits in the cell. To address this issue we have generated a toolkit of conditionally degradable or stabilisable orthologous dCas9 or Cpf1 effector proteins, thus opening options for multidimensional control of functional activities through combinations of orthogonal, drug-tunable artificial transcription factors.
Combining chemical and genetic approaches to increase drought resistance in plants
Authors: Cao Min-Jie , Zhang Yu-Lu , Liu Xue , Huang Huan , Zhou X. Edward , Wang Wen-Long , Zeng Ai , Zhao Chun-Zhao , Si Tong , Du Jiamu , Wu Wen-Wu , Wang Fu-Xing , Xu H. Eric , Zhu Jian-Kang 
Published: October 2017

AbstractDrought stress is a major threat to crop production, but effective methods to mitigate the adverse effects of drought are not available. Here, we report that adding fluorine atoms in the benzyl ring of the abscisic acid (ABA) receptor agonist AM1 optimizes its binding to ABA receptors by increasing the number of hydrogen bonds between the compound and the surrounding amino acid residues in the receptor ligand-binding pocket. The new chemicals, known as AMFs, have long-lasting effects in promoting stomatal closure and inducing the expression of stress-responsive genes. Application of AMFs or transgenic overexpression of the receptor PYL2 in Arabidopsis and soybean plants confers increased drought resistance. The greatest increase in drought resistance is achieved when AMFs are applied to the PYL2-overexpression transgenic plants. Our results demonstrate that the combining of potent chemicals with transgenic overexpression of an ABA receptor is very effective in helping plants combat drought stress.
Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates
Authors: Frøslev Tobias Guldberg , Kjøller Rasmus , Bruun Hans Henrik , Ejrnæs Rasmus , Brunbjerg Ane Kirstine , Pietroni Carlotta , Hansen Anders Johannes 
Published: October 2017

AbstractDNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants paired with plant ITS2 metabarcoding data of DNA extracted from soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves α-diversity estimates and other biodiversity metrics, and does not require a sequence reference database; thus, it represents a promising method for reliable biodiversity estimation.
Suppression of mRNAs encoding CD63 family tetraspanins from the carcinogenic liver fluke Opisthorchis viverrini results in distinct tegument phenotypes
Authors: Chaiyadet Sujittra , Krueajampa Watchara , Hipkaeo Wiphawi , Plosan Yada , Piratae Supawadee , Sotillo Javier , Smout Michael , Sripa Banchob , Brindley Paul J. , Loukas Alex , Laha Thewarach 
Published: October 2017

AbstractThe liver fluke Opisthorchis viverrini infects 10 million people in Southeast Asia and causes cholangiocarcinoma (CCA). Fluke secreted and tegumental proteins contribute to the generation of a tumorigenic environment and are targets for drug and vaccine-based control measures. Herein, we identified two tetraspanins belonging to the CD63 family (Ov-TSP-2 and Ov-TSP-3) that are abundantly expressed in the tegument proteome of O. viverrini. Ov-tsp-2 and tsp-3 transcripts were detected in all developmental stages of O. viverrini. Protein fragments corresponding to the large extracellular loop (LEL) of each TSP were produced in recombinant form and antibodies were raised in rabbits. Ov-TSP-2 and TSP-3 were detected in whole worm extracts and excretory/secretory products of O. viverrini and reacted with sera from infected hamsters and humans. Antibodies confirmed localization of Ov-TSP-2 and TSP-3 to the adult fluke tegument. Using RNA interference, Ov-tsp-2 and tsp-3 mRNA expression was significantly suppressed for up to 21 days in vitro. Ultrastructural observation of tsp-2 and tsp-3 dsRNA-treated flukes resulted in phenotypes with increased tegument thickness, increased vacuolation (tsp-2) and reduced electron density (tsp-3). These studies confirm the importance of CD63 family tegument tetraspanins in parasitic flukes and support efforts to target these proteins for vaccine development.
Synthesis of graphene/DPA composite for determination of nicotine in tobacco products
Authors: Jing Yanqiu , Yu Baohua , Li Penghui , Xiong Bin , Cheng Yuyuan , Li Yaoguang , Li Chunguang , Xiao Xianyi , Chen Mengqi , Chen Liangyuan , Zhang Yu , Zhao Mingqin , Cheng Chuance 
Published: October 2017

AbstractIn this contribution, the azo dye (E)-1-(4-((4-(phenylamino)phenyl)diazenyl) phenyl)ethanone (DPA) was combined with reduced graphene oxide (RGO) for the electrochemical modification of a pencil graphite electrode (RGO/DPA/PGE) surface. A series of electrochemical measurements were used for the characterization of the modified electrode surfaces. At the modified electrode, nicotine was irreversibly reduced. An obvious increase was observed in the reductive peak current of nicotine at the modified electrode, indicating the capability of the RGO/DPA composite to increase the electron transfer rate. The current was found proportional to the nicotine concentration in a range of 31 to 1900 μM, and the limit of detection (LOD) was calculated as 7.6 μM.
Reinstatement of memory representations for lifelike events over the course of a week
Authors: Oedekoven Christiane S. H. , Keidel James L. , Berens Sam C. , Bird Chris M. 
Published: October 2017

AbstractWhen we remember an event, the content of that memory is represented across the brain. Detailed memory retrieval is thought to involve the reinstatement of those representations. Functional MRI combined with representational similarity analyses (RSA) of spatial patterns of brain activity has revealed reinstatement of recently-experienced events throughout a core memory retrieval network. In the present study, participants were scanned while they watched, immediately retrieved and then retrieved after a week, 24 short videos. Following the delayed retrieval, they freely recalled all videos outside of the scanner. We observed widespread within- and between-subject reinstatement effects within a posterior midline core memory retrieval network during all phases of the experiment. Within precuneus, bilateral middle temporal gyrus and the left hippocampus, reinstatement effects between the retrieval phases correlated with memory performance. These findings extend previous studies that have only employed short retention periods or highly rehearsed materials, demonstrating that memory representations for unique events are reliably reinstated over longer timeframes that are meaningful in the context of real-world episodic memory.
A-ZIP53, a dominant negative reveals the molecular mechanism of heterodimerization between bZIP53, bZIP10 and bZIP25 involved in Arabidopsis seed maturation
Authors: Jain Prateek , Shah Koushik , Sharma Nishtha , Kaur Raminder , Singh Jagdeep , Vinson Charles , Rishi Vikas 
Published: October 2017

AbstractIn Arabidopsis, maturation phase, an intricate process in seed formation is tightly regulated by the DNA binding activity of protagonist basic leucine zipper 53 (bZIP53) transcription factor and its heterodimerizing partners, bZIP10 and bZIP25. Structural determinants responsible for heterodimerization specificity of bZIP53 are poorly understood. Analysis of amino acid sequences of three bZIPs does not identify interactions that may favor heterodimerization. Here, we describe a designed dominant negative termed A-ZIP53 that has a glutamic acid-rich amphipathic peptide sequence attached to N-terminal of bZIP53 leucine zipper. Circular dichroism (CD) and mass spectrometry studies with equimolar mixture of three bZIP proteins in pairs showed no heterodimer formation whereas A-ZIP53 interacted and formed stable heterodimers with bZIP53, bZIP10, and bZIP25. A-ZIP53 electrostatically mimics DNA and can overcome repulsion between basic DNA binding regions of three bZIP proteins. Gel shift experiments showed that A-ZIP53 can inhibit the DNA binding of three proteins. CD studies demonstrated the specificity of A-ZIP53 as it did not interact with bZIP39 and bZIP72. Transient co-transfections in Arabidopsis protoplasts showed that A-ZIP53 inhibited three bZIPs and their putative heterodimers-mediated transactivation of GUS reporter gene. Furthermore, four newly designed acidic extensions were evaluated for their ability to interact with three bZIPs.
MIF Inhibitor ISO-1 Protects Photoreceptors and Reduces Gliosis in Experimental Retinal Detachment
Authors: Kim Bongsu , Kusibati Rania , Heisler-Taylor Tyler , Mantopoulos Dimosthenis , Ding Jiaxi , Abdel-Rahman Mohamed H. , Satoskar Abhay R. , Godbout Jonathan P. , Bhattacharya Sanjoy K. , Cebulla Colleen M. 
Published: October 2017

AbstractPhotoreceptor death and retinal gliosis underlie the majority of vision threatening retinal diseases including retinal detachment (RD). Although the underlying pathobiology of vision limiting processes in RD is not fully understood, inflammation is known to play a critical role. We conducted an iTRAQ proteomic screen of up- and down-regulated proteins in a murine model of RD to identify potential targetable candidates. Macrophage migration inhibitory factor (MIF) was identified and evaluated for neurotoxic and pro-gliotic effects during RD. Systemic administration of the MIF inhibitor ISO-1 significantly blocked photoreceptor apoptosis, outer nuclear layer (ONL) thinning, and retinal gliosis. ISO-1 and MIF knockout (MIFKO) had greater accumulation of Müller glia pERK expression in the detached retina, suggesting that Müller survival pathways might underlie the neuroprotective response. Our data show the feasibility of the MIF-inhibitor ISO-1 to block pathological damage responses in retinal detachment and provide a rationale to explore MIF inhibition as a potential therapeutic option for RD.
Polyphyletic ancestry of expanding Patagonian Chinook salmon populations
Authors: Correa Cristian , Moran Paul 
Published: October 2017

AbstractChinook salmon native to North America are spreading through South America’s Patagonia and have become the most widespread anadromous salmon invasion ever documented. To better understand the colonization history and role that genetic diversity might have played in the founding and radiation of these new populations, we characterized ancestry and genetic diversity across latitude (39–48°S). Samples from four distant basins in Chile were genotyped for 13 microsatellite loci, and allocated, through probabilistic mixture models, to 148 potential donor populations in North America representing 46 distinct genetic lineages. Patagonian Chinook salmon clearly had a diverse and heterogeneous ancestry. Lineages from the Lower Columbia River were introduced for salmon open-ocean ranching in the late 1970s and 1980s, and were prevalent south of 43°S. In the north, however, a diverse assembly of lineages was found, associated with net-pen aquaculture during the 1990s. Finally, we showed that possible lineage admixture in the introduced range can confound allocations inferred from mixture models, a caveat previously overlooked in studies of this kind. While we documented high genetic and lineage diversity in expanding Patagonian populations, the degree to which diversity drives adaptive potential remains unclear. Our new understanding of diversity across latitude will guide future research.
Incidence and mortality of lung cancer: global trends and association with socioeconomic status
Authors: Wong Martin C. S. , Lao Xiang Qian , Ho Kin-Fai , Goggins William B. , Tse Shelly L. A. 
Published: October 2017

AbstractWe examined the correlation between lung cancer incidence/mortality and country-specific socioeconomic development, and evaluated its most recent global trends. We retrieved its age-standardized incidence rates from the GLOBOCAN database, and temporal patterns were assessed from global databases. We employed simple linear regression analysis to evaluate their correlations with Human Development Index (HDI) and Gross Domestic Product (GDP) per capita. The average annual percent changes (AAPC) of the trends were evaluated from join-point regression analysis. Country-specific HDI was strongly correlated with age-standardized incidence (r = 0.70) and mortality (r = 0.67), and to a lesser extent GDP (r = 0.24 to 0.55). Among men, 22 and 30 (out of 38 and 36) countries showed declining incidence and mortality trends, respectively; whilst among women, 19 and 16 countries showed increasing incidence and mortality trends, respectively. Among men, the AAPCs ranged from −2.8 to −0.6 (incidence) and −3.6 to −1.1 (mortality) in countries with declining trend, whereas among women the AAPC range was 0.4 to 8.9 (incidence) and 1 to 4.4 (mortality) in countries with increasing trend. Among women, Brazil, Spain and Cyprus had the greatest incidence increase, and all countries in Western, Southern and Eastern Europe reported increasing mortality. These findings highlighted the need for targeted preventive measures.