bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small room for compromise between oil palm cultivation and primate conservation in Africa
Authors: Strona Giovanni , Stringer Simon D. , Vieilledent Ghislain , Szantoi Zoltan , Garcia-Ulloa John , A. Wich Serge 
Published: August 2018

Significance
Although oil palm cultivation represents an important source of income for many tropical countries, its future expansion is a primary threat to tropical forests and biodiversity. In this context, and especially in regions where industrial palm oil production is still emerging, identifying “areas of compromise,” that is, areas with high productivity and low biodiversity importance, could be a unique opportunity to reconcile conservation and economic growth. We applied this approach to Africa, by combining data on oil palm suitability with primate distribution, diversity, and vulnerability. We found that such areas of compromise are very rare throughout the continent (0.13 Mha), and that large-scale expansion of oil palm cultivation in Africa will have unavoidable, negative effects on primates.
International approaches to developing healthy eating patterns for national dietary guidelines
Authors: Davis Karelyn A , Esslinger Krista , Elvidge Munene Lisa-Anne , St-Pierre Sylvie 
Published: August 2018

Abstract
As part of the revision of the 2007 Eating Well with Canada’s Food Guide, a literature scan on statistical modeling approaches used in developing healthy eating patterns for national food guides was conducted. The scan included relevant literature and online searches, primarily since the 2007 Canada’s Food Guide was released. Eight countries were identified as utilizing a statistical model or analysis to help inform their healthy eating pattern, defined as the amounts and types of food recommended, with many common characteristics noted. Detail on international modeling approaches is presented, highlighting similarities and differences as well as strengths and challenges.
SHP2 protects endothelial cell barrier through suppressing VE‐cadherin internalization regulated by MET‐ARF1
Authors: Zhang Jie , Huang Jiaqi , Qi Tongyun , Huang Yizhou , Lu Yuting , Zhan Tianwei , Gong Hui , Zhu Zhengyi , Shi Yueli , Zhou Jianhong , Yu Luyang , Zhang Xue , Cheng Hongqiang , Ke Yuehai 
Published: August 2018

ABSTRACTVascular endothelial (VE)–cadherin junctional localization is known to play a central role in vascular development, endothelial barrier integrity, and homeostasis. The sarcoma homology domain containing protein tyrosine phosphatase (SHP)2 has been shown to be involved in regulating endothelial barrier function; however, the mechanisms remain largely unknown. In this work SHP2 knockdown in an HUVEC monolayer increased VE‐cadherin internalization and endothelial barrier permeability. Loss of SHP2 specifically augmented the GTPase activity of ADP‐ribosylation factor (ARF)‐1. ARF1 knockdown or inhibition of its guanine nucleotide exchange factors (GEFs) markedly attenuated VE‐cadherin internalization and barrier hyperpermeability induced by SHP2 deficiency. SHP2 knockdown increased the total and phosphorylated levels of MET, whose activity was necessary for ARF1 activation and VE‐cadherin internalization. Furthermore, constitutive endothelium‐specific deletion of Shp2 in mice led to disrupted endothelial cell junctions, massive hemorrhage, and lethality in embryos. Induced and endothelium‐specific deletion of Shp2 in adult mice resulted in lung hyperpermeability. Inhibitors for ARF1–GEF or MET used in pregnant mice prevented the vascular leakage in endothelial Shp2‐deleted embryos. Together, our findings define a novel role of SHP2 in stabilizing junctional VE‐cadherin in the resting endothelial barrier through suppressing MET and ARF1 activation.—Zhang, J., Huang, J., Qi, T., Huang, Y., Lu, Y., Zhan, T., Gong, H., Zhu, Z., Shi, Y., Zhou, J., Yu, L., Zhang, X., Cheng, H., Ke, Y. SHP2 protects endothelial cell barrier through suppressing VE‐cadherin internalization regulated by MET‐ARF1. FASEB J. 33, 1124–1137 (2019). www.fasebj.org
Microbial Diversity in a Military Impacted Lagoon (Vieques, Puerto Rico) as Revealed by Metagenomics
Authors: Dávila-Santiago Lizbeth , DeLeón-Rodriguez Natasha , LaSanta-Pagán Katia , Hatt Janet K. , Kurt Zohre , Massol-Deyá Arturo , Konstantinidis Konstantinos T. 
Published: August 2018

AbstractThe Anones Lagoon, located in the island municipality of Vieques, Puerto Rico (PR), received extensive bombing during military practices by the US Navy for decades. After military activities ceased in 2003, the bombing range was designated as part of a larger Superfund site by US EPA. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0-5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PR’s capital city). Consistent with selection under low anthropogenic impacts, Guaniquilla exhibited the highest degree of diversity with lower frequency of genes related to xenobiotics metabolism among the three lagoons. Notably, a clear shift was observed in Anones, withEuryarchaeotabecoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique population genomes were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants. Collectively, these results provided new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and could serve as reference points to enhance bioremediation actions at this site and for assessing other similarly impacted sites.ImportanceThis study represents the first assessment of the benthic microbial community in the Anones Lagoon in Vieques, Puerto Rico after the impact of intense pollution by bombs and unconventional weapons during military training exercises. Evaluating the microbial diversity of Anones, represents an opportunity to assess the microbial succession patterns during the active process of natural attenuation of pollutants. The culture-independent techniques employed to study these environmental samples allowed the recovery of almost complete genomes of several abundant species that were likely involved in the biodegradation of pollutants and thus, represented species responding to the strong selection pressure posed by military activities. Further, our results showed that natural attenuation has proceeded to a great extend ten years after the cease of military activities.
Magic-BLAST, an accurate DNA and RNA-seq aligner for long and short reads
Authors: Boratyn Grzegorz M , Thierry-Mieg Jean , Thierry-Mieg Danielle , Busby Ben , Madden Thomas L 
Published: August 2018

ABSTRACTNext-generation sequencing technologies can produce tens of millions of reads, often paired-end, from transcripts or genomes. But few programs can align RNA on the genome and accurately discover introns, especially with long reads. We introduce Magic-BLAST, a new aligner based on ideas from the Magic pipeline. It uses innovative techniques that include the optimization of a spliced alignment score and selective masking during seed selection. We evaluate the performance of Magic-BLAST to accurately map short or long sequences and its ability to discover introns on real RNA-seq data sets from PacBio, Roche and Illumina runs, and on six benchmarks, and compare it to other popular aligners. Additionally, we look at alignments of human idealized RefSeq mRNA sequences perfectly matching the genome. We show that Magic-BLAST is the best at intron discovery over a wide range of conditions and the best at mapping reads longer than 250 bases, from any platform. It is versatile and robust to high levels of mismatches or extreme base composition, and reasonably fast. It can align reads to a BLAST database or a FASTA file. It can accept a FASTQ file as input or automatically retrieve an accession from the SRA repository at the NCBI.
TranslucentID: Detecting Individuals with High Confidence in Saturated DNA SNP Mixtures
Authors: Ricke Darrell O. , Watkins James , Fremont-Smith Philip , Boettcher Tara , Schwoebel Eric 
Published: August 2018

AbstractHigh throughput sequencing (HTS) of complex DNA mixtures with single nucleotide polymorphisms (SNPs) panels can identify multiple individuals in forensic DNA mixture samples. SNP mixture analysis relies upon the exclusion of non-contributing individuals with the subset of SNP loci with no detected minor alleles in the mixture. Few, if any, individuals are anticipated to be detectable in saturated mixtures by this mixture analysis approach because of the increased probability of matching random individuals. Being able to identify a subset of the contributors in saturated HTS SNP mixtures is valuable for forensic investigations. A desaturated mixture can be created by treating a set of SNPs with the lowest minor allele ratios as having no minor alleles. Leveraging differences in DNA contributor concentrations in saturated mixtures, we introduce TranslucentID for the identification of a subset of individuals with high confidence who contributed DNA to saturated mixtures by desaturating the mixtures.
Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program
Authors: Chagoyen Mónica , Poyatos Juan F 
Published: August 2018

AbstractEnvironmental or genetic perturbations lead to gene expression changes. While most analyses of these changes emphasize the presence of qualitative differences on just a few genes, we now know that changes are widespread. This large-scale variation has been linked to the exclusive influence of a global transcriptional program determined by the new physiological state of the cell. However, given the sophistication of eukaryotic regulation, we expect to have a complex architecture of specific control affecting this program. Here, we examine this architecture. Using data of Saccharomyces cerevisiae expression in different nutrient conditions, we first propose a five-sector genome partition, which integrates earlier models of resource allocation, as a framework to examine the deviations from the global control. In this scheme, we recognize invariant genes, whose regulation is dominated by physiology, specific genes, which substantially depart from it, and two additional classes that contain the frequently assumed growth-dependent genes. Whereas the invariant class shows a considerable absence of specific regulation, the rest is enriched by regulation at the level of transcription factors (TFs) and epigenetic modulators. We nevertheless find markedly different strategies in how these classes deviate. On the one hand, there are TFs that act in a unique way between partition constituents, and on the other, the action of chromatin modifiers is significantly diverse. The balance between regulatory strategies ultimately modulates the action of the general transcription machinery and therefore limits the possibility of establishing a unifying program of expression change at a genomic scale.
Chemical characterization, biological assessment and molecular docking studies of essential oil ofOcimum viridefor potential antimicrobial and anticancer activities
Authors: Bhagat Madhulika , Sangral Monica , Arya Khushboo , Rather Rafiq A. 
Published: August 2018

ABSTRACTOcimum viride(family: Lamiaceae) is a medicinally important aromatic plant that grows widely in north western Himalayan range of Indian subcontinent. Essentials oils (EOs) and purified aromatic compounds derived from plants of genusOcimumhave long been used in traditional system of medicine to treat various chronic disorders. In this study we made an attempt to assess the chemical composition of essential oil (EO) obtained fromOcimum viridefor potential antimicrobial and anticancer properties. Gas chromatography-mass spectrometry (GCMS) analysis revealed that EOs of aerial parts (leaves) ofOcimum viridecontain high amounts of oxygenated monoterpenes, thymol and gamma terpinene. Notably, thymol (~50%) and γ-terpinene (~18%) were identified as the most abundant components of the oil. EOs showed most prominent antibacterial effect againstBacillus subtilisandin silicomolecular docking analyses of antibacterial action against bacterial cell wall ofBacillus subtilisshowed interaction of thymol with Sec A protein ofBacillus subtilis(binding energy of-15 kcal/mol) with active site Lys284, Trp275, Leu269, Arg19, Glu277, pro270. While,in vitrocytotoxic effect of EO against six human cancer cell lines showed maximum effect with IC50value of ~0.034 ± 0.001μL/ mL against HT-29 colon cancer cell line. DNA fragmentation analysis and cell cycle analysis revealed that EO inhibits the growth of HT-29 colon cancer cells probably through induction of unrepairable DNA damage and subsequent cell death. Taken together, our results indicate that EO possesses potent antimicrobial and anticancer properties, and may find applications in bacterial growth inhibition and cancer therapeutics.
Spatial dynamics within and between brain functional domains: A hierarchical approach to study time-varying brain function
Authors: Iraji A. , Fu Z. , Damaraju E. , DeRamus T.P. , Lewis N. , Bustillo J.R. , Lenroot R.K. , Belger A. , Ford J.M. , McEwen S. , Mathalon D.H. , Mueller B.A. , Pearlson G.D. , Potkin S.G. , Preda A. , Turner J.A. , Vaidya J.G. , van Erp T.G.M. , Calhoun V.D. 
Published: August 2018

AbstractThe analysis of time-varying activity and connectivity patterns (i.e., the chronnectome) using resting-state magnetic resonance imaging has become an important part of ongoing neuroscience discussions. The majority of previous work has focused on variations of temporal coupling among fixed spatial nodes or transition of the dominant activity/connectivity pattern over time. Here, we introduce an approach to capture spatial dynamics within functional domains (FD), as well as temporal dynamics within and between FD. The approach models the brain as a hierarchical functional architecture with different levels of granularity, where lower levels have higher functional homogeneity and less dynamic behavior and higher levels have less homogeneity and more dynamic behavior. First, a high-order spatial independent component analysis is used to approximate functional units. A functional unit is a pattern of regions with very similar functional activity over time. Next, functional units are used to construct FDs. Finally, functional modules (FMs) are calculated from FDs, providing an overall view of brain dynamics. Results highlight the spatial fluidity within FDs, including a broad spectrum of changes in regional associations from strong coupling to complete decoupling. Moreover, FMs capture the dynamic interplay between FDs. Patients with schizophrenia show transient reductions in functional activity and state connectivity across several FDs, particularly the subcortical domain. Activity and connectivity differences convey unique information in many cases (e.g. the default mode) highlighting their complementarity information. The proposed hierarchical model to capture FD spatiotemporal variation provides new insight into the macroscale chronnectome and identifies changes hidden from existing approaches.
Multiple interfacial hydration of dihydro-sphingomyelin bilayer reported by the Laurdan fluorescence
Authors: Watanabe (N. W.) N. , Goto (Y. G) Y. , Suga (K. S.) K. , Nyholm (T. N.) T. , Slotte (J. P. S.) J. P. , Umakoshi (H. U.) H. 
Published: August 2018

AbstractThe hydration properties of the lipid bilayer interface are important for determining membrane characteristics. The hydration properties of different lipid bilayer species were evaluated using the solvent sensitive fluorescence probe, 6-lauroyl-2-dimethylamino naphthalene (Laurdan). Sphingolipids, D-erythro-N-palmitoyl-sphingosylphosphorylcholine (PSM) and D-erythro-N-palmitoyl-dihydrosphingomyelin (DHPSM) showed specific, interfacial hydration properties stemming from their intra- and intermolecular hydrogen bonds. As control, the bilayers of glycerophospholipids, such as 1-palmitoyl-2-palmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1-oleoyl-2-oleoyl-sn-glycero-3-phosphocholine (DOPC), were also evaluated. The fluorescence properties of Laurdan in sphingolipids indicated multiple excited states according to the results obtained from the emission spectra, fluorescence anisotropy, and the center of mass spectra during the decay time. Deconvolution of the Laurdan emission spectra into four components enabled us to identify the variety of hydration and the configurational states derived from intermolecular hydrogen bonding in sphingolipids. Particularly, the Laurdan in DHPSM revealed more hydrated properties compared to the case in PSM, even though DHPSM has a higher Tm than PSM. Since DHPSM forms hydrogen bonds with water molecules (in 2NH configurational functional groups) and the different flexibility among the head groups compared with PSM, which could modulate space to retain a high amount of water molecules. The careful analysis of Laurdan such as the deconvolution of emission spectra into four components performed in this study gives the important view for understanding the membrane hydration property.
Optimal wingtip device design for transport airplane
Authors: de Mattos Bento Silva , Komatsu Paulo Jiniche , Tomita Jesuíno Takachi 
Published: August 2018

Purpose
The present work aims to analyze the feasibility of wingtip device incorporation into transport airplane configurations considering many aspects such as performance, cost and environmental impact. A design framework encompassing optimization for wing-body configurations with and without winglets is described and application examples are presented and discussed.

Design/methodology/approach
modeFrontier, an object-oriented optimization design framework, was used to perform optimization tasks of configurations with wingtip devices. A full potential code with viscous effects correction was used to calculate the aerodynamic characteristics of the fuselage–wing–winglet configuration. MATLAB® was also used to perform some computations and was easily integrated into the modeFrontier frameworks. CFD analyses of transport airplanes configurations were also performed with Fluent and CFD++ codes.

Findings
Winglet provides considerable aerodynamic benefits regarding similar wings without winglets. Drag coefficient reduction in the order of 15 drag counts was achieved in the cruise condition. Winglet also provides a small boost in the clean-wing maximum lift coefficient. In addition, less fuel burn means fewer emissions and contributes toward preserving the environment.

Practical implications
More efficient transport airplanes, presenting considerable lower fuel burn.

Social implications
Among other contributions, wingtip devices reduce fuel burn, engine emissions and contribute to a longer engine lifespan, reducing direct operating costs. This way, they are in tune with a greener world.

Originality/value
The paper provides valuable wind-tunnel data of several winglet configurations, an impact of the incorporation of winglets on airplane design diagram and a direct comparison of two optimizations, one performed with winglets in the configuration and the other without winglets. These simulations showed that their Pareto fronts are clearly apart from each other, with the one from the configuration with winglets placed well above the other without winglets. The present simulations indicate that there are always aerodynamic benefits present regardless the skeptical statements of some engineers. that a well-designed wing does not need any winglet.
Informal payments for health care in Iran
Authors: Meskarpour Amiri Mohammad , Assari Abbas , Bahadori Mohammadkarim , Ravangard Ramin , Hosseini-Shokouh Sayyed Morteza 
Published: August 2018

Purpose
Reducing informal payments (IPs) for health services has always been a top priority for health policymakers all over the world. As the newest attempts to reduce IPs, Iran’s Government applied a set of reforms in the health care system in 2014 called “Health Sector Evolution Plan” (HSEP). The purpose of this paper is to investigate the prevalence and nature of IPs one year after implementing this plan.

Design/methodology/approach
This descriptive and cross-sectional study was a nationwide survey on Iran's health sector informal payments carried out in 2016. To do this, a sample of 1,112 Iranain households was selected from all over the country using a multistage cluster-stratified sampling method. The prevalence and nature of IPs were determined through conducting face-to-face interviews using a standard questionnaire.

Findings
One year after implementing the HSEP, about 27.7 percent of sampled Iranians had at least one experience of IPs for health services. The prevalences of compulsory and voluntary IPs were 21.4 and 11.5 percent, respectively. IPs were reported by 26.1 and 12.5 percent in the inpatient and outpatient services, respectively.

Originality/value
According to the results, compulsory IPs are still prevalent in both the outpatient and inpatient services of Iran’s health system and it seems that the HSEP has not been completely successful in achieving the goal of eradicating IPs. It can be said that the HSEP has been the first step toward eradicating IPs in Iran and should not be the last one. The study provides useful results of the prevalence and nature of IPs after implementing the HSEP, which should be considered in designing the next steps.
The effect of soft skills on French post-secondary graduates’ earnings
Authors: Albandea Ines , Giret Jean-François 
Published: August 2018

PurposeThe purpose of this paper is to construct soft-skill indicators and measure their effects on graduates’ earnings using survey data from a sample of master’s degree graduates in France.Design/methodology/approachThe authors use a quantile analysis to measure the effects of soft skills on income.FindingsCertain soft skills explain a proportion of the earnings of recent master’s graduates. In particular, they influence the highest salaries and are important for the most highly skilled jobs.Research limitations/implicationsMost of these soft skills are measured using declarative responses and may result from the feeling of having skills rather than actually possessing the skill. Moreover, this paper only looks at graduates who are employed, and a deficit in soft skills may be more penalising for job seekers.Social implicationsWhile some young people take advantage of soft skills early and benefit from them in the labour market, it is likely that it is even more important for those less endowed with these skills to further develop them before entering the labour market.Originality/valueThis research illustrates the heterogeneous nature of the skills that young post-secondary graduates acquire. French diplomas do not seem to homogenise all of the skills that young people develop through their academic and professional experiences.