bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of the Effect of Nd Content and Extrusion Process on Thermal Conductivity of Mg-Mn-Zn-Nd Alloys
Authors: Zhou Ying-Long , Liu Jie , Luo Dong-Mei , Chen Dong-Chu
Published: November 2018

The thermal conductivity of the Mg-1Mn-2Zn-xNd alloys (x = 0.5, 1.0, 1.5 wt. %) was studied for the potential applications of heat dissipation. The phase constituents were examined by X-ray diffraction analysis, and the microstructure was observed by light and scanning electron microscopes. The thermal conductivity of the Mg alloys was gauged at room temperature using laser flash method. The experimental results indicate that the thermal conductivity of both the cast and extruded Mg alloys decreases slowly with Nd content, and the extrusion process remarkably reduces the grain sizes and thermal conductivity of the Mg alloys. The thermal conductivity of cast Mg-1Mn-2Zn-xNd alloys exceeds the required critical value (100 W/(m·k)) for the cast Mg alloys. Among them, the cast Mg-1Mn-2Zn-1Nd alloy has great potential to be a good candidate of heat dissipation materials due to its good combination of thermal and mechanical properties.
Parametric Analysis of a Spiraled Shell: Learning from Nature’s Adaptable Structures
Authors: Chen Diana A. , Ross Brandon E. , Klotz Leidy E.
Published: November 2018

In our current building design philosophy, structural design is based on static predictions of the loads a building will need to withstand and the services it will need to provide. However, one study found that 60% of all buildings are demolished due to obsolescence. To combat our obsolescence-demolition culture, we turn to Nature for lessons about adaptable structural design. In this paper, we investigate the structural adaptability of the T. terebra spiraled turret shell through finite element modeling and parametric studies. The shell is able to change its structure over time to meet changing performance demands—a feat of adaptability that could transform our current infrastructure design. Modeling the shell’s growth process is an early and simple attempt at characterizing adaptability. As the mollusk deposits material overtime, its shell wall thickness changes, and its number of whorls increases. We designed parametric studies around these two modes of growth and investigated their effect on structural integrity and living convenience for the mollusk. By drawing parallels between the shell structure and human structures, we demonstrate connections between engineering challenges and Nature’s solutions. We encourage readers to consider biomimicry as a source of inspiration for their own quantitative studies for a more sustainable world.
A New CUK-Based Z-Source Inverter
Authors: Wang Baocheng , Tang Wei
Published: November 2018

This paper proposes a new three-switch single-phase Z-source inverter (ZSI) based on a CUK converter, which is named a CUK-based ZSI. This topology has characteristics of buck‒boost capability and dual grounding. In addition, the voltage gain of proposed inverter is higher than those of the single-phase quasi-Z-source and semi-Z-source inverters. Aside from that, a simple control method is presented to achieve the linear voltage gain. The operational principle of the proposed topology is described. Finally, a performance evaluation is carried out and the test results verify the effectiveness of the proposed solution.
Turbojet Engine Industrial Min–Max Controller Performance Improvement Using Fuzzy Norms
Authors: Jafari Soheil , Nikolaidis Theoklis
Published: November 2018

The Min–Max control strategy is the most widely used control algorithm for gas turbine engines. This strategy uses minimum and maximum mathematical functions to select the winner of different transient engine control loops at any instantaneous time. This paper examines the potential of using fuzzy T and S norms in Min–Max selection strategy to improve the performance of the controller and the gas turbine engine dynamic behavior. For this purpose, different union and intersection fuzzy norms are used in control strategy instead of using minimum and maximum functions to investigate the impact of this idea in gas turbine engines controller design and optimization. A turbojet engine with an industrial Min–Max control strategy including steady-state and transient control loops is selected as the case study. Different T and S norms including standard, bounded, Einstein, algebraic, and Hamacher norms are considered to be used in control strategy to select the best transient control loop for the engine. Performance indices are defined as pilot command tracking as well as the engine response time. The simulation results confirm that using Einstein and Hamacher norms in the Min–Max selection strategy could enhance the tracking capability and the response time to the pilot command respectively. The limitations of the proposed method are also discussed and potential solutions for dealing with these challenges are proposed. The methodological approach presented in this research could be considered for enhancement of control systems in different types of gas turbine engines from practical point of view.
Downlink Spectral Efficiency Analysis in Distributed Massive MIMO with Phase Noise
Authors: Lv Qian , Li Jiamin , Zhu Pengcheng , Wang Dongming , You Xiaohu
Published: November 2018

To achieve the advantages provided by massive multiple-input multiple-output (MIMO), a large number of antennas need to be deployed at the base station. However, for the reason of cost, inexpensive hardwares are employed in the realistic scenario, which makes the system distorted by hardware impairments. Hence, in this paper, we analyze the downlink spectral efficiency in distributed massive MIMO with phase noise and amplified thermal noise. We provide an effective channel model considering large-scale fading, small-scale fast fading and phase noise. Based on the model, the estimated channel state information (CSI) is obtained during the pilot phase. Under the imperfect CSI, the closed-form expressions of downlink achievable rates with maximum ratio transmission (MRT) and zero-forcing (ZF) precoders in distributed massive MIMO are derived. Furthermore, we also give the user ultimate achievable rates when the number of antennas tends to infinity with both precoders. Based on these expressions, we analyze the impacts of phase noise on the spectral efficiency. It can be concluded that the same limit rate is achieved with both precoders when phase noise is present, and phase noise limits the spectral efficiency. Numerical results show that ZF outdoes MRT precoder in spectral efficiency and ZF precoder is more affected by phase noise.
A Novel Synchronization Technique for Wireless Power Transfer Systems
Authors: Liu Xin , Jin Nan , Yang Xijun , Wang Tianfeng , Hashmi Khurram , Tang Houjun
Published: November 2018

Recently, wireless power transfer (WPT) systems with active receivers have been proposed for conduction loss reduction, bidirectional power transfer and efficiency improvement. However, the synchronization of WPT systems is complex in nature with the selection of high operating frequencies. Without proper synchronization, power oscillations appear and the system can become unstable. In this paper, a detailed analysis of different WPT systems is presented and the essence of the synchronization technique is derived as being composed of two functions: independent frequency locking and reference phase calibration. The voltage across the receiver-side compensation capacitor is divided and utilized for frequency locking, whereas the reference phase calibration is realized through software code. The proposed method is effective and easy to implement, with a lower overall cost due to its simplicity. The technique can work effectively at high frequency and withstand large variations of operating frequency, load and mutual inductance. In addition, it can address the synchronization problem of multiple active receiver WPT systems with and without cross coupling among the receiving coils. Theoretical analysis and experimental results validate the proposed technique.
Hardware Considerations for Tensor Implementation and Analysis Using the Field Programmable Gate Array
Authors: Grout Ian , Mullin Lenore
Published: November 2018

In today’s complex embedded systems targeting internet of things (IoT) applications, there is a greater need for embedded digital signal processing algorithms that can effectively and efficiently process complex data sets. A typical application considered is for use in supervised and unsupervised machine learning systems. With the move towards lower power, portable, and embedded hardware-software platforms that meet the current and future needs for such applications, there is a requirement on the design and development communities to consider different approaches to design realization and implementation. Typical approaches are based on software programmed processors that run the required algorithms on a software operating system. Whilst such approaches are well supported, they can lead to solutions that are not necessarily optimized for a particular problem. A consideration of different approaches to realize a working system is therefore required, and hardware based designs rather than software based designs can provide performance benefits in terms of power consumption and processing speed. In this paper, consideration is given to utilizing the field programmable gate array (FPGA) to implement a combined inner and outer product algorithm in hardware that utilizes the available hardware resources within the FPGA. These products form the basis of tensor analysis operations that underlie the data processing algorithms in many machine learning systems.
An All-Region State-of-Charge Estimator Based on Global Particle Swarm Optimization and Improved Extended Kalman Filter for Lithium-Ion Batteries
Authors: Lai Xin , Yi Wei , Zheng Yuejiu , Zhou Long
Published: November 2018

In this paper, a novel model parameter identification method and a state-of-charge (SOC) estimator for lithium-ion batteries (LIBs) are proposed to improve the global accuracy of SOC estimation in the all SOC range (0–100%). Firstly, a subregion optimization method based on particle swarm optimization is developed to find the optimal model parameters of LIBs in each subregion, and the optimal number of subregions is investigated from the perspective of accuracy and computation time. Then, to solve the problem of a low accuracy of SOC estimation caused by large model error in the low SOC range, an improved extended Kalman filter (IEKF) algorithm with variable noise covariance is proposed. Finally, the effectiveness of the proposed methods are verified by experiments on two kinds of batteries under three working cycles, and case studies show that the proposed IEKF has better accuracy and robustness than the traditional extended Kalman filter (EKF) in the all SOC range.
Cloning and Expression of the Chitinase Encoded by ChiKJ406136 from Streptomyces Sampsonii (Millard & Burr) Waksman KJ40 and Its Antifungal Effect
Authors: Li Shujiang , Zhang Boyang , Zhu Hanmingyue , Zhu Tianhui
Published: November 2018

The present study demonstrated that the chitinase gene ChiKJ406136 of Streptomyces sampsonii (Millard & Burr) Waksman KJ40 could be cloned using a PCR protocol and expressed in Escherichia coli (Migula) Castellani & Chalmers BL21 (DE3), and the recombinant protein had antifungal effect on four forest pathogens (Cylindrocladium scoparium Morgan, Cryphonectria parasitica (Murrill) Barr, Neofusicoccum parvum Crous, and Fusarium oxysporum Schl.) and also had the biological control effects on Eucalyptus robusta Smith leaf blight, Castanea mollissima BL. blight, Juglans regia L. blight and J. regia root rot. The results showed that ChiKJ406136 was efficiently expressed and a 48 kilodalton (kDa) recombinant protein was obtained. No significant change in protein production was observed in the presence of different concentrations of IPTG (isopropyl-b-D-thio-galactoside). The purified protein yield was greatest in the 150 mmol/L imidazole elution fraction, and the chitinase activities of the crude protein and purified protein solutions were 0.045 and 0.033 U/mL, respectively. The antifungal effects indicated that mycelial cells of the four fungi were disrupted, and the control effects of the chitinase on four forest diseases showed significant differences among the undiluted 10- and 20-fold dilutions and the control. The undiluted solution exhibited best effect. The results of this study provide a foundation for the use of S. sampsonii as a biocontrol agent and provides a new source for the chitinase gene, providing a theoretical basis for its application.
Embryo Development, Seed Germination, and the Kind of Dormancy of Ginkgo biloba L.
Authors: Feng Jing , Shen Yongbao , Shi Fenghou , Li Chengzhong
Published: November 2018

The embryos of Ginkgo biloba L. are generally reported to undergo after-ripening and be underdeveloped at the time of dispersal, which suggests that the seeds have morphological dormancy (MD) or morphological physiological dormancy (MPD). The aim of this work is to determine whether embryos of a G. biloba population are well-developed at the time of seed dispersal, and whether the seeds are dormant or not. From 8 September, which was the 140th day after flowering (140 DAF), seeds were collected separately from trees (T) and the ground (G) every 10 days until 7 December (230 DAF), resulting in a total of 10 samples. The changes in vertical diameter, transverse diameter, fresh weight, water content, and embryo length during seed development were measured. Simultaneously, the effects of different temperatures (15, 25, 30, and 35 °C) on seed germination, dormancy, and germination characteristics of G. biloba seeds were studied. Results showed that the embryos of G. biloba seeds were well developed and had no morphological dormancy. On 18 September (150 DAF), embryos were visible with a length of 2.5 mm. On 7 December (230 DAF), at the time of seed dispersal, their length was 17.1 mm. The germination percentage of the isolated embryos and seeds increased as the delay in seed collection increased, but there was no significant difference between T and G (p > 0.05). On 7 December (230 DAF), the germination of the isolated embryos reached 98%, indicating that the embryos were nondormant. Without pretreatment, seed germination was 82.57% within four weeks at 25 °C. Furthermore, the germination test at different temperatures showed the highest germination percentage at 30 °C (84.82%). Obviously, the G. biloba seeds were nondormant. The mean germination time (MGT) of the seeds at 30 and 35 °C was significantly lower than that of the seeds at 15 and 25 °C, and the speed of germination (SG) was significantly higher than that of the seeds at 15 and 25 °C. Although there was no significant difference in the seed-germination percentage between 30 and 35 °C, a portion of the seeds (9.5%) rotted at 35 °C. Therefore, 30 °C was the most favorable germination temperature for G. biloba seeds. This is the first study that reports G. biloba seeds with no dormancy.
LiDAR-Based Regional Inventory of Tall Trees—Wellington, New Zealand
Authors: Zörner Jan , Dymond John R. , Shepherd James D. , Wiser Susan K. , Jolly Ben
Published: November 2018

Indigenous forests cover 23.9% of New Zealand’s land area and provide highly valued ecosystem services, including climate regulation, habitat for native biota, regulation of soil erosion and recreation. Despite their importance, information on the number of tall trees and the tree height distribution across different forest classes is scarce. We present the first region-wide spatial inventory of tall trees (>30 m) based on airborne LiDAR (Light Detection and Ranging) measurements in New Zealand—covering the Greater Wellington region. This region has 159,000 ha of indigenous forest, primarily on steep mountainous land. We implement a high-performance tree mapping algorithm that uses local maxima in a canopy height model (CHM) as initial tree locations and accurately identifies the tree top positions by combining a raster-based tree crown delineation approach with information from the digital surface and terrain models. Our algorithm includes a check and correction for over-estimated heights of trees on very steep terrain such as on cliff edges. The number of tall trees (>30 m) occurring in indigenous forest in the Wellington Region is estimated to be 286,041 (±1%) and the number of giant trees (>40 m tall) is estimated to be 7340 (±1%). Stereo-analysis of aerial photographs was used to determine the accuracy of the automated tree mapping. The giant trees are mainly in the beech-broadleaved-podocarp and broadleaved-podocarp forests, with density being 0.04 and 0.12 (trees per hectare) respectively. The inventory of tall trees in the Wellington Region established here improves the characterization of indigenous forests for management and provides a useful baseline for long-term monitoring of forest conditions. Our tree top detection scheme provides a simple and fast method to accurately map overstory trees in flat as well as mountainous areas and can be directly applied to improve existing and build new tree inventories in regions where LiDAR data is available.
Assessing Spatial Equity and Accessibility of Public Green Spaces in Aleppo City, Syria
Authors: Almohamad Hussein , Knaack Anna Lisa , Habib Badriah Mohammed
Published: November 2018

This paper examines the accessibility of urban green spaces within the Syrian city of Aleppo before the civil war using an environmental justice approach by indicating the current state of the parameters proximity and quantity in relation to the socioeconomic status of the inhabitants. Therefore, we conducted the average nearest neighbour analysis, facilities over and under coverage analysis, network analysis and a one-way analysis of variance (ANOVA) test followed by a post-hoc Tukey honestly significant difference (HSD) test. The findings clearly indicate that the spatial pattern of the distribution of public parks facilities was significantly clustered (p-value < 0.0001), with a z-score of −16.4. Several neighbourhoods within the western and central parts of the city were identified to have a higher density of facilities, while the majority of the neighbourhoods located in the marginal parts in eastern Aleppo (low income) lack access to urban green spaces. The hierarchy-wise analysis reveals a strong deficit of urban green spaces at lower hierarchies, for example pocket parks and neighbourhood parks, while access to quarter parks and district parks is high. The urban green spaces at higher hierarchies are located in high and middle socioeconomic status areas. Regarding social segregation in park distribution and their accessibility, the data showed that high income neighbourhoods enjoy a significantly higher percentage of park facilities. The approach presented in this paper offers a generic method for the future development of public green spaces for balanced and sustainable planning.
Assessing the Long-Term Ecosystem Productivity Benefits and Potential Impacts of Forests Re-Established on a Mine Tailings Site
Authors: Metsaranta Juha M. , Beauchemin Suzanne , Langley Sean , Tisch Bryan , Dale Phyllis
Published: November 2018

Restoring sites disturbed by industrial activity to a forested condition can ensure the continued provision of economic and ecosystem services from these areas. Impounded mine tailings are particularly challenging sites, and positive benefits of establishing trees must be balanced against risks associated with metal contamination, ongoing tailings stability, and the possibility of acid mine drainage. We used a hybrid biometric modelling approach based on dendrochronological reconstruction to retrospectively (1980–2015) quantify productivity and carbon dynamics of pine plantations growing on impounded mine tailings at the Vale waste management facility near Sudbury, Canada. Historical reclamation practices had remediated conditions sufficiently to allow conifer plantation establishment in the late 1970s. The revegetated sites were highly productive, when compared to reference conditions based on site index, wood volume growth, and ecosystem production, congruent with other studies showing that forests on revegetated post mining sites can be highly productive. However, metal concentrations in the forest floor were high, and further research is warranted to evaluate ecosystem impacts. Due to the requirement for energy-intensive inputs, we estimated that it took 12 years or more to recover the emissions associated with the revegetation process through C accumulated in biomass and soil at the revegetated sites.
The Yeast Torulaspora delbrueckii: An Interesting But Difficult-To-Use Tool for Winemaking
Authors: Ramírez Manuel , Velázquez Rocío
Published: November 2018

Torulaspora delbrueckii is probably the non-Saccharomyces yeast that is currently most used for winemaking. Multiple advantages have been claimed for it relative to conventional S. cerevisiae strains. However, many of these claimed advantages are based on results in different research studies that are contradictory or non-reproducible. The easiest way to explain these discrepancies is to attribute them to the possible differences in the behaviour of the different strains of this yeast that have been used in different investigations. There is much less knowledge of the physiology, genetics, and biotechnological properties of this yeast than of the conventional yeast S. cerevisiae. Therefore, it is possible that the different results that have been found in the literature are due to the variable or unpredictable behaviour of T. delbrueckii, which may depend on the environmental conditions during wine fermentation. The present review focusses on the analysis of this variable behaviour of T. delbrueckii in the elaboration of different wine types, with special emphasis on the latest proposals for industrial uses of this yeast.
Live Fuel Moisture Content: The ‘Pea Under the Mattress’ of Fire Spread Rate Modeling?
Authors: Rossa Carlos G. , Fernandes Paulo M.
Published: November 2018

Currently, there is a dispute on whether live fuel moisture content (FMC) should be accounted for when predicting a real-world fire-spread rate (RoS). The laboratory and field data results are conflicting: laboratory trials show a significant effect of live FMC on RoS, which has not been convincingly detected in the field. It has been suggested that the lack of influence of live FMC on RoS might arise from differences in the ignition of dead and live fuels: flammability trials using live leaves subjected to high heat fluxes (80–140 kW m−2) show that ignition occurs before all of the moisture is vaporized. We analyze evidence from recent studies, and hypothesize that differences in the ignition mechanisms between dead and live fuels do not preclude the use of overall fine FMC for attaining acceptable RoS predictions. We refer to a simple theory that consists of two connected hypotheses to explain why the effect of live FMC on field fires RoS has remained elusive so far: H1, live tree foliage FMC remains fairly constant over the year; and H2, the seasonal variation of live shrubs’ FMC correlates with the average dead FMC. As a result, the effect of live FMC is not easily detected by statistical analysis.
miRNA Mediated Noise Making of 3′UTR Mutations in Cancer
Authors: Wu Wei , Wu Lingxiang , Zhu Mengyan , Wang Ziyu , Wu Min , Li Pengping , Nie Yumin , Lin Xue , Hu Jie , Eskilsson Eskil , Wang Qh , Shao Jiaofang , Lyu Sali
Published: November 2018

Somatic mutations in 3′-untranslated regions (3′UTR) do not alter amino acids and are considered to be silent in cancers. We found that such mutations can promote tumor progression by altering microRNA (miRNA) targeting efficiency and consequently affecting miRNA–mRNA interactions. We identified 67,159 somatic mutations located in the 3′UTRs of messenger RNAs (mRNAs) which can alter miRNA–mRNA interactions (functional somatic mutations, funcMutations), and 69.3% of these funcMutations (the degree of energy change > 12 kcal/mol) were identified to significantly promote loss of miRNA-mRNA binding. By integrating mRNA expression profiles of 21 cancer types, we found that the expression of target genes was positively correlated with the loss of absolute affinity level and negatively correlated with the gain of absolute affinity level. Functional enrichment analysis revealed that genes carrying funcMutations were significantly enriched in the MAPK and WNT signaling pathways, and analysis of regulatory modules identified eighteen miRNA modules involved with similar cellular functions. Our findings elucidate a complex relationship between miRNA, mRNA, and mutations, and suggest that 3′UTR mutations may play an important role in tumor development.
Dissecting the Contribution of Release Factor Interactions to Amber Stop Codon Reassignment Efficiencies of the Methanocaldococcus jannaschii Orthogonal Pair
Authors: Schwark David G. , Schmitt Margaret A. , Fisk John D.
Published: November 2018

Non-canonical amino acids (ncAAs) are finding increasing use in basic biochemical studies and biomedical applications. The efficiency of ncAA incorporation is highly variable, as a result of competing system composition and codon context effects. The relative quantitative contribution of the multiple factors affecting incorporation efficiency are largely unknown. This manuscript describes the use of green fluorescent protein (GFP) reporters to quantify the efficiency of amber codon reassignment using the Methanocaldococcus jannaschii orthogonal pair system, commonly employed for ncAA incorporation, and quantify the contribution of release factor 1 (RF1) to the overall efficiency of amino acid incorporation. The efficiencies of amber codon reassignments were quantified at eight positions in GFP and evaluated in multiple combinations. The quantitative contribution of RF1 competition to reassignment efficiency was evaluated through comparisons of amber codon suppression efficiencies in normal and genomically recoded Escherichia coli strains. Measured amber stop codon reassignment efficiencies for eight single stop codon GFP variants ranged from 51 to 117% in E. coli DH10B and 76 to 104% in the RF1 deleted E. coli C321.ΔA.exp. Evaluation of efficiency changes in specific sequence contexts in the presence and absence of RF1 suggested that RF1 specifically interacts with +4 Cs and that the RF1 interactions contributed approximately half of the observed sequence context-dependent variation in measured reassignment efficiency. Evaluation of multisite suppression efficiencies suggests that increasing demand for translation system components limits multisite incorporation in cells with competing RF1.
Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes
Authors: Wang Shuaibin , Song Qingwei , Li Shanshan , Hu Zhigang , Dong Gangqiang , Song Chi , Huang Hongwen , Liu Yifei
Published: November 2018

Diversity in structure and organization is one of the main features of angiosperm mitochondrial genomes (mitogenomes). The ultra-long reads of Oxford Nanopore Technology (ONT) provide an opportunity to obtain a complete mitogenome and investigate the structural variation in unprecedented detail. In this study, we compared mitogenome assembly methods using Illumina and/or ONT sequencing data and obtained the complete mitogenome (208 kb) of Chrysanthemum nankingense based on the hybrid assembly method. The mitogenome encoded 19 transfer RNA genes, three ribosomal RNA genes, and 34 protein-coding genes with 21 group II introns disrupting eight intron-contained genes. A total of seven medium repeats were related to homologous recombination at different frequencies as supported by the long ONT reads. Subsequently, we investigated the variations in gene content and constitution of 28 near-complete mitogenomes from Asteraceae. A total of six protein-coding genes were missing in all Asteraceae mitogenomes, while four other genes were not detected in some lineages. The core fragments (~88 kb) of the Asteraceae mitogenomes had a higher GC content (~46.7%) than the variable and specific fragments. The phylogenetic topology based on the core fragments of the Asteraceae mitogenomes was highly consistent with the topologies obtained from the corresponding plastid datasets. Our results highlighted the advantages of the complete assembly of the C. nankingense mitogenome and the investigation of its structural variation based on ONT sequencing data. Moreover, the method based on local collinear blocks of the mitogenomes could achieve the alignment of highly rearrangeable and variable plant mitogenomes as well as construct a robust phylogenetic topology.
Unintentional Genomic Changes Endow Cupriavidus metallidurans with an Augmented Heavy-Metal Resistance
Authors: Millacura Felipe A. , Janssen Paul J. , Monsieurs Pieter , Janssen Ann , Provoost Ann , Van Houdt Rob , Rojas Luis A.
Published: November 2018

For the past three decades, Cupriavidus metallidurans has been one of the major model organisms for bacterial tolerance to heavy metals. Its type strain CH34 contains at least 24 gene clusters distributed over four replicons, allowing for intricate and multilayered metal responses. To gain organic mercury resistance in CH34, broad-spectrum mer genes were introduced in a previous work via conjugation of the IncP-1β plasmid pTP6. However, we recently noted that this CH34-derived strain, MSR33, unexpectedly showed an increased resistance to other metals (i.e., Co2+, Ni2+, and Cd2+). To thoroughly investigate this phenomenon, we resequenced the entire genome of MSR33 and compared its DNA sequence and basal gene expression profile to those of its parental strain CH34. Genome comparison identified 11 insertions or deletions (INDELs) and nine single nucleotide polymorphisms (SNPs), whereas transcriptomic analysis displayed 107 differentially expressed genes. Sequence data implicated the transposition of IS1088 in higher Co2+ and Ni2+ resistances and altered gene expression, although the precise mechanisms of the augmented Cd2+ resistance in MSR33 remains elusive. Our work indicates that conjugation procedures involving large complex genomes and extensive mobilomes may pose a considerable risk toward the introduction of unwanted, undocumented genetic changes. Special efforts are needed for the applied use and further development of small nonconjugative broad-host plasmid vectors, ideally involving CRISPR-related and advanced biosynthetic technologies.
The Emerging Role of Epitranscriptomics in Cancer: Focus on Urological Tumors
Authors: Lobo João , Barros-Silva Daniela , Henrique Rui , Jerónimo Carmen
Published: November 2018

Epitranscriptomics has gained ground in recent years, especially after the advent of techniques for accurately studying these mechanisms. Among all modifications occurring in RNA molecules, N6-methyladenosine (m6A) is the most frequent, especially among mRNAs. m6A has been demonstrated to play important roles in many physiological processes and several disease states, including various cancer models (from solid to liquid tumors). Tumor cells’ epitranscriptome is indeed disrupted in a way to promote cancer-prone features, by means of up/downregulating m6A-related players: the so-called writers, readers and erasers. These proteins modulate m6A establishment, removal and determine mRNAs fate, acting in a context-dependent manner, so that a single player may act as an oncogenic signal in one tumor model (methyltransferase like 3 (METTL3) in lung cancer) and as a tumor suppressor in another context (METTL3 in glioblastoma). Despite recent advances, however, little attention has been directed towards urological cancer. By means of a thorough analysis of the publicly available TCGA (The Cancer Genome Atlas) database, we disclosed the most relevant players in four major urogenital neoplasms—kidney, bladder, prostate and testicular cancer—for prognostic, subtype discrimination and survival purposes. In all tumor models assessed, the most promising player was shown to be Vir like m6A methyltransferase associated (VIRMA), which could constitute a potential target for personalized therapies.
Large-Scale Analyses of Site-Specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure, and Functional Domains
Authors: Ahrens Joseph B. , Rahaman Jordon , Siltberg-Liberles Jessica
Published: November 2018

Various structural and functional constraints govern the evolution of protein sequences. As a result, the relative rates of amino acid replacement among sites within a protein can vary significantly. Previous large-scale work on Metazoan (Animal) protein sequence alignments indicated that amino acid replacement rates are partially driven by a complex interaction among three factors: intrinsic disorder propensity; secondary structure; and functional domain involvement. Here, we use sequence-based predictors to evaluate the effects of these factors on site-specific sequence evolutionary rates within four eukaryotic lineages: Metazoans; Plants; Saccharomycete Fungi; and Alveolate Protists. Our results show broad, consistent trends across all four Eukaryote groups. In all four lineages, there is a significant increase in amino acid replacement rates when comparing: (i) disordered vs. ordered sites; (ii) random coil sites vs. sites in secondary structures; and (iii) inter-domain linker sites vs. sites in functional domains. Additionally, within Metazoans, Plants, and Saccharomycetes, there is a strong confounding interaction between intrinsic disorder and secondary structure—alignment sites exhibiting both high disorder propensity and involvement in secondary structures have very low average rates of sequence evolution. Analysis of gene ontology (GO) terms revealed that in all four lineages, a high fraction of sequences containing these conserved, disordered-structured sites are involved in nucleic acid binding. We also observe notable differences in the statistical trends of Alveolates, where intrinsically disordered sites are more variable than in other Eukaryotes and the statistical interactions between disorder and other factors are less pronounced.
Rare Biosphere Archaea Assimilate Acetate in Precambrian Terrestrial Subsurface at 2.2 km Depth
Authors: Nuppunen-Puputti Maija , Purkamo Lotta , Kietäväinen Riikka , Nyyssönen Mari , Itävaara Merja , Ahonen Lasse , Kukkonen Ilmo , Bomberg Malin
Published: November 2018

The deep biosphere contains a large portion of the total microbial communities on Earth, but little is known about the carbon sources that support deep life. In this study, we used Stable Isotope Probing (SIP) and high throughput amplicon sequencing to identify the acetate assimilating microbial communities at 2260 m depth in the bedrock of Outokumpu, Finland. The long-term and short-term effects of acetate on the microbial communities were assessed by DNA-targeted SIP and RNA targeted cell activation. The microbial communities reacted within hours to the amended acetate. Archaeal taxa representing the rare biosphere at 2260 m depth were identified and linked to the cycling of acetate, and were shown to have an impact on the functions and activity of the microbial communities in general through small key carbon compounds. The major archaeal lineages identified to assimilate acetate and metabolites derived from the labelled acetate were Methanosarcina spp., Methanococcus spp., Methanolobus spp., and unclassified Methanosarcinaceae. These archaea have previously been detected in the Outokumpu deep subsurface as minor groups. Nevertheless, their involvement in the assimilation of acetate and secretion of metabolites derived from acetate indicated an important role in the supporting of the whole community in the deep subsurface, where carbon sources are limited.
Dehydration and Malnutrition in Residential Care: Recommendations for Strategies for Improving Practice Derived from a Scoping Review of Existing Policies and Guidelines
Authors: Bunn Diane , Hooper Lee , Welch Ailsa
Published: November 2018

Preventing malnutrition and dehydration in older care home residents is a complex task, with both conditions remaining prevalent, despite numerous guidelines spanning several decades. This policy-mapping scoping review used snowballing search methods to locate publicly-available policies, reports and best practice guidelines relating to hydration and nutrition in UK residential care homes, to describe the existing knowledge base and pinpoint gaps in practice, interpretation and further investigation. The findings were synthesised narratively to identify solutions. Strategies for improvements to nutritional and hydration care include the development of age and population-specific nutrient and fluid intake guidelines, statutory regulation, contractual obligations for commissioners, appropriate menu-planning, the implementation and auditing of care, acknowledgment of residents’ eating and drinking experiences, effective screening, monitoring and treatment and staff training. The considerable body of existing knowledge is failing to influence practice, relating to translational issues of implementing knowledge into care at the point of delivery, and this is where future research and actions should focus.
Postcards from Chile and Images from an Archive: Lighting the Nitrate of the 1973 Coup
Authors: Purbrick Louise
Published: November 2018

This article examines a mass produced postcard image as a picture of conflict. It considers the postcard as a Benjaminian ‘prismatic fringe’ through which an archive can be viewed, wherein documents of the British trade in Chilean nitrate are juxtaposed with those of General Pinochet’s 1973 military coup. The archive itself is explored as a site of loss and its postcard, an unvarying idealisation, as a particularly problematic but powerful image that renders conflict out of sight.
The Agency of the Displaced? Roman Expansion, Environmental Forces, and the Occupation of Marginal Landscapes in Ancient Italy
Authors: Perego Elisa , Scopacasa Rafael
Published: November 2018

This article approaches the agency of displaced people through material evidence from the distant past. It seeks to construct a narrative of displacement where the key players include human as well as non-human agents—namely, the environment into which people move, and the socio-political and environmental context of displacement. Our case-study from ancient Italy involves potentially marginalized people who moved into agriculturally challenging lands in Daunia (one of the most drought-prone areas of the Mediterranean) during the Roman conquest (late fourth-early second centuries BCE). We discuss how the interplay between socio-political and environmental forces may have shaped the agency of subaltern social groups on the move, and the outcomes of this process. Ultimately, this analysis can contribute towards a framework for the archaeological study of marginality and mobility/displacement—while addressing potential limitations in evidence and methods.
RNA Helicase Mediates Competitive Fitness of Listeria monocytogenes on the Surface of Cantaloupe
Authors: Price Robert , Parsons Cameron , Kathariou Sophia
Published: November 2018

Listeria monocytogenes is a foodborne pathogen that is implicated in numerous outbreaks of disease (listeriosis) via fresh produce. The genetic features of L. monocytogenes that allow adherence and growth on produce remain largely uncharacterized. In this study, two non-motile transposon mutants were characterized for attachment, growth, and survival on the surface of cantaloupe rind. One of the mutants, L1E4, harbored a single transposon insertion in a DEAD-box RNA helicase gene (lmo0866 homolog), while the other, M1A5, harbored an insertion in a gene from a flagellum biosynthesis and chemotaxis gene cluster (lmo0694 homolog). When inoculated alone, neither mutant was significantly impaired in growth or survival on the surface of cantaloupe at either 25 or 37 °C. However, when co-inoculated with the wildtype parental strain, the RNA helicase mutant L1E4 had a clear competitive disadvantage, while the relative fitness of M1A5 was not noticeably impacted. Genetic complementation of L1E4 with the intact RNA helicase gene restored relative fitness on cantaloupe. The findings suggest that the DEAD-box RNA helicase encoded by the lmo0866 homolog is critical for relative fitness of L. monocytogenes on cantaloupe. Mutant L1E4 was pleiotropic, being not only non-motile but also cold-sensitive and with reduced hemolytic activity, warranting further studies to elucidate the role of this helicase in the competitive fitness of L. monocytogenes on produce.
Aircraft-Assisted Pilot Suicides in the General Aviation Increased for One-Year Period after 11 September 2001 Attack in the United States
Authors: Vuorio Alpo , Laukkala Tanja , Junttila Ilkka , Bor Robert , Budowle Bruce , Pukkala Eero , Navathe Pooshan , Sajantila Antti
Published: November 2018

Pilot aircraft-assisted suicides (AAS) are rare, and there is limited understanding of copycat phenomenon among aviators. The aim of this study was to evaluate the possible effect the 11 September 2001, terrorist attacks had on pilot AASs in the U.S. Fatal aviation accidents in the National Transportation Safety Board (NTSB) database were searched using the following search words: “suicide”, “murder-suicide” and “homicide-suicide”. The timeline between 11 September 1996, and 11 September 2004, was analyzed. Only those accidents in which NTSB judged that the cause of the accident was suicide were included in the final analysis. The relative risk (RR) of the pilot AASs in all fatal accidents in the U.S. was calculated in order to compare the one, two, and three-year periods after the September 11 terrorist attacks with five years preceding the event. The RR of a fatal general aviation aircraft accident being due to pilot suicide was 3.68-fold (95% confidence interval 1.04–12.98) during the first year after 11 September 2001, but there was not a statistically significant increase in the later years. This study showed an association, albeit not determinate causal effect, of a very specific series of simultaneous terrorist murder-suicides with subsequent pilot AASs.
Factors Associated with Cervical Cancer Screening among Married Female Immigrants with Korean Husbands in South Korea
Authors: Chang Ha Kyun , Seo Sang-Soo , Myong Jun-Pyo , Koo Jung-Wan , Jeong Jinhee
Published: November 2018

Background. The purpose of this study was to identify factors associated with the national cervical cancer screening behaviors of married female immigrants living in South Korea. Methods. The present study dataset was collected by the National Health Insurance Services in 2014–2015. A final study population of 15,935 was considered eligible for inclusion in this study if they met the criteria for participation in the national cervical cancer screening program in 2014–2015. Results. Of the 15,935 subjects, 7837 (49%) participated in cervical cancer screening. Based on the results of the logistic regression analysis of the association between cervical cancer screening behaviors and related factors, the odds ratio (OR) for participation in cervical cancer screening among individuals older than 50 years was the highest (OR: 2.13; 95% confidence interval (CI): 1.82–2.51), and the OR increased as their duration of stay in South Korea decreased. The OR of Chinese women for cervical cancer screening participation was higher than that of non-Chinese women (OR: 1.83; 95% CI: 1.69–1.99). The OR value was 29.4 (95% CI: 25.9–33.3) among those who participated in the general health screening compared with those who did not participate. Conclusions. To improve awareness about cervical cancer screening and reduce disparities in access to healthcare, appropriate programs should be developed to promote cervical cancer screening participation to socially vulnerable classes. Continuous social attention is needed to address these issues and encourage participation in general health screening to improve the rate of cervical cancer screening.
The Impact of Backpack Loads on School Children: A Critical Narrative Review
Authors: Perrone Michelle , Orr Robin , Hing Wayne , Milne Nikki , Pope Rodney
Published: November 2018

Background: Backpack loads of school students during school days have been suggested to range from 10% to as high as 25% of their body weight and may have a negative impact on their body. The aim of this review was to identify and review studies that have examined impacts of contemporary backpack loads on school children. Methods: A systematic search was conducted of the literature using key search terms. After relevant studies published in recent years were selected using strict inclusion and exclusion criteria, the studies were critically appraised and relevant data were extracted and tabulated prior to conducting a critical narrative synthesis of findings. Results: Twenty-one studies were included, ranging in methodological quality from poor to good (critical appraisal scores 22% to 77%). Students carried on average over 15% of their own body weight, which caused biomechanical and physiological adaptations that could increase musculoskeletal injury risk, fatigue, redness, swelling and discomfort. Conclusion: Considering the limited methodological quality and variations in foci across studies, further research is needed to elucidate: (1) the loads students carry around on a school day in their school backpacks and; (2) the biomechanical, physiological and physical effects of load carriage on students.
Characteristics of Climate Change and Extreme Weather from 1951 to 2011 in China
Authors: Zhao Chunli , Chen Jianguo , Du Peng , Yuan Hongyong
Published: November 2018

It has been demonstrated that climate change is an established fact. A good comprehension of climate and extreme weather variation characteristics on a temporal and a spatial scale is important for adaptation and response. In this work, the characteristics of temperature, precipitation, and extreme weather distribution and variation is summarized for a period of 60 years and the seasonal fluctuation of temperature and precipitation is also analyzed. The results illustrate the reduction in daily and annual temperature divergence on both temporal and spatial scales. However, the gaps remain relatively significant. Furthermore, the disparity in daily and annual precipitation are found to be increasing on both temporal and spatial scales. The findings indicate that climate change, to a certain extent, narrowed the temperature gap while widening the precipitation gap on temporal and spatial scales in China.