bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of plastic mulch and nitrogen fertilizer on the soil microbial community, enzymatic activity and yield performance in a dryland maize cropping system
Authors: Wang Xiukang , Wang Ge , Guo Tao , Xing Yingying , Mo Fei , Wang Haidong , Fan Junliang , Zhang Fucang 
Published: February 2020

AbstractFarming practices that integrate plastic film mulching and nitrogen (N) fertilization have been extensively used to enhance crop productivity. However, the interactive effects of mulching and N application on soil microbial properties and crop yields have received little attention. A 2‐year field experiment was carried out in the Loess Plateau to investigate the independent and combined effects of plastic mulch and N application rate on the soil microbial population, enzymatic activity and grain yield. From 2016 to 2017, two mulching patterns (i.e., plastic mulching and no mulching) were exposed to five different N application rates (0 (N0), 80 (N80), 160 (N160), 200 (N200) and 240 (N240) kg N ha−1). N application significantly affected the soil microbial community composition, as suggested by significant increases in soil total bacteria, cellulose‐decomposing bacteria and the bacterial‐to‐fungal ratio with N rates. In contrast, the mulching pattern significantly affected soil extracellular enzyme production. Furthermore, there were significant effects of mulching, N application and their interaction on grain yield. The highest grain yield (11,728 kg N ha−1 in 2016 and 12,350 kg N ha−1 in 2017) in both growing seasons was consistently obtained under plastic mulching with a N level of 200 kg N ha−1. Our study showed that plastic mulching significantly affected extracellular enzyme production, and N fertilizer application significantly affected the composition of the soil microbial community.Highlights
Independent and coupled effects of mulching and N application on soil biological properties and grain performance were explored.
N application significantly influenced soil microbial community composition.
Mulching pattern rather than N application independently and significantly affected soil extracellular enzyme production
The combined application of plastic mulching with 200 kg N ha−1 should be seem as an optimum crop production pattern in this area.
Functional analysis of epilepsy‐associated variants in STXBP1/Munc18‐1 using humanizedCaenorhabditis elegans
Authors: Zhu Bangfu , Mak Jennifer C. H. , Morris Andrew P. , Marson Anthony G. , Barclay Jeff W. , Sills Graeme J. , Morgan Alan 
Published: February 2020

AbstractObjectiveGenetic variants inSTXBP1, which encodes the conserved exocytosis protein Munc18‐1, are associated with a variety of infantile epilepsy syndromes. We aimed to develop an in vivoCaenorhabditis elegansmodel that could be used to test the pathogenicity of such variants in a cost‐effective manner.MethodsThe CRISPR/Cas9 method was used to introduce a null mutation into theunc‐18gene (theC. elegansorthologue ofSTXBP1), thereby creating a paralyzed worm strain. We subsequently rescued this strain with transgenes encoding the human STXBP1/Munc18‐1 protein (wild‐type and eight different epilepsy‐associated missense variants). The resulting humanized worm strains were then analyzed via behavioral, electrophysiological, and biochemical approaches.ResultsTransgenic expression of wild‐type human STXBP1 protein fully rescued locomotion in both solid and liquid media to the same level as the standard wild‐type worm strain, Bristol N2. Six variant strains (E59K, V84D, C180Y, R292H, L341P, R551C) exhibited impaired locomotion, whereas two (P335L, R406H) were no different from worms expressing wild‐type STXBP1. Electrophysiological recordings revealed that all eight variant strains displayed less frequent and more irregular pharyngeal pumping in comparison to wild‐type STXBP1‐expressing strains. Four strains (V84D, C180Y, R292H, P335L) exhibited pentylenetetrazol‐induced convulsions in an acute assay of seizure‐like activity, in contrast to worms expressing wild‐type STXBP1. No differences were seen between wild‐type and variant STXBP1 strains in terms of mRNA abundance. However, STXBP1 protein levels were reduced to 20%‐30% of wild‐type in all variants, suggesting that the mutations result in STXBP1 protein instability.SignificanceThe approach described here is a cost‐effective in vivo method for establishing the pathogenicity of genetic variants in STXBP1 and potentially other conserved neuronal proteins. Furthermore, the humanized strains we created could potentially be used in the future for high‐throughput drug screens to identify novel therapeutics.
Do dogs mind the dots? Investigating domestic dogs' (Canis familiaris) preferential looking at human‐shaped point‐light figures
Authors: Delanoeije Joni , Gerencsér Linda , Miklósi Ádám 
Published: February 2020

AbstractIt is generally assumed that dogs show increased attention towards humans. A major part of this includes attention towards visual cues such as bodily gestures. We tested empirically whether dogs are visually attentive towards human body movement. Based on methods from visual perception research in humans, we used point‐light figures (PLFs) to investigate whether dogs attend to human body movement compared to other forms of motion. We investigated dogs' attentiveness towards vocalisation‐paired PLFs by adopting a preferential looking paradigm. Results indicate that dogs show increased attention towards vocalisation‐paired human‐shaped PLFs in comparison with inverted and non‐inverted scrambled configurations of the same PLFs. This increased attention, however, was only present in the case of PLFs that simulated a human in frontal orientation but not for PLFs in lateral orientation. We conclude that dogs prefer to look at PLFs of socially relevant (i.e. frontally facing) human body (i.e. natural) movement rather than scrambled (i.e. unnatural) displays. Our results indicate that PLFs may function as a promising tool to investigate dogs' visual perceptual preferences and mechanisms.
Opportunities for agent‐based modelling in human dimensions of fisheries
Authors: Burgess Matthew G. , Carrella Ernesto , Drexler Michael , Axtell Robert L. , Bailey Richard M. , Watson James R. , Cabral Reniel B. , Clemence Michaela , Costello Christopher , Dorsett Chris , Gaines Steven D. , Klein Emily S. , Koralus Philipp , Leonard George , Levin Simon A. , Little Lorne Richard , Lynham John , Madsen Jens Koed , Merkl Andreas , Owashi Brandon , Saul Steven E. , van Putten Ingrid E. , Wilcox Sharon 
Published: February 2020

AbstractModels of human dimensions of fisheries are important to understanding and predicting how fishing industries respond to changes in marine ecosystems and management institutions. Advances in computation have made it possible to construct agent‐based models (ABMs)—which explicitly describe the behaviour of individual people, firms or vessels in order to understand and predict their aggregate behaviours. ABMs are widely used for both academic and applied purposes in many settings including finance, urban planning and the military, but are not yet mainstream in fisheries science and management, despite a growing literature. ABMs are well suited to understanding emergent consequences of fisher interactions, heterogeneity and bounded rationality, especially in complex ecological, social and institutional contexts. For these reasons, we argue that ABMs of human behaviour can contribute significantly to human dimensions of fisheries in three areas: (a) understanding interactions between multiple management institutions; (b) incorporating cognitive and behavioural sciences into fisheries science and practice; and (c) understanding and projecting the social consequences of management institutions. We provide simple examples illustrating the potential for ABMs in each of these areas, using conceptual (“toy”) versions of the POSEIDON model. We argue that salient strategic advances in these areas could pave the way for increased tactical use of ABMs in fishery management settings. We review common ABM development and application challenges, with the aim of providing guidance to beginning ABM developers and users studying human dimensions of fisheries.
Density‐dependent growth and survival in salmonids: Quantifying biological mechanisms and methodological biases
Authors: Matte Jean‐Michel , Fraser Dylan J. , Grant James W. A. 
Published: February 2020

AbstractUnderstanding the complex variation in patterns of density‐dependent individual growth and survival across populations is critical to adaptive fisheries management, but the extent to which this variation is caused by biological or methodological differences is unclear. Consequently, we conducted a correlational meta‐analysis of published literature to investigate the relative importance of methodological and biological predictors on the shape and strength of density‐dependent individual growth and survival in salmonids. We obtained 160 effect sizes from 75 studies of 12 species conducted between 1977 and 2019 that differed in experimental approach (sensuEcological Monographs,54, 187–211; 65 laboratory experiments, 60 observational field studies, and 35 field experiments). The experimental approach was the strongest factor influencing the strength of density dependence across studies: density‐dependent survival was stronger than growth in field observational studies, whereas laboratory experiments detected stronger density‐dependent growth than survival. The difference between density‐dependent growth and survival was minimal in field experiments, and between lotic and lentic habitats. The shape of density dependence (logarithmic, linear, exponential or density‐independent) could be predicted with 66.7% accuracy based solely on the experimental approach and the density gradient (highest/lowest*100) of the study. Overall, the strength and shape of density dependence were primarily influenced by methodological predictors, while biological factors (predator presence, food abundance, and species) had predictable but modest effects. For both empirical studies and adaptive fisheries management, we recommend using field experiments with a density gradient of at least 470% to detect the proper shape of the density‐dependent response, or accounting for potential biases if observational or laboratory studies are conducted.
The crystal structure of the tetrameric DABA‐aminotransferase EctB, a rate‐limiting enzyme in the ectoine biosynthesis pathway
Authors: Hillier Heidi Therese , Altermark Bjørn , Leiros Ingar 
Published: February 2020

l‐2,4‐diaminobutyric acid (DABA) aminotransferases can catalyze the formation of amines at the distal ω‐position of substrates, and is the intial and rate‐limiting enzyme in the biosynthesis pathway of the cytoprotecting molecule (S)‐2‐methyl‐1,4,5,6‐tetrahydro‐4‐pyrimidine carboxylic acid (ectoine). Although there is an industrial interest in the biosynthesis of ectoine, the DABA aminotransferases remain poorly characterized. Herein, we present the crystal structure of EctB (2.45 Å), a DABA aminotransferase from Chromohalobacter salexigens DSM 3043, a well‐studied organism with respect to osmoadaptation by ectoine biosynthesis. We investigate the enzyme’s oligomeric state to show that EctB from C. salexigens is a tetramer of two functional dimers, and suggest conserved recognition sites for dimerization that also includes the characteristic gating loop that helps shape the active site of the neighboring monomer. Although ω‐transaminases are known to have two binding pockets to accommodate for their dual substrate specificity, we herein provide the first description of two binding pockets in the active site that may account for the catalytic character of DABA aminotransferases. Furthermore, our biochemical data reveal that the EctB enzyme from C. salexigens is a thermostable, halotolerant enzyme with a broad pH tolerance which may be linked to its tetrameric state. Put together, this study creates a solid foundation for a deeper structural understanding of DABA aminotransferases and opening up for future downstream studies of EctB’s catalytic character and its redesign as a better catalyst for ectoine biosynthesis. In summary, we believe that the EctB enzyme from C. salexigens can serve as a benchmark enzyme for characterization of DABA aminotransferases.DatabaseStructural data are available in PDB database under the accession number 6RL5.
A triclosan‐resistance protein from the soil metagenome is a novel enoyl‐acyl carrier protein reductase: Structure‐guided functional analysis
Authors: Kim Sang‐Hoon , Khan Raees , Choi Kihyuck , Lee Seon‐Woo , Rhee Sangkee 
Published: February 2020

The synthetic biocide triclosan targets enoyl‐acyl carrier protein reductase(s) (ENR) in bacterial type II fatty acid biosynthesis. Screening and sequence analyses of the triclosan resistome from the soil metagenome identified a variety of triclosan‐resistance ENRs. Interestingly, the mode of triclosan resistance by one hypothetical protein was elusive, mainly due to a lack of sequence similarity with other proteins that mediate triclosan resistance. Here, we carried out a structure‐based function prediction of the hypothetical protein, herein referred to as FabMG, and in vivo and in vitro functional analyses. The crystal structure of FabMG showed limited structural homology with FabG and FabI, which are also involved in type II fatty acid synthesis. In vivo complementation and in vitro activity assays indicated that FabMG is functionally a FabI‐type ENR that employs NADH as a coenzyme. Variations in the sequence and structure of FabMG are likely responsible for inefficient binding of triclosan, resulting in triclosan resistance. These data unravel a previously uncharacterized FabMG, which is prevalent in various microbes in triclosan‐contaminated environments and provide mechanistic insight into triclosan resistance.
Mangrove blue carbon stocks and dynamics are controlled by hydrogeomorphic settings and land‐use change
Authors: Sasmito Sigit D. , Sillanpää Mériadec , Hayes Matthew A. , Bachri Samsul , Saragi‐Sasmito Meli F. , Sidik Frida , Hanggara Bayu B. , Mofu Wolfram Y. , Rumbiak Victor I. , Hendri  , Taberima Sartji , Suhaemi  , Nugroho Julius D. , Pattiasina Thomas F. , Widagti Nuryani , Barakalla  , Rahajoe Joeni S. , Hartantri Heru , Nikijuluw Victor , Jowey Rina N. , Heatubun Charlie D. , zu Ermgassen Philine , Worthington Thomas A. , Howard Jennifer , Lovelock Catherine E. , Friess Daniel A. , Hutley Lindsay B. , Murdiyarso Daniel 
Published: February 2020

AbstractGlobally, carbon‐rich mangrove forests are deforested and degraded due to land‐use and land‐cover change (LULCC). The impact of mangrove deforestation on carbon emissions has been reported on a global scale; however, uncertainty remains at subnational scales due to geographical variability and field data limitations. We present an assessment of blue carbon storage at five mangrove sites across West Papua Province, Indonesia, a region that supports 10% of the world's mangrove area. The sites are representative of contrasting hydrogeomorphic settings and also capture change over a 25‐years LULCC chronosequence. Field‐based assessments were conducted across 255 plots covering undisturbed and LULCC‐affected mangroves (0‐, 5‐, 10‐, 15‐ and 25‐year‐old post‐harvest or regenerating forests as well as 15‐year‐old aquaculture ponds). Undisturbed mangroves stored total ecosystem carbon stocks of 182–2,730 (mean ± SD: 1,087 ± 584) Mg C/ha, with the large variation driven by hydrogeomorphic settings. The highest carbon stocks were found in estuarine interior (EI) mangroves, followed by open coast interior, open coast fringe and EI forests. Forest harvesting did not significantly affect soil carbon stocks, despite an elevated dead wood density relative to undisturbed forests, but it did remove nearly all live biomass. Aquaculture conversion removed 60% of soil carbon stock and 85% of live biomass carbon stock, relative to reference sites. By contrast, mangroves left to regenerate for more than 25 years reached the same level of biomass carbon compared to undisturbed forests, with annual biomass accumulation rates of 3.6 ± 1.1 Mg C ha−1 year−1. This study shows that hydrogeomorphic setting controls natural dynamics of mangrove blue carbon stocks, while long‐term land‐use changes affect carbon loss and gain to a substantial degree. Therefore, current land‐based climate policies must incorporate landscape and land‐use characteristics, and their related carbon management consequences, for more effective emissions reduction targets and restoration outcomes.
DISOLV: A Python Package for the Interpretation of Borehole Dilution Tests
Authors: Collins Sarah L. , Bianchi Marco 
Published: February 2020

AbstractSingle borehole dilution tests (SBDTs) are an inexpensive but effective technique for hydrogeological characterization of hard‐rock aquifers. We present a freely available, easy‐to‐use, open‐source Python package, DISOLV, for plotting, analyzing, and modeling SBDT data. DISOLV can significantly reduce the time spent interpreting field data by helping to identify flowing fractures intersecting the borehole and estimate the corresponding flow rates. DISOLV is successfully benchmarked against two analytical solutions. We also present an example application to real data collected in a borehole in a crystalline basement aquifer in southern India.
Groundwater Impacts from the M5.8 Earthquake in Korea as Determined by Integrated Monitoring Systems
Authors: Lee Soo‐Hyoung , Lee Jae Min , Yoon Heesung , Kim Yongcheol , Hwang Seho , Ha Kyoochul , Kim Yongje 
Published: February 2020

AbstractThis paper describes the impacts of the M5.8(5.1) Gyeongju earthquakes on groundwater levels using data obtained from a unique coastal monitoring well. The monitoring strategy integrates conventional water level monitoring with periodic, continuous measurements of temperature and electrical conductivity (EC) within the water column of the well. Another important component of the monitoring system is a new instrument, the InterfacEGG, which is capable of dynamically tracking the freshwater‐saltwater interface. Although the system was set up to monitor seawater intrusion related to over‐pumping, as well as rainfall and tidal effects, it recorded impacts associated with a large earthquake and aftershocks approximately 241 km away. Seismic energies associated with the M5.8(5.1) Gyeongju earthquakes induced groundwater flows to the monitoring well through fractures and joints in the crystalline basement rocks. Temperature and EC logging data showed that the EC vertical profile declined from an average of approximately 5300 to 4800 μS/cm following the earthquakes. The temperature profile showed a trend toward lower temperatures as the depth increased, a feature not commonly observed in previous studies. Data from the InterfacEGG suggested that the rise in EC was not due to the saltwater intrusion, but from the tendency for brackish water entering the borehole to induce convective mixing at deeper depths as the seismic waves travel through the well‐aquifer system. The increase in groundwater levels was caused by pulse of colder, less brackish water flowing into the well because of the earthquake. This behavior reflects an enhancement in rock permeability by removing precipitates and colloidal particles from clogged fractures, which improve the hydraulic connection with a nearby unit with a higher hydraulic head. This study suggests there is value added with a more aggressive monitoring strategy.
‘There is no choice apart from antibiotics…’: Qualitative analysis of views on urinary infections in pregnancy and antimicrobial resistance
Authors: Ghouri Flavia , Hollywood Amelia , Ryan Kath 
Published: February 2020

AbstractBackgroundAntimicrobial resistance (AMR) is a health risk as it can lead to life‐threatening infections. There has been a rise in resistant urinary tract infections (UTIs) which is the most common infection in pregnancy. This can be challenging in pregnancy due to the additional need to safeguard foetal development. The study's aim was to explore views about AMR in women who experienced UTIs in pregnancy.DesignFifteen semi‐structured interviews were conducted in the UK and analysed using thematic analysis.ResultsResults highlighted two themes: conceptualization of AMR and pregnancy as a deviation from the norm, with an overarching theme of ‘self‐efficacy’. Results show that participants were concerned about AMR but uncertain about the effect on society compared to individual's taking antibiotics and about completing antibiotic courses. Participants reported an unsparing use of antibiotics was justified in pregnancy, and behaviours like drinking adequate water were ineffective at preventing UTIs. In summary, women had low self‐efficacy regards tackling AMR and managing their health.ConclusionMisconceptions about how AMR affects society vs the individual translated into viewing it as a future problem to be tackled by the health‐care sector. Consequently, AMR requires reconceptualization as a current problem requiring collective action. This research also indicates women endorse a biomedical model of UTIs in pregnancy which attributes resolving illness to interventions such as medicines, implying an automatic reliance on antibiotics. Subsequently, there is a need for self‐efficacy by focusing on a behavioural model which emphasizes behaviours for infection prevention, thus reducing the need for antibiotics.
Effects of different ATP contents on phosphorylation level of glycogen phosphorylase and its activity in lamb during incubation at 4 ℃ in vitro
Authors: Bai Yuqiang , Li Xin , Zhang Dequan , Hou Chengli , Zheng Xiaochun , Chen Li , Ren Chi 
Published: February 2020

AbstractThe aim of this study was to investigate the effects of ATP on glycogen phosphorylase activity in lamb during incubation at 4℃ in vitro. Sarcoplasmic proteins from lamb were extracted and treated with different contents of ATP to get three groups of glycogen phosphorylase with low, middle and high ATP content groups, the amount of ATP were 0.5, 2.0 and 2.5 μM per 100 μg protein, respectively. The control group was without ATP adding. The results showed that ATP promoted the phosphorylation of glycogen phosphorylase, and phosphorylation modification promoted its activity. But ATP inhibited the activity of glycogen phosphorylase and ATP preferentially participated in phosphorylation. When ATP concentration was 0.5 μM per 100 μg protein, the effect of phosphorylation modification on the activity of glycogen phosphorylase was equal to the inhibition of ATP. The effect of glycogen phosphorylase phosphorylation on its activity gradually became dominant as incubation time prolonged.