bluuebunny/crossref_metadata_2025_split huggingface dataset:
Summer heat waves over Eastern China: dynamical processes and trend attribution
Authors: Freychet Nicolas , Tett Simon , Wang Jun , Hegerl Gabriele 
Published: February 2017

Abstract
Recent trends in summer heat waves (HW) over Central-Eastern China and their atmospheric drivers are investigated using the ERA Interim re-analysis. A composite analysis shows that these events are preceded by an increase in 500 hPa geopotential height. Consequently, a subsidence anomaly develops over the region and surface solar radiation increases. An increase in the northward moisture transport from the tropical region is also found to increase specific humidity, leading to warmer night-time temperatures. Feedback effects are also important: decrease of precipitation and enhanced evaporation also increases the specific humidity and North-Westerlies due to the low pressure lead to more heat convergence. HW occurrence increases, especially during the last decade, and is largely due to an increase in the mean temperature rather than to a change in dynamics, suggesting a human influence.
Similar Clinical Severity and Outcomes for Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Pediatric Musculoskeletal Infections
Authors: An Thomas J. , Benvenuti Michael A. , Mignemi Megan E. , Martus Jeffrey , Wood James B. , Thomsen Isaac P. , Schoenecker Jonathan G. 
Published: February 2017

Abstract

Background
Prior studies of pediatric musculoskeletal infection have suggested that methicillin-resistant Staphylococcus aureus (MRSA) infections result in worse outcomes compared with infections with methicillin-susceptible S aureus (MSSA) strains. Based on these results, clinical prediction algorithms have been developed to differentiate between MRSA and MSSA early in a patient’s clinical course. This study compares hospital outcomes for pediatric patients with MRSA and MSSA musculoskeletal infection presenting to the emergency department at a large tertiary care children’s hospital.

Methods
A retrospective study identified pediatric patients with S aureus musculoskeletal infection over a 5-year period (2008–2013) by sequential review of all pediatric orthopedic consults. Relevant demographic information, laboratory values, and clinical outcomes were obtained from the electronic medical record.

Results
Of the 91 identified cases of S aureus pediatric musculoskeletal infection, there were 49 cases of MRSA infection (53%) and 42 cases of MSSA infection (47%). There were no significant differences between MRSA and MSSA infections in median hospital length of stay (4.8 vs 5.7 days, P = .50), febrile days (0.0 vs 1.5 days, P = .10), and antibiotic duration (28 vs 34 days, P = .18). Methicillin-resistant S aureus infections were more likely to require operative intervention than MSSA infection (85% vs 62%, P = .15). A logistic regression model based on C-reactive protein, temperature, white blood cell count, pulse, and respiratory rate at presentation demonstrated poor ability to differentiate between MRSA and MSSA infection.

Conclusions
The results demonstrated no significant differences between MSSA and MRSA musculoskeletal infections for most hospital outcomes measured. However, MRSA infections required more operative interventions than MSSA infections. In addition, a predictive model based on severity markers obtained at presentation was unable to effectively differentiate between MRSA and MSSA infection. The clinical utility and capacity for early differentiation of MRSA and MSSA depends on virulence patterns that may vary temporally and geographically.
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Authors: Oertlin Christian , Lorent Julie , Gandin Valentina , Murie Carl , Masvidal Laia , Cargnello Marie , Furic Luc , Topisirovic Ivan , Larsson Ola 
Published: February 2017

ABSTRACTmRNA translation plays an evolutionarily conserved role in homeostasis and when dysregulated results in various disorders. Optimal and universally applicable analytical methods to study transcriptome-wide changes in translational efficiency are therefore critical for understanding the complex role of translation regulation under physiological and pathological conditions. Techniques used to interrogate translatomes, including polysome- and ribosome-profiling, require adjustment for changes in total mRNA levels to capturebona fidealterations in translational efficiency. Herein, we present the anota2seq algorithm for such analysis using data from ribosome- or polysome-profiling quantified by DNA-microarrays or RNA sequencing, which outperforms current methods for identification of changes in translational efficiency. In contrast to available analytical methods, anota2seq also allows capture of an underappreciated mode for regulation of gene expression whereby translation acts as a buffering mechanism which maintains constant protein levels despite fluctuations in mRNA levels (“translational buffering”). Application of anota2seq shows that insulin affects gene expression at multiple levels, in a largely mTOR-dependent manner. Moreover, insulin induces levels of a subset of mRNAs independently of mTOR that undergo translational buffering upon mTOR inhibition. Thus, the universal anota2seq algorithm allows efficient and hitherto unprecedented interrogation of translatomes and enables studies of translational buffering which represents an unexplored mechanism for regulating of gene expression.
Habitat generalists or specialists, insights from comparative genomic analyses ofThermosipholineages
Authors: Haverkamp Thomas H.A. , Geslin Claire , Lossouarn Julien , Podosokorskaya Olga A. , Kublanov Ilya , Nesbø Camilla L. 
Published: February 2017

AbstractThermosiphospecies inhabit various extreme environments such as marine hydrothermal vents, petroleum reservoirs and terrestrial hot springs. A 16S rRNA phylogeny of availableThermosiphospp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents and hotsprings. Comparative genomics and recombination analysis of the genomes of 15Thermosiphoisolates separated them into three species with different habitat distributions, the widely distributedT. africanusand the more specialized,T. melanesiensisandT. affectus. The threeThermosiphospecies can also be differentiated on the basis of genome content. For instance theT. africanusgenomes had the largest repertoire of carbohydrate metabolism, which could explain why these isolates were obtained from ecologically more divergent habitats. The three species also show different capacities for defense against foreign DNA.T. melanesiensisandT. africanusboth had a complete RM system, while this was missing inT. affectus. These observations also correlated with Pacbio sequencing, which revealed a methylatedT. melanesiensisBI431 genome, while no methylation was detected among twoT. affectusisolates. All the genomes carry CRISPR arrays accompanied by more or less complete CRISPR-cas systems. Interestingly, some isolates of bothT. melanesiensisandT. africanuscarry integrated prophage elements, with spacers matching these in their CRISPR arrays. Taken together, the comparative genomic analyses ofThermosiphospp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA that is present in subsurface ecosystems.
Broad-spectrum inhibition ofPhytophthora infestansby root endophytes
Authors: de Vries Sophie , von Dahlen Janina K. , Schnake Anika , Ginschel Sarah , Schulz Barbara , Rose Laura E. 
Published: February 2017

SummaryPhytophthora infestans(Phy. infestans) is a devastating pathogen of tomato and potato. It readily overcomes resistance genes and applied agrochemicals. Fungal endophytes provide a largely unexplored avenue of control againstPhy. infestans. Not only do endophytes produce a wide array of bioactive metabolites, they may also directly compete with and defeat pathogensin planta.Twelve isolates of fungal endophytes from different plant species were testedin vitrofor their production of metabolites with anti-Phy. infestansactivity. Four well-performing isolates were evaluated for their ability to suppress nine isolates ofPhy. infestanson agar medium andin planta.Two endophytes reliably inhibited allPhy. infestansisolates on agar medium, of whichPhoma eupatoriiisolate 8082 was the most promising. It nearly abolished infection byPhy. infestans in planta.Here we present a biocontrol agent, which can inhibit a broad-spectrum ofPhy. infestansisolates. Such broadly acting inhibition is ideal, because it allows for effective control of genetically diverse pathogen isolates and may slow the adaptation ofPhy. infestans.
Robust and Efficient Coding with Grid Cells
Authors: Vágó Lajos , Ujfalussy Balázs B 
Published: February 2017

AbstractThe neuronal code arising from the coordinated population activity of grid cells in the rodent entorhinal cortex can uniquely represent space across large distances but the precise conditions for efficient coding are unknown. Here we present a number-theoretic analysis of grid coding and derive an upper bound on the distance that a population of grid cells can represent without error. We show that in the absence of neuronal noise, the capacity of the system would be extremely sensitive to the choice of the grid periods. However, when the accuracy of the representation is limited by neuronal noise, the capacity becomes gradually more robust against the choice of grid scales as the number of modules increases and remains near optimal even for random scale choices. Our study reveals that robust and efficient coding can be achieved without parameter tuning in the case of grid cell representation.
Division of labor, bet hedging, and the evolution of mixed biofilm investment strategies
Authors: Lowery Nick Vallespir , McNally Luke , Ratcliff William C. , Brown Sam P. 
Published: February 2017

ABSTRACTBacterial cells, like many other organisms, face a tradeoff between longevity and fecundity. Planktonic cells are fast growing and fragile, while biofilm cells are often slower growing but stress resistant. Here we ask: why do bacterial lineages invest simultaneously in both fast and slow growing types? We develop a population dynamical model of lineage expansion across a patchy environment, and find that mixed investment is favored across a broad range of environmental conditions, even when transmission is entirely via biofilm cells. This mixed strategy is favored because of a division of labor, where exponentially dividing planktonic cells can act as an engine for the production of future biofilm cells, which grow more slowly. We use experimental evolution to test our predictions, and show that phenotypic heterogeneity is persistent even under selection for purely planktonic or purely biofilm transmission. Furthermore, simulations suggest that maintenance of a biofilm subpopulation serves as a cost-effective hedge against environmental uncertainty, which is also consistent with our experimental findings.
Using constrained inversion of gravity and magnetic field to produce a 3D litho‐prediction model
Authors: Mahmoodi Omid , Smith Richard S. , Spicer Bill 
Published: February 2017

ABSTRACTGeologically constrained inversion of gravity and magnetic field data of the Victoria property (located in Sudbury, Canada) was undertaken in order to update the present three‐dimensional geological model. The initial and reference model was constructed based on geological information from over 950 drillholes to constrain the inversion. In addition, downhole density and magnetic susceptibility measured in six holes were statistically analysed to derive lower and upper bounds on the physical properties attributed to the lithological units in the reference model. Constrained inversion of the ground gravity and the airborne magnetic data collected at the Victoria property were performed using GRAV3D and MAG3D, respectively. A neural network was trained to predict lithological units from the physical properties measured in six holes. Then, the trained network was applied on the three‐dimensional distribution of physical properties derived from the inversion models to produce a three‐dimensional litho‐prediction model. Some of the features evident in the lithological model are remnants of the constraints, where the data did not demand a significant change in the model from the initial constraining model (e.g., the thin pair of diabase dykes). However, some important changes away from the initial model are evident; for example, a larger body was predicted for quartz diorite, which may be related to the prospective offset dykes; a new zone was predicted as sulfide, which may represent potential mineralisation; and a geophysical subcategory of metabasalt was identified with high magnetic susceptibility and high density. The litho‐prediction model agrees with the geological expectation for the three‐dimensional structure at Victoria and is consistent with the geophysical data, which results in a more holistic understanding of the subsurface lithology.
Functional outcomes of fungal community shifts driven by tree genotype and spatial‐temporal factors in Mediterranean pine forests
Authors: Pérez‐Izquierdo Leticia , Zabal‐Aguirre Mario , Flores‐Rentería Dulce , González‐Martínez Santiago C. , Buée Marc , Rincón Ana 
Published: February 2017

SummaryFungi provide relevant ecosystem services contributing to primary productivity and the cycling of nutrients in forests. These fungal inputs can be decisive for the resilience of Mediterranean forests under global change scenarios, making necessary an in‐deep knowledge about how fungal communities operate in these ecosystems. By using high‐throughput sequencing and enzymatic approaches, we studied the fungal communities associated with three genotypic variants of Pinus pinaster trees, in 45‐year‐old common garden plantations. We aimed to determine the impact of biotic (i.e., tree genotype) and abiotic (i.e., season, site) factors on the fungal community structure, and to explore whether structural shifts triggered functional responses affecting relevant ecosystem processes. Tree genotype and spatial‐temporal factors were pivotal structuring fungal communities, mainly by influencing their assemblage and selecting certain fungi. Diversity variations of total fungal community and of that of specific fungal guilds, together with edaphic properties and tree's productivity, explained relevant ecosystem services such as processes involved in carbon turnover and phosphorous mobilization. A mechanistic model integrating relations of these variables and ecosystem functional outcomes is provided. Our results highlight the importance of structural shifts in fungal communities because they may have functional consequences for key ecosystem processes in Mediterranean forests.
Back on the water margin: the ethical fixes of sustainable water provisions in rural China
Authors: Pia Andrea E. 
Published: February 2017

The classical Chinese novelThe water margintells the story of a group of petty officials who take a collective stance against the widespread corruption and unfairness of imperial Chinese society. At the root of this story lies the deeply ethical conundrum of redressing injustice when unchecked power prevails. This article draws from this insight to explore some of the ethical dilemmas Chinese state bureaucrats in Yunnan face today when provisioning drinking water to rural communities. Yunnanese officials are burdened with these dilemmas by the state's conspicuous retreat from rural public services in favour of market‐based supply. Through their ethical interventions, Chinese bureaucrats are able to temporarily defer the collapsing of rural water provisions which is caused by the contradictions introduced by the marketization of water. However, such interventions may be followed by further damage to the environment.
Determination of Time since Death using Vitreous Humor Tryptophan
Authors: Ansari Niha , Menon Shobhana K. 
Published: February 2017

AbstractDetermination of time since death (TSD) plays very important role in forensic examination as it narrows down field of suspects and aids in deceased identification. This study utilizes the fluorescence property of vitreous humor (VH) tryptophan to determine TSD using o‐phthalaldehyde (OPA). The detection limit of these fluorometric studies was found to be 8 ppb indicating sensitivity and high accuracy in TSD determination. The study was performed on selected 76 cadaver with known TSD ranging from 3 to 90 h. Excellent correlation between VH tryptophan and TSD was obtained with a coefficient of correlationR2= 0.9590. Results showed statistically significant increase in vitreous tryptophan with TSD up to 90 h, and the proposed method was efficaciously applied for prediction of TSD as no systematic error exist. The regression equation obtained from the study is [Trp] = 2.21 + 2.98 * TSD.
Inhibitory Effects of Red Wine on Lipid Oxidation in Fish Oil Emulsion and Angiogenesis in Zebrafish Embryo
Authors: Sun Haiyan , Zhang Yulin , Shen Yixiao , Zhu Yongchao , Wang Hua , Xu Zhimin 
Published: February 2017

AbstractThe capabilities of red wine against lipid oxidation and angiogenesis were evaluated by using a fish oil emulsion system and an in vivo zebrafish embryos model, respectively. The red wine contained 12 different antioxidant phenolics which levels were led by anthocyanins (140.46 mg/L), catechin (55.08 mg/L), and gallic acid (46.76 mg/L). The diversity of the phenolics in red wine was greater than the tea, coffee, or white wine selected as a peer control in this study. The total phenolics concentration of red wine was 305.53 mg/L, although the levels of tea, coffee, and white wine were 85.59, 76.85, and 26.57 mg/L, respectively. The activity of red wine in scavenging DPPH (2,2‐diphenyl‐1‐picrylhydrazyl) free radicals was approximately 4 times higher than the tea and 8 times than the coffee or white wine. The red wine showed the highest capability in preventing long chain PUFA oxidation in the fish oil emulsion. Because of the outstanding antioxidant activity of red wine, the red wine dried extract was used to monitor its inhibitory effect against angiogenesis by using transgenic zebrafish embryos (Tg[fli1:egfp]y1) with fluorescent blood vessels. After incubated in 100 μg/mL of the extract solution for 26 h pf, each of the embryos had a lower number of intersegmental vessel than the control embryo. The inhibition rate of red wine extract against growing of angiogenic blood vessel reached 100%.
Characterizing change points and continuous transitions in movement behaviours using wavelet decomposition
Authors: Soleymani Ali , Pennekamp Frank , Dodge Somayeh , Weibel Robert 
Published: February 2017

Summary

Individual behaviour, that is, the reaction of an organism to internal state, conspecifics and individuals of other species as well as the environment, is a crucial building block of their ecology. Modern tracking techniques produce high‐frequency observations of spatial positions of animals and accompanying speed and tortuosity measurements. However, inferring behavioural modes from movement trajectories remains a challenge.

Changes in behavioural modes occur at different temporal and spatial scales and may take two forms: abrupt, representing distinct change points; or continuous, representing smooth transitions between movement modes. The multi‐scale nature of these behavioural changes necessitates development of methods that can pinpoint behavioural states across spatial and temporal scales.

We propose a novel segmentation method based on the discrete wavelet transform (DWT), where the movement signal is decomposed into low‐frequency approximation and high‐frequency detail sub‐bands to screen for behavioural changes at multiple scales. Approximation sub‐bands characterizes broad changes by taking the continuous variations between behavioural modes into account, whereas detail sub‐bands are employed to detect abrupt, finer scale change points.

We tested the ability of our method to identify behavioural modes in simulated trajectories by comparing it to three state‐of‐the‐art methods from the literature. We further validated the method using an annotated dataset of turkey vultures (Cathartes aura) relating extracted segments to the expert knowledge of migratory vs. non‐migratory patterns. Our results show that the proposed DWT segmentation is more versatile than other segmentation methods, as it can be applied to different movement parameters, performs better or equally well on the simulated data, and correctly identifies behavioural modes identified by the experts. It is hence a valuable addition to the toolbox of land managers and conservation practitioners to understand the behavioural patterns expressed by animals in natural and human‐dominated landscapes.
Grain spilled from moving trains create a substantial wildlife attractant in protected areas
Authors: Gangadharan A. , Pollock S. , Gilhooly P. , Friesen A. , Dorsey B. , St. Clair C. C. 
Published: February 2017

AbstractTransportation corridors can attract threatened wildlife via habitat enhancement and foraging opportunities, leading to collisions with vehicles. But wildlife may also be attracted to energy‐dense food products that are spilled or discarded from moving vehicles, which is rarely studied. Therefore, we quantified train‐spilled attractants in Banff and Yoho National Parks, Canada, where agricultural products (hereafter, grain) are transported along 134 km of railway and may contribute to wildlife mortality. We measured grain deposition from 2012 to 2015 at 19 sites and assessed the performance of three structures developed to measure spilled grain. We then modeled grain deposition with respect to four types of spatial and temporal variables: those related to grain shipment, physical habitat characteristic, train‐related characteristics and variables specific to the study site. Grain was spilled at a mean rate of 1.64 g m−2 day−1 (sd = 3.60) from April to October (n = 3 years) and 1.52 (sd = 2.37) from November to March (n = 1 year). Extrapolating annual deposition across the study area yielded enough grain (110 tons) to provide 4.77 × 108 kcal of gross energy, which is equivalent to the average annual caloric needs of 42–54 grizzly bears Ursus arctos horribilis; the regional population is estimated at 50–73 animals. Much of this energy will not be accessible or available to bears; however, their attraction to it could contribute to rising and unsustainable rates of mortality. Models explained 9–31% of the variance in deposition for each grain type, primarily via coarse temporal variables of shipping rates and month. The absence of more specific predictive variables suggests that mitigation should target broader policies, such as prompt reporting and repair of leaky hopper cars, and limits to train stoppage in protected areas. We encourage more global assessment of the under‐studied issue of food attractants spilled by vehicles along transportation corridors.