bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated ecological–economic fisheries models—Evaluation, review and challenges for implementation
Authors: Nielsen J Rasmus , Thunberg Eric , Holland Daniel S , Schmidt Jorn O , Fulton Elizabeth A , Bastardie Francois , Punt Andre E , Allen Icarus , Bartelings Heleen , Bertignac Michel , Bethke Eckhard , Bossier Sieme , Buckworth Rik , Carpenter Griffin , Christensen Asbjørn , Christensen Villy , Da‐Rocha José M , Deng Roy , Dichmont Catherine , Doering Ralf , Esteban Aniol , Fernandes Jose A. , Frost Hans , Garcia Dorleta , Gasche Loic , Gascuel Didier , Gourguet Sophie , Groeneveld Rolf A , Guillén Jordi , Guyader Olivier , Hamon Katell G , Hoff Ayoe , Horbowy Jan , Hutton Trevor , Lehuta Sigrid , Little L Richard , Lleonart Jordi , Macher Claire , Mackinson Steven , Mahevas Stephanie , Marchal Paul , Mato‐Amboage Rosa , Mapstone Bruce , Maynou Francesc , Merzéréaud Mathieu , Palacz Artur , Pascoe Sean , Paulrud Anton , Plaganyi Eva , Prellezo Raul , van Putten Elizabeth I , Quaas Martin , Ravn‐Jonsen Lars , Sanchez Sonia , Simons Sarah , Thébaud Olivier , Tomczak Maciej T , Ulrich Clara , van Dijk Diana , Vermard Youen , Voss Rudi , Waldo Staffan 
Published: July 2017

AbstractMarine ecosystems evolve under many interconnected and area‐specific pressures. To fulfil society's intensifying and diversifying needs while ensuring ecologically sustainable development, more effective marine spatial planning and broader‐scope management of marine resources is necessary. Integrated ecological–economic fisheries models (IEEFMs) of marine systems are needed to evaluate impacts and sustainability of potential management actions and understand, and anticipate ecological, economic and social dynamics at a range of scales from local to national and regional. To make these models most effective, it is important to determine how model characteristics and methods of communicating results influence the model implementation, the nature of the advice that can be provided and the impact on decisions taken by managers. This article presents a global review and comparative evaluation of 35 IEEFMs applied to marine fisheries and marine ecosystem resources to identify the characteristics that determine their usefulness, effectiveness and implementation. The focus is on fully integrated models that allow for feedbacks between ecological and human processes although not all the models reviewed achieve that. Modellers must invest more time to make models user friendly and to participate in management fora where models and model results can be explained and discussed. Such involvement is beneficial to all parties, leading to improvement of mo‐dels and more effective implementation of advice, but demands substantial resources which must be built into the governance process. It takes time to develop effective processes for using IEEFMs requiring a long‐term commitment to integrating multidisciplinary modelling advice into management decision‐making.
Deformation behavior of nanocrystalline titania particles accessed by complementary in situ electron microscopy techniques
Authors: Herre Patrick , Romeis Stefan , Mačković Mirza , Przybilla Thomas , Paul Jonas , Schwenger Jan , Torun Boray , Grundmeier Guido , Spiecker Erdmann , Peukert Wolfgang 
Published: July 2017

AbstractThe mechanical behavior of nanostructured spherical submicrometer titania particles was studied by in situ uniaxial compression experiments in the scanning and transmission electron microscope (SEM and TEM). Mesoporous and amorphous titania particles were prepared by a wet chemical sol‐gel approach. To obtain nanocrystalline (nc) single‐phase anatase and rutile particles the amorphous particles were crystallized by high‐temperature annealing. For each sample the deformation behavior of at least 50 particles was investigated by in situ compression experiments in the SEM. In all cases an elastic – predominantly plastic deformation behavior accompanied by crack initiation at exceptionally high engineering strain values of several percent were observed. Crack propagation presumably along grain boundaries and a Weibull distributed fracture stress was shown for all nc particles. Complementary in situ TEM experiments and ex situ analysis of focused ion beam prepared particle cross‐sections were carried out to identify the underlying deformation mechanisms. Grain rotations and grain sliding are observed for nc anatase particles during in situ compression and are further identified to be linked to a densification of the mesoporous particle structure. Our dedicated preparation and quantitative in situ characterization methodology provides an excellent basis for a better understanding of the mechanical behavior of advanced ceramics.
Octahedral distortion, phase structural stability, and microwave dielectric properties in equivalently substituted LaTiNbO6 ceramics
Authors: Zhang Jian , Zuo Ruzhong 
Published: July 2017

AbstractThe room‐temperature phase composition, microstructural characteristic, and microwave dielectric properties of equivalently substituted LaTiNbO6 ceramics were investigated by means of the Rietveld structural refinement, scanning electron microscopy, and network analyzer. A special interest was focused on the influence of the variation in bond length and octahedral distortion on the phase structural stability. A monoclinic (M) aeschynite phase was obtained in B‐site ions (Ta5+ and [W0.5Ti0.5]5+) substituted LaTiNbO6 ceramics while an orthorhombic (O) aeschynite structure appeared in B‐site ions (Zr4+) or A‐site ions (Ce3+ and Sm3+) substituted LaTiNbO6 ceramics, which owned typical polygonal and short rod‐like grain morphologies, respectively. Compared with the octahedral bond length, a straightforward relation between the phase structural stability and the octahedral distortion was established, in which a reduced octahedral distortion was directly correlated with the destabilization of O or M phases or vice versa, irrespective of the substitution ionic radius. The experimentally observed giant difference in dielectric performance of LaTiNbO6 based ceramics was believed to mainly originate from their distinct phase structure and grain morphology.
Unilateral vocal cord paralysis after surgical closure of a patent ductus arteriosus in extremely preterm infants
Authors: Pharande Pramod , Karthigeyan Sathiyapriya , Walker Karen , D'Cruz Daphne , Badawi Nadia , Luig Melissa , Winlaw David , Popat Himanshu 
Published: July 2017

AimLeft vocal cord paralysis (LVCP) is variably reported post ligation of patent ductus arteriosus (PDA). Our objective was to determine the incidence of LVCP and identify predictive factors and associated morbidities in preterm infants post PDA ligation.MethodsThis is a retrospective cohort study of infants less than 29 weeks gestational age from 2006 to 2014 who underwent PDA ligation. Infants with laryngeal symptoms underwent flexible fibreoptic nasopharyngolaryngoscopy to evaluate vocal cord function. We compared short‐ and long‐term morbidities among infants with and without symptomatic LVCP.ResultsA total of 35 infants underwent PDA ligation in the study period, of which 11 infants (31%) developed symptomatic LVCP. Dysphonia was the presenting symptom in all neonates with LVCP and stridor was present in 46% (5/11) of them. The median (interquartile range) gestation (25 weeks (24–27) vs. 25 weeks (23–28)), birthweight (810 g (550–1180) vs. 825 g (550–1220)) and age at surgery (19 days (9–27) vs. 20 (5–69)) were similar in infants with and without LVCP, respectively. Infants with LVCP took significantly longer to reach suck feeds (128 vs. 90 days, P = <0.001), stayed longer in hospital (119 vs. 95 days, P = 0.01) and were more likely to go home on oxygen (73 vs. 27%; P = 0.024). Neurodevelopmental outcomes were similar in the two groups.ConclusionsLVCP was noted in 31% of infants post PDA ligation and was associated with prolonged hospital stay, a longer time to reach suck feeds and a need for home oxygen. No predictive factors for development of LVCP were identified.
Long‐term native liver survival in infants with biliary atresia and use of a stool color card: Case–control study
Authors: Gu Yan‐Hong , Matsui Akira 
Published: July 2017

AbstractBackgroundSo far, there has been no epidemiological study on whether long‐term native liver survival (NLS) in infants with biliary atresia (BA) is associated with use of a stool color card (SCC).MethodsA case–control study was performed, involving two associations for patients with BA in Japan. Participants were patients with BA who were born and underwent their first open Kasai procedures (KP) between August 1994 and March 2011, and who were also members of either of two associations for patients with BA in Japan. SCC users were classified as cases and SCC non‐users as controls.ResultsMean age at the time of the first open KP was 59.7 and 68.2 days in SCC users and non‐users, respectively (P < 0.05). According to Kaplan–Meier analysis, the probability of NLS at 12.5 years was 48.5% and 36.6% in SCC users and non‐users (P < 0.05), respectively. On Cox proportional hazard modeling, not using an SCC was harmful to long‐term NLS (hazard ratio, 2.61; 95% CI: 1.20–5.70; P = 0.016), adjusted for sex, age of timing of KP and type of BA.ConclusionsLong‐term NLS is associated with SCC for early detection, but not associated with age or a threshold of age at KP (<90 days) in patients with BA.
The application of 3‐dimensional printing for preoperative planning in oral and maxillofacial surgery in dogs and cats
Authors: Winer Jenna N. , Verstraete Frank J. M. , Cissell Derek D. , Lucero Steven , Athanasiou Kyriacos A. , Arzi Boaz 
Published: July 2017

AbstractObjectiveTo describe the application of 3‐dimensional (3D) printing in advanced oral and maxillofacial surgery (OMFS) and to discuss the benefits of this modality in surgical planning, student and resident training, and client education.Study designRetrospective case series.AnimalsClient‐owned dogs (n = 28) and cats (n = 4) with 3D printing models of the skulls.MethodsThe medical records of 32 cases with 3D printing prior to major OMFS were reviewed.ResultsIndications for 3D printing included preoperative planning for mandibular reconstruction after mandibulectomy (n = 12 dogs) or defect nonunion fracture (n = 6 dogs, 2 cats), mapping of ostectomy location for temporomandibular joint ankylosis or pseudoankylosis (n = 4 dogs), assessment of palatal defects (n = 2 dogs, 1 cat), improved understanding of complex anatomy in cases of neoplasia located in challenging locations (n = 2 dogs, 1 cat), and in cases of altered anatomy secondary to trauma (n = 2 dogs).ConclusionIn the authors' experience, 3D printed models serve as excellent tools for OMFS planning and resident training. Furthermore, 3D printed models are a valuable resource to improve clients' understanding of the pet's disorder and the recommended treatment.Clinical relevanceThree‐dimensional printed models should be considered viable tools for surgical planning, resident training, and client education in candidates for complex OMFS.
Serologic evidence of West Nile virus and Usutu virus infections in Eurasian coots in the Netherlands
Authors: Lim S. M. , Geervliet M. , Verhagen J. H. , Müskens G. J. D. M. , Majoor F. A. , Osterhaus A. D. M. E. , Martina B. E. E. 
Published: July 2017

SummaryWest Nile virus (WNV) and Usutu virus (USUV) are arboviruses that are maintained in enzootic transmission cycles between mosquitoes and birds and are occasionally transmitted to mammals. As arboviruses are currently expanding their geographic range and emerging in often unpredictable locations, surveillance is considered an important element of preparedness. To determine whether sera collected from resident and migratory birds in the Netherlands as part of avian influenza surveillance would also represent an effective source for proactive arbovirus surveillance, a random selection of such sera was screened for WNV antibodies using a commercial ELISA. In addition, sera of jackdaws and carrion crows captured for previous experimental infection studies were added to the selection. Of the 265 screened serum samples, 27 were found to be WNV–antibody‐positive, and subsequent cross‐neutralization experiments using WNV and USUV confirmed that five serum samples were positive for only WNV‐neutralizing antibodies and seven for only USUV. The positive birds consisted of four Eurasian coots (Fulica atra) and one carrion crow (Corvus corone) for WNV, of which the latter may suggest local presence of the virus, and only Eurasian coots for USUV. As a result, the screening of a small selection of serum samples originally collected for avian influenza surveillance demonstrated a seroprevalence of 1.6% for WNV and 2.8% for USUV, suggesting that this sustained infrastructure could serve as a useful source for future surveillance of arboviruses such as WNV and USUV in the Netherlands.
Transcriptomic analysis identifies a role of PI3K–Akt signalling in the responses of skeletal muscle to acute hypoxia in vivo
Authors: Gan Zhuohui , Powell Frank L. , Zambon Alexander C. , Buchholz Kyle S. , Fu Zhenxing , Ocorr Karen , Bodmer Rolf , Moya Esteban A. , Stowe Jennifer C. , Haddad Gabriel G. , McCulloch Andrew D. 
Published: July 2017

Key points
Changes in gene expression that occur within hours of exposure to hypoxia in in vivo skeletal muscles remain unexplored.
Two hours of hypoxia caused significant down‐regulation of extracellular matrix genes followed by a shift at 6 h to altered expression of genes associated with the nuclear lumen while respiratory and blood gases were stabilized.
Enrichment analysis of mRNAs classified by stability rates suggests an attenuation of post‐transcriptional regulation within hours of hypoxic exposure, where PI3K–Akt signalling was suggested to have a nodal role by pathway analysis.
Experimental measurements and bioinformatic analyses suggested that the dephosphorylation of Akt after 2 h of hypoxic exposure might deactivate RNA‐binding protein BRF1, hence resulting in the selective degradation of mRNAs.
AbstractThe effects of acute hypoxia have been widely studied, but there are few studies of transcriptional responses to hours of hypoxia in vivo, especially in hypoxia‐tolerant tissues like skeletal muscles. We used RNA‐seq to analyse gene expression in plantaris muscles while monitoring respiration, arterial blood gases, and blood glucose in mice exposed to 8% O2 for 2 or 6 h. Rapid decreases in blood gases and a slower reduction in blood glucose suggest stress, which was accompanied by widespread changes in gene expression. Early down‐regulation of genes associated with the extracellular matrix was followed by a shift to genes associated with the nuclear lumen. Most of the early down‐regulated genes had mRNA half‐lives longer than 2 h, suggesting a role for post‐transcriptional regulation. These transcriptional changes were enriched in signalling pathways in which the PI3K–Akt signalling pathway was identified as a hub. Our analyses indicated that gene targets of PI3K–Akt but not HIF were enriched in early transcriptional responses to hypoxia. Among the PI3K–Akt targets, 75% could be explained by a deactivation of adenylate–uridylate‐rich element (ARE)‐binding protein BRF1, a target of PI3K–Akt. Consistent decreases in the phosphorylation of Akt and BRF1 were experimentally confirmed following 2 h of hypoxia. These results suggest that the PI3K–Akt signalling pathway might play a role in responses induced by acute hypoxia in skeletal muscles, partially through the dephosphorylation of ARE‐binding protein BRF1.
Aerobiological Stabilities of Different Species of Gram-Negative Bacteria, Including Well-Known Biothreat Simulants, in Single-Cell Particles and Cell Clusters of Different Compositions
Authors: Dybwad Marius , Skogan Gunnar 
Published: July 2017

ABSTRACTThe ability to perform controlled experiments with bioaerosols is a fundamental enabler of many bioaerosol research disciplines. A practical alternative to using hazardous biothreat agents, e.g., for detection equipment development and testing, involves using appropriate model organisms (simulants). Several species of Gram-negative bacteria have been used or proposed as biothreat simulants. However, the appropriateness of different bacterial genera, species, and strains as simulants is still debated. Here, we report aerobiological stability characteristics of four species of Gram-negative bacteria (Pantoea agglomerans,Serratia marcescens,Escherichia coli, andXanthomonas arboricola) in single-cell particles and cell clusters produced using four spray liquids (H2O, phosphate-buffered saline[PBS], spent culture medium[SCM], and a SCM-PBS mixture).E. colishowed higher stability in cell clusters from all spray liquids than the other species, but it showed similar or lower stability in single-cell particles. The overall stability was higher in cell clusters than in single-cell particles. The highest overall stability was observed for bioaerosols produced using SCM-containing spray liquids. A key finding was the observation that stability differences caused by particle size or compositional changes frequently followed species-specific patterns. The results highlight how even moderate changes to one experimental parameter, e.g., bacterial species, spray liquid, or particle size, can strongly affect the aerobiological stability of Gram-negative bacteria. Taken together, the results highlight the importance of careful and informed selection of Gram-negative bacterial biothreat simulants and also the accompanying particle size and composition. The outcome of this work contributes to improved selection of simulants, spray liquids, and particle size for use in bioaerosol research.IMPORTANCEThe outcome of this work contributes to improved selection of simulants, spray liquids, and particle size for use in bioaerosol research. Taken together, the results highlight the importance of careful and informed selection of Gram-negative bacterial biothreat simulants and also the accompanying particle size and composition. The results highlight how even moderate changes to one experimental parameter, e.g., bacterial species, spray liquid, or particle size, can strongly affect the aerobiological stability of Gram-negative bacteria. A key finding was the observation that stability differences caused by particle size or compositional changes frequently followed species-specific patterns.
Parallel Evolution of Two Clades of an Atlantic-Endemic Pathogenic Lineage of Vibrio parahaemolyticus by Independent Acquisition of Related Pathogenicity Islands
Authors: Xu Feng , Gonzalez-Escalona Narjol , Drees Kevin P. , Sebra Robert P. , Cooper Vaughn S. , Jones Stephen H. , Whistler Cheryl A. 
Published: July 2017

ABSTRACT

Shellfish-transmitted
Vibrio parahaemolyticus
infections have recently increased from locations with historically low disease incidence, such as the Northeast United States. This change coincided with a bacterial population shift toward human-pathogenic variants occurring in part through the introduction of several Pacific native lineages (ST36, ST43, and ST636) to nearshore areas off the Atlantic coast of the Northeast United States. Concomitantly, ST631 emerged as a major endemic pathogen. Phylogenetic trees of clinical and environmental isolates indicated that two clades diverged from a common ST631 ancestor, and in each of these clades, a human-pathogenic variant evolved independently through acquisition of distinct
Vibrio
pathogenicity islands (VPaI). These VPaI differ from each other and bear little resemblance to hemolysin-containing VPaI from isolates of the pandemic clonal complex. Clade I ST631 isolates either harbored no hemolysins or contained a chromosome I-inserted island we call VPaIβ that encodes a type 3 secretion system (T3SS2β) typical of Trh hemolysin producers. The more clinically prevalent and clonal ST631 clade II had an island we call VPaIγ that encodes both
tdh
and
trh
and that was inserted in chromosome II. VPaIγ was derived from VPaIβ but with some additional acquired elements in common with VPaI carried by pandemic isolates, exemplifying the mosaic nature of pathogenicity islands. Genomics comparisons and amplicon assays identified VPaIγ-type islands containing
tdh
inserted adjacent to the
ure
cluster in the three introduced Pacific and most other emergent lineages that collectively cause 67% of infections in the Northeast United States as of 2016.

IMPORTANCE
The availability of three different hemolysin genotypes in the ST631 lineage provided a unique opportunity to employ genome comparisons to further our understanding of the processes underlying pathogen evolution. The fact that two different pathogenic clades arose in parallel from the same potentially benign lineage by independent VPaI acquisition is surprising considering the historically low prevalence of community members harboring VPaI in waters along the Northeast U.S. coast that could serve as the source of this material. This illustrates a possible predisposition of some lineages to not only acquire foreign DNA but also become human pathogens. Whereas the underlying cause for the expansion of
V. parahaemolyticus
lineages harboring VPaIγ along the U.S. Atlantic coast and spread of this element to multiple lineages that underlies disease emergence is not known, this work underscores the need to define the environment factors that favor bacteria harboring VPaI in locations of emergent disease.
Deep-Sea Bacterium Shewanella piezotolerans WP3 Has Two Dimethyl Sulfoxide Reductases in Distinct Subcellular Locations
Authors: Xiong Lei , Jian Huahua , Xiao Xiang 
Published: July 2017

ABSTRACTDimethyl sulfoxide (DMSO) acts as a substantial sink for dimethyl sulfide (DMS) in deep waters and is therefore considered a potential electron acceptor supporting abyssal ecosystems.Shewanella piezotoleransWP3 was isolated from west Pacific deep-sea sediments, and two functional DMSO respiratory subsystems are essential for maximum growth of WP3 underin situconditions (4°C/20 MPa). However, the relationship between these two subsystems and the electron transport pathway underlying DMSO reduction by WP3 remain unknown. In this study, both DMSO reductases (type I and type VI) in WP3 were found to be functionally independent despite their close evolutionary relationship. Moreover, immunogold labeling of DMSO reductase subunits revealed that the type I DMSO reductase was localized on the outer leaflet of the outer membrane, whereas the type VI DMSO reductase was located within the periplasmic space. CymA, a cytoplasmic membrane-bound tetrahemec-type cytochrome, served as a preferential electron transport protein for the type I and type VI DMSO reductases, in which type VI accepted electrons from CymA in a DmsE- and DmsF-independent manner. Based on these results, we proposed a core electron transport model of DMSO reduction in the deep-sea bacteriumS. piezotoleransWP3. These results collectively suggest that the possession of two sets of DMSO reductases with distinct subcellular localizations may be an adaptive strategy for WP3 to achieve maximum DMSO utilization in deep-sea environments.IMPORTANCEAs the dominant methylated sulfur compound in deep oceanic water, dimethyl sulfoxide (DMSO) has been suggested to play an important role in the marine biogeochemical cycle of the volatile anti-greenhouse gas dimethyl sulfide (DMS). Two sets of DMSO respiratory systems in the deep-sea bacteriumShewanella piezotoleransWP3 have previously been identified to mediate DMSO reduction underin situconditions (4°C/20 MPa). Here, we report that the two DMSO reductases (type I and type VI) in WP3 have distinct subcellular localizations, in which type I DMSO reductase is localized to the exterior surface of the outer membrane and type VI DMSO reductase resides in the periplasmic space. A core electron transport model of DMSO reduction in WP3 was constructed based on genetic and physiological data. These results will contribute to a comprehensive understanding of the adaptation mechanisms of anaerobic respiratory systems in benthic microorganisms.