bluuebunny/crossref_metadata_2025_split huggingface dataset:
Some like it deep: Intraspecific niche segregation in ruffe (Gymnocephalus cernua)
Authors: Eloranta Antti P. , Vejříková Ivana , Čech Martin , Vejřík Lukáš , Holubová Michaela , Šmejkal Marek , Frouzová Jaroslava , Kiljunen Mikko , Jones Roger I. , Peterka Jiří 
Published: June 2017

Abstract

Generalist fishes commonly show intraspecific niche segregation along the littoral–pelagic resource axis in lakes. Recent studies have shown that the deep, cold and seemingly unproductive profundal zone can also offer underutilised resources and facilitate specialised individuals, and can contribute to lake food webs via methane‐derived carbon pathways. Despite numerous examples from salmonid fish species, such intraspecific niche segregation along a littoral–profundal resource axis has not been reported in percids or other predominantly littoral benthivorous fishes.

Here, we describe a case of ruffe (Gymnocephalus cernua: Percidae) populations consisting of shallow‐ and deep‐water dwelling individuals in two post‐mining lakes in the northern Czech Republic. Results from stable isotope (δ15N and δ13C) mixing models indicated that littoral and profundal food resources dominated the long‐term diets of ruffe individuals caught from shallow‐ and deep‐water habitats, respectively. No similar niche segregation along the littoral–profundal gradient was observed in coexisting perch (Perca fluviatilis: Percidae) which used more pelagic food than the benthivorous ruffe.

The observed littoral–profundal niche segregation in ruffe was more pronounced in the macrophyte‐rich and poorly oxygenated Lake Milada, where high habitat complexity and strong interspecific interactions in the littoral zone as well as the absence of competing fish species in the profundal zone likely promote narrow trophic niches of shallow‐ and deep‐water dwelling ruffe

Our study provides novel evidence of littoral–profundal niche segregation in a predominantly benthivorous fish species. The results also show that intraspecific niche variation can be affected by lake ecosystem characteristics, in particular by the availability of and competition for littoral and profundal resources. Although more research is needed to confirm potential early divergence of shallow‐ and deep‐water dwelling ruffe as well as cascading effects on lake ecosystem processes (e.g. nutrient cycling and competitive and predatory interactions), our study indicates that individual ruffe may show limited habitat and food‐web coupling due to their restricted use of shallow or deep resources.
Alternative operation models for using a feed‐in terminal as a part of the forest chip supply system for a CHP plant
Authors: Väätäinen Kari , Prinz Robert , Malinen Jukka , Laitila Juha , Sikanen Lauri 
Published: June 2017

AbstractThe fuel supply of forest chips has to adapt to the annual fluctuations of power and heat generation. This creates inefficiency and unbalances the capacity utilization of the fuel supply fleet in the direct fuel supplies from roadside storages to power and heat generation. Terminals can offer an alternative approach for the fleet management of fuel supplies in terms of smoothing the unbalanced fleet use towards more even year‐round operations. The aim of the study was to compare the supply costs of a conventional direct forest chip supply to an alternative fuel supply with the use of a feed‐in terminal using the discrete‐event simulation method. The influences of the terminal location, terminal investment cost, outbound terminal transport method, terminal truck utilization and quality changes of terminal‐stored forest chips for the fuel supply cost were studied in the case environment. By introducing a feed‐in terminal and a shuttle truck for the transports of terminal‐stored forest chips, the total supply cost was 1.4% higher than the direct fuel supply scenario. In terminal scenarios, the supply costs increased 1–2% if the cost of the terminal investment increased 30%, the distance to the terminal increased from 5 to 30 km or the total annual use of a terminal truck decreased 1500 h. Moreover, a 1 per cent point per month increase in the dry matter loss of terminal‐stored chips increased the total supply cost 1%. The study revealed that with the relatively low additional cost, the feed‐in terminal can be introduced to the conventional forest chip supply. Cost compensation can be gained through the higher annual use of a fuel supply fleet and more secured fuel supply to power plants by decreasing the need for supplement fuel, which can be more expensive at a time of the highest fuel demand.
Sillimanite‐mullite transformation observed in synchrotron X‐ray diffraction experiments
Authors: Igami Yohei , Ohi Shugo , Miyake Akira 
Published: June 2017

AbstractHigh‐resolution synchrotron powder X‐ray diffraction (XRD) experiments were conducted to clarify the transformation of sillimanite to mullite (mullitization) and determine the mullitization temperature (Tc). We were able to distinguish sillimanite and mullite in the XRD patterns, despite their very similar crystallographic parameters, and to detect the appearance of small mullite peaks among sillimanite peaks. Analysis of the Johnson‐Mehl‐Avrami (JMA) equation for mullitization ratio (ζ) revealed that at temperatures T≥1240°C the mullitization had the same kinetics. The activation energy E at T≥1240°C obtained from the Arrhenius plot was 679.8 kJ mol−1. In analysis using a time‐temperature‐transformation diagram for mullitization, a mullitization curve of ζ=1% can be described as urn:x-wiley:00027820:media:jace15020:jace15020-math-0001where t is time, n is a reaction‐mechanism‐dependent parameter determined as 0.324 by JMA‐analysis, k0 is the frequency factor, EA is the activation energy for atomic diffusion, and represents the activation energy for nucleation. The results of fitting the data to this equation were Tc=1199°C, A=3.9×106 kJ mol−1 K−2, EA=605 kJ mol−1, and k0=3.65×1015. We conclude that the boundary between sillimanite and mullite+SiO2 in the phase diagram is ~1200°C.
miR‐181a and miR‐150 regulate dendritic cell immune inflammatory responses and cardiomyocyte apoptosis via targeting JAK1–STAT1/c‐Fos pathway
Authors: Zhu Jianbing , Yao Kang , Guo Junjie , Shi Hongtao , Ma Leilei , Wang Qian , Liu Haibo , Gao Wei , Sun Aijun , Zou Yunzeng , Ge Junbo 
Published: June 2017

AbstractThe immune inflammatory response plays a crucial role in many cardiac pathophysiological processes, including ischaemic cardiac injury and the post‐infarction repair process. MicroRNAs (miRNAs) regulate the development and function of dendritic cells (DCs), which are key players in the initiation and regulation of immune responses; however, the underlying regulatory mechanisms remain unclear. Here, we used the supernatants of necrotic primary cardiomyocytes (Necrotic‐S) to mimic the myocardial infarction (MI) microenvironment to investigate the role of miRNAs in the regulation of DC‐mediated inflammatory responses. Our results showed that Necrotic‐S up‐regulated the DC maturation markers CD40, CD83 and CD86 and increased the production of inflammatory cytokines, concomitant with the up‐regulation of miR‐181a and down‐regulation of miR‐150. Necrotic‐S stimulation activated the JAK/STAT pathway and promoted the nuclear translocation of c‐Fos and NF‐κB p65, and silencing of STAT1 or c‐Fos suppressed Necrotic‐S‐induced DC maturation and inflammatory cytokine production. The effects of Necrotic‐S on DC maturation and inflammatory responses, its activation of the JAK/STAT pathway and the induction of cardiomyocyte apoptosis under conditions of hypoxia were suppressed by miR‐181a or miR‐150 overexpression. Taken together, these data indicate that miR‐181a and miR‐150 attenuate DC immune inflammatory responses via JAK1–STAT1/c‐Fos signalling and protect cardiomyocytes from cell death under conditions of hypoxia.
Epigenetics in natural animal populations
Authors: Hu J. , Barrett R. D. H. 
Published: June 2017

AbstractPhenotypic plasticity is an important mechanism for populations to buffer themselves from environmental change. While it has long been appreciated that natural populations possess genetic variation in the extent of plasticity, a surge of recent evidence suggests that epigenetic variation could also play an important role in shaping phenotypic responses. Compared with genetic variation, epigenetic variation is more likely to have higher spontaneous rates of mutation and a more sensitive reaction to environmental inputs. In our review, we first provide an overview of recent studies on epigenetically encoded thermal plasticity in animals to illustrate environmentally‐mediated epigenetic effects within and across generations. Second, we discuss the role of epigenetic effects during adaptation by exploring population epigenetics in natural animal populations. Finally, we evaluate the evolutionary potential of epigenetic variation depending on its autonomy from genetic variation and its transgenerational stability. Although many of the causal links between epigenetic variation and phenotypic plasticity remain elusive, new data has explored the role of epigenetic variation in facilitating evolution in natural populations. This recent progress in ecological epigenetics will be helpful for generating predictive models of the capacity of organisms to adapt to changing climates.
An Evolutionary Concept Analysis of Compassion Fatigue
Authors: Sorenson Claire , Bolick Beth , Wright Karen , Hamilton Rebekah 
Published: June 2017

AbstractPurposeThe purpose of this article is to fill the need for an updated concept analysis of compassion fatigue.MethodsThis review used Rodgers’ Evolutionary Model to direct the analysis of 25 papers published between 2005 and 2015. This review focused strictly on healthcare providers in the formal healthcare setting.ConclusionsThe authors provided an analysis of the evolution of compassion fatigue and identified surrogate terms, attributes and defining characteristics, and antecedents and consequences of the term, true to Rodgers’ Evolutionary Model. Related terms are also discussed and a brief case model is provided.Clinical RelevanceA better understanding of compassion fatigue will allow researchers and clinicians to identify its causes, prevention, and treatment. This could impact the rate at which healthcare providers leave clinical practice and their ability to compassionately engage with patients.
Next‐generation sequencing of oncogenes and tumor suppressor genes in odontogenic myxomas
Authors: Santos Jean Nunes , Sousa Neto Ernesto Santos , França Josiane Alves , Diniz Marina Gonçalves , Moreira Rennan Garcias , Castro Wagner Henriques , Gomez Ricardo Santiago , de Sousa Silvia Ferreira , Gomes Carolina Cavalieri 
Published: June 2017

BackgroundMutations previously considered drivers of malignant neoplasms also occur in benign tumors. From the biological perspective, the study of malignant and benign neoplasms is equally relevant. The study of rare tumors contributes to the understanding of the more common ones, as both could share the same hallmark genetic drivers. The identification of driver mutations in benign tumors is facilitated by the fact that they harbor quiet genomes. Pathogenic mutations have being described in benign epithelial odontogenic tumors, such as ameloblastomas and adenomatoid odontogenic tumors. However, the molecular pathogenesis of odontogenic myxoma (OM), a benign aggressive ectomesenchymal tumor, is still poorly characterized, precluding the development of personalized therapy. Aiming to find druggable genetic mutations, we investigated in OM mutations in 50 genes commonly mutated in cancer.MethodsWe used targeted next‐generation sequencing to interrogate over 2,800 COSMIC mutations in OM.ResultsMissense single nucleotide variants were detected in KDR, TP53, PIK3CA, KIT, JAK3; however, these did not include pathogenic mutations.ConclusionThese aggressive tumors do not harbor pathogenic mutations in genes commonly mutated in human cancers or if they do, these mutations probably occur in a low proportion of cases.
Effect of Split‐File Digital Workflow on Crown Margin Adaptation
Authors: Sheridan Ryan R. , Verrett Ronald , Haney Stephan , Schoolfield John 
Published: June 2017

AbstractPurposeComputer‐aided design/computer‐aided manufacturing (CAD/CAM) is becoming increasingly integrated into dental practice workflow at a pace that exceeds scientific validation. The aim of this study is to evaluate a complete digital split‐file protocol relative to segmental digital and analog techniques for restoring a single maxillary anterior edentulous space with custom abutment and crown.Materials and MethodsFour treatment workflows were assessed: complete digital (CD), segmental digital (SD), milled wax (AM), and heat pressed and hand waxed (AH) and heat pressed. The CD workflow “split” an abutment and crown into separate files to fabricate a zirconia abutment and both zirconia/lithium disilicate crown restorations. The SD workflow scanned the existing abutment for design of segmental restorations in zirconia, lithium disilicate, and milled wax (AM). The AH specimens were conventionally hand waxed. Both the AM and AH specimens were heat pressed with lithium disilicate. All restorations were evaluated with standardized measurements using scanning electron microscopy (SEM) as manufactured without internal adjustments and after manual adjustment. The number of adjustments, adjustment time, and location of adjustments were recorded. One‐way ANOVA with repeated measures was used to report geometric means with 95% confidence intervals.ResultsThe mean marginal gap after adjustment of the CD group was 69 μm, with an upper bound (UB) of 79 μm and a lower bound (LB) of 60 μm. SD group mean was 26 μm with an UB of 31 μm and LB of 22 μm. The AM group mean was 32 μm, with an UB of 49 μm and a LB of 20 μm; AH group mean of 26 μm with an UB of 34 μm and a LB of 20 μm. The SD, AM, and AH workflows were statistically similar (p = 1.000), and the CD workflow was statistically greater than the other three (p < 0.001).ConclusionsThe split‐file (CD) protocol results in marginal gap size within clinical standards after adjustment; however, 52 of the 60 digitally produced restorations showed a horizontal marginal offset that required adjustment for proper contours.
The Effect of Temporary Cement Cleaning Methods on the Retention of Crowns
Authors: Song Mi‐Young , An Hongseok , Park Eun‐Jin 
Published: June 2017

AbstractPurposeTo evaluate the effect of temporary cement cleaning methods on the retention of cemented crowns using zinc phosphate cement and resin‐modified glass ionomer cement.Materials and MethodsForty titanium specimens were fabricated to simulate prepared molars with minimally retentive taper. The Ni‐Cr cast crowns were fabricated, temporarily cemented, and separated. The specimens were divided into four groups according to the temporary cement cleaning method (n = 10) as follows: control group (no temporary cementation), orange solvent group, ultrasonic cleaning group, and air‐abrasion group. After the cleaning procedures, the specimens were cemented with definitive cements (zinc phosphate cement and resin‐modified glass ionomer, RMGI, cement) and subjected to thermocycling (5000 cycles, 5‐55°C, dwell time, 10 seconds). The tensile bond strength of each specimen was measured using a universal testing machine, and the results were analyzed using the Kruskal‐Wallis and Mann‐Whitney U test (α = 0.05).ResultsWhen cemented with zinc phosphate cement, the statistical analysis showed that the value of the air‐abrasion group was significantly higher than those of the other groups (p < 0.01). There was no statistically significant difference among the other groups. When cemented with RMGI cement, the air‐abrasion group showed the lowest value, and the control group showed the highest value (p < 0.01). The difference between the ultrasonic cleaning group and the orange solvent group was not statistically significant.ConclusionThe use of temporary cement did not have a significant influence on retention of permanently cemented crowns when zinc phosphate cement was used for permanent cementation. Airborne‐particle abrasion after provisional cementation improved retention of crowns cemented with zinc phosphate cement; however, the use of temporary cement significantly decreased retention of permanently cemented crowns when RMGI cement was used regardless of the temporary cement cleaning method.
Impact of Denture Cleansing Solution Immersion on Some Properties of Different Denture Base Materials: An In Vitro Study
Authors: Al‐Thobity Ahmad M. , Gad Mohammed , ArRejaie Aws , Alnassar Talal , Al‐Khalifa Khalifa S. 
Published: June 2017

AbstractPurposeTo evaluate the effect of several denture cleansing solutions on the color stability, surface roughness, and flexural strength of three denture base materials.Materials and MethodsTwenty‐seven specimens were prepared using heat‐polymerized (HP) denture base material, 27 using autopolymerized (AP) denture base material, and 27 using visible‐light‐polymerized (VLP) denture base, creating a total of 81 specimens. The specimens were randomly divided into three groups (n = 27): the distilled water group (DWG), Corega group (CG), and Renew group (RG). Color changes (ΔE), surface roughness (Ra, nm), and flexural strength (MPa) of each specimen were measured using a spectrophotometer, an optical profilometer, and a universal testing machine, respectively. The results were statistically analyzed using a one‐way ANOVA and a post hoc Tukey's test (α = 0.05).ResultsThe only statistically significant color change detected was in the VLP resin treated with Corega and Renew. There was a significant increase in the surface roughness of all denture resin groups after immersion in Corega. Immersion in Renew significantly increased surface roughness only in the HP and AP specimens. The only significant reduction in flexural strength was detected in the HP resin after immersion in Corega (p < 0.05).ConclusionsWithin the limitations of this study, it can be concluded that Corega has a significantly greater negative impact than distilled water on the flexural strength of HP resin base materials. Renew significantly increased the surface roughness of AP and HP, while Corega increased the surface roughness of all resin materials.
Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae)
Authors: Passow Courtney N. , Brown Anthony P. , Arias‐Rodriguez Lenin , Yee Muh‐Ching , Sockell Alexandra , Schartl Manfred , Warren Wesley C. , Bustamante Carlos , Kelley Joanna L. , Tobler Michael 
Published: June 2017

AbstractVariation in gene expression can provide insights into organismal responses to environmental stress and physiological mechanisms mediating adaptation to habitats with contrasting environmental conditions. We performed an RNA‐sequencing experiment to quantify gene expression patterns in fish adapted to habitats with different combinations of environmental stressors, including the presence of toxic hydrogen sulphide (H2S) and the absence of light in caves. We specifically asked how gene expression varies among populations living in different habitats, whether population differences were consistent among organs, and whether there is evidence for shared expression responses in populations exposed to the same stressors. We analysed organ‐specific transcriptome‐wide data from four ecotypes of Poecilia mexicana (nonsulphidic surface, sulphidic surface, nonsulphidic cave and sulphidic cave). The majority of variation in gene expression was correlated with organ type, and the presence of specific environmental stressors elicited unique expression differences among organs. Shared patterns of gene expression between populations exposed to the same environmental stressors increased with levels of organismal organization (from transcript to gene to physiological pathway). In addition, shared patterns of gene expression were more common between populations from sulphidic than populations from cave habitats, potentially indicating that physiochemical stressors with clear biochemical consequences can constrain the diversity of adaptive solutions that mitigate their adverse effects. Overall, our analyses provided insights into transcriptional variation in a unique system, in which adaptation to H2S and darkness coincide. Functional annotations of differentially expressed genes provide a springboard for investigating physiological mechanisms putatively underlying adaptation to extreme environments.
A novel RNA polymerase‐binding protein that interacts with a sigma‐factor docking site
Authors: Wang Erickson Anna F. , Deighan Padraig , Chen Shanshan , Barrasso Kelsey , Garcia Cinthia P. , Martínez‐Lumbreras Santiago , Alfano Caterina , Krysztofinska Ewelina M. , Thapaliya Arjun , Camp Amy H. , Isaacson Rivka L. , Hochschild Ann , Losick Richard 
Published: June 2017

SummarySporulation in Bacillus subtilis is governed by a cascade of alternative RNA polymerase sigma factors. We previously identified a small protein Fin that is produced under the control of the sporulation sigma factor σF to create a negative feedback loop that inhibits σF‐directed gene transcription. Cells deleted for fin are defective for spore formation and exhibit increased levels of σF‐directed gene transcription. Based on pull‐down experiments, chemical crosslinking, bacterial two‐hybrid experiments and nuclear magnetic resonance chemical shift analysis, we now report that Fin binds to RNA polymerase and specifically to the coiled‐coil region of the β′ subunit. The coiled‐coil is a docking site for sigma factors on RNA polymerase, and evidence is presented that the binding of Fin and σF to RNA polymerase is mutually exclusive. We propose that Fin functions by a mechanism distinct from that of classic sigma factor antagonists (anti‐σ factors), which bind directly to a target sigma factor to prevent its association with RNA polymerase, and instead functions to inhibit σF by competing for binding to the β′ coiled‐coil.
Mechanistic insight into acrylate metabolism and detoxification in marine dimethylsulfoniopropionate‐catabolizing bacteria
Authors: Wang Peng , Cao Hai‐Yan , Chen Xiu‐Lan , Li Chun‐Yang , Li Ping‐Yi , Zhang Xi‐Ying , Qin Qi‐Long , Todd Jonathan D. , Zhang Yu‐Zhong 
Published: June 2017

SummaryDimethylsulfoniopropionate (DMSP) cleavage, yielding dimethyl sulfide (DMS) and acrylate, provides vital carbon sources to marine bacteria, is a key component of the global sulfur cycle and effects atmospheric chemistry and potentially climate. Acrylate and its metabolite acryloyl‐CoA are toxic if allowed to accumulate within cells. Thus, organisms cleaving DMSP require effective systems for both the utilization and detoxification of acrylate. Here, we examine the mechanism of acrylate utilization and detoxification in Roseobacters. We propose propionate‐CoA ligase (PrpE) and acryloyl‐CoA reductase (AcuI) as the key enzymes involved and through structural and mutagenesis analyses, provide explanations of their catalytic mechanisms. In most cases, DMSP lyases and DMSP demethylases (DmdAs) have low substrate affinities, but AcuIs have very high substrate affinities, suggesting that an effective detoxification system for acylate catabolism exists in DMSP‐catabolizing Roseobacters. This study provides insight on acrylate metabolism and detoxification and a possible explanation for the high Km values that have been noted for some DMSP lyases. Since acrylate/acryloyl‐CoA is probably produced by other metabolism, and AcuI and PrpE are conserved in many organisms across all domains of life, the detoxification system is likely relevant to many metabolic processes and environments beyond DMSP catabolism.