bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ambient changes exceed treatment effects on plant species abundance in global change experiments
Authors: Langley J. Adam , Chapman Samantha K. , La Pierre Kimberly J. , Avolio Meghan , Bowman William D. , Johnson David S. , Isbell Forest , Wilcox Kevin R. , Foster Bryan L. , Hovenden Mark J. , Knapp Alan K. , Koerner Sally E. , Lortie Christopher J. , Megonigal James P. , Newton Paul C. D. , Reich Peter B. , Smith Melinda D. , Suttle Kenwyn B. , Tilman David 
Published: October 2018

AbstractThe responses of species to environmental changes will determine future community composition and ecosystem function. Many syntheses of global change experiments examine the magnitude of treatment effect sizes, but we lack an understanding of how plant responses to treatments compare to ongoing changes in the unmanipulated (ambient or background) system. We used a database of long‐term global change studies manipulating CO2, nutrients, water, and temperature to answer three questions: (a) How do changes in plant species abundance in ambient plots relate to those in treated plots? (b) How does the magnitude of ambient change in species‐level abundance over time relate to responsiveness to global change treatments? (c) Does the direction of species‐level responses to global change treatments differ from the direction of ambient change? We estimated temporal trends in plant abundance for 791 plant species in ambient and treated plots across 16 long‐term global change experiments yielding 2,116 experiment–species–treatment combinations. Surprisingly, for most species (57%) the magnitude of ambient change was greater than the magnitude of treatment effects. However, the direction of ambient change, whether a species was increasing or decreasing in abundance under ambient conditions, had no bearing on the direction of treatment effects. Although ambient communities are inherently dynamic, there is now widespread evidence that anthropogenic drivers are directionally altering plant communities in many ecosystems. Thus, global change treatment effects must be interpreted in the context of plant species trajectories that are likely driven by ongoing environmental changes.
Global geographic patterns in the colours and sizes of animal‐dispersed fruits
Authors: Sinnott‐Armstrong Miranda A. , Downie Alexander E. , Federman Sarah , Valido Alfredo , Jordano Pedro , Donoghue Michael J. 
Published: October 2018

AbstractAimFruit colours attract animal seed dispersers, yet the causes of fruit colour diversity remain controversial. The lack of knowledge of large‐scale spatial patterns in fruit colours has limited our ability to formulate and test alternative hypotheses to explain fruit colour, fruit size and fruit colour diversity. We describe spatial (especially latitudinal) variation in fruit colour, colour diversity and length, and test for correlations between fruit colour, length and plant habit.LocationGlobal.Time periodPresent day.Major taxa studiedSeed plants.MethodsWe assembled a database of fruit traits for 13,178 fleshy fruited plant species spanning 136 sites around the world. To assess whether fruit colour categories correspond with spectral reflectances, we tested for clustering of hue, chroma and saturation for 236 species for which we had reflectance data. We then quantified latitudinal gradients in fruit colour, fruit length and fruit colour diversity while controlling for the effects of plant habit and whether colour categories varied with respect to average fruit size.ResultsColour categories corresponded well with reflectance data. The tropics show high colour diversity, while red fruits progressively constitute a higher proportion of the fleshy‐fruited plant community towards high latitudes. All mammal‐associated colours (green, orange, brown and yellow) are more common in the tropics than at high latitudes. Fruit length also increases towards the tropics.Main conclusionsTropical communities tend to have diverse fruit colours, including many mammal‐associated fruit colours, while high latitude communities contain a higher percentage of red‐fruited species. The correlation between colour and size is strong, and some latitudinal patterns may be partly driven by changes in fruit size. Differences in geography and in the history of plant lineages in the Southern versus the Northern Hemisphere may help to explain some biogeographic patterns, but alternative hypotheses related to fruit defence, development and metabolic costs are plausible.
Gauging support for macroecological patterns in helminth parasites
Authors: Dallas Tad A. , Aguirre A. Alonso , Budischak Sarah , Carlson Colin , Ezenwa Vanessa , Han Barbara , Huang Shan , Stephens Patrick R. 
Published: October 2018

AbstractAimTo explore spatial patterns of helminth parasite diversity, and to investigate three main macroecological patterns – (a) latitude–diversity relationships, (b) positive scaling between parasite and host diversity, and (c) species–area relationships – using a largely underutilized global database of helminth parasite occurrence records.LocationGlobal.MethodsWe examined the London Natural History Museum’s collection of helminth parasite occurrence records, consisting of over 18,000 unique host species and 27,000 unique helminth parasite species distributed across over 350 distinct terrestrial and aquatic localities.ResultsWe find support for latitudinal gradients in parasite diversity and a strong relationship between host and parasite diversity at the global scale. Helminth species diversity–area relationships were not detectable as a function of host body mass, but larger geographic areas supported higher parasite richness, potentially mediated through higher host richness.Main conclusionsOur findings indicate that helminth parasites may obey some of the macroecological relationships found in free‐living species, suggesting that parasites may offer further support for the generality of these patterns, while offering interesting counterexamples for others. We conclude with a discussion of future directions and potential challenges in the newly emerging macroecology of infectious disease.
Homogenization of species composition and species association networks are decoupled
Authors: Li Daijiang , Poisot Timothée , Waller Donald M. , Baiser Benjamin 
Published: October 2018

AbstractAimEcological communities are composed of both species and the biotic relationships (interactions or spatial associations) among them. Biotic homogenization in species composition (i.e., increased site‐to‐site similarity) is recognized as a common consequence of global change, but less is known about how the similarity of species relationships changes over space and time. Does homogenization of species composition lead to homogenization of species relationships or are the dynamics of species relationships decoupled from changes in species composition?LocationWisconsin, USA.Time period1950–2012.Major taxa studiedVascular plants.MethodsWe used long‐term resurvey data to analyse changes in plant species association patterns between the 1950s and 2000s at 266 sites distributed among three community types in Wisconsin, USA. We used species associations (quantified via local co‐occurrence patterns) to represent one type of relationship among species. Species pairs that co‐occur more or less than expected by chance have positive or negative associations, respectively. We then measured beta diversity in both species composition and species association networks over time and space.ResultsShifts in species associations consistently exceeded the shifts observed in species composition. Less disturbed forests of northern Wisconsin have converged somewhat in species composition but little in species associations. In contrast, forests in central Wisconsin succeeding from pine barrens to closed‐canopy forests have strongly homogenized in both species composition and species associations. More fragmented forests in southern Wisconsin also tended to converge in species composition and in the species’ negative associations, but their positive associations diverged over the last half century. Species composition and associations are generally affected by a similar set of environmental variables. Their relative importance, however, has changed over time.Main conclusionsLong‐term shifts in species relationships appear to be decoupled from shifts in species composition despite being affected by similar environmental variables.
Expression of epithelial‐mesenchymal transition regulators TWIST, SLUG and SNAIL in follicular thyroid tumours may relate to widely invasive, poorly differentiated and distant metastasis
Authors: Wu Jianghua , Zhang Yanhui , Cheng Runfen , Gong Wenchen , Ding TingTing , Zhai Qiongli , Wang Yong , Meng Bin , Sun Baocun 
Published: October 2018

AimsTo assess the expression of epithelial–mesenchymal transition (EMT) regulators in follicular thyroid tumours.Methods and resultsThe expression of E‐cadherin (E‐CAD) and transcription factors TWIST, SLUG and SNAIL in follicular thyroid tumours was examined by immunohistochemistry in tissue samples, including 18 follicular adenomas (FA), 12 minimally invasive follicular thyroid carcinomas (MI‐FTC), 16 widely invasive follicular thyroid carcinomas (WI‐FTC), 10 poorly differentiated follicular thyroid carcinomas (PDTC) and six anaplastic thyroid carcinomas (ATC). Metastatic tumour tissues from six of these cases were also examined. The results showed an increasing expression trend of EMT regulators in a panel of follicular tumour cases with a spectrum of morphological subtypes from low‐ to high‐risk malignancy. The expression of EMT regulators was higher in the WI‐FTC, PDTC and ATC groups but focal and lower in the FA and MI‐FTC groups. Different expression intensity of E‐CAD and EMT regulators at the tumour centre part and the invasive front (IF) was observed. The loss of E‐CAD and expression of EMT regulators was significantly correlated with distant metastasis and vascular invasion (VI) in the well‐differentiated follicular carcinoma (WD‐FTC), and six tumours of metastatic sites also showed variables positive for EMT regulators. The disease‐free survival analysis showed an apparent relationship between the expression of EMT regulators and the tumour disease‐free outcomes in WD‐FTC.ConclusionsOur study supported the role of EMT in the development of follicular thyroid carcinoma and indicated that EMT regulatory proteins may play an important role in WD‐FTC that are widely invasive and exhibit distant metastasis.
Lithium isotope variations in Tonga–Kermadec arc–Lau back‐arc lavas and Deep Sea Drilling Project (DSDP) Site 204 sediments
Authors: Brens Raul , Liu Xiao‐Ming , Turner Simon , Rushmer Tracy 
Published: October 2018

AbstractLithium isotopes have been identified as a promising tracer of subducted materials in arc lavas due to the observable variations in related reservoirs such as subducting sediments and altered oceanic crust. The Tonga–Kermadec arc–Lau back‐arc provides an end‐member of subduction zones with the coldest thermal structure on Earth. Reported here are Li isotope data for 14 lavas from the arc front and 7 back‐arc lavas as well as 12 pelagic and volcaniclastic sediments along a profile through the sedimentary sequence at DSDP Site 204. The arc and back‐arc lavas range from basalts to dacites in composition with SiO2 = 48.3–65.3 wt% over which Li concentrations increase from 2 ppm to 16 ppm. Li/Y ratios range from 0.08 to 0.77 and from 0.24 to 0.65 in the arc and back‐arc lavas, respectively. The majority of the lavas have δ7Li that ranges from 2.5 ‰ to 5.0 ‰ with an average of (3.6 ±0.7) ‰, similar to that reported from other arcs and there is no distinction between the arc front and back‐arc lavas. The pelagic sediments have variable Li concentrations (33–133 ppm) and δ7Li that ranges from 1.2 ‰ to 10.2 ‰ while the volcaniclastic sediments have an even greater range of Li concentrations (3.6–165 ppm) and generally higher δ7Li values (8–14 ‰). However, δ7Li in the lavas does not correlate with commonly used trace element ratio or isotope signatures indicative of slab‐derived fluids or the sediments. This is probably because the range of δ7Li in the lavas and sediments overlap. Calculated sediment mass‐balance models require significantly more sediment than previous estimates based on Th–Nd–Be isotopes. This may indicate that a sizeable proportion of the total Li budget in the lavas is provided by Li‐enriched fluids from the subducting sediments and/or altered oceanic crust.
Inflammation‐induced overexpression of microRNA‐223‐3p regulates odontoblastic differentiation of human dental pulp stem cells by targeting SMAD3
Authors: Huang X. , Liu F. , Hou J. , Chen K. 
Published: October 2018

AbstractAimTo profile miRNA expression between inflamed and healthy human dental pulp tissues and to investigate how the upregulation of miR‐223‐3p in the inflamed pulp tissue regulates odontoblast differentiation and regeneration.MethodologyMicroarray analysis was used to identify differences in miRNA expression patterns between healthy and inflamed pulp tissue. The results were validated using quantitative real‐time PCR. To determine the effect of miR‐223‐3p on odontoblast differentiation, miR‐223‐3p was overexpressed in human dental pulp stem cells (DPSCs), which were cultured in mineralizing induction medium (to induce odontoblast differentiation). To identify the target genes of miR‐223‐3p, an SABiosciences Human Osteogenesis PCR Array, combined with bioinformatics, was used. Furthermore, a dual‐luciferase reporter assay and a small interfering RNA (siRNA) experiment were used to confirm the relationship between miR‐223‐3p and its target gene. Statistical analysis was performed using the Student's t‐test or one‐way analysis of variance (anova); P < 0.05 was considered statistically significant.ResultsSeventy‐nine miRNAs were significantly differentially expressed (fold change >2.0; P < 0.05) between the two tissues. In particular, miR‐223‐3p was markedly upregulated in inflamed dental pulp. Overexpression of miR‐223‐3p in DPSCs significantly increased the protein levels of dentine sialophosphoprotein (DSPP) and dentine matrix protein 1 (DMP‐1) (P < 0.05). However, the SMAD family member 3 (SMAD3) protein level was significantly lower than in control DPSCs (P < 0.05). Bioinformatics and the dual‐luciferase assay reporter assay indicated that Smad3 was a potential target of miR‐223‐3p. Knockdown of Smad3 in DPSCs subjected to mineralization induction resulted in detection of DSPP and DMP‐1 earlier than in control DPSCs, and it increased the protein level of alkaline phosphatase (ALP), thereby promoting odontoblast differentiation.ConclusionsmiR‐223‐3p is implicated in the regulation of odontoblast differentiation, which may be involved in the process of pulpitis repair.
Characterisation of sorghum starch granules using SAXS: effects of moisture on crystallinity and structure
Authors: Subzwari Sana , Bryant Gary , Small Darryl M. 
Published: October 2018

SummaryIn order to further characterise sorghum starch as a potential ingredient in food formulations, starch granules have been extracted from sorghum flour and characterised. The lamellar structure of granules and the uptake of water under ambient conditions have been investigated using small‐angle X‐ray scattering (SAXS). The lamellar structure was affected by the uptake of water and crystallinity was disrupted as water was absorbed. The diameter of sorghum granules had a bimodal distribution and the lamellar patterns were similar to those of other cereal starches. Moisture uptake occurred within the first four hours of exposure to water and SAXS provides a valuable technique for further studies of granular starch, including changes during the uptake of water.
Predictive ability of renal cortex enhancement in dynamic computed tomography for residual renal function after nephroureterectomy: Comparison with 99mTc‐diethylenetriaminopentacetic acid renography and validation study
Authors: Waseda Yuma , Saito Kazutaka , Ishikawa Yudai , Kawano Keizo , Yokoyama Minato , Ishioka Junichiro , Matsuoka Yoh , Morimoto Shinji , Kihara Kazunori , Fujii Yasuhisa 
Published: October 2018

ObjectiveTo estimate postoperative residual renal function after radical nephroureterectomy for upper tract urothelial carcinoma using the preoperative dynamic computed tomography renal cortex enhancement ratio in comparison with the split kidney glomerular filtration rate measured by 99mTc‐diethylenetriaminopentacetic acid renography.MethodsA total of 47 patients who received radical nephroureterectomy and underwent both preoperative dynamic computed tomography and renography were the model‐development cohort; and 109 patients who underwent dynamic computed tomography alone were the validation cohort. Postoperative renal function of the unremoved kidney was estimated using the following formulas: preoperative estimated glomerular filtration rate × the percentage of total renal cortex radiodensity for the intact kidney in Hounsfield units obtained from corticomedullary phase images in the computed tomography‐based model, or the percentage of the total glomerular filtration rate measured by renography in the nuclear model. The correlation between observed and estimated postoperative renal function was determined. The computed tomography‐based prediction model derived from linear regression analysis was validated externally.ResultsThe correlation of computed tomography‐based split renal function with the observed postoperative estimated glomerular filtration rate (r = 0.80) was equivalent to that of nuclear split renal function (r = 0.78). In the validation cohort, the computed tomography‐based prediction model showed an equivalently strong correlation (r = 0.78).ConclusionsThe present study showed that the percentage of total renal cortex radiodensity for the intact kidney is a useful tool for predicting unremoved kidney function in upper tract urothelial carcinoma patients, thereby allowing appropriate patient selection for perioperative cisplatin‐based combination chemotherapy.
Infants’ Biological Sensitivity to the Effects of Maternal Social Support: Evidence Among Mexican American Families
Authors: Somers Jennifer A. , Jewell Shannon L. , Hanna Ibrahim Mariam , Luecken Linda J. 
Published: October 2018

The identification of infants who are most susceptible to both negative and positive social environments is critical for understanding early behavioral development. This study longitudinally assessed the interactive effects of infant vagal tone (respiratory sinus arrhythmia; RSA) and maternal social support on behavioral problems and competence among 322 low‐income Mexican American mother–infant dyads (infants: 54.1% female) and explored sex differences. Infant RSA was calculated from resting HR data at 6 weeks of age. Mothers reported on general social support, partner support, and family support at 6 months, and infant behavioral problems and competence at 1 year. Two‐way interactions (RSA × support source) were evaluated to predict behavioral problems and competence, adjusting for covariates. Results indicated higher competence among infants with lower RSA whose mothers reported higher general support or higher partner support. Interactive effects on behavior problems of RSA with maternal partner or family support were only found for female infants: Girls with higher RSA showed more behavior problems when mothers reported low support, but fewer problem levels in the context of high support. Our results suggest that infant RSA is an important moderator of the effects of the early social environment on early development.
Statistical Analysis with Linked Data
Authors: Han Ying , Lahiri Partha 
Published: October 2018

SummaryComputerised Record Linkage methods help us combine multiple data sets from different sources when a single data set with all necessary information is unavailable or when data collection on additional variables is time consuming and extremely costly. Linkage errors are inevitable in the linked data set because of the unavailability of error‐free unique identifiers. A small amount of linkage errors can lead to substantial bias and increased variability in estimating parameters of a statistical model. In this paper, we propose a unified theory for statistical analysis with linked data. Our proposed method, unlike the ones available for secondary data analysis of linked data, exploits record linkage process data as an alternative to taking a costly sample to evaluate error rates from the record linkage procedure. A jackknife method is introduced to estimate bias, covariance matrix and mean squared error of our proposed estimators. Simulation results are presented to evaluate the performance of the proposed estimators that account for linkage errors.
Charted waters? Tracking the production of conservation territories on the high seas
Authors: Gray Noella J. 
Published: October 2018

AbstractMarine protected areas (MPAs), a common marine conservation tool, function as both objects of governance and as a form of territory. This article tracks the long‐term effort to produce conservation territories on the high seas, in areas beyond national jurisdiction. Drawing on data collected at five international environmental meetings, the paper demonstrates how an imaginative geography of the high seas is being simultaneously constituted by scientific and technological advances, particularly geospatial visualisations, as well as coordinated efforts to advocate for and develop a new international conservation instrument (an implementing agreement under the United Nations Convention on the Law of the Sea). Conventional understandings of territory constrain this effort by equating territory with the state. At the same time, the case of high seas conservation contributes to critiques of this conceptualisation of territory, by showcasing the role of multiple actors in seeing and controlling ocean space. Overall, the production of territory on the high seas both reflects and informs a shift in the “frontier mentality” of the oceans, as conservation and science frontier as well as economic frontier. Diverse responses to representations of, and policies for, the high seas point to both possibilities and limits of territorial thinking in the oceans.
Surface shape development of the pitch lap under the loading of the conditioner in continuous polishing process
Authors: Liao Defeng , Xie Ruiqing , Zhao Shijie , Ren Lele , Zhang Feihu , Wang Jian , Xu Qiao 
Published: October 2018

AbstractContinuous polishing using the pitch lap is a key process in finishing large flat optical elements. The optical elements’ surface figure is primarily dependent on the surface shape of the pitch lap, which is controlled by a large‐size conditioner. However, underlying fundamentals of the process control is not yet clear, and it remains empirical and nondeterministic to date. In this study, a novel analysis model is proposed for exploring the surface shape development of the pitch lap under the conditioner loading. The analysis model divides the polishing time into a series of segments, in which the shape variation of the pitch lap due to viscoelastic creep is derived from the pressure distribution at the conditioner‐lap contact interface. Further, a contact model of the lap and conditioner is built to obtain the pressure distribution at the interface, and a novel creep model is proposed for the viscoelastic behavior of the pitch lap under the pressure. The analysis model combined with the contact and viscoelastic models can be used to explore the pitch lap shape development under various conditions and hence reveal the underlying fundamentals of controlling the lap shape by the conditioner.