bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered spring phenology of North American freshwater turtles and the importance of representative populations
Authors: Janzen Fredric J. , Hoekstra Luke A. , Brooks Ronald J. , Carroll David M. , Gibbons J. Whitfield , Greene Judith L. , Iverson John B. , Litzgus Jacqueline D. , Michael Edwin D. , Parren Steven G. , Roosenburg Willem M. , Strain Gabriel F. , Tucker John K. , Ultsch Gordon R. 
Published: May 2018

AbstractGlobally, populations of diverse taxa have altered phenology in response to climate change. However, most research has focused on a single population of a given taxon, which may be unrepresentative for comparative analyses, and few long‐term studies of phenology in ectothermic amniotes have been published. We test for climate‐altered phenology using long‐term studies (10–36 years) of nesting behavior in 14 populations representing six genera of freshwater turtles (Chelydra, Chrysemys, Kinosternon, Malaclemys, Sternotherus, and Trachemys). Nesting season initiation occurs earlier in more recent years, with 11 of the populations advancing phenology. The onset of nesting for nearly all populations correlated well with temperatures during the month preceding nesting. Still, certain populations of some species have not advanced phenology as might be expected from global patterns of climate change. This collection of findings suggests a proximate link between local climate and reproduction that is potentially caused by variation in spring emergence from hibernation, ability to process food, and thermoregulatory opportunities prior to nesting. However, even though all species had populations with at least some evidence of phenological advancement, geographic variation in phenology within and among turtle species underscores the critical importance of representative data for accurate comprehensive assessments of the biotic impacts of climate change.
Woodland caribou habitat selection patterns in relation to predation risk and forage abundance depend on reproductive state
Authors: Viejou Rebecca , Avgar Tal , Brown Glen S. , Patterson Brent R. , Reid Doug E. B. , Rodgers Arthur R. , Shuter Jennifer , Thompson Ian D. , Fryxell John M. 
Published: May 2018

AbstractThe ideal free distribution assumes that animals select habitats that are beneficial to their fitness. When the needs of dependent offspring differ from those of the parent, ideal habitat selection patterns could vary with the presence or absence of offspring. We test whether habitat selection depends on reproductive state due to top‐down or bottom‐up influences on the fitness of woodland caribou (Rangifer tarandus caribou), a threatened, wide‐ranging herbivore. We combined established methods of fitting resource and step selection functions derived from locations of collared animals in Ontario with newer techniques, including identifying calf status from video collar footage and seasonal habitat selection analysis through latent selection difference functions. We found that females with calves avoided predation risk and proximity to roads more strongly than females without calves within their seasonal ranges. At the local scale, females with calves avoided predation more strongly than females without calves. Females with calves increased predation avoidance but not selection for food availability upon calving, whereas females without calves increased selection for food availability across the same season. These behavioral responses suggest that habitat selection by woodland caribou is influenced by reproductive state, such that females with calves at heel use habitat selection to offset the increased vulnerability of their offspring to predation risk.
Density‐dependent and density‐independent drivers of population change in Barton Springs salamanders
Authors: Bendik Nathan F. , Dries Laurie A. 
Published: May 2018

AbstractUnderstanding population change is essential for conservation of imperiled species, such as amphibians. Worldwide amphibian declines have provided an impetus for investigating their population dynamics, which can involve both extrinsic (density‐independent) and intrinsic (density‐dependent) drivers acting differentially across multiple life stages or age classes. In this study, we examined the population dynamics of the endangered Barton Springs Salamander (Eurycea sosorum) using data from a long‐term monitoring program. We were interested in understanding both the potential environmental drivers (density‐independent factors) and demographic factors (interactions among size classes, negative density dependence) to better inform conservation and management activities. We used data from three different monitoring regimes and multivariate autoregressive state‐space models to quantify environmental effects (seasonality, discharge, algae, and sediment cover), intraspecific interactions among three size classes, and intra‐class density dependence. Results from our primary data set revealed similar patterns among sites and size classes and were corroborated by our out‐of‐sample data. Cross‐correlation analysis showed juvenile abundance was most strongly correlated with a 9‐month lag in aquifer discharge, which we suspect is related to inputs of organic carbon into the aquifer. However, sedimentation limited juvenile abundance at the surface, emphasizing the importance of continued sediment management. Recruitment from juveniles to the sub‐adult size class was evident, but negative density‐dependent feedback ultimately regulated each size class. Negative density dependence may be an encouraging sign for the conservation of E. sosorum because populations that can reach carrying capacity are less likely to go extinct compared to unregulated populations far below their carrying capacity. However, periodic population declines coupled with apparent migration into the aquifer complicate assessments of species status. Although both density‐dependent and density‐independent drivers of population change are not always apparent in time series of animal populations, both have important implications for conservation and management of E. sosorum.
Empowerment and threat in response to mass protest shape public support for a social movement and social change: A panel study in the context of the Bersih movement in Malaysia
Authors: Selvanathan Hema Preya , Lickel Brian 
Published: May 2018

AbstractOne path to social change is through sustained collective action. Although such actions often explicitly target the public audience to raise support for a movement's cause, we know little about how the public psychologically responds to protests. To examine this question, a sample of Malaysians was surveyed before and immediately after the occurrence of mass street protests in Malaysia (N = 422) using a two‐wave longitudinal design. Analyses revealed that (beyond pre‐existing levels of movement identity and support for social change) experiencing empowerment in response to the protests promoted a supportive movement identity and more support for social change after the protests, whereas experiencing threat in response to the protests promoted an oppositional movement identity and less support for social change after the protests. This research suggests that the psychological impact of ongoing protests on the public can determine subsequent public support for the movement and its goals.
Shaking table tests and numerical analyses of an RC coupled wall structure with replaceable coupling beams
Authors: Lu Xilin , Chen Cong , Jiang Huanjun , Wang Shanshan 
Published: May 2018

SummaryThe replaceable coupling beam (RCB) is an innovative structural component developed to increase the seismic resilience of reinforced concrete (RC) shear wall structures. In this study, two 1/5‐scale 5‐story 3‐dimensional RC shear wall structures—one with conventional RC coupling beams and the other with RCBs—were designed, constructed, and tested on a shaking table. The failure pattern, dynamic properties, and structural responses, including the acceleration, displacement, story force, and strain responses, of the 2 structures are compared under earthquake excitations. The test results demonstrate that the seismic performance of the structure with RCBs was improved when RCBs were working compared with the structure with conventional RC coupling beams. In addition, the replaceable devices suffering the severe damage during an earthquake can be conveniently replaced after the earthquake. However, after the sudden failure of RCBs during the severe earthquakes, the inter‐story drift and floor acceleration of the structure with RCBs became larger. The design and manufacture quality of RCBs should be improved to avoid the sudden failure. Then, numerical models for the test structures were established using the commercial software PERFORM‐3D. Numerical simulations of the tests were conducted. The simulation results correspond well with the experimental results, thus verifying the accuracy of the numerical models. The RC shear wall structure installed with RCBs can be applied as a new type of earthquake‐resilient structure in engineering practice.
Badlands as a hot spot of petrogenic contribution to riverine particulate organic carbon to the Gulf of Lion (NW Mediterranean Sea)
Authors: Copard Yoann , Eyrolle Frédérique , Radakovitch Olivier , Poirel Alain , Raimbault Patrick , Gairoard Stéphanie , Di‐Giovanni Christian 
Published: May 2018

AbstractDetermining the riverine carbon fluxes to oceans is critical for an improved understanding of C budgets and biogeochemical cycles (C, O) over a broad range of spatial and time scales. Among the particulate organic carbon (POC) involved in these fluxes, those yielded by sedimentary rocks (petrogenic POC: pPOC) remain somewhat uncertain as to their source on continental surfaces. Based on time series from long‐term observatories, we refine the POC and sediments flux of the Rhône River, one of the major tributaries to the Mediterranean Sea. Radiocarbon measurements on a set of riverine samples and forward modelling were used to (i) determine a modelled pPOC content and pPOC/POC ratio for each sample set, (ii) assess pPOC flux delivered to the NW Mediterranean Sea, and (iii) estimate the badlands contribution from the Durance catchment to both the pPOC and to sediment discharges. The weighted pPOC flux contributes up to 26% of the POC flux (145 Gg yr‐1) discharged into the Mediterranean Sea, whereas the weighted pPOC content reaches 0.31 wt%. Despite their low contributive surface area (0.2%), badlands provide, respectively, 12, 3.5 and 14% of the pPOC, POC and sediment fluxes to the Rhône River. Consequently, such rocks can be considered as a major source of pPOC and sediments for the NW Mediterranean Sea and potentially for oceans. We suggest that river‐dominated ocean margins, such as the Rhône River, with badlands in their catchment could export a significant amount of pPOC to the oceans. Copyright © 2018 John Wiley & Sons, Ltd.
Hierarchically nested river landform sequences. Part 2: Bankfull channel morphodynamics governed by valley nesting structure
Authors: Pasternack Gregory B. , Baig Dastagir , Weber Matthew D. , Brown Rocko A. 
Published: May 2018

AbstractRiver corridors exhibit landforms nested within landforms repeatedly down spatial scales. In Pasternack et al. (), a new, scale‐independent, hierarchical river classification was developed that uses five landform types to map the domains of a single fluvial process – flow convergence routing – at each of three–five spatial scales. Given those methods, this study investigated the details of how flow convergence routing organizes nested landform sequences. The method involved analyzing landform abundance, sequencing, and hierarchical nesting along the 35 km gravel/cobble lower Yuba River in California. Independent testing of flow convergence routing found that hydraulic patterns at every flow matched the essential predictions from classification, substantiating the process–morphology link. River width and bed elevation sequences exhibit large, nonrandom, and linked oscillations structured to preferentially yield wide bars and constricted pools at base flow and bankfull flow. At a flow of 8.44 times bankfull, there is still an abundance of wide bar and constricted pool landforms, but larger topographic drivers also yield an abundance of nozzle and oversized landforms. The nested structure of flow convergence routing landforms reveals that base flow and bankfull landforms are nested together within specific floodprone valley landform types, and these landform types control channel morphodynamics during moderate to large floods. As a result, this study calls into question the prevailing theory that the bankfull channel of a gravel/cobble river is controlled by in‐channel, bankfull, and/or small flood flows. Such flows may initiate sediment transport, but they are too small to control landform organization in a gravel/cobble river with topographic complexity. Copyright © 2018 John Wiley & Sons, Ltd.
Chromosomal rearrangements in uveal melanoma: Chromothripsis
Authors: van Poppelen Natasha M. , Yavuzyigitoglu Serdar , Smit Kyra N. , Vaarwater Jolanda , Eussen Bert , Brands Tom , Paridaens Dion , Kiliç Emine , de Klein Annelies 
Published: May 2018

AbstractUveal melanoma (UM) is the most common primary intraocular malignancy in the Western world. Recurrent mutations in GNAQ, GNA11, CYSLTR2, PLCB4, BAP1, EIF1AX, and SF3B1 are described as well as non‐random chromosomal aberrations. Chromothripsis is a rare event in which chromosomes are shattered and rearranged and has been reported in a variety of cancers including UM. SNP arrays of 249 UM from patients who underwent enucleation, biopsy or endoresection were reviewed for the presence of chromothripsis. Chromothripsis was defined as ten or more breakpoints per chromosome involved. Genetic analysis of GNAQ, GNA11, BAP1, SF3B1, and EIF1AX was conducted using Sanger and next‐generation sequencing. In addition, immunohistochemistry for BAP1 was performed. Chromothripsis was detected in 7 out of 249 tumors and the affected chromosomes were chromosomes 3, 5, 6, 8, 12, and 13. The mean total of fragments per chromosome was 39.8 (range 12‐116). In 1 UM, chromothripsis was present in 2 different chromosomes. GNAQ, GNA11 or CYSLTR2 mutations were present in 6 of these tumors and 5 tumors harbored a BAP1 mutation and/or lacked BAP1 protein expression by immunohistochemistry. Four of these tumors metastasized and for the fifth only short follow‐up data are available. One of these metastatic tumors harbored an SF3B1 mutation. No EIF1AX mutations were detected in any of the tumors. To conclude, chromothripsis is a rare event in UM, occurring in 2.8% of samples and without significant association with mutations in any of the common UM driver genes.
Copy number variant analysis using genome‐wide mate‐pair sequencing
Authors: Smadbeck James B. , Johnson Sarah H. , Smoley Stephanie A. , Gaitatzes Athanasios , Drucker Travis M. , Zenka Roman M. , Kosari Farhad , Murphy Stephen J. , Hoppman Nicole , Aypar Umut , Sukov William R. , Jenkins Robert B. , Kearney Hutton M. , Feldman Andrew L. , Vasmatzis George 
Published: May 2018

AbstractCopy number variation (CNV) is a common form of structural variation detected in human genomes, occurring as both constitutional and somatic events. Cytogenetic techniques like chromosomal microarray (CMA) are widely used in analyzing CNVs. However, CMA techniques cannot resolve the full nature of these structural variations (i.e. the orientation and location of associated breakpoint junctions) and must be combined with other cytogenetic techniques, such as karyotyping or FISH, to do so. This makes the development of a next‐generation sequencing (NGS) approach capable of resolving both CNVs and breakpoint junctions desirable. Mate‐pair sequencing (MPseq) is a NGS technology designed to find large structural rearrangements across the entire genome. Here we present an algorithm capable of performing copy number analysis from mate‐pair sequencing data. The algorithm uses a step‐wise procedure involving normalization, segmentation, and classification of the sequencing data. The segmentation technique combines both read depth and discordant mate‐pair reads to increase the sensitivity and resolution of CNV calls. The method is particularly suited to MPseq, which is designed to detect breakpoint junctions at high resolution. This allows for the classification step to accurately calculate copy number levels at the relatively low read depth of MPseq. Here we compare results for a series of hematological cancer samples that were tested with CMA and MPseq. We demonstrate comparable sensitivity to the state‐of‐the‐art CMA technology, with the benefit of improved breakpoint resolution. The algorithm provides a powerful analytical tool for the analysis of MPseq results in cancer.
Two novel fusion genes, AIF1L‐ETV6 and ABL1‐AIF1L, result together with ETV6‐ABL1 from a single chromosomal rearrangement in acute lymphoblastic leukemia with prenatal origin
Authors: Lukes Jr Julius , Potuckova Eliska , Sramkova Lucie , Stary Jan , Starkova Julia , Trka Jan , Votava Felix , Zuna Jan , Zaliova Marketa 
Published: May 2018

AbstractFusion genes resulting from chromosomal rearrangements represent a hallmark of childhood acute lymphoblastic leukemia (ALL). Unlike more common fusion genes generated via simple reciprocal chromosomal translocations, formation of the ETV6‐ABL1 fusion gene requires 3 DNA breaks and usually results from an interchromosomal insertion. We report a child with ALL in which a single interchromosomal insertion led to the formation of ETV6‐ABL1 and 2 novel fusion genes: AIF1L‐ETV6 and ABL1‐AIF1L. We demonstrate the prenatal origin of this complex chromosomal rearrangement, which apparently initiated the leukemogenic process, by successful backtracking of the ETV6‐ABL1 fusion into the patient's archived neonatal blood. We cloned coding sequences of AIF1L‐ETV6 and ABL1‐AIF1L in‐frame fusion transcripts from the patient's leukemic blasts and we show that the chimeric protein containing the DNA binding domain of ETV6 is expressed from the AIF1L‐ETV6 transcript and localized in both the cytoplasm and nucleus of transfected HEK293T cells. Transcriptomic and genomic profiling of the diagnostic bone marrow sample revealed Ph‐like gene expression signature and loss of the IKZF1 and CDKN2A/B genes, the typical genetic lesions accompanying ETV6‐ABL1‐positive ALL. The prenatal origin of the rearrangement confirms that ETV6‐ABL1 is not sufficient to cause overt leukemia, even when combined with the 2 novel fusions. We did not find the AIF1L‐ETV6 and ABL1‐AIF1L fusions in other ETV6‐ABL1‐positive ALL. Nevertheless, functional studies would be needed to establish the biological role of AIF1L‐ETV6 and ABL1‐AIF1L and to determine whether they contribute to leukemogenesis and/or to the final leukemia phenotype.
Geochemistry of silicate melt inclusions in middle and southern Okinawa Trough rocks: Implications for petrogenesis and variable subducted sediment component injection
Authors: Li Xiaohui , Zeng Zhigang , Yang Huixin , Yin Xuebo , Wang Xiaoyuan , Chen Shuai , Ma Yao , Guo Kun 
Published: May 2018

Silicate melt inclusions (SMIs) in olivine, clinopyroxene, and orthopyroxene in basalt and trachyandesite of the middle Okinawa Trough (MOT) and in basaltic andesites of the southern Okinawa Trough (SOT) were investigated in detail to understand the evolution of magma and geochemical characteristics of the basaltic magma source. Both the SMIs and host bulk rocks are more heavily enriched with Pb and large ion lithophile elements than with high field strength elements and rare earth elements. The major element compositions of SMIs in the MOT trachyandesite show a scattered variation trend of medium‐K to shoshonitic series and suggest that a K‐rich magma source may exist in the Okinawa Trough. Two groups with distinct element distribution patterns observed in SMIs of the MOT trachyandesite may represent magmas with different evolutionary histories. Compared with fractional crystallization and partial melting processes, magma mixing may serve as a reasonable process for the production of trachyandesite in the MOT. Fractional crystallization has played an important role in basaltic magma evolution in the MOT and SOT. Simulations conducted using MELTS show that the fractional crystallization evolution trends observed correspond well to the presence of a magma chamber at 300 MPa with an H2O content level of 0.2 wt% in the MOT and to the presence of a magma chamber at 300 MPa with an H2O content level of 0.4 wt% in the SOT. Ratios of incompatible trace elements (e.g., Th/Ce, Th/Sm, Ba/Th, and Th/Nb); positive Pb anomalies; negative Nb, Ta, and Ti anomalies; and the existence of organic hydrocarbons (CnHm) in the SMIs can be attributed to the involvement of subducted sediment from the subducting slab. Modelling results suggest that more primitive magma represented by SMIs from the MOT has formed through the melting of less than 6% of a metasomatized depleted mantle with contributions of 1.2% sediment melt and 0.8% sediment fluid. In contrast, more primitive magma from the SOT formed through the melting of 4–10% of the depleted mantle with contributions of 3% sediment melt and 1% sediment fluid. The different features of the SMIs together with different tectonic settings of the MOT and SOT have formed in response to the westward subduction of the Philippine Sea Plate.
The roles of extracellular vesicle microRNAs in the central nervous system
Authors: Blandford Stephanie N. , Galloway Dylan A. , Moore Craig S. 
Published: May 2018

AbstractMicroRNAs (miRNAs) are small, highly conserved non‐coding RNA molecules that post‐transcriptionally regulate protein expression and most biological processes. Mature miRNAs are recruited to the RNA‐induced silencing complex (RISC) and target mRNAs via complementary base‐pairing, thus resulting in translational inhibition and/or transcript degradation. Here, we present evidence implicating miRNAs within extracellular vesicles (EVs), including microvesicles and exosomes, as mediators of central nervous system (CNS) development, homeostasis, and injury. EVs are extracellular vesicles that are secreted by all cells and represent a novel method of intercellular communication. In glial cells, the transfer of miRNAs via EVs can alter the function of recipient cells and significantly impacts cellular mechanisms involved in both injury and repair. This review discusses the value of information to be gained by studying miRNAs within EVs in the context of CNS diseases and their potential use in the development of novel disease biomarkers and therapeutic strategies.
Chest width, waist circumference, and thigh circumference are predictors of dementia
Authors: Liao Pei‐Ju , Lin Tzu‐Yu , Ting Ming‐Kuo , Peng Tsung‐I , Chiou Wen‐Ko , Chen Li‐Hsuan , Hsu Kuang‐Hung 
Published: May 2018

ObjectiveFew studies have investigated the relationship between specific body measures and dementia.MethodsThree‐dimensional anthropometric body surface scanning data containing 38 body measures were collected from 6831 participants from the health examination department of a medical center in Taiwan during 2000 to 2008, and 236 dementia cases were identified during the 10‐year follow‐up. A multiple Cox regression analysis was performed.ResultsSpecific body measures, namely chest width (hazard ratio [HR] = 0.90; 95% confidence interval [CI] = 0.83–0.98), and right thigh circumference (HR = 0.93; 95% CI = 0.90–0.96), were protective predictors to dementia occurrence. Waist circumference (HR = 1.03; 95% CI = 1.02–1.05) was a risk factor in dementia occurrence. Among the combinations, dementia risk was higher in participants with a larger waist circumference and a smaller right thigh circumference, with the highest HR of 2.49 (95% CI = 1.54–4.03).ConclusionThe body measures provide clues for future applications and scientific merits in both clinical and preventive medicine.