bluuebunny/crossref_metadata_2025 huggingface dataset:
Long‐term outcomes of patent foramen ovale closure or medical therapy after cryptogenic stroke: A meta‐analysis of randomized trials
Authors: Abdelaziz Hesham K. , Saad Marwan , Abuomara Hossamaldin Z. , Nairooz Ramez , Pothineni Naga Venkata K. , Madmani Mohamed E. , Roberts David H. , Mahmud Ehtisham
Published: May 2018

Objectives

To examine long‐term clinical outcomes with transcatheter patent foramen ovale (PFO) closure versus medical therapy alone in patients with cryptogenic stroke.

Background

A long‐standing debate regarding the optimal approach for the management of patients with PFO after a cryptogenic stroke exists.

Methods

An electronic search was performed for randomized clinical trials (RCTs) reporting clinical outcomes with PFO closure vs. medical therapy alone after stroke. Random effects DerSimonian‐Laird risk ratios (RR) were calculated. The main outcome was recurrence of stroke. Other outcomes included transient ischemic attack (TIA), new‐onset atrial fibrillation/flutter (AF/AFL), major bleeding, serious adverse events, and device‐related complications. All‐cause mortality was also examined.

Results

Five RCTs with a total of 3,440 patients were included. At a mean follow‐up of 4.02 ± 1.57 years, PFO closure was associated with less recurrence of stroke (RR = 0.43; 95% CI 0.19–0.91; P = .027) compared with medical therapy alone. No difference was observed between both strategies for TIA (P = .21), major bleeding (P = .69), serious adverse events (P = .35), and all‐cause death (P = .48). However, PFO closure, was associated with increased new‐onset AF/AFL (P < .001), risk of pulmonary embolism (P = .04), and device‐related complications (P < .001). On a subgroup analysis, stroke recurrence rate remained lower in PFO closure arm regardless of the type of closure device used (Pinteraction = .50), or the presence of substantial shunt in the majority of study population (Pinteraction = .13).

Conclusions

Transcatheter PFO closure reduces the recurrence of stroke compared with medical therapy alone, with no significant safety concerns. Close follow‐up of patients after PFO closure is recommended to detect new‐onset atrial arrhythmias.
Comparison of paravalvular aortic leak characteristics in the Medtronic CoreValve versus Edwards Sapien Valve: Paravalvular aortic leak characteristics
Authors: Gilbert Olivia N. , Choi Charles H. , Franzil Jodie L. , Caughey Melissa , Qureshi Waqas , Stacey R. Brandon , Pu Min , Applegate Robert J. , Gandhi Sanjay K. , Zhao David X. M.
Published: May 2018

Objectives

Temporally quantify and localize paravalvular aortic leak (PVL) after transcatheter aortic valve replacement (TAVR) in the Medtronic CoreValve (MCV) versus the Edwards Sapien Valve (ESV).

Background

In order to increase the precision of THV selection and PVL intervention, an understanding of PVL characteristics is essential.

Methods

The frequency, severity, and location of post‐TAVR PVL were evaluated with transthoracic echocardiography pre‐discharge, one month, and one‐year post‐procedure in 202 patients receiving a MCV (N = 120) or ESV (N = 81). This was done through application of a clock face to the short axis of the aortic valve in order to divide the area into three tertiles.

Results

Pre‐discharge differences between PVL frequency and severity in the MCV and ESV lost significance over time. Localizing these trends, MCV PVL frequency and severity significantly decreased in the first and third tertiles during most time periods while PVL in the second tertile of the MCV or in any of the tertiles of the ESV failed to improve. Presence of pre‐discharge PVL was predictive of 30‐day HF readmission and/or death (OR = 3.16, 95% CI: 0.99–10.12). Presence of pre‐discharge and 30‐day PVL was predictive of 1‐year HF readmissions and/or death (OR = 2.12, 95% CI: 1.09–4.13 and OR = 1.99, 95% CI: 0.96–4.12).

Conclusions

When comparing the MCV and ESV, not all locations of PVL improve equally over time, which has implications for heart failure readmissions. This could be used to influence valve selection and to identify cases in which earlier intervention on PVL may be appropriate.
Successful exclusion of an aortic aneurysm with a novel PTFE‐tube covered cobalt‐chromium stent in a pediatric patient with native coarctation of the aorta
Authors: Nordmeyer Johannes , Kramer Peter , Berger Felix , Schubert Stephan
Published: May 2018

Treatment of aneurysmal lesions in the context of coarctation of the aorta (CoA) is a challenging task and these lesions are rare in children. An 11‐year‐old boy was incidentally diagnosed with native CoA and concomitant complex aneurysmal lesions during medical check‐up for arterial hypertension. Pre‐catheterization imaging was performed with computed tomography (CT), which showed a mild CoA and two native aneurysms that were juxtaposed to the origin of the left subclavian artery. For planning and guidance of the catheter procedure, image fusion software was used with an overlay from pre‐registered three‐dimensional reconstruction images on live fluoroscopy. Here, we report the first case of successful treatment of an aneurysmal lesion in the context of native coarctation with a novel PTFE‐tube covered cobalt‐chromium stent (BeGraft, Bentley) in a pediatric patient.
Automated chemical imaging identification of illegal drugs in correctional facilities mail
Authors: Schweitzer Robert C. , Treado Patrick J. , Olkhovyk Oksana , Zbur Lucas
Published: May 2018

The current opioid epidemic represents a significant health and security threat. This epidemic has affected correctional facilities with an increased smuggling of illicit drugs concealed in envelopes, letters, greeting cards, and business cards to inmates. Short‐wave infrared chemical imaging sensors are being successfully applied to the automated, high confidence detection of drugs concealed in prison mail. Once detected, end users have a need to confirm the detection and to identify the specific drug being detected. The challenge for identification is that the spectral signature of the concealed drug is often convolved with the spectral signature of the piece of mail (substrate) in which the drug is concealed. This paper presents a method to remove the substrate signal from the substrate/drug mixture signal followed by a set of 3 spectral identification methods. The substrate signature is estimated by a region of interest that is spatially local to the detection, and linear unmixing uses this substrate signature to calculate the residual spectra in the detection pixels. These residual spectra represent the isolated drug spectra, and they are compared with a spectral drug library via Euclidean distance, target factor analysis, and adaptive cosine estimator methods. This methodology was applied to a set of 116 positive‐ and negative‐control samples spanning a range of drugs and concealment methods with the result that 90 of the 104 positive‐control samples were identified correctly (86.5%) and 0 of the 12 negative‐control samples were incorrectly identified as a drug in the library (0%).
Unconventional Synthesis of a CuI Rotaxane with a Superacceptor Stopper: Ultrafast Excited‐State Dynamics and Near‐Infrared Luminescence
Authors: Trolez Yann , Finke Aaron D. , Silvestri Fabio , Monti Filippo , Ventura Barbara , Boudon Corinne , Gisselbrecht Jean‐Paul , Schweizer W. Bernd , Sauvage Jean‐Pierre , Armaroli Nicola , Diederich François
Published: May 2018

A CuI bis‐phenanthroline rotaxane was prepared by using the [2+2] cycloaddition‐retroelectrocyclization (CA‐RE) reaction to graft a bulky dicyanoquinodimethane (DCNQ) stopper. The electronic properties were investigated with electrochemical and photophysical techniques, in parallel with three reference compounds, namely, the DCNQ derivative alone, the DCNQ‐based phenanthroline ligand, and an analogue CuI complex lacking the DCNQ moiety. In all the systems containing the DCNQ unit, the lowest electronic excited states are centered thereon, with the singlet level (S1) located at about 1.0 eV, as suggested by TDDFT calculations. Accordingly, in the DCNQ‐equipped rotaxane, the typical metal‐to‐ligand charge‐transfer luminescence of the CuI center is totally quenched. Ultrafast transient absorption and emission studies show that, in the rotaxane, the final sink of photoinduced processes is the lowest singlet state of the DCNQ moiety (S1), which exhibits strong charge‐transfer character and a lifetime of 0.4 ps. Its deactivation leads to population of another excited state with a lifetime of 1.3 ps, which can be the related triplet state (T1) or a vibrationally hot level (hot‐S0). Notably, S1 also shows stimulated fluorescence in the near‐infrared (NIR) region between 1100 and 1500 nm, corroborating the TDDFT prediction. This unusual finding opens up the study of ultrashort‐lived NIR luminescence in organic donor–acceptor systems.
Exploration of Novel Chemical Space: Synthesis and in vitro Evaluation of N‐Functionalized Tertiary Sulfonimidamides
Authors: Izzo Flavia , Schäfer Martina , Lienau Philip , Ganzer Ursula , Stockman Robert , Lücking Ulrich
Published: May 2018

An unprecedented set of structurally diverse sulfonimidamides (47 compounds) has been prepared by various N‐functionalization reactions of tertiary =NH sulfonimidamide 2 aa. These N‐functionalization reactions of model compound 2 aa include arylation, alkylation, trifluoromethylation, cyanation, sulfonylation, alkoxycarbonylation (carbamate formation) and aminocarbonylation (urea formation). Small molecule X‐ray analyses of selected N‐functionalized products are reported. To gain further insight into the properties of sulfonimidamides relevant to medicinal chemistry, a variety of structurally diverse reaction products were tested in selected in vitro assays. The described N‐functionalization reactions provide a short and efficient approach to structurally diverse sulfonimidamides which have been the subject of recent, growing interest in the life sciences.
Three‐month posttreatment prostate‐specific antigen level as a biomarker of treatment response in patients with intermediate‐risk or high‐risk prostate cancer treated with androgen deprivation therapy and radiotherapy
Authors: Bryant Alex K. , D'Amico Anthony V. , Nguyen Paul L. , Einck John P. , Kane Christopher J. , McKay Rana R. , Simpson Daniel R. , Mundt Arno J. , Murphy James D. , Rose Brent S.
Published: May 2018

BACKGROUND

Prostate‐specific antigen (PSA) measurement after definitive radiotherapy (RT) and androgen deprivation therapy for localized prostate cancer has been proposed as an early prognostic biomarker. In the current study, the authors investigated the association between 3‐month post‐RT PSA level and biochemical progression‐free survival (bPFS), prostate cancer‐specific survival (PCSS), and overall survival (OS).

METHODS

A total of 5783 patients with intermediate‐risk or high‐risk localized prostate cancer who were diagnosed between 2000 and 2015 and treated with RT and androgen deprivation therapy were identified from Veterans Affairs data. Patients were divided into groups based on 3‐month post‐RT PSA values: <0.10 ng/mL, 0.10 to 0.49 ng/mL, and ≥0.50 ng/mL. The effect of the 3‐month PSA group on bPFS, PCSS, and OS was evaluated in multivariable Cox models adjusting for potential confounders.

RESULTS

There were 2651 patients with intermediate‐risk and 3132 with high‐risk disease; approximately 11% had a 3‐month PSA level of ≥0.50 ng/mL. A higher 3‐month PSA level was found to be strongly associated with each outcome; compared with patients in the group with a 3‐month PSA value <0.10 ng/mL, the authors noted greater hazards for the patients with a 3‐month PSA value ≥0.50 ng/mL (hazard ratio for bPFS: 5.23; PCSS: 3.97; and OS: 1.50 [P<.001 for all]) and the patients with a 3‐month PSA value of 0.10 to 0.49 ng/mL (hazard ratio for bPFS: 2.41 [P<.001]; PCSS: 2.29 [P<.001]; and OS: 1.21 [P = .003]). When analyzed separately, the 3‐month PSA level was found to be predictive of OS in the high‐risk group (P<.001) but not the intermediate‐risk group (P = .21).

CONCLUSIONS

The 3‐month post‐RT PSA level appears to be a strong prognostic biomarker for bPFS, PCSS, and OS in patients with intermediate‐risk and high‐risk prostate cancer, particularly those with high‐risk disease. The 3‐month PSA measurement may augment clinical decision making and holds promise as a potential surrogate endpoint in clinical trials. Cancer 2018;124:2939‐47. © 2018 American Cancer Society.
A generic methodology for geo‐related data semantic annotation
Authors: Malik Kaleem Razzaq , Habib Muhammad Asif , Khalid Shehzad , Ahmad Mudassar , Alfawair Mai , Ahmad Awais , Jeon Gwanggil
Published: May 2018

Geo‐related data, also known as spatial data, is represented using a vector used for representing longitude, elevation, and latitude. Specially built systems, well known as Geographical Information Systems (GIS), made use of such data for querying, manipulating, navigation, and analyzing. In the current era of data, science needs to involve smart interactive investigation involving Internet of Data (IoD) on predicting upcoming changes and spatial updates on the map is growing rapidly. To resolve issues concerning real‐time spatial data, transformation using semantic annotation can provide a better way to translate spatial relationships. These spatial relationships will support spatial analysis by linking different cause and effect with the help of reasoning mechanism. This research's major focus is on a data transformation methodology for geo‐related semantic annotation. Spatial dataset gets stored in a database and then transformed into Extensible Markup Language (XML) and Resource Description Framework (RDF). Even for bi‐directional transformation to work properly, we need to map different schema level transformations. A deep research is conducted to consider available mappings, implementations, and updates to further improving data fusion for having better compatibility. Then, transformed data as results get analyzed and discussed based on the data mapping rules formulated. It is aimed to show the importance of reducing the response time of investigation and offer compatibility between the web and semantically enriched spatial data.
Generation of Human Induced Pluripotent Stem Cells Using a Defined, Feeder‐Free Reprogramming System
Authors: Park Seonmi , Mostoslavsky Gustavo
Published: May 2018

Human induced pluripotent stem cells (hiPSCs) offer great opportunities for the study of human development and disease modeling and have enormous potential for use in future clinical cell‐based therapies. However, most current systems to create hiPSCs often expose the cells to animal feeder layers or xenogeneic reagents; this raises safety concerns about using hiPSC‐derived cells for therapeutic purposes. Here, we describe protocols to generate hiPSCs without exposing the cells to xenogeneic materials that uses a defined, feeder‐free reprogramming system. With this method, we were able to successfully reprogram not only patient‐derived peripheral blood mononuclear cells but also amniocytes from the amniotic fluid of stillborn fetuses using two independent reprogramming platforms. Importantly, hiPSCs generated in this fashion expressed pluripotent markers and had normal karyotypes. The protocols allowed us to generate and culture hiPSCs under Good Manufacturing Practice–like conditions, a necessary step for the future clinical application of these cells. © 2018 by John Wiley & Sons, Inc.
Fifth‐order Π‐type load resonant converters analysis based‐on immittance property for constant output current applications
Authors: Khoshsaadat Alireza , Moghani Javad Shokrollahi , Ehsanipour Mansour
Published: May 2018

Passive resonant tanks (PRTs) with immittance property are suitable candidates to achieve constant output current in load resonant converters (LRCs). In this paper, fifth‐order Π‐type LC networks are investigated to accede this target. At the first step, fifth‐order Π‐type passive LC networks that can be applied as a PRT are specified based on source and sink natures. Also, their structural advantages are described in detail to give a suitable perspective for the topology selection. At the second step, immittance property is verified for the proposed topologies and immittance PRTs (IPRTs), with their immittance operation conditions, are derived. To confirm the effectiveness, a 150‐W LRC is implemented leveraging new Π‐type IPRTs. A deep investigation is devoted to analyze the current/voltage stress in the components of the designed LRC. Moreover, kVA/kW ratio is considered as a key parameter for the reactive component size minimization. The proposed constant current LRC presents high load regulation capability in addition to the minimum reactive power and zero‐voltage switching (ZVS) on the inverter MOSFETs under the various loads. A significant robustness against load variations, less sensitivity versus parameters variation, and relatively higher efficiency are the main superiorities of the fifth‐order IPRTs to the lower order counterparts.
A programmable analog baseband filter with DC offset reduction using servo loop feedback
Authors: Chang Chia‐Hung
Published: May 2018

This paper presents a programmable analog baseband filter with direct current (DC) offset cancelling, using the standard complementary metal‐oxide‐semiconductor process. The servo loop feedback topology is adopted to reject in‐band DC offset at each stage of the receiving system. Furthermore, the proposed back‐to‐back diode‐connected configuration forms an ultrahigh pseudo resistor, which is applied in the feedback path of the integrator to obtain an ultralow cut‐off frequency (<1 Hz) for the high‐pass response. Therefore, low‐frequency application is possible for simultaneously in‐band DC offset and out‐band interference suppression. A servo loop feedback system with a pseudo resistor is used in the analog baseband filter to verify the concept. The chip is fabricated by using the TSMC 0.13‐um complementary metal‐oxide‐semiconductor process and consumes 43.8 mA from a 1.2 V DC supply voltage. The measured gain variation is from 65.6 to −3.3 dB with a resolution of 1 dB at a bandwidth of 5 MHz. The bandwidth is adjustable from 1.75 to 10 MHz.
Electrical circuits described by fractional conformable derivative
Authors: Martínez L. , Rosales J.J. , Carreño C.A. , Lozano J.M.
Published: May 2018

In the last 3 years, the fractional conformable derivative and its properties have been introduced. Unlike other definitions, this new fractional derivative is based on the basic limit definition of the derivative and satisfies the same formulas of derivation, such as product and quotient of 2 functions and the chain rule. Using this new derivative, we obtain a new class of linear ordinary differential equations with noninteger power variable coefficients for the Resistance Capacitance (RC), Inductance Capacitance (LC), and Resistance, Inductance Capacitance (RLC) electric circuits. The numerical solutions are solved through the Matlab software. Solutions depend on time and on the fractional order parameter 0 < γ ≤ 1. The computing using this new derivative is much easier than using other definitions of fractional derivative. It has been shown that in the particular case γ = 1, these solutions become the ordinary ones. Also, a comparison has been made with the Caputo fractional derivative for the case of the RC circuit with constant source.
A spatial genetics approach to inform vector control of tsetse flies (Glossina fuscipes fuscipes) in Northern Uganda
Authors: Saarman Norah , Burak Mary , Opiro Robert , Hyseni Chaz , Echodu Richard , Dion Kirstin , Opiyo Elizabeth A. , Dunn Augustine W. , Amatulli Giuseppe , Aksoy Serap , Caccone Adalgisa
Published: May 2018

Tsetse flies (genus Glossina) are the only vector for the parasitic trypanosomes responsible for sleeping sickness and nagana across sub‐Saharan Africa. In Uganda, the tsetse fly Glossina fuscipes fuscipes is responsible for transmission of the parasite in 90% of sleeping sickness cases, and co‐occurrence of both forms of human‐infective trypanosomes makes vector control a priority. We use population genetic data from 38 samples from northern Uganda in a novel methodological pipeline that integrates genetic data, remotely sensed environmental data, and hundreds of field‐survey observations. This methodological pipeline identifies isolated habitat by first identifying environmental parameters correlated with genetic differentiation, second, predicting spatial connectivity using field‐survey observations and the most predictive environmental parameter(s), and third, overlaying the connectivity surface onto a habitat suitability map. Results from this pipeline indicated that net photosynthesis was the strongest predictor of genetic differentiation in G. f. fuscipes in northern Uganda. The resulting connectivity surface identified a large area of well‐connected habitat in northwestern Uganda, and twenty‐four isolated patches on the northeastern margin of the G. f. fuscipes distribution. We tested this novel methodological pipeline by completing an ad hoc sample and genetic screen of G. f. fuscipes samples from a model‐predicted isolated patch, and evaluated whether the ad hoc sample was in fact as genetically isolated as predicted. Results indicated that genetic isolation of the ad hoc sample was as genetically isolated as predicted, with differentiation well above estimates made in samples from within well‐connected habitat separated by similar geographic distances. This work has important practical implications for the control of tsetse and other disease vectors, because it provides a way to identify isolated populations where it will be safer and easier to implement vector control and that should be prioritized as study sites during the development and improvement of vector control methods.
Discovering variation of secondary metabolite diversity and its relationship with disease resistance inCornus floridaL.
Authors: Pais Andrew L. , Li Xu , (Jenny) Xiang Qiu‐Yun
Published: May 2018

Understanding intraspecific relationships between genetic and functional diversity is a major goal in the field of evolutionary biology and is important for conserving biodiversity. Linking intraspecific molecular patterns of plants to ecological pressures and trait variation remains difficult due to environment‐driven plasticity. Next‐generation sequencing, untargeted liquid chromatography–mass spectrometry (LC‐MS) profiling, and interdisciplinary approaches integrating population genomics, metabolomics, and community ecology permit novel strategies to tackle this problem. We analyzed six natural populations of the disease‐threatenedCornus floridaL. from distinct ecological regions using genotype‐by‐sequencing markers and LC‐MS‐based untargeted metabolite profiling. We tested the hypothesis that higher genetic diversity inC. floridayielded higher chemical diversity and less disease susceptibility (screening hypothesis), and we also determined whether genetically similar subpopulations were similar in chemical composition. Most importantly, we identified metabolites that were associated with candidate loci or were predictive biomarkers of healthy or diseased plants after controlling for environment. Subpopulation clustering patterns based on genetic or chemical distances were largely congruent. While differences in genetic diversity were small among subpopulations, we did observe notable similarities in patterns between subpopulation averages of rarefied‐allelic and chemical richness. More specifically, we found that the most abundant compound of a correlated group of putative terpenoid glycosides and derivatives was correlated with tree health when considering chemodiversity. Random forest biomarker and genomewide association tests suggested that this putative iridoid glucoside and other closely associated chemical features were correlated to SNPs under selection.
Insights from modeling studies on how climate change affects invasive alien species geography
Authors: Bellard Celine , Jeschke Jonathan M. , Leroy Boris , Mace Georgina M.
Published: May 2018

Climate change and biological invasions are threatening biodiversity and ecosystem services worldwide. It has now been widely acknowledged that climate change will affect biological invasions. A large number of studies have investigated predicted shifts and other changes in the geographic ranges of invasive alien species related to climate change using modeling approaches. Yet these studies have provided contradictory evidence, and no consensus has been reached. We conducted a systematic review of 423 modeling case studies included in 71 publications that have examined the predicted effects of climate change on those species. We differentiate the approaches used in these studies and synthesize their main results. Our results reaffirm the major role of climate change as a driver of invasive alien species distribution in the future. We found biases in the literature both regarding the taxa, toward plants and invertebrates, and the areas of the planet investigated. Despite these biases, we found for the plants and vertebrates studied that climate change will more frequently contribute to a decrease in species range size than an increase in the overall area occupied. This is largely due to oceans preventing terrestrial invaders from spreading poleward. In contrast, we found that the ranges of invertebrates and pathogens studied are more likely to increase following climate change. An important caveat to these findings is that researchers have rarely considered the effects of climate change on transport, introduction success, or the resulting impacts. We recommend closing these research gaps, and propose additional avenues for future investigations, as well as opportunities and challenges for managing invasions under climate change.
Long‐term regeneration of a tropical plant community after sand mining
Authors: Garbin Mário L. , Misaki Flora , Ferreira Poliana F. , Guidoni‐Martins Karlo G. , Soares Rayara B. , Mariotte Pierre , Sansevero Jerônimo B. B. , Rocha Patryck Gouvea , Silva Ary G.
Published: May 2018

Sandy coastal plant communities in tropical regions have been historically under strong anthropic pressure. In Brazil, these systems shelter communities with highly plastic plant species. However, the potential of these systems to regenerate without human assistance after disturbances has hardly been examined. We determined the natural regeneration of a coastal sandy plain vegetation (restinga) in Brazil, 16 years after the end of sand removal. We inventoried 38 plots: 20 within a sand‐mined site and 18 in an adjacent undisturbed site. We expected lower diversity values in the sand‐mined site compared to the undisturbed site, but similar species composition between the two sites due to the spatial proximity of the two sites and the high plasticity of restinga species. Species were ranked using abundance and importance value index in both sites, and comparisons were performed using Rényi entropy profiles, rarefaction curves, principal component analysis, and redundancy analysis. Species composition and dominant species differed markedly between the two sites. Bromeliads andClusia hilariana, well‐known nurse plants, dominated the undisturbed site but were almost absent in the regenerating site. Species richness did not differ between both sites, but diversity was higher in the undisturbed site. Within‐site composition differences in the mined area were associated with field characteristics. Interestingly, species classified as subordinate or rare in the undisturbed site became dominants in the regenerating site. These newer dominants in the sand‐mined site are not those known as nurse plants in other restingas, thus yielding strong implications for restoration.
Carbon allocation and competition maintain variation in plant root mutualisms
Authors: Christian Natalie , Bever James D.
Published: May 2018

Plants engage in multiple root symbioses that offer varying degrees of benefit. We asked how variation in partner quality persists using a resource‐ratio model of population growth. We considered the plant's ability to preferentially allocate carbon to mutualists and competition for plant carbon between mutualist and nonmutualist symbionts. We treated carbon as two nutritionally interchangeable, but temporally separated, resources—carbon allocated indiscriminately for the construction of the symbiosis, and carbon preferentially allocated to the mutualist after symbiosis establishment and assessment. This approach demonstrated that coexistence of mutualists and nonmutualists is possible when fidelity of the plant to the mutualist and the cost of mutualism mediate resource competition. Furthermore, it allowed us to trace symbiont population dynamics given varying degrees of carbon allocation. Specifically, coexistence occurs at intermediate levels of preferential allocation. Our findings are consistent with previous empirical studies as well the application of biological market theory to plantroot symbioses.
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

Globally, 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

The 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

Understanding 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

One 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

The 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

Determining 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

River 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

Uveal 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

Copy 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

Fusion 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.