bluuebunny/crossref_metadata_2025 huggingface dataset:
Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior
Authors: Balakrishnan Christopher N , Mukai Motoko , Gonser Rusty A , Tuttle Elaina M , Clayton David F , London Sarah E , Wingfield John C
Published: January 2018

Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel’s white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, 80% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with transcript assembly N50s ranging from 2,557 to 4,072. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as a primary determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.
HIV-positive parents, HIV-positive children, and HIV-negative children’s perspectives on disclosure of a parent’s and child’s illness in Kenya
Authors: Gachanja Grace , Burkholder Gary J , Ferraro Aimee
Published: January 2018

HIV disclosure from parent to child is complex and challenging to HIV-positive parents and healthcare professionals. This study was conducted to understand the lived experiences of HIV-positive parents and their children during the disclosure process in Kenya. Sixteen HIV-positive parents, seven HIV-positive children, and five HIV-negative children underwent semistructured in-depth interviews. Data was analyzed using the Van Kaam method in NVivo 8. Seven themes emerged that spanned the disclosure process. Presented here is data on the theme about how participants recommend full disclosure be approached to HIV-positive and negative children. Participants recommended disclosure as a process starting at five years with full disclosure delivered at 10 years when the child was capable of understanding the illness; or by 14 years when the child was mature enough to receive the news if full disclosure had not been conducted earlier. Important disclosure considerations include the parent’s and/or child’s health statuses, the number of infected persons’ illnesses to be disclosed to the child, the child’s maturity and understanding level, addressing important life events (e.g., taking a national school examination), and the person best suited to deliver full disclosure to the child. Recommendations are made for inclusion into HIV disclosure guidelines, manuals, and programs.
The relationship between managed bees and the prevalence of parasites in bumblebees
Authors: Graystock Peter , Goulson Dave , Hughes William O
Published: January 2018

Honey bees have been domesticated for centuries, and are now managed commercially to pollinate crops and produce hive products. Recently, bumblebee colonies have also been reared commercially and transported worldwide for crop pollination.Mounting evidence suggests that use of managed honey bees or commercially reared bumblebees may affect the health of local bumblebees. The increase in pollinator density and the mixing of managed and wild pollinator populations may augment parasite prevalence in wild bumblebees. Here, we screened 764bumblebees from around five greenhouses that either used commercially reared bumblebees or did not, as well as bumblebees from 10 colonies placed at two sites either close to or far from a honey bee apiary, for the parasites Apicystis bombi, Crithidia bombi, Nosema bombi, N. ceranae, N. apis and deformed wing virus. We found that two of the parasites were more prevalent in bumblebees that were close to managed honey bees or commercially reared bumblebees. Apicystis bombi and C. bombi were more prevalent around greenhouses using commercially reared bumblebees, while bumblebees from near to the honey bee apiary had an 18% greater prevalence of C. bombi compared to bumblebees far from the apiary. Whilst these results support previous reports of parasite spillover from commercial bumblebees, they also suggest that the prevalence of C. bombi may be elevated by stress or increased pollinator density, in addition potentially to direct spillover from commercial bumblebees. The use of managed bees clearly comes at a cost of increased parasites in wild bumblebees, which is not only a concern for bumblebee conservation, but also a phenomenon that is likely found in other sympatric pollinators around managed bees.
SKIMMR: Facilitating knowledge discovery in life sciences by machine-aided skim reading
Authors: Novacek Vit , Burns Gully APC
Published: January 2018

Background: Unlike full reading, 'skim-reading' involves the process of looking quickly over information in an attempt to cover more material whilst still being able to retain a superficial view of the underlying content. Within this work, we specifically emulate this natural human activity by providing a dynamic graph-based view of entities automatically extracted from text. For the extraction, we use shallow parsing, co-occurrence analysis and semantic similarity computation techniques. Our main motivation is to assist biomedical researchers and clinicians in coping with increasingly large amounts of potentially relevant articles that are being published ongoingly in life sciences.

Methods: To construct the high-level network overview of articles, we extract weighted binary statements from the text. We consider two types of these statements, co-occurrence and similarity, both organised in the same distributional representation (i.e., in a vector-space model). For the co-occurrence weights, we use point-wise mutual information that indicates the degree of non-random association between two co-occurring entities. For computing the similarity statement weights, we use cosine distance based on the relevant co-occurrence vectors. These statements are used to build fuzzy indices of terms, statements and provenance article identifiers, which support fuzzy querying and subsequent result ranking. These indexing and querying processes are then used top construct a graph-based interface for searching and browsing entity networks extracted from articles, as well as articles relevant to the networks being browsed.

Results: We provide a prototype (called SKIMMR) that generates a network of inter-related entities from a set of documents which users may explore through our interface. When a particular area of the entity network looks interesting to a user, the tool displays the documents that are most relevant entities currently shown in the network. We present this as a methodology for browsing a collection of research articles. To illustrate the practical applicability of SKIMMR, we present examples of its use in the domains of Spinal Muscular Atrophy and Parkinson's Disease. Finally, we describe a methodology for automated experimental evaluation of SKIMMR instances. The method uses formal comparison of the graphs generated by our tool to relevant gold standards based on manually curated PubMed, TREC challenge and MeSH data. The results of experiments performed on three different instances of SKIMMR show that the presented method for machine-aided skim reading outperforms state of the art tools like PubMed regarding focused browsing and informativeness of the browsing context.

Conclusions: In preliminary trials, sample users find new, interesting and non-trivial facts with the tool. Our evaluation showed a high potential of the presented work for facilitating knowledge discovery in life sciences.
Women are underrepresented on editorial boards
Authors: Cho Alyssa , Johnson Shelly A , Schuman Carrie , Adler Jennifer , Gonzalez Oscar , Graves Sarah J , Huebner Jana , Marchant D Blaine , Rifai Sami , Skinner Irina , Bruna Emilio M
Published: January 2018

Despite women earning similar numbers of graduate degrees as men in STEM disciplines, they are underrepresented in upper level positions in both academia and industry. Editorial board memberships are an important example of such positions; membership is both a professional honor in recognition of achievement and an opportunity for professional advancement. We surveyed 10 highly regarded journals in environmental biology, natural resource management, and plant sciences to quantify the number of women on their editorial boards and in positions of editorial leadership from 1985-2013. We found that during this time period, only 16% of editorial board members were women, with more pronounced disparities in positions of editorial leadership (i.e., Associate Editors, Editors-in-Chief). Although the trend was towards improvement over time, there was surprising variation between journals. We argue editorial boards should strive for gender parity to increase the number of women afforded the opportunities and benefits that accompany membership, as well as increase the number of role models and mentors for early-career scientists and students.
A genetic manipulation of motor neuron excitability does not alter locomotor output in Drosophila larvae
Authors: McKiernan Erin C.
Published: January 2018

Motor activity, like that producing locomotion, is generated by networks of neurons. At the last output level of these networks are the motor neurons, which send signals to the muscles, causing them to contract. Current research in motor control is focused on finding out how motor neurons contribute to shaping the timing of motor behaviors. Are motor neurons just passive relayers of the signals they receive? Or, do motor neurons shape the signals before passing them on to the muscles, thereby influencing the timing of the behavior? It is now well accepted that motor neurons have active, intrinsic membrane properties - there are ion channels in the cell membrane that allow motor neurons to respond to input in non-linear and diverse ways. However, few direct tests of the role of motor neuron intrinsic properties in shaping motor behavior have been carried out, and many questions remain about the role of specific ion channel genes in motor neuron function. In this study, two potassium channel transgenes were expressed in Drosophila larvae, causing motor neurons to fire at lower levels of current stimulation and at higher frequencies, thereby increasing excitability. Mosaic animals were created in which some identified motor neurons expressed the transgenes while others did not. Motor output underlying crawling was compared in muscles innervated by control and experimental neurons in the same animals. Counterintuitively, no effect of the transgenic manipulation on motor output was seen. Future experiments are outlined to determine how the larval nervous system produces normal motor output in the face of altered motor neuron excitability.
The first occurrence of the enigmatic archosaur Crosbysaurus (Heckert 2004) from the Chinle Formation of Southern Utah
Authors: Gay Robert J , St. Aude Isabella
Published: January 2018

Originally identified as an ornithisichian dinosaur, Crosbysaurus has been found in New Mexico, Arizona, and the type locality in Texas. The genus has been reassessed by other workers in light of revelations about the postcrania of another putative Triassic ornithischian, Revueltosaurus. The understanding of Triassic dental faunas has become more complicated by the extreme convergence between pseudosuchian archosaurus and ornithichian dinosaur dental morphologies. We report here on a new specimen of Crosbysaurus from the Petrified Forest Member of the Chinle Formation at Comb Ridge in southeastern Utah. This new specimen is assigned to Crosbysaurus on the basis of the unique compound posterior denticles, mediolateral width, and curvature. While this specimen, MNA V10666, does not help resolve the affinities of Crosbysaurus it does represent an approximately 250 kilometer extension of the geographic range of this taxon. This is the first record of this taxon in Utah and as such it represents the northernmost known record of Crosbysaurus. This indicates that Crosbysaurus was not limited to the southern area of Chinle/Dockum deposition but instead was widespread across the paleoriver systems of the Late Triassic in western Pangea. The specimen we report on here was found in close association with a typical Late Triassic Chinle fauna, including phytosaurs, metoposaurs, and dinosauromorphs.
Seven years of experimental warming and nutrient addition causes decline of bryophytes and lichens in alpine meadow and heath communities
Authors: Alatalo Juha M , Jägerbrand Annika K , Molau Ulf
Published: January 2018

Global change is predicted to have large and rapid impact on polar and alpine regions. Bryophytes and lichens increase their importance in terms of biomass, carbon/nutrient cycling, cover and ecosystem functioning at higher latitudes/altitudes. Here we report from a seven year factorial experiment with nutrient addition and warming on the abundance of bryophytes and lichens in an alpine meadow and heath community. Treatments had significant negative effect on relative change of total abundance bryophytes and lichens, the largest decline to the nutrient addition and the combined nutrient addition and warming treatments, bryophytes decreasing most in the meadow, lichens most in the heath. Nutrient addition, and the combined nutrient addition and warming brought rapid decrease in both bryophytes and lichens, while warming had a delayed negative impact. Of sixteen species that were included the statistical analyses, we found significant negative effects on seven species. We show that impact of simulated global change on bryophytes and lichens differ in time and magnitude among treatments and plant communities. Our results point out the importance of longer-term studies to improve the quality of climate change models, as short-term studies are poor predictors of longer-term responses of bryophytes and lichens, similar to what have been shown for vascular plants. Species-specific responses may differ in time, and this will likely cause changes in the dominance structures of bryophytes and lichens over time.
Russula senecis: an unexplored wild mushroom for your healthy lunch basket
Authors: Khatua Somanjana , Dutta Arun Kumar , Acharya Krishnendu
Published: January 2018

Russula senecis, a worldwide distributed mushroom, is exclusively popular among the tribal communities of West Bengal for food purposes. The present study focuses on its reliable taxonomic identification through macro-, micro-morphological features and DNA barcoding, confirmation of its systematic placement by phylogenetic analyses, myco-chemicals and functional activities. For the first time, complete Internal Transcribed Spacer region of R. senecis has been sequenced and its taxonomic position within subsection Foetentinae under series Ingratae of the subgen. Ingratula is confirmed through phylogenetic analysis. For exploration of its medicinal properties, dried basidiocarps were subjected for preparation of a heat stable phenol rich extract (RusePre) using water and ethanol as solvent system. The antioxidant activity was evaluated through hydroxyl radical scavenging (EC50 µg/ml), chelating ability of ferrous ion (EC50 0.158 mg/ml), DPPH radical scavenging (EC50 1.34 mg/ml), reducing power (EC50 2.495 mg/ml) and total antioxidant activity methods (13.44 µg ascorbic acid equivalent/mg of extract). RusePre exhibited antimicrobial potentiality against Listeria monocytogenes, Bacillus subtilis, Pseudomonas aeruginosa and Staphylococcus aureus. Furthermore, different parameters were tested to investigate its chemical composition which revealed the presence of appreciable quantity of phenolic compounds along with carotenoids and ascorbic acid. HPLC-UV fingerprint indicated existence of at least 13 phenolics of which 10 were identified (pyrogallol> kaempferol> quercetin> chlorogenic acid> ferulic acid, cinnamic acid> vanillic acid> salicylic acid> p-coumaric acid> gallic acid). Result from the present work suggests that the fraction, RusePre, may open novel prospection as a functional ingredient in antioxidant supplements and in drugs to treat infectious disease.
A new method to analyze species abundances in space using generalized dimensions
Authors: Saravia Leonardo A
Published: January 2018

Species-area relationships (SAR) and species abundance distributions (SAD) are among the most studied patterns in ecology, due to their application in both theoretical and conservation issues. One problem with these general patterns is that different theories can generate the same predictions, and for this reason they can not be used to detect different mechanisms. A solution for this is to search for more sensitive patterns. One possibility is to extend the SAR to the whole species abundance distribution. A generalized dimension ($D_q$) approach has been proposed to study the scaling of SAD, but there has been no evaluation of the ability of this pattern to detect different mechanisms. An equivalent way to express SAD is the rank abundance distribution (RAD). Here I introduce a new way to study scaling of SAD using a spatial version of RAD: the species-rank surface (SRS), which can be analyzed using $D_q$. Thus there is an old $D_q$ based on SAR ($D_q^{SAD}$), and a new one based on SRS ($D_q^{SRS}$). I perform spatial simulations to relate both $D_q$ with SAD, spatial patterns and number of species. Finally I compare the power of both $D_q$, SAD, SAR exponent, and the fractal information dimension to detect different community patterns using a continuum of hierarchical and neutral spatially explicit models. The SAD, $D_q^{SAD}$ and $D_q^{SRS}$ all had good performance in detecting models with contrasting mechanisms. $D_q^{SRS}$ had a better fit to data and a strong ability to compare between hierarchical communities where the other methods failed. The SAR exponent and information dimension had low power and should not be used. SRS and $D_q^{SRS}$ could be an interesting addition to study community or macroecological patterns.
CRISPR-Cas9 in gene therapy: much control on breaking, little control on repairing
Authors: Daneshvar Kaveh
Published: January 2018

Recent advances in CRISPR-Cas9 genome editing tool have made great promises to basic and biomedical research as well as gene therapy. Efforts to make the CRISPR-Cas9 system applicable in gene therapy are largely focused on two aspects: 1) increasing the specificity of this system by eliminating off-target effects, and 2) optimizing in vivo delivery of the CRISPR-Cas9 DNA constructs to target cells and limiting the expression of Cas9 and gRNA to prevent immune responses. Moreover, there is an unnoted but crucial consideration about the mode of DNA repair at the lesion caused by CRISPR-Cas9. In this commentary, I briefly highlight recent publications on in vivo use of the CRISPR-Cas9 system in gene therapy. I then discuss concerns about the off-target activity and immune responses triggered by the use CRISPR-Cas9 in gene therapy. Following this, I focus on the undesired on-target DNA repair events that can occur as a result of the activity of CRISPR-Cas9. This concise commentary sets itself apart from previous perspectives by focusing on the modes of DNA repair employed following a CRISPR-Cas9 induced genomic insult, and by carefully weighing the benefits of the outcomes. In particular, the present manuscript underscores the need for more study on controlled DNA repair in systems targeted with CRISPR-Cas9 genome editing tools.
Direct dilution of cell aliquot for high temporal resolution bacterial surface charge measurement
Authors: Ng Wenfa
Published: January 2018

Bacterial surface charge (SC) mediates important cell-environment and microbe-host interactions, and its accurate and precise measurement by microelectrophoresis requires removing metabolites adhered to the cell surface - where repeated centrifugation and washing by buffers is the gold standard approach. Unfortunately, the need for time-consuming centrifugation limits the temporal resolution of sampling and interrogation of experimental dynamics; especially for samples requiring immediate treatment post sampling. Herein, the feasibility of diluting cell aliquots with buffer as a one-step sample preparation technique for SC measurement was investigated by characterising the effects of dilution factor, type of cation, and buffer conductivity on measuring SC of Escherichia coli DH5α grown in LB medium. Results indicated that dilution factor was critical to accurate SC measurement since low signal-to-noise ratios in high or low cell concentration samples generated substantial error. Type of buffer cation was also important since putative binding of high affinity cations to the cell surface underestimated SC of negatively-charged bacteria. Finally, although high conductivity buffers enabled greater removal of adsorbed metabolites through increased charge screening, a broader statistical distribution of measured SC was also observed – which, at extreme conductivity values, led to inaccurate data, probably due to removal of both intrinsic cell surface ions and exogenous adsorbed metabolites. Altogether, one-step dilution of cell aliquot with deionized water reliably reproduced E. coli SC values obtained via the gold standard approach; however, since the ensemble of secreted metabolites is bacteria/medium specific, distinct diluent and optimal parameters exist for each system. The described methodology may find use in preparing samples for cell surface characterisation studies, where it would help reduce sample preparation time – and thus, improve temporal resolution at which scientific questions can be probed and answered.
Internationalising Nordic higher education: comparing the imagined with actual worlds of international scholar-practitioners
Authors: Hellstén Meeri
Published: January 2018

This comparative case study addresses a timely issue engaging researchers involved in the internationalisation of Nordic Higher Education, in the context of Sweden and Finland. The study examines a hypothetical imaginary in the transition between university international policy statements and their understandings from the position of a globalised episteme. The investigation forms a tag-project as part of a funded large international research project examining ethical internationalism in times of global crises, involving a partnership between more than twenty higher education institutions in excess of ten countries across five continents. The data was collected using a mixed-methods design, whilst being controlled across the matched data collection period in 2013-2014. Data consisted of policy texts, surveys and interviews. The current research inquiry reports on a within and across comparative analyses of certain policy texts and follow-up interviews with university management. The results yield logical support for a global higher education imaginary driving internationalisation in ways which reveal paradoxical associations between the imagined and the real worlds of international scholar-practitioners.
Integrated genomic analyses of lung squamous cell carcinoma for identification of a possible competitive endogenous RNA network by means of TCGA datasets
Authors: Ning Pengbo , Wu Zhongxing , Hu Aoxue , Li Xuepeng , He Jun , Gong Xiaocheng , Xia Yuqiong , Shang Yukui , Bian Huijie
Published: January 2018

The etiology of cancer includes aberrant cellular homeostasis where a compromised RNA regulatory network is a prominent contributing factor. In particular, noncoding RNAs including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) were recently shown to play important roles in the initiation, progression, and metastasis of human cancers. Nonetheless, a mechanistic understanding of noncoding RNA functions in lung squamous cell carcinoma (LUSC) is lacking. To fill this critical gap in knowledge, we obtained mRNA, miRNA, and lncRNA expression data on patients with LUSC from the updated Cancer Genome Atlas (TCGA) database (2016). We successfully identified 3,366 mRNAs, 79 miRNAs, and 151 lncRNAs as key contributing factors of a high risk of LUSC. Furthermore, we hypothesized that the lncRNA–miRNA–mRNA regulatory axis positively correlates with LUSC and constructed a competitive endogenous RNA (ceRNA) network of LUSC by targeting interrelations with significantly aberrant expression data between miRNA and mRNA or lncRNA. Six ceRNAs (PLAU, miR-31-5p, miR-455-3p, FAM83A-AS1, MIR31HG, and MIR99AHG) significantly correlated with survival (P< 0.05). Finally, real-time quantitative PCR analysis showed that PLAU is significantly upregulated in SK-MES-1 cells compared with 16-BBE-T cells. Taken together, our findings represent new knowledge for a better understanding the ceRNA network in LUSC biology and pave the way to improved diagnosis and prognosis of LUSC.
The Potential for Metamorphic Thermal Pulses to Develop During Compaction‐Driven Fluid Flow
Authors: Tian Meng , Ague Jay J. , Chu Xu , Baxter Ethan F. , Dragovic Nora , Chamberlain C. Page , Rumble Douglas
Published: January 2018

Compaction‐driven fluid flow below the brittle‐ductile transition may be a means of transporting fluids during metamorphism. In particular, when a decompaction weakening mechanism is introduced to account for the rock viscosity reduction due to fluid overpressures, channeling instabilities evolve into high‐porosity/permeability fluid conduits that focus mass and energy transfer. In this study, we consider a crustal rheology that accounts simultaneously for upward‐increasing viscosity and decompaction weakening to examine the nucleation and evolution of fluid channelization in two dimensions (2‐D). The model shows that plume‐shaped flow patterns can develop on time scales as short as 104 years, during which the plume tails act as fluid conduits and the plume heads act as fluid dispersion zones near the brittle‐ductile transition. Collection of fluids into conduits is accomplished by a basal fluid catchment zone characterized by strong lateral fluid pressure gradients but low porosity/permeability. Relatively narrow ranges of viscous activation energy (∼100 kJ mol−1) and decompaction weakening factor (∼10−4) are constrained if the fluid conduits are of kilometer scale in width. Significant thermal excursions (∼65 °C) can be induced if a high flow rate, potentially from rapid intermittent dehydration, is realized within channels. Moreover, if the focused fluids emanate from external anomalously hot sources (e.g., magma intrusion), thermal pulses (>100°C), and steep lateral temperature gradients (>50°C km−1) can be generated. Given the focusing efficiency estimated from our 2‐D compaction model, simple 3‐D modeling further shows that tubular conduits have the potential to cause thermal pulses >200°C within 104 years.
Analytical Expressions for Thermo‐Osmotic Permeability of Clays
Authors: Gonçalvès J. , Ji Yu C. , Matray J.‐M. , Tremosa J.
Published: January 2018

In this study, a new formulation for the thermo‐osmotic permeability of natural pore solutions containing monovalent and divalent cations is proposed. The mathematical formulation proposed here is based on the theoretical framework supporting thermo‐osmosis which relies on water structure alteration in the pore space of surface‐charged materials caused by solid‐fluid electrochemical interactions. The ionic content balancing the surface charge of clay minerals causes a disruption in the hydrogen bond network when more structured water is present at the clay surface. Analytical expressions based on our heuristic model are proposed and compared to the available data for NaCl solutions. It is shown that the introduction of divalent cations reduces the thermo‐osmotic permeability by one third compared to the monovalent case. The analytical expressions provided here can be used to advantage for safety calculations in deep underground nuclear waste repositories.
Low‐Frequency Variability and the Unusual Indian Ocean Dipole Events in 2015 and 2016
Authors: Zhang Lianyi , Du Yan , Cai Wenju
Published: January 2018

An unusual positive Indian Ocean Dipole (IOD) event occurred in 2015 associated with the 2015/2016 extreme El Niño. Unlike the canonical IOD, sea surface temperature (SST) warming in the west central tropical Indian Ocean (TIO) dominated the strong zonal SST gradient as cooling off Sumatra‐Java was weak. Over the southeastern TIO, deeper thermocline has suppressed the upwelling cooling since 2012. Such deepened thermocline related to a low‐frequency adjustment and curtailed cool anomalies in the 2015 positive IOD but favored warm anomalies in the 2016 negative IOD. Based on statistical analyses, ocean assimilation data confirm that an IOD‐like pattern exists in the TIO on decadal timescale. During a negative decadal IOD‐like phase, thermocline is deeper in the southeastern TIO; the thermocline‐SST feedback is unfavorable for positive IOD occurrence and intensity, but conducive to negative IOD events. Thus, we propose that the 2015–2016 IOD events are modulated by the low‐frequency variability of thermocline.
Alfvénic Dynamics and Fine Structuring of Discrete Auroral Arcs: Swarm and e‐POP Observations
Authors: Miles D. M. , Mann I. R. , Pakhotin I. P. , Burchill J. K. , Howarth A. D. , Knudsen D. J. , Lysak R. L. , Wallis D. D. , Cogger L. L. , Yau A. W.
Published: January 2018

The electrodynamics associated with dual discrete arc aurora with antiparallel flow along the arcs were observed nearly simultaneously by the enhanced Polar Outflow Probe (e‐POP) and the Swarm A and C spacecraft. Auroral imaging from e‐POP reveals 1–10 km structuring of the arcs, which move and evolve on second timescales and confound the traditional single‐spacecraft field‐aligned current algorithms. High‐cadence magnetic data from e‐POP show 1–10 Hz, inferred Alfvénic, perturbations coincident with and at the same scale size as the observed dynamic auroral fine structures. High‐cadence electric and magnetic field data from Swarm A reveal nonstationary electrodynamics involving reflected and interfering Alfvén waves and modulation consistent with trapping in the ionospheric Alfvén resonator (IAR). These observations suggest a role for Alfvén waves, perhaps also the IAR, in discrete arc dynamics on 0.2–10 s timescales and ~1–10 km spatial scales and reinforce the importance of considering Alfvén waves in magnetosphere‐ionosphere coupling.
Meridional Modes and Increasing Pacific Decadal Variability Under Anthropogenic Forcing
Authors: Liguori Giovanni , Di Lorenzo Emanuele
Published: January 2018

Pacific decadal variability has strong impacts on the statistics of weather, atmosphere extremes, droughts, hurricanes, marine heatwaves, and marine ecosystems. Sea surface temperature (SST) observations show that the variance of the El Niño‐like decadal variability has increased by ~30% (1920–2015) with a stronger coupling between the major Pacific climate modes. Although we cannot attribute these trends to global climate change, the examination of 30 members of the Community Earth System Model Large Ensemble (LENS) forced with the RCP8.5 radiative forcing scenario (1920–2100) suggests that significant anthropogenic trends in Pacific decadal variance will emerge by 2020 in response to a more energetic North Pacific Meridional Mode (PMM)—a well‐known El Niño precursor. The PMM is a key mechanism for energizing and coupling tropical and extratropical decadal variability. In the LENS, the increase in PMM variance is consistent with an intensification of the winds‐evaporation‐SST thermodynamic feedback that results from a warmer mean climate.
Statistically Self‐Consistent and Accurate Errors for SuperDARN Data
Authors: Reimer A. S. , Hussey G. C. , McWilliams K. A.
Published: January 2018

The Super Dual Auroral Radar Network (SuperDARN)‐fitted data products (e.g., spectral width and velocity) are produced using weighted least squares fitting. We present a new First‐Principles Fitting Methodology (FPFM) that utilizes the first‐principles approach of Reimer et al. (2016) to estimate the variance of the real and imaginary components of the mean autocorrelation functions (ACFs) lags. SuperDARN ACFs fitted by the FPFM do not use ad hoc or empirical criteria. Currently, the weighting used to fit the ACF lags is derived from ad hoc estimates of the ACF lag variance. Additionally, an overcautious lag filtering criterion is used that sometimes discards data that contains useful information. In low signal‐to‐noise (SNR) and/or low signal‐to‐clutter regimes the ad hoc variance and empirical criterion lead to underestimated errors for the fitted parameter because the relative contributions of signal, noise, and clutter to the ACF variance is not taken into consideration. The FPFM variance expressions include contributions of signal, noise, and clutter. The clutter is estimated using the maximal power‐based self‐clutter estimator derived by Reimer and Hussey (2015). The FPFM was successfully implemented and tested using synthetic ACFs generated with the radar data simulator of Ribeiro, Ponomarenko, et al. (2013). The fitted parameters and the fitted‐parameter errors produced by the FPFM are compared with the current SuperDARN fitting software, FITACF. Using self‐consistent statistical analysis, the FPFM produces reliable or trustworthy quantitative measures of the errors of the fitted parameters. For an SNR in excess of 3 dB and velocity error below 100 m/s, the FPFM produces 52% more data points than FITACF.
Tectonic Regimes of the Central and Southern Andes: Responses to Variations in Plate Coupling During Subduction
Authors: Horton Brian K.
Published: January 2018

Construction of the Andes has been governed largely by fluctuating contractional, neutral, and extensional tectonic regimes during differing degrees of mechanical coupling along the convergent plate boundary. These three contrasting regimes are likely regulated by geodynamic variations in absolute trenchward motion of South America and episodic regional shifts in the geometry of the subducting oceanic slab. Alternations among these three modes are revealed in syntheses of Mesozoic‐Cenozoic crustal deformation, basin evolution, and arc magmatism along orogen‐perpendicular transects across the central and southern Andes at 23°S, 35°S, and 43°S. Despite considerable along‐strike dissimilarities in the magnitude of deformation, a comparable tectonic regime typified the early Andean history, as defined by a transition from Late Jurassic‐Early Cretaceous postrift thermal subsidence to Late Cretaceous retroarc shortening. A key contradiction is expressed for the late middle Eocene to earliest Miocene, when neutral to extensional conditions affected retroarc to forearc regions, except in parts of the central Andes, which experienced retroarc shortening with only localized forearc extension. This mixed‐mode scenario during Paleogene time may reflect decoupling along the plate boundary (possibly during slab rollback within a retreating subduction system) in which widespread stasis or low‐magnitude extension dominated the southern Andes but was inhibited in the strongly shortened central Andes at 15–25°S where shallow subduction and/or high topography boosted plate coupling. Comparable temporal and spatial shifts in tectonic regime along the Andes and other convergent margins can be related to variable degrees of coupling during first‐order plate‐scale changes in convergence and second‐order regional cycles of slab shallowing and steepening.
Preserved Neoproterozoic Continental Collision in Southeastern North America: The Brunswick Suture Zone and Osceola Continental Margin Arc
Authors: Boote Susannah K. , Knapp James H. , Mueller Paul A.
Published: January 2018

A series of exotic terranes were accreted to the eastern margin of southeastern Laurentia beginning in the Siluro‐Devonian (Acadian event), and to the northeastern Laurentian margin beginning earlier (late Taconian). Many of these terranes have unclear tectonostratigraphic relationships to each other and to their parental cratons, but their accretionary history is critical to understanding the evolution of the Appalachian orogen. Two of these, the Gondwanan Suwannee and Charleston terranes, accreted during the Alleghanian orogeny and now lie beneath the Atlantic Coastal Plain in southeastern North America. Reanalysis of deep seismic reflection and well data reveals a preserved Neoproterozoic continental collision zone and associated continental margin arc, the Osceola arc, related to their juxtaposition. The subduction zone and associated strain are recorded in the newly termed Brunswick suture zone (BSZ). The BSZ is readily identified on a series of eight deep seismic reflection transects across the Brunswick Magnetic Anomaly (BMA), which we interpret as the boundary between the Charleston and Suwannee terranes. While originally interpreted to be the Late Paleozoic Alleghanian suture, new age constraints provided by the overlapping Gondwanan Paleozoic Suwannee Basin strata require the BSZ to predate the Early to Middle Paleozoic passive margin sequence of the Suwannee Basin. These results provide new insights into the tectonostratigraphic evolution of the Charleston and Suwannee terranes, the controversy surrounding the age and origin of the dipping seismic reflectors, previously attributed to the suturing of the Suwannee terrane to Laurentia, and the relationship of this suture zone to the origin of the BMA.
Strain Localization Within a Syntectonic Intrusion in a Back‐Arc Extensional Context: The Naxos Monzogranite (Greece)
Authors: Bessiere Eloïse , Rabillard Aurelien , Précigout Jacques , Arbaret Laurent , Jolivet Laurent , Augier Romain , Menant Armel , Mansard Nicolas
Published: January 2018

Although fundamental to the understanding of crustal dynamics in extensional setting, the relationships between the emplacement of granitic intrusions and activity of detachments still remain very elusive. Through a multiscale approach, we here document a continuous deformation history between the monzogranitic intrusion of Naxos and the Naxos‐Paros Detachment System (Cyclades, Greece). Field observations first show an early magmatic deformation followed by solid‐state, ductile, and then brittle deformation when approaching the detachment zone, as evidenced by the overprinting of mylonites by cataclastes and pseudotachylites. From these observations, we define six strain facies that characterize a positive strain gradient from core to rim of the Naxos monzogranite. Based on field pictures, X‐ray tomography, and electron backscatter diffraction (EBSD) analyses along the strain gradient, we then quantify the intensity of mineralogical fabrics in 2‐D and 3‐D and better characterize the deformation mechanisms. Our measured shape variations of the strain ellipsoid corroborate the large‐scale strain gradient, showing a good correlation between qualitative and quantitative studies. In addition, EBSD data indicate that dislocation creep was predominant during cooling from more than 500°C to temperature conditions of the ductile‐to‐brittle transition. However, (1) a weakening of quartz lattice preferred orientation with increasing strain and (2) evidence of numerous four‐grain junctions in high‐strain shear bands also indicate that grain boundary sliding significantly contributed to the deformation. Although the source of grain boundary sliding remains to be constrained, it provides a consistent approach to account for strain localization in Naxos.
The T‐TEL Method for Assessing Water, Sediment, and Chemical Connectivity
Authors: Ali Genevieve , Oswald Claire , Spence Christopher , Wellen Christopher
Published: January 2018

The concept of connectivity has been the subject of a great deal of recent research and provided new insights and breakthroughs on runoff generation processes and watershed biogeochemistry. However, a consensus definition and cohesive mathematical framework that would permit the consistent quantification of hydrologic connectivity, the examination of the interrelationships between water and material (e.g., sediment and chemicals) connectivity, or rigorous study intercomparison, have not been presented by the water resource community. Building on previous conceptualizations and site‐specific or process‐specific metrics, this paper aimed to review the current state of science on hydrologic connectivity and its role in water‐mediated connectivity of material such as solutes and sediment before introducing a conceptual and a mathematical connectivity assessment framework. These frameworks rely on the quantification of Time scales, Thresholds, Excesses and Losses related to water and water‐mediated material transport dynamics and are referred to as the T‐TEL method. Through a small case study, we show how the T‐TEL method allows a wide range of properties to be quantified, namely the occurrence, frequency, duration, magnitude, and spatial extent of water and water‐mediated material connectivity. We also propose a research agenda to refine the T‐TEL method and ensure its usefulness for facilitating the research and management of connectivity in pristine and human‐impacted landscapes.
Accounting for the Decreasing Reaction Potential of Heterogeneous Aquifers in a Stochastic Framework of Aquifer‐Scale Reactive Transport
Authors: Loschko Matthias , Wöhling Thomas , Rudolph David L. , Cirpka Olaf A.
Published: January 2018

Many groundwater contaminants react with components of the aquifer matrix, causing a depletion of the aquifer's reactivity with time. We discuss conceptual simplifications of reactive transport that allow the implementation of a decreasing reaction potential in reactive‐transport simulations in chemically and hydraulically heterogeneous aquifers without relying on a fully explicit description. We replace spatial coordinates by travel‐times and use the concept of relative reactivity, which represents the reaction‐partner supply from the matrix relative to a reference. Microorganisms facilitating the reactions are not explicitly modeled. Solute mixing is neglected. Streamlines, obtained by particle tracking, are discretized in travel‐time increments with variable content of reaction partners in the matrix. As exemplary reactive system, we consider aerobic respiration and denitrification with simplified reaction equations: Dissolved oxygen undergoes conditional zero‐order decay, nitrate follows first‐order decay, which is inhibited in the presence of dissolved oxygen. Both reactions deplete the bioavailable organic carbon of the matrix, which in turn determines the relative reactivity. These simplifications reduce the computational effort, facilitating stochastic simulations of reactive transport on the aquifer scale. In a one‐dimensional test case with a more detailed description of the reactions, we derive a potential relationship between the bioavailable organic‐carbon content and the relative reactivity. In a three‐dimensional steady‐state test case, we use the simplified model to calculate the decreasing denitrification potential of an artificial aquifer over 200 years in an ensemble of 200 members. We demonstrate that the uncertainty in predicting the nitrate breakthrough in a heterogeneous aquifer decreases with increasing scale of observation.
Unraveling the Hydrology of the Glacierized Kaidu Basin by Integrating Multisource Data in the Tianshan Mountains, Northwestern China
Authors: Shen Yan‐Jun , Shen Yanjun , Fink Manfred , Kralisch Sven , Brenning Alexander
Published: January 2018

Understanding the water balance, especially as it relates to the distribution of runoff components, is crucial for water resource management and coping with the impacts of climate change. However, hydrological processes are poorly known in mountainous regions due to data scarcity and the complex dynamics of snow and glaciers. This study aims to provide a quantitative comparison of gridded precipitation products in the Tianshan Mountains, located in Central Asia and in order to further understand the mountain hydrology and distribution of runoff components in the glacierized Kaidu Basin. We found that gridded precipitation products are affected by inconsistent biases based on a spatiotemporal comparison with the nearest weather stations and should be evaluated with caution before using them as boundary conditions in hydrological modeling. Although uncertainties remain in this data‐scarce basin, driven by field survey data and bias‐corrected gridded data sets (ERA‐Interim and APHRODITE), the water balance and distribution of runoff components can be plausibly quantified based on the distributed hydrological model (J2000). We further examined parameter sensitivity and uncertainty with respect to both simulated streamflow and different runoff components based on an ensemble of simulations. This study demonstrated the possibility of integrating gridded products in hydrological modeling. The methodology used can be important for model applications and design in other data‐scarce mountainous regions. The model‐based simulation quantified the water balance and how the water resources are partitioned throughout the year in Tianshan Mountain basins, although the uncertainties present in this study result in important limitations.
Biomimetic and Superwettable Nanofibrous Skins for Highly Efficient Separation of Oil‐in‐Water Emulsions
Authors: Ge Jianlong , Zong Dingding , Jin Qing , Yu Jianyong , Ding Bin
Published: January 2018

Developing a feasible and efficient separation membrane for the purification of highly emulsified oily wastewater is of significance but challenging due to the critical limitations of low flux and serious membrane fouling. Herein, a biomimetic and superwettable nanofibrous skin on an electrospun fibrous membrane via a facile strategy of synchronous electrospraying and electrospinning is created. The obtained nanofibrous skin possesses a lotus‐leaf‐like micro/nanostructured surface with intriguing superhydrophilicity and underwater superoleophobicity, which are due to the synergistic effect of the hierarchical roughness and hydrophilic polymeric matrix. The ultrathin, high porosity, sub‐micrometer porous skin layer results in the composite nanofibrous membranes exhibiting superior performances for separating both highly emulsified surfactant‐free and surfactant‐stabilized oil‐in‐water emulsions. An ultrahigh permeation flux of up to 5152 L m−2 h−1 with a separation efficiency of >99.93% is obtained solely under the driving of gravity (≈1 kPa), which was one order of magnitude higher than that of conventional filtration membranes with similar separation properties, showing significant applicability for energy‐saving filtration. Moreover, with the advantage of an excellent antioil fouling property, the membrane exhibits robust reusability for long‐term separation, which is promising for large‐scale oily wastewater remediation.