bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards Real‐Time Continental Scale Streamflow Simulation in Continuous and Discrete Space
Authors: Salas Fernando R. , Somos‐Valenzuela Marcelo A. , Dugger Aubrey , Maidment David R. , Gochis David J. , David Cédric H. , Yu Wei , Ding Deng , Clark Edward P. , Noman Nawajish 
Published: October 2017

AbstractThe National Weather Service (NWS) forecasts floods at approximately 3,600 locations across the United States (U.S.). However, the river network, as defined by the 1:100,000 scale National Hydrography Dataset‐Plus (NHDPlus) dataset, consists of 2.7 million river segments. Through the National Flood Interoperability Experiment, a continental scale streamflow simulation and forecast system was implemented and continuously operated through the summer of 2015. This system leveraged the WRF‐Hydro framework, initialized on a 3‐km grid, the Routing Application for the Parallel Computation of Discharge river routing model, operating on the NHDPlus, and real‐time atmospheric forcing to continuously forecast streamflow. Although this system produced forecasts, this paper presents a study of the three‐month nowcast to demonstrate the capacity to seamlessly predict reach scale streamflow at the continental scale. In addition, this paper evaluates the impact of reservoirs, through a case study in Texas. Validation of the uncalibrated model using observed hourly streamflow at 5,701 U.S. Geological Survey gages shows 26% demonstrate PBias ≤ |25%|, 11% demonstrate Nash‐Sutcliffe Efficiency (NSE) ≥ 0.25, and 6% demonstrate both PBias ≤ |25%| and NSE ≥ 0.25. When evaluating the impact of reservoirs, the analysis shows when reservoirs are included, NSE ≥ 0.25 for 56% of the gages downstream while NSE ≥ 0.25 for 11% when they are not. The results presented here provide a benchmark for the evolving hydrology program within the NWS and supports their efforts to develop a reach scale flood forecasting system for the country.
Quantifying population size of migrant birds at stopover sites: Combining count data with stopover length estimated from stable isotope analysis
Authors: Catry Teresa , Lourenço Pedro M. , Granadeiro José P. 
Published: October 2017

Abstract

Regular counts of migrating animals at stopover sites have been used as a measure of site importance at the global scale as well as for monitoring long‐term population changes. However, migratory passage can last for several weeks and the turnover rate of individuals is often high, preventing the use of peak counts to estimate the total number of migrants. This estimate can be achieved, however, by combining count data with information on stopover length.

Here, we developed a new method to quantify the total number of migrant birds using stopover areas hosting overlapping populations of local (breeding or wintering) and passage individuals of a given species. We illustrate the application of this method by estimating the number of spring migrant dunlins Calidris alpina stopping over at the Tagus estuary (Portugal). We used carbon and nitrogen isotopic signatures in toenails to identify migrants and to estimate their proportion in total counts. We then employed isotopic clock models to determine time since arrival (TSA) of individuals from signatures in red blood cells and plasma and, using a simulation approach, we derived the relationship between TSA and stopover length. Finally, by dividing the number of migrants.day (obtained from counts) by the stopover length, we assessed the size of the migrant population.

We demonstrated that stopover length can be directly predicted from mean TSA values of birds sampled during migration, regardless of variations in (1) migratory rate, that is, the phenology of arrivals throughout the migratory period and (2) the number of birds involved in the migratory event. Migrant dunlins stayed on average 7.5 days at the Tagus estuary during spring migration, which combined with count data resulted in an estimate of c. 30,000 passage dunlins, using the study site.

Our novel approach is not strict in its assumptions, and therefore can be customised to the specificities of different taxa and study areas. Estimates of total number of migrants along migratory flyways are critical to identify priority sites for conservation action. In fact, single stopover sites may host a very significant proportion of a global population albeit for a short period.
Quantitative evolutionary patterns in bipartite networks: Vicariance, phylogenetic tracking or diffuse co‐evolution?
Authors: Russo Laura , Miller Adam D. , Tooker John , Bjornstad Ottar N. , Shea Katriona 
Published: October 2017

Abstract

Many pairwise interactions in ecological communities are thought to be structured by co‐evolution, a process difficult to study on a community level. Traditional methods can reveal correlated phylogenies between interacting organisms, suggesting a co‐evolutionary association. However, several processes could lead to cophylogeny, including (1) vicariance, (2) phylogenetic tracking and (3) co‐evolution.

We present a framework to investigate diffuse co‐evolution between groups of interacting taxa. Our methodology incorporates two complementary statistical methods to test for evolutionary signals. First, we test for correlated taxonomies between interacting species, and then we test for an association between the pattern of interactions and taxonomy of interacting species. We use these methods to clearly distinguish between three possible explanations of cophylogenies, when present.

Our methodology is designed to explore diffuse evolutionary signals among many interacting taxa: it is robust to polytomies and generalization and can use taxonomic trees in place of phylogenies. Thus, we use taxonomic distances to identify groups of associated taxa, as opposed to specific co‐evolutionary relationships.

In a case study, we find significant evidence for phylogenetic tracking, vicariance and asymmetry. Generally, our method can be applied whenever relevant taxonomy is well resolved and includes sufficient variation at multiple taxonomic ranks between two groups of interacting taxa. This adaptable method can incorporate many types of data on species traits or behaviours, such as phylogenetic relatedness, pollination efficacy, interaction strengths and visitation rates. The analysis we provide here may be of use to a broad range of ecologists interested in evaluating diffuse evolutionary patterns in groups of interacting species.
AutoMorph: Accelerating morphometrics with automated 2D and 3D image processing and shape extraction
Authors: Hsiang Allison Y. , Nelson Kaylea , Elder Leanne E. , Sibert Elizabeth C. , Kahanamoku Sara S. , Burke Janet E. , Kelly Abigail , Liu Yusu , Hull Pincelli M. 
Published: October 2017

Abstract

Large‐scale, comparative studies of morphological variation are rare due to the time‐intensive nature of shape quantification. This data gap is important to address, as intraspecific and interspecific morphological variation underpins and reflects ecological and evolutionary processes.

Here, we detail a novel software package, AutoMorph, for high‐throughput object and shape extraction. AutoMorph can batch image many types of organisms (e.g. foraminifera, molluscs and fish teeth), allowing for rapid generation of assemblage‐scale morphological data.

We used AutoMorph to image and generate 2D and 3D morphological data for >100,000 marine microfossils in about a year. Our collaborators have used AutoMorph to process >12,000 patellogastropod shells and >50,000 fish teeth.

AutoMorph allows users to rapidly produce large amounts of morphological data, facilitating community‐scale evolutionary and ecological studies. To hasten the adoption of automated approaches, we have made AutoMorph freely available and open source. AutoMorph runs on all UNIX‐like systems; future versions will run across all platforms.
Evaluation of a method for isocapnic hyperventilation: a clinical pilot trial
Authors: Hallén K. , Jildenstål P. , Stenqvist O. , Ricksten S.‐E. , Lindgren S. 
Published: October 2017

BackgroundIsocapnic hyperventilation (IHV) is a method that shortens time to extubation after inhalation anaesthesia using hyperventilation (HV) without lowering airway CO2. In a clinical trial on patients undergoing long‐duration sevoflurane anaesthesia for major ear–nose–throat (ENT) surgery, we evaluated the utility of a technique for CO2 delivery (DCO2) to the inspiratory limb of a closed breathing circuit, during HV, to achieve isocapnia.MethodsFifteen adult ASA 1–3 patients were included. After end of surgery, mechanical HV was started by doubling baseline minute ventilation. Simultaneously, CO2 was delivered and dosed using a nomogram developed in a previous experimental study. Time to extubation and eye opening was recorded. Inspired (FICO2) and expired (FETCO2) CO2 and arterial CO2 levels were monitored during IHV. Cognition was tested pre‐operatively and at 20, 40 and 60 min after surgery.ResultsA DCO2 of 285 ± 45 ml/min provided stable isocapnia during HV (13.5 ± 4.1 l/min). The corresponding FICO2 level was 3.0 ± 0.3%. Time from turning off the vaporizer (1.3 ± 0.1 MACage) to extubation (0.2 ± 0.1 MACage) was 11.3 ± 1.8 min after 342 ± 131 min of anaesthesia. PaCO2 and FETCO2 remained at normal levels during and after IHV. In 85% of the patients, post‐operative cognition returned to pre‐operative values within 60 min.ConclusionsIn this cohort of patients, a DCO2 nomogram for IHV was validated. The patients were safely extubated shortly after discontinuing long‐term sevoflurane anaesthesia. Perioperatively, there were no adverse effects on arterial blood gases or post‐operative cognition. This technique for IHV can potentially be used to decrease emergence time from inhalation anaesthesia.
Context‐Specific Inhibition is Related to Craving in Alcohol Use Disorders: A Dangerous Imbalance
Authors: Stein Maria , Fey Werner , Koenig Thomas , Oehy Jacqueline , Moggi Franz 
Published: October 2017

BackgroundMost contemporary neuroscientific models of alcohol use disorders (AUD) incorporate an imbalance between enhanced cue reactivity, which results in a strong urge to consume, and the impaired inhibitory control of that urge. While these phenomena have been frequently investigated separately, studies involving both aspects and thus precisely investigating the postulated imbalance are rare. In this study, inhibition was investigated in an addiction‐specific context and individual craving levels were also examined.MethodsThis study compared inhibition in alcohol‐related and neutral contexts in patients with AUD and healthy controls, while also taking into account the individual amount of craving. All subjects performed a Go/NoGo task involving neutral and alcohol‐related NoGo trials, while their brain activity was recorded using multichannel electroencephalography. The map strength and topography of the N2 and P3 components of the NoGo event‐related potentials were compared between groups and contexts using whole‐scalp randomization‐based methods. The effects of interest were further investigated with sLORETA source analysis.ResultsFor the N2 component, the context by craving interaction was strong for map strength and map topography. The source analysis indicated that in subjects with high craving, alcohol‐related context led to enhanced and prolonged activation in the posterior cingulate and premotor cortical areas. This interaction was specific for craving, but not for diagnostic classification. The amplitude of the P3 component was reduced in subjects with AUD, which replicated previous findings.ConclusionsIn subjects with strong craving, the conflict reflected in the NoGo‐N2 was enhanced in the alcohol‐related context. Such enhanced conflict probably makes the successful inhibition of the urge to drink in high‐risk situations even more difficult for this subgroup of patients and should therefore be addressed in individualized treatment planning.
Hemispheric asymmetry of the frontolimbic cortex in young adults with borderline personality disorder
Authors: Zhou Q. , Zhong M. , Yao S. , Jin X. , Liu Y. , Tan C. , Zhu X. , Yi J. 
Published: October 2017

ObjectiveAlthough the frontolimbic cortex has been implicated in borderline personality disorder (BPD), information about possible asymmetries in this region in patients with BPD is limited. This study aimed to examine whether frontolimbic cortex asymmetries differ between patients with BPD and healthy individuals.MethodsThe brains of 30 young adult patients with BPD and 32 healthy control subjects were scanned with magnetic resonance imaging (MRI). The participants completed self‐report scales assessing impulsivity, affect intensity and other psychological variables. Gray matter volume, surface area, and cortical thickness in regions of interest (ROIs), namely anterior insula (AI) and anterior cingulate cortex (ACC) were determined and the data were probed for hemisphere‐group interactions.ResultsRelative to controls, patients with BPD had reduced cortical thickness in left ACC and less surface area and gray matter volume in left AI. Significant group‐hemisphere interactions were observed for gray matter volume and surface area of AI and for cortical thickness of ACC. Post hoc analysis showed that the BPD patients had greater frontolimbic cortex asymmetry than healthy controls; furthermore, greater asymmetry of AI&ACC correlated with a higher score in attention subscale of Barratt Impulsiveness Scale.ConclusionPatients with BPD have greater frontolimbic asymmetry than healthy individuals.
The role of Rhytidoponera metallica (Hymenoptera, Formicidae) in facilitating post‐fire seed germination of three ant‐dispersed legume species
Authors: Beaumont Kieren P. , Mackay Duncan A. , Whalen Molly A. 
Published: October 2017

AbstractThe fire avoidance hypothesis proposes that a benefit of seed dispersal by ants (myrmecochory) is to protect seeds from being killed during fire and to facilitate post‐fire germination of seeds that require heat shock to break their physical dormancy. The aim of this study was to quantify the effect of fire and seed burial by a predominant seed‐dispersing ant, Rhytidoponera metallica (subfamily: Ectatomminae) on germination levels of three ant‐dispersed legume species (Pultenaea daphnoides, Acacia myrtifolia and Acacia pycnantha). Experimental burial of seeds within aluminium cans at a site prior to being burnt and at an adjacent unburnt site showed that fire increased germination levels, particularly for seeds buried at 1‐ and 2‐cm deep and that overall, germination levels differed among the three plant species. To quantify seed burial depths and post‐fire germination levels facilitated by R. metallica ants, seeds were fed to colonies prior to fire at the burnt and unburnt sites. Of the seeds buried within nests that were recovered, between 45% and 75% occurred within the upper 6 cm of the soil profile, although unexpectedly, greater percentages of seeds were recovered from the upper 0–2 cm of nests in the unburnt site compared with nests in the burnt site. Germination levels of buried seeds associated with R. metallica nests ranged from 21.2% to 29.5% in the burnt site compared with 3.1–14.8% in the unburnt site. While increased seed germination levels were associated with R. metallica nests following fire, most seeds were buried at depths below those where optimal temperatures for breaking seed dormancy occurred during the fire. We suggest that R. metallica ants may provide fire avoidance benefits to myrmecochorous seeds by burying them at a range of depths within a potential germination zone defined by intra‐ and inter‐fire variation in levels of soil heating.
Gender and arch effects on the use of non‐opioid analgesics for post endodontic pain reduction
Authors: Elzaki Wail M. , Ziada Hassan M. , Abubakr Neamat H. , Ibrahim Yahia E. 
Published: October 2017

AbstractThis study aimed to evaluate the secondary outcomes of gender and arch and their impact on pain reduction following initial endodontic therapy. 185 medications, including placebo were prepared, and 170 participants completed the trial. Group 1, received a single dose of Paracetamol alone (G‐1), Group 2 received combined Ibuprofen/Paracetamol (G‐2). Group 3 received combined Mefenamic acid/Paracetamol (G‐3), group 4 received combined Diclofenac K/Paracetamol (G‐4) and Group 5 received a placebo (G‐5). There were no statistically significant differences in pain reduction between males and females whilst there were statistically significant differences between them and the placebo group. All combinations of Paracetamol performed better in pain reduction than the placebo among females, while there were no statistically significant differences among males. In conclusion, there were no differences in pain reduction between males and females, and arch for the tested analgesics taken immediately following initial endodontic therapy in teeth with irreversible pulpitis.
Review article: hepatitis B core‐related antigen (HBcrAg): an emerging marker for chronic hepatitis B virus infection
Authors: Mak L.‐Y. , Wong D. K.‐H. , Cheung K.‐S. , Seto W.‐K. , Lai C.‐L. , Yuen M.‐F. 
Published: October 2017

SummaryBackgroundChronic hepatitis B (CHB) cannot be completely eradicated due to the presence of covalently closed circular DNA (cccDNA) in the nuclei of infected hepatocytes. While quantification of intrahepatic cccDNA requires liver biopsies, serological markers can be non‐invasive alternatives to reflect intrahepatic viral replicative activity. Recently, hepatitis B core‐related antigen (HBcrAg) has been advocated as a novel serum marker for disease monitoring and prognostication of CHB.AimTo examine the virological aspect and clinical application of HBcrAg with respect to the natural history and treatment of CHB.MethodsWe reviewed all papers published in the PubMed journal list and abstracts from major international meetings that included the keyword “HBcrAg” or “hepatitis B core‐related antigen” until March 2017. Selected studies were compared and summarised on the basis of existing theories, as well as the authors’ experience.ResultsHBcrAg exhibited good correlation with intrahepatic (ih) cccDNA, ih total hepatitis B virus (HBV) DNA, serum HBV DNA and to a lesser extent HBV surface antigen (HBsAg). In situations where serum HBV DNA levels become undetectable or HBsAg loss is achieved, HBcrAg can still be detectable. This marker is helpful in differentiation of HBeAg‐negative chronic hepatitis from HBeAg‐negative chronic infection, predicting spontaneous or treatment‐induced HBeAg seroconversion, sustained response to nucleos(t)ide analogue (NA), risk of HBV reactivation in occult HBV infection under immunosuppressive therapies, and risk of hepatocellular carcinoma (HCC) development as well as post‐operative HCC recurrence.ConclusionsHBcrAg is a potential surrogate marker of cccDNA. It may soon become a useful marker for disease monitoring, predicting treatment response and disease outcome of chronic hepatitis B.
Innovation not recovery: dynamic redox promotes metazoan radiations
Authors: Wood Rachel , Erwin Douglas H. 
Published: October 2017

ABSTRACTEnvironmental fluctuations in redox may reinforce rather than hinder evolutionary transitions, such that variability in near‐surface oceanic oxygenation can promote morphological evolution and novelty. Modern, low‐oxygen regions are heterogeneous and dynamic habitats that support low diversity and are inhabited by opportunistic and non‐skeletal metazoans. We note that several major radiation episodes follow protracted or repeating intervals (>1 million years) of persistent and dynamic shallow marine redox (oceanic anoxic events). These are also often associated with short‐lived mass‐extinction events (<0.5 million years) where skeletal benthic incumbents are removed, and surviving or newly evolved benthos initially inhabit transient oxic habitats. We argue that such intervals create critical opportunities for the generation of evolutionary novelty, followed by innovation and diversification.We develop a general model for redox controls on the distribution and structure of the shallow marine benthos in a dominantly anoxic world, and compile data from the terminal Ediacaran–mid‐Cambrian (∼560–509 Ma), late Cambrian–Ordovician (∼500–445 Ma), and Permo‐Triassic (∼255–205 Ma) to test these predictions. Assembly of phylogenetic data shows that prolonged and widespread anoxic intervals indeed promoted morphological novelty in soft‐bodied benthos, providing the ancestral stock for subsequently skeletonized lineages to appear as innovations once oxic conditions became widespread and stable, in turn promoting major evolutionary diversification. As a result, we propose that so‐called ‘recovery’ intervals after mass extinctions might be better considered as ‘innovation’ intervals.
Involvement of local renin‐angiotensin system in immunosuppression of tumor microenvironment
Authors: Nakamura Kenta , Yaguchi Tomonori , Ohmura Gaku , Kobayashi Asuka , Kawamura Naoshi , Iwata Takashi , Kiniwa Yukiko , Okuyama Ryuhei , Kawakami Yutaka 
Published: October 2017

AbstractTo improve current cancer immunotherapies, strategies to modulate various immunosuppressive cells including myeloid derived suppressor cells (MDSC) which were shown to be negative factors in immune‐checkpoint blockade therapy, need to be developed. In the present study, we evaluated the role of the local renin‐angiotensin system (RAS) in the tumor immune‐microenvironment using murine models bearing tumor cell lines in which RAS was not involved in their proliferation and angiogenetic ability. Giving angiotensin II receptor blockers (ARB) to C57BL/6 mice bearing murine colon cancer cell line MC38 resulted in significant enhancement of tumor antigen gp70 specific T cells. ARB administration did not change the numbers of CD11b+ myeloid cells in tumors, but significantly reduced their T‐cell inhibitory ability along with decreased production of various immunosuppressive factors including interleukin (IL)‐6, IL‐10, vascular endothelial growth factor (VEGF), and arginase by CD11b+ cells in tumors. ARB also decreased expression of immunosuppressive factors such as chemokine ligand 12 and nitric oxide synthase 2 in cancer‐associated fibroblasts (CAF). Last, combination of ARB and anti‐programmed death‐ligand 1 (PD‐L1) antibodies resulted in significant augmentation of anti‐tumor effects in a CD8+ T cell‐dependent way. These results showed that RAS is involved in the generation of an immunosuppressive tumor microenvironment caused by myeloid cells and fibroblasts, other than the previously shown proliferative and angiogenetic properties of cancer cells and macrophages, and that ARB can transform the immunosuppressive properties of MDSC and CAF and could be used in combination with PD‐1/PD‐L1 immune‐checkpoint blockade therapy.