bluuebunny/crossref_metadata_2025 huggingface dataset:
Climbing halo merger trees with TreeFrog
Authors: Elahi Pascal J. , Poulton Rhys J. J. , Tobar Rodrigo J. , Cañas Rodrigo , Lagos Claudia del P. , Power Chris , Robotham Aaron S. G.
Published: August 2019

We present TreeFrog, a massively parallel halo merger tree builder that is capable comparing different halo catalogues and producing halo merger trees. The code is written in c++11, use the MPI and OpenMP API’s for parallelisation, and includes python tools to read/manipulate the data products produced. The code correlates binding energy sorted particle ID lists between halo catalogues, determining optimal descendant/progenitor matches using multiple snapshots, a merit function that maximises the number of shared particles using pseudo-radial moments, and a scheme for correcting halo merger tree pathologies. Focusing on VELOCIraptor catalogues for this work, we demonstrate how searching multiple snapshots spanning a dynamical time significantly reduces the number of stranded halos, those lacking a descendant or a progenitor, critically correcting poorly resolved halos. We present a new merit function that improves the distinction between primary and secondary progenitors, reducing tree pathologies. We find FOF accretion rates and merger rates show similar mass ratio dependence. The model merger rates from Poole, et al. [2017, 472, 3659] agree with the measured net growth of halos through mergers.
Mucosal microbial parasites/symbionts in health and disease: an integrative overview
Authors: Hirt Robert P.
Published: August 2019

Microbial parasites adapted to thrive at mammalian mucosal surfaces have evolved multiple times from phylogenetically distant lineages into various extracellular and intracellular life styles. Their symbiotic relationships can range from commensalism to parasitism and more recently some host–parasites interactions are thought to have evolved into mutualistic associations too. It is increasingly appreciated that this diversity of symbiotic outcomes is the product of a complex network of parasites–microbiota–host interactions. Refinement and broader use of DNA based detection techniques are providing increasing evidence of how common some mucosal microbial parasites are and their host range, with some species being able to swap hosts, including from farm and pet animals to humans. A selection of examples will illustrate the zoonotic potential for a number of microbial parasites and how some species can be either disruptive or beneficial nodes in the complex networks of host–microbe interactions disrupting or maintaining mucosal homoeostasis. It will be argued that mucosal microbial parasitic diversity will represent an important resource to help us dissect through comparative studies the role of host–microbe interactions in both human health and disease.
Healthy retirement begins at school: educational differences in the health outcomes of early transitions into retirement
Authors: Allel Kasim , León Ana Sofía , Staudinger Ursula M. , Calvo Esteban
Published: August 2019

The literature on socio-economic variations in the association between retirement timing and health is inconclusive and largely limited to the moderating role of occupation. By selecting the sample case of Mexico where a sizeable number of older adults have no or very little formal education, this study allows the moderating role of education to be tested properly. Drawing on panel data for 2,430 individuals age 50 and over from the Mexican Health and Aging Study (MHAS) and combining propensity score matching models with fixed-effects regressions, this article investigates differences in the health effects of retirement timing between older adults with varying years of education. Subjective health is measured using a self-reported assessment of respondents’ overall health and physical health as a reverse count of doctor-diagnosed chronic diseases. The results indicate that early transitions into retirement are associated with worse health outcomes, but education fully compensates for the detrimental association with subjective and physical health, while adjusting for baseline health, demographics and socio-economic characteristics. In conclusion, formal education during childhood and adolescence is associated with a long-term protective effect on health. It attenuates negative health consequences of early retirement transitions. Policies and programmes promoting healthy and active ageing would benefit from considering the influence of formal education in shaping older adults’ health after the transition into retirement.
Third time lucky: challenging secundum atrial septal defect
Authors: Ordoñez Maria Victoria , Moharem-Elgamal Sarah , Bedair Radwa
Published: August 2019

Secundum atrial septal defect is the most common form of interatrial communication. Atrial septal defects can present in young adults with a variety of clinical presentations, including breathlessness on effort, palpitations, or stroke. Clinical heart failure and resting desaturation are both rarely seen in young patients. We present a case of a young man with a secundum atrial septal defect and a diagnosis of constrictive pericarditis, only made after two attempts at surgical correction of the atrial septal defect, with pericardiectomy at the third attempt and subsequent symptomatic improvement.
Measuring adherence in social recovery therapy with people with first episode psychosis
Authors: Lowen Christine , Hodgekins Jo , Pugh Katherine , Berry Clio , Fitzsimmons Mike , French Paul , Sacadura Catarina , Birchwood Max , Jackson Chris , Baggott Eleanor , Bernard Mark , Fowler David
Published: August 2019

Background:

The SUPEREDEN3 study, a phase II randomized controlled trial, suggests that social recovery therapy (SRT) is useful in improving functional outcomes in people with first episode psychosis. SRT incorporates cognitive behavioural therapy (CBT) techniques with case management and employment support, and therefore has a different emphasis to traditional CBT for psychosis, requiring a new adherence tool.

Aims:

This paper describes the SRT adherence checklist and content of the therapy delivered in the SUPEREDEN3 trial, outlining the frequency of SRT techniques and proportion of participants who received a full therapy dose. It was hypothesized that behavioural techniques would be used frequently, consistent with the behavioural emphasis of SRT.

Method:

Research therapists completed an adherence checklist after each therapy session, endorsing elements of SRT present. Data from 1236 therapy sessions were reviewed to determine whether participants received full, partial or no therapy dose.

Results:

Of the 75 participants randomized to receive SRT, 57.3% received a full dose, 24% a partial dose, and 18.7% received no dose. Behavioural techniques were endorsed in 50.5% of sessions, with cognitive techniques endorsed in 34.9% of sessions.

Conclusions:

This report describes an adherence checklist which should be used when delivering SRT in both research and clinical practice. As hypothesized, behavioural techniques were a prominent feature of the SRT delivered in SUPEREDEN3, consistent with the behavioural emphasis of the approach. The use of this adherence tool would be considered essential for anyone delivering SRT looking to ensure adherence to the model.
THE RELATIVE VALUATION OF GOLD
Authors: Baur Dirk G. , Beckmann Joscha , Czudaj Robert L.
Published: August 2019

Gold is a globally traded asset and held in large quantities by investors and central banks. Since there is no established model to assess whether the price of gold is overvalued or undervalued, we propose a relative valuation framework based on gold price ratios. This idea is not confined to gold but offers the foundation for relative valuation of a broad range of different assets or asset classes. We analyze gold prices relative to commodity prices, consumer prices, stock prices, dividend, and bond yields and find that the relative value of gold varies significantly over time. An analysis of the factors which drive these variations demonstrates that inflation expectations and uncertainty have a strong influence on gold ratios while macroeconomic fundamentals are less important. More specifically, a boost in confidence decreases the relative price of gold while heightened uncertainty increases the relative price of gold, which confirms the role of gold as a safe haven.
Real-world evaluation of digital CBT for insomnia in the primary care setting – many should not log on to doze off
Authors: Xu Zheyu , Anderson Kirstie N.
Published: August 2019

Cognitive behaviour therapy for insomnia (CBTi) has emerged as the first-line treatment for insomnia where available. Clinical trials of digital CBTi (dCBTi) have demonstrated similar efficacy and drop-out rates to face-to-face CBTi. Most patients entering clinical trials are carefully screened to exclude other sleep disorders. This is a case series review of all those referred to a dCBTi within an 18-month time period. Those initially screened, accepted after exclusion of other sleep disorders, commencing and completing therapy were assessed to understand patient population referred from general practice in the UK. 390 patient referrals were analysed. 135 were suitable for dCBTi with a high rate of other sleep disorders detected in screening. 78 completed therapy (20.0%) and 44.9% had significant improvement in sleep outcomes, achieving ≥20% improvement in final sleep efficiency. dCBTi can be used within the UK NHS with good benefit for those who are selected as having insomnia and who then complete therapy. Many referrals are made with those likely to have distinct primary sleep disorders highlighting the need for education regarding sleep and sleep disorders prior to dCBTi therapy.

Key learning aims

(1)

The use of unsupported digital cognitive behavioural therapy for insomnia (dCBTi) requires proper patient selection.

(2)

There are many insomnia mimics and also previously unrecognized sleep and psychiatric disturbances that are under-diagnosed in the primary care setting that are contraindications for unsupported dCBTi.

(3)

The use of a stepped care approach similar to the UK’s Improving Access to Psychological Therapies (IAPT) model using dCBTi could be feasible in the public health setting.
Method to Derive Ion Properties From Juno JADE Including Abundance Estimates for O+ and S2+
Authors: Kim Thomas K. , Ebert R. W. , Valek P. W. , Allegrini F. , McComas D. J. , Bagenal F. , Chae K. , Livadiotis G. , Loeffler C. E. , Pollock C. , Ranquist D. A. , Thomsen M. F. , Wilson R. J. , Clark G. , Kollmann P. , Mauk B. H. , Bolton S. , Levin S. , Nicolaou G.
Published: August 2019

The Jovian Auroral Distributions Experiment Ion sensor (JADE‐I) on Juno is a plasma instrument that measures the energy‐per‐charge (E/Q) distribution of 0.01 to 46.2 keV/q ions over a mass‐per‐charge (M/Q) range of 1– 64 amu/q. However, distinguishing O+ and S2+ from JADE‐I's measurements is a challenging task due to similarities in their M/Q (∼16 amu/q). Because of this, O+ and S2+ have not been fully resolved in the in situ measurements made by plasma instruments at Jupiter (e.g., Voyager PLS and Galileo PLS) and their relative ratios has been studied using physical chemistry models and ultraviolet remote observations. To resolve this ambiguity, a ray tracing simulation combined with carbon foil effects is developed and used to obtain instrument response functions for H+, O+, O2+, O3+, Na+, S+, S2+, and S3+. The simulation results indicate that JADE‐I can resolve the M/Q ambiguity between O+ and S2+ due to a significant difference in their charge state modification process and a presence of a large electric potential difference (∼8 kV) between its carbon foils and MCPs. A forward model based on instrument response functions and convected kappa distributions is then used to obtain ion properties at the equatorial plasma sheet (∼36 RJ) in the predawn sector of magnetosphere. The number density ratio between O+ and S2+ for the selected plasma sheet crossings ranges from 0.2 to 0.7 (0.37 ± 0.12) and the number density ratio between total oxygen ions to total sulfur ions ranges from 0.2 to 0.6 (0.41 ± 0.09).
Multimode 3‐D Kirchhoff Migration of Receiver Functions at Continental Scale
Authors: Millet F. , Bodin T. , Rondenay S.
Published: August 2019

Receiver function analysis is widely used to image sharp structures in the Earth, such as the Moho or transition zone discontinuities. Standard procedures either rely on the assumption that underlying discontinuities are horizontal (common conversion point stacking) or are computationally expensive and usually limited to 2‐D geometries (reverse time migration and generalized Radon transform). Here, we develop a teleseismic imaging method that uses fast 3‐D traveltime calculations with minimal assumption about the underlying structure. This allows us to achieve high computational efficiency without limiting ourselves to 1‐D or 2‐D geometries. In our method, we apply acoustic Kirchhoff migration to transmitted and reflected teleseismic waves (i.e., receiver functions). The approach expands on the work of Cheng et al. (2016, https://doi.org/10.1093/gji/ggw062) to account for free surface multiples. We use an Eikonal solver based on the fast marching method to compute traveltimes for all scattered phases. Three‐dimensional scattering patterns are computed to correct the amplitudes and polarities of the three component input signals. We consider three different stacking methods (linear, phase weighted, and second root) to enhance the structures that are most coherent across scattering modes and find that second‐root stack is the most effective. Results from synthetic tests show that our imaging principle can recover scattering structures accurately with minimal artifacts. Application to real data from the Multidisciplinary Experiments for Dynamic Understanding of Subduction under the Aegean Sea experiment in the Hellenic subduction zone yields images that are similar to those obtained by 2‐D generalized Radon transform migration at no additional computational cost, further supporting the robustness of our approach.
Tempo‐Spatial Variations of the Kuroshio Current in the Tokara Strait Based on Long‐Term Ferryboat ADCP Data
Authors: Liu Zhao‐Jun , Nakamura Hirohiko , Zhu Xiao‐Hua , Nishina Ayako , Guo Xinyu , Dong Menghong
Published: August 2019

Transverse‐vertical structure and temporal variability of the Kuroshio current across the Tokara Strait during 2003–2012 measured by a ferryboat acoustic Doppler current profiler with a 2‐km horizontal resolution and a two‐day interval are presented. The Kuroshio passing through the Tokara Strait exhibits a multicore velocity structure. Its seasonal volume transport variation is biannual for baroclinic components relative to 700 m, peaking in July and December–January. However, the barotropic transport component exhibits an annual cycle with a maximum in December. Empirical orthogonal function analysis of the cross‐sectional velocity is performed. The first two empirical orthogonal function modes reveal the north‐south shift of the Kuroshio current axis and the change in Kuroshio volume transport, respectively. Temporal variabilities of the leading two modes correspond to those of the Kuroshio Position Index and the sea level difference across the strait, respectively. The third empirical orthogonal function mode, with a relatively smaller horizontal scale, was examined in terms of turbulent mixing. The banded structure captured by this mode is likely induced by flow‐topography interaction because islands in the Kuroshio route could cause horizontal and vertical flow separation. Additional analysis based on high‐resolution reanalysis data suggested that (1) inertial instability, which is expected in the areas with negative Ertel's potential vorticity, arises to enhance vertical mixing around the islands in the Tokara Strait, and (2) when the Kuroshio directly impinges the islands, flow divergence in the lee of the islands drives upwelling and leads to uplift of isotherms.
Benefits of Explicit Treatment of Zero Flows in Probabilistic Hydrological Modeling of Ephemeral Catchments
Authors: McInerney David , Kavetski Dmitri , Thyer Mark , Lerat Julien , Kuczera George
Published: August 2019

Probabilistic modeling of streamflow in ephemeral catchments, where streamflow is frequently zero or negligible, is a major scientific and operational challenge. This paper evaluates the benefits of an explicit treatment of zero flows in the residual error models used for hydrological model calibration and prediction. In this approach, the lower bound of zero for streamflow is implemented using a censoring approach. The explicit approach is compared to a simpler pragmatic approach, which imposes the zero streamflow bound in prediction but not in calibration. Following a theoretical exposition, empirical comparisons are reported using a daily rainfall‐runoff model (GR4J), four residual error schemes (based on log, log‐sinh, and Box‐Cox [BC] transformations withλ= 0.2 and 0.5), 74 Australian catchments with diverse hydroclimatology, and five performance metrics (reliability, precision, bias, proportion of zero flow days, and Continuous Ranked Probability skill score). The key findings are as follows: (1) inmid‐ephemeralcatchments (5–50% zero flows) the explicit approach improves predictive performance, especially reliability, through better characterization of residual errors; (2) BC0.2 and BC0.5 schemes are Pareto optimal in mid‐ephemeral catchments (when the explicit approach is used): BC0.2 achieves better reliability and is recommended for probabilistic prediction, whereas BC0.5 attains lower volumetric bias; (3) inlow‐ephemeralcatchments (<5% zero flows) the pragmatic approach is sufficient; (4) inhigh‐ephemeralcatchments (>50% zero flows) theoretical limitations result in poor performance of these particular explicit and pragmatic approaches, and further development is needed. The findings provide guidance on improving probabilistic streamflow predictions in ephemeral catchments.
Effects of Liquid Clouds on GPS Radio Occultation Profiles in Superrefractions
Authors: Hordyniec P. , Norman R. , Rohm W. , Huang C.‐Y. , Le Marshall J.
Published: August 2019

Inversion of radio occultation (RO) measurements to atmospheric parameters in the neutral atmosphere utilizes the assumption of spherical symmetry by implementation of the Abel transform. The main contribution to the retrieved refractional angle and other geophysical parameters comes from gaseous properties of the atmosphere. The atmospheric refraction is expressed by a function of air pressure, air temperature, and water vapor pressure. Such commonly adopted methodology results in highly comparable RO retrievals with background models. However, in the lowermost troposphere referred to as planetary boundary layer, inversion in spherically symmetric atmosphere is an ill‐conditioned problem. The presence of superrefractions introduces negative errors in the RO‐retrieved refractivity (N‐bias). We show that significant refractivity gradients are frequently collocated with clouds over oceans in tropical and subtropical regions. Based on gridded monthly means we show that superrefractions usually occur at altitudes up to 2 km and the largest cloud fractions tend to suspend at underlying layers. The magnitude of clouds expressed in terms of refractivity units can exceed 1.5, which corresponds to 0.5% in terms of fractional differences. We use both geometrical optics and wave optics techniques to illustrate propagation mechanisms in RO retrievals. Simulation experiments suggest that RO inversions in cloudy planetary boundary layer lead to larger negative N‐biases. Low‐level clouds retrieved from numerical weather prediction model could therefore be used as an indicator of erroneous RO observations. A better agreement with RO refractivity could be achieved by incorporating cloud variables into background fields especially over the Pacific and Atlantic Oceans.
Mars Upper Atmospheric Responses to the 10 September 2017 Solar Flare: A Global, Time‐Dependent Simulation
Authors: Fang Xiaohua , Pawlowski David , Ma Yingjuan , Bougher Stephen , Thiemann Edward , Eparvier Francis , Wang Wenbin , Dong Chuanfei , Lee Christina O. , Dong Yaxue , Benna Mehdi , Elrod Meredith , Chamberlin Phillip , Mahaffy Paul , Jakosky Bruce
Published: August 2019

We report the first global, time‐dependent simulation of the Mars upper atmospheric responses to a realistic solar flare event, an X8.2 eruption on 10 September 2017. The Mars Global Ionosphere‐Thermosphere Model runs with realistically specified flare irradiance, giving results in reasonably good agreement with the Mars Atmosphere and Volatile EvolutioN spacecraft measurements. It is found that the ionized and neutral regimes of the upper atmosphere are significantly disturbed by the flare but react differently. The ionospheric electron density enhancement is concentrated below ∼110‐km altitude due to enhanced solar X‐rays, closely following the time evolution of the flare. The neutral atmospheric perturbation increases with altitude and is important above ∼150‐km altitude, in association with atmospheric upwelling driven by solar extreme ultraviolet heating. It takes ∼2.5 hr past the flare peak to reach the maximum disturbance and then additional ∼10 hr to generally settle down to preflare levels.
Benguela Niños and Benguela Niñas in Forced Ocean Simulation From 1958 to 2015
Authors: Imbol Koungue Rodrigue Anicet , Rouault Mathieu , Illig Serena , Brandt Peter , Jouanno Julien
Published: August 2019

A systematic study of Benguela Niño and Benguela Niña events during 1958 to 2015 including those that developed before the satellite era (1982) is carried out using an ocean general circulation model in combination with a linear equatorial model. Altogether, 21 strong warm and cold anomalous coastal events are identified among which 6 undocumented extreme coastal events are reported. Results suggest that most of these extreme coastal events including the newly identified ones are linked to remote equatorial forcing via mode 2 equatorial Kelvin waves. The latter propagates after approaching the African coast poleward as coastally trapped waves leading surface temperature anomalies along the Angola‐Benguela current system by one month. One to two months before the peak of Benguela Niños or Niñas usually occurring in March–April, a large‐scale wind stress forcing is observed with both local (variations of alongshore coastal wind stress) and remote forcing developing simultaneously. Results further suggest that surface temperature anomalies off Southern Angola and in the Angola‐Benguela Front are associated with equatorial dynamics and meridional wind stress fluctuations off the southwestern African coast north of 15°S. Similar mechanisms are observed for Northern Namibia in combination with forcing by local meridional wind stress variations.
The Plasma Nature of Lightning Channels and the Resulting Nonlinear Resistance
Authors: da Silva C. L. , Sonnenfeld R. G. , Edens H. E. , Krehbiel P. R. , Quick M. G. , Koshak W. J.
Published: August 2019

Lightning channels are made of plasma. As a consequence, the driving electrical current changes the channel's resistance in a nonlinear fashion. The resistance has an intricate dependence on the history of Joule heating and various cooling processes, as well as on the various kinetic processes that dictate the population balance of electrons within the channel. Such dependence cannot be captured by an analytic function, as often attempted. In this paper, we introduce a minimal numerical model that can qualitatively capture the temporal dynamics of the key plasma properties of a lightning channel, including its electric field, temperature, plasma density, radius, and the resulting nonlinear resistance. Through a series of novel parameterizations, we introduce six zero‐dimensional equations that can capture both nonequilibrium/low‐temperature and local thermodynamic equilibrium/high‐temperature plasma regimes. In this manuscript, we go to great lengths to validate the model, showing that it can reproduce the finite time scale of streamer‐to‐leader transition, replicate the negative differential resistance behavior of steady‐state plasma arcs, and properly describe the temporal evolution of temperature in a return stroke channel. Finally, the model is applied to the simulation of optical emissions from rocket‐triggered lightning strikes, explaining the measured delay between the rise of current and visible light, as well as reproducing the direct relationship between peak current and peak radiated power and between charge transferred to ground and total radiated energy.
Diagnosing Bias in Modeled Soil Moisture/Runoff Coefficient Correlation Using the SMAP Level 4 Soil Moisture Product
Authors: Crow W. T. , Chen F. , Reichle R. H. , Xia Y.
Published: August 2019

The physical parameterization of key processes in land surface models (LSMs) remains uncertain, and new techniques are required to evaluate LSMs accuracy over large spatial scales. Given the role of soil moisture in the partitioning of surface water fluxes (between infiltration, runoff, and evapotranspiration), surface soil moisture (SSM) estimates represent an important observational benchmark for such evaluations. Here, we apply SSM estimates from the NASA Soil Moisture Active Passive Level‐4 product (SMAP_L4) to diagnose bias in the correlation between SSM and surface runoff for multiple Noah‐Multiple Physics (Noah‐MP) LSM parameterization cases. Results demonstrate that Noah‐MP surface runoff parameterizations often underestimate the correlation between prestorm SSM and the event‐scale runoff coefficient (RC; defined as the ratio between event‐scale streamflow and precipitation volumes). This bias can be quantified against an observational benchmark calculated using streamflow observations and SMAP_L4 SSM and applied to explain a substantial fraction of the observed basin‐to‐basin (and case‐to‐case) variability in the skill of event‐scale RC estimates from Noah‐MP. Most notably, a low bias in LSM‐predicted SSM/RC correlation squanders RC information contained in prestorm SSM and reduces LSM RC estimation skill. Based on this concept, a novel case selection strategy for ungauged basins is introduced and demonstrated to successfully identify poorly performing Noah‐MP parameterization cases.
Selection for antimicrobial resistance is reduced when embedded in a natural microbial community
Authors: Klümper Uli , Recker Mario , Zhang Lihong , Yin Xiaole , Zhang Tong , Buckling Angus , Gaze William H
Published: August 2019

Antibiotic resistance has emerged as one of the most pressing, global threats to public health. In single-species experiments selection for antibiotic resistance occurs at very low antibiotic concentrations. However, it is unclear how far these findings can be extrapolated to natural environments, where species are embedded within complex communities. We competed isogenic strains of Escherichia coli, differing exclusively in a single chromosomal resistance determinant, in the presence and absence of a pig faecal microbial community across a gradient of antibiotic concentration for two relevant antibiotics: gentamicin and kanamycin. We show that the minimal selective concentration was increased by more than one order of magnitude for both antibiotics when embedded in the community. We identified two general mechanisms were responsible for the increase in minimal selective concentration: an increase in the cost of resistance and a protective effect of the community for the susceptible phenotype. These findings have implications for our understanding of the evolution and selection of antibiotic resistance, and can inform future risk assessment efforts on antibiotic concentrations.
Efficacy of omega-3 PUFAs in depression: A meta-analysis
Authors: Liao Yuhua , Xie Bo , Zhang Huimin , He Qian , Guo Lan , Subramanieapillai Mehala , Fan Beifang , Lu Ciyong , McIntyre Roger S.
Published: August 2019

We conducted this meta-analysis of double-blind randomized placebo-controlled trials to estimate the efficacy of omega-3 polyunsaturated fatty acids (PUFAs), especially docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), in the improvement of depression. We applied a systematic bibliographic search in PubMed and EMBASE for articles published prior to 20 December 2017. This meta-analysis was performed using RevMan 5.3 and R 3.4.3, and means and standard deviations were calculated in fixed- or random-effects models based on the results of the Q-test. A sensitivity analysis was also conducted to evaluate the stability of the results, and publication bias was evaluated by a funnel plot and Egger’s linear regression analysis. Our search resulted in 180 articles; we analyzed 26 studies, which included 2160 participants. The meta-analysis showed an overall beneficial effect of omega-3 polyunsaturated fatty acids on depression symptoms (SMD = −0.28,P = 0.004). Compared with placebo, EPA-pure (=100% EPA) and EPA-major formulations (≥60% EPA) demonstrated clinical benefits with an EPA dosage ≤1 g/d (SMD = −0.50,P = 0.003, and SMD = −1.03,P = 0.03, respectively), whereas DHA-pure and DHA-major formulations did not exhibit such benefits.

Current evidence supports the finding that omega-3 PUFAs with EPA ≥ 60% at a dosage of ≤1 g/d would have beneficial effects on depression. Further studies are warranted to examine supplementation with omega-3 PUFAs for specific subgroups of subjects with inflammation, severity of depression, and the dose response for both EPA and DHA supplementation.
Treatment response classes in major depressive disorder identified by model-based clustering and validated by clinical prediction models
Authors: Paul Riya , Andlauer Till. F. M. , Czamara Darina , Hoehn David , Lucae Susanne , Pütz Benno , Lewis Cathryn M. , Uher Rudolf , Müller-Myhsok Bertram , Ising Marcus , Sämann Philipp G.
Published: August 2019

The identification of generalizable treatment response classes (TRC[s]) in major depressive disorder (MDD) would facilitate comparisons across studies and the development of treatment prediction algorithms. Here, we investigated whether such stable TRCs can be identified and predicted by clinical baseline items. We analyzed data from an observational MDD cohort (Munich Antidepressant Response Signature [MARS] study, N = 1017), treated individually by psychopharmacological and psychotherapeutic means, and a multicenter, partially randomized clinical/pharmacogenomic study (Genome-based Therapeutic Drugs for Depression [GENDEP], N = 809). Symptoms were evaluated up to week 16 (or discharge) in MARS and week 12 in GENDEP. Clustering was performed on 809 MARS patients (discovery sample) using a mixed model with the integrated completed likelihood criterion for the assessment of cluster stability, and validated through a distinct MARS validation sample and GENDEP. A random forest algorithm was used to identify prediction patterns based on 50 clinical baseline items. From the clustering of the MARS discovery sample, seven TRCs emerged ranging from fast and complete response (average 4.9 weeks until discharge, 94% remitted patients) to slow and incomplete response (10% remitted patients at week 16). These proved stable representations of treatment response dynamics in both the MARS and the GENDEP validation sample. TRCs were strongly associated with established response markers, particularly the rate of remitted patients at discharge. TRCs were predictable from clinical items, particularly personality items, life events, episode duration, and specific psychopathological features. Prediction accuracy improved significantly when cluster-derived slopes were modelled instead of individual slopes. In conclusion, model-based clustering identified distinct and clinically meaningful treatment response classes in MDD that proved robust with regard to capturing response profiles of differently designed studies. Response classes were predictable from clinical baseline characteristics. Conceptually, model-based clustering is translatable to any outcome measure and could advance the large-scale integration of studies on treatment efficacy or the neurobiology of treatment response.
Ankylosing spondylitis: etiology, pathogenesis, and treatments
Authors: Zhu Wei , He Xuxia , Cheng Kaiyuan , Zhang Linjie , Chen Di , Wang Xiao , Qiu Guixing , Cao Xu , Weng Xisheng
Published: August 2019

Ankylosing spondylitis (AS), a common type of spondyloarthropathy, is a chronic inflammatory autoimmune disease that mainly affects spine joints, causing severe, chronic pain; additionally, in more advanced cases, it can cause spine fusion. Significant progress in its pathophysiology and treatment has been achieved in the last decade. Immune cells and innate cytokines have been suggested to be crucial in the pathogenesis of AS, especially human leukocyte antigen (HLA)‑B27 and the interleukin‑23/17 axis. However, the pathogenesis of AS remains unclear. The current study reviewed the etiology and pathogenesis of AS, including genome-wide association studies and cytokine pathways. This study also summarized the current pharmaceutical and surgical treatment with a discussion of future potential therapies.
Conditional disruption of the osterix gene in chondrocytes during early postnatal growth impairs secondary ossification in the mouse tibial epiphysis
Authors: Xing Weirong , Godwin Catrina , Pourteymoor Sheila , Mohan Subburaman
Published: August 2019

In our previous studies, we have found that the prepubertal increase in thyroid hormone levels induces osterix (Osx) signaling in hypertrophic chondrocytes to transdifferentiate them into osteoblasts. To test if Osx expressed in chondrocytes directly contributes to transdifferentiation and secondary ossification, we generated Osxflox/flox; Col2-Cre-ERT2 mice and knocked out Osx with a single injection of tamoxifen at postnatal day (P) 3 prior to evaluation of the epiphyseal bone phenotype by µCT, histology, and immunohistochemistry (IHC) at P21. Vehicle (oil)-treated Osxflox/flox; Col2-Cre-ERT2 and tamoxifen-treated, Cre-negative Osxflox/flox mice were used as controls. µCT analysis of tibial epiphyses revealed that trabecular bone mass was reduced by 23% in the Osx conditional knockout (cKO) compared with control mice. Trabecular number and thickness were reduced by 28% and 8%, respectively, while trabecular separation was increased by 24% in the cKO mice. Trichrome staining of longitudinal sections of tibial epiphyses showed that bone area and bone area adjusted for total area were decreased by 22% and 18%, respectively. IHC studies revealed the presence of abundant Osx-expressing prehypertrophic chondrocytes in the epiphyses of control mice at P10, but not in the cKO mice. Furthermore, expression levels of MMP13, COL10, ALP, and BSP were considerably reduced in the epiphyses of cKO mice. We also found that Osx overexpression in ATDC5 chondrocytes increased expression of Col10, Mmp13, Alp, and Bsp. Our data indicate that Osx expressed in chondrocytes plays a significant role in secondary ossification by regulating expression of genes involved in chondrocyte hypertrophy and osteoblast transdifferentiation.
Dataset of three-dimensional traces of roads
Authors: Ariza-López Francisco Javier , Mozas-Calvache Antonio Tomás , Ureña-Cámara Manuel Antonio , Gil de la Vega Paula
Published: August 2019

We present a dataset consisting of three-dimensional traces, captured by Global Navigation Satellite System techniques with three-dimensional coordinates. It offers 138 traces (69 going and 69 returning), in addition to the actual mean axis of the road determined by precise surveying techniques to be used as ground truth for research activities. These data may serve as a test bed for research on data mining applications related to Global Navigation Satellite System multitraces, particularly the development and testing of algorithms intended for mining mean axis data from road multitraces. The data are suitable for the statistical analysis of both single-trace and multitrace datasets (e.g., outliers and biases).
Does nesfatin-1 influence the hypothalamic–pituitary–gonadal axis in adult males with obstructive sleep apnoea?
Authors: Batura-Gabryel Halina , Bromińska Barbara , Sawicka-Gutaj Nadia , Cyrańska-Chyrek Ewa , Kuźnar-Kamińska Barbara , Winiarska Hanna , Kostrzewska Magdalena , Zybek-Kocik Ariadna , Hernik Aleksandra , Wrotkowska Elżbieta , Bielawska Lena , Cofta Szczepan , Ruchała Marek
Published: August 2019

There is growing evidence that obstructive sleep apnoea (OSA) influences the hypothalamic–pituitary–gonadal axis (HPG axis) in men. The aim of the study was to assess the association of nesfatin-1 with HPG axis disturbances in OSA. This is a prospective study with consecutive enrolment. It comprises 72 newly diagnosed OSA patients ((AHI: apnoea-hypopnea index) 18 subjects: 5 ≤ AHI < 15; 24: 15 ≤ AHI < 30; 30: AHI ≥ 30) and a control group composed of 19 patients (AHI < 5). All patients underwent polysomnography and fasting blood collection for nesfatin-1, testosterone, luteinising hormone (LH), high-sensitivity C-reactive protein (hsCRP), aspartate transaminase (AST), alanine aminotransferase (ALT), creatinine and glucose. Groups had similar levels of LH, nesfatin-1 and testosterone (p = 0.87; p = 0.24; p = 0.08). Nesfatin-1 was not correlated to LH (p = 0.71), testosterone (p = 0.38), AHI (p = 0.34) or the oxygen desaturation index (ODI) (p = 0.69) either in the whole group, or in sub-groups. The study did not reveal any association between the HPG axis and nesfatin-1 in OSA adult males. It is possible that nesfatin-1 is not a mediator of HPG axis disturbances in adult patients with OSA.
Sublethal Pyrethroid Insecticide Exposure Carries Positive Fitness Effects Over Generations in a Pest Insect
Authors: Margus Aigi , Piiroinen Saija , Lehmann Philipp , Tikka Santtu , Karvanen Juha , Lindström Leena
Published: August 2019

Stress tolerance and adaptation to stress are known to facilitate species invasions. Many invasive species are also pests and insecticides are used to control them, which could shape their overall tolerance to stress. It is well-known that heavy insecticide usage leads to selection of resistant genotypes but less is known about potential effects of mild sublethal insecticide usage. We studied whether stressful, sublethal pyrethroid insecticide exposure has within-generational and/or maternal transgenerational effects on fitness-related traits in the Colorado potato beetle (Leptinotarsa decemlineata) and whether maternal insecticide exposure affects insecticide tolerance of offspring. Sublethal insecticide stress exposure had positive within-and transgenerational effects. Insecticide-stressed larvae had higher adult survival and higher adult body mass than those not exposed to stress. Furthermore, offspring whose mothers were exposed to insecticide stress had higher larval and pupal survival and were heavier as adults (only females) than those descending from control mothers. Maternal insecticide stress did not explain differences in lipid content of the offspring. To conclude, stressful insecticide exposure has positive transgenerational fitness effects in the offspring. Therefore, unsuccessful insecticide control of invasive pest species may lead to undesired side effects since survival and higher body mass are known to facilitate population growth and invasion success.
VO2-based switchable radiator for spacecraft thermal control
Authors: Kim Heungsoo , Cheung Kwok , Auyeung Raymond C. Y. , Wilson Donald E. , Charipar Kristin M. , Piqué Alberto , Charipar Nicholas A.
Published: August 2019

Direct calorimetric measurements of a solid state passive switchable radiator for spacecraft thermal control have been performed in a simulated space environment. Dynamic emissivity control is provided by the thermochromic phase change in a multilayer VO2 thin film based resonant absorber. The measured radiated power difference between 300 K and 373 K was 480 W/m2 corresponding to a 7× difference in radiative cooling power. We present theoretical and experimental radiator values for both normal and hemispherical as well the optical properties of VO2 as determined via infrared spectroscopic ellipsometry.
Publisher Correction: SOX9 regulated matrix proteins are increased in patients serum and correlate with severity of liver fibrosis
Authors: Athwal Varinder S. , Pritchett James , Martin Katherine , Llewellyn Jessica , Scott Jennifer , Harvey Emma , Zaitoun Abed M. , Mullan Aoibheann F. , Zeef Leo A. H. , Friedman Scott L. , Irving William L. , Hanley Neil A. , Guha Indra N. , Piper Hanley Karen
Published: August 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Publisher Correction: Potential landscape of high dimensional nonlinear stochastic dynamics with large noise
Authors: Tang Ying , Yuan Ruoshi , Wang Gaowei , Zhu Xiaomei , Ao Ping
Published: August 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos
Authors: Rodrigues Andreia S. , Chaves Inês , Costa Bruno Vasques , Lin Yao-Cheng , Lopes Susana , Milhinhos Ana , Van de Peer Yves , Miguel Célia M.
Published: August 2019

Regulation of seed development by small non-coding RNAs (sRNAs) is an important mechanism controlling a crucial phase of the life cycle of seed plants. In this work, sRNAs from seed tissues (zygotic embryos and megagametophytes) and from somatic embryos of Pinus pinaster were analysed to identify putative regulators of seed/embryo development in conifers. In total, sixteen sRNA libraries covering several developmental stages were sequenced. We show that embryos and megagametophytes express a large population of 21-nt sRNAs and that substantial amounts of 24-nt sRNAs were also detected, especially in somatic embryos. A total of 215 conserved miRNAs, one third of which are conifer-specific, and 212 high-confidence novel miRNAs were annotated. MIR159, MIR171 and MIR394 families were found in embryos, but were greatly reduced in megagametophytes. Other families, like MIR397 and MIR408, predominated in somatic embryos and megagametophytes, suggesting their expression in somatic embryos is associated with in vitro conditions. Analysis of the predicted miRNA targets suggests that miRNA functions are relevant in several processes including transporter activity at the cotyledon-forming stage, and sulfur metabolism across several developmental stages. An important resource for studying conifer embryogenesis is made available here, which may also provide insightful clues for improving clonal propagation via somatic embryogenesis.
The silencing of indoleamine 2,3-dioxygenase 1 (IDO1) in dendritic cells by siRNA-loaded lipid nanoparticles enhances cell-based cancer immunotherapy
Authors: Endo Rikito , Nakamura Takashi , Kawakami Kyoko , Sato Yusuke , Harashima Hideyoshi
Published: August 2019

Cell-based therapy using dendritic cells (DC) represents a potent cancer immunotherapy. However, activated DC express indoleamine 2,3-dioxygenase 1 (IDO1), a counter-regulatory and tolerogenic molecule, leading to the inhibition of T cell activation and the promotion of T cell differentiation into regulatory T cells. Silencing the IDO1 gene in DC by small interfering RNA (siRNA) represents a potent therapeutic strategy. We report on the successful and efficient introduction of a siRNA targeting IDO1 into mouse DCs by a means of a multifunctional envelope-type nanodevice (MEND) containing a YSK12-C4 (YSK12-MEND). The YSK12-C4 has both fusogenic and cationic properties. The YSK12-MEND induced an effective level of gene silencing of IDO1 at siRNA doses in the range of 1–20 nM, a concentration that commercially available transfection reagents are not able to silence. The YSK12-MEND mediated IDO1 silencing had no effect on the characteristic determinants of DC phenotype such as CD11c, CD80 and MHC class II. The silencing of IDO1 in DC by the YSK12-MEND significantly enhanced the antitumor effect against E.G7-OVA tumor. Moreover, a decrease in the numbers of regulatory T cells in the tumor was observed in mice that were treated with the IDO1-silenced DC. The YSK12-MEND appears to be a potent delivery system for IDO1-silenced DC based cancer immunotherapy.
Filter paper supported nZVI for continuous treatment of simulated dyeing wastewater
Authors: Yu Pingping , Yu Haifan , Sun Qisong , Ma Bomou
Published: August 2019

In this study, polyacrylic acid modified filter paper (FP/PAA) was synthesized by in-situ polymerization of acrylic acid, which was used as a matrix to chelate nano-scale zero valent iron (nZVI). The loading content of nZVI in the filter paper reached 24.8%. The fabricated composite FP/PAA/nZVI was characterized by SEM, FT-IR and TGA respectively. Moreover, it was used for the removal of methyl blue and methylene blue as model anionic and cationic dyes. The effect of initial dye concentration on decolorization efficiency was investigated. The results showed that FP/PAA/nZVI enhanced the removal of dye from the simulated dye wastewater and the decolorization efficiency exceeded 95% for the dye solutions lower than 20 mg/L. More importantly, the filter paper supported nZVI realized the continuous treatment of simulated dye wastewater by a simple filtration process. This study hopes to serve as a basis for the application of nZVI in textile wastewater treatment.
Relationships between cardiorespiratory fitness/muscular strength and 18F-fluorodeoxyglucose uptake in brown adipose tissue after exposure to cold in young, sedentary adults
Authors: Martinez-Tellez Borja , Sanchez-Delgado Guillermo , Amaro-Gahete Francisco J. , Acosta Francisco M. , Ruiz Jonatan R.
Published: August 2019

Humans have metabolically active brown adipose tissue (BAT). However, what is the relation between exercise or physical activity with this tissue remains controversial. Therefore, the main aim of the present study is to examine whether cardiorespiratory fitness and muscular strength are associated with brown adipose tissue (BAT) volume and activity after exposure to cold in young, sedentary adults. Cardiorespiratory fitness was determined in 119 young, healthy, sedentary adults (68% women, age 21.9 ± 2.1 years, body mass index 25 ± 4.8 kg/m2) via the maximum treadmill exercise test, and their muscular strength assessed by the handgrip strength test and the 1-repetition maximum bench and leg press tests. Some days later, all subjects were exposed to 2 h of personalized exposure to cold and their cold-induced BAT volume and activity determined by a combination of 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography and computed tomography scan. Cardiorespiratory fitness was associated with neither the BAT volume nor BAT activity (P ≥ 0.05). However, handgrip strength with respect to lean body mass was positively (though weakly) associated with BAT activity as represented by the 18F-FDG mean standardised uptake value (SUV) (β = 3.595, R2 = 0.039, P = 0.031) and SUVpeak value (β = 15.314, R2 = 0.037, P = 0.035). The above relationships remained after adjusting for several confounders. No other associations were found. Handgrip strength with respect to lean body mass is positively associated with BAT activity (SUVmean and SUVpeak) in young adults after exposure to cold - but only weakly. Further studies are needed to reveal the relationship between muscular fitness and human BAT characteristics.