bluuebunny/crossref_metadata_2025 huggingface dataset:
Generating Survival Times Using Cox Proportional Hazards Models with Cyclic and Piecewise Time-Varying Covariates
Authors: Huang Yunda , Zhang Yuanyuan , Zhang Zong , Gilbert Peter B.
Published: January 2020

Time-to-event outcomes with cyclic time-varying covariates are frequently encountered in biomedical studies that involve multiple or repeated administrations of an intervention. In this paper, we propose approaches to generating event times for Cox proportional hazards models with both time-invariant covariates and a continuous cyclic and piecewise time-varying covariate. Values of the latter covariate change over time through cycles of interventions and its relationship with hazard differs before and after a threshold within each cycle. The simulations of data are based on inverting the cumulative hazard function and a log link function for relating the hazard function to the covariates. We consider closed-form derivations with the baseline hazard following the exponential, Weibull, or Gompertz distribution. We propose two simulation approaches: one based on simulating survival data under a single-dose regimen first before data are aggregated over multiple-dosing cycles and another based on simulating survival data directly under a multiple-dose regimen. We consider both fixed intervals and varying intervals of the drug administration schedule. The method’s validity is assessed in simulation experiments. The results indicate that the proposed procedures perform well in generating data that conform to their cyclic nature and assumptions of the Cox proportional hazards model.
Perspectives on permaculture for commercial farming: aspirations and realities
Authors: Fiebrig Immo , Zikeli Sabine , Bach Sonja , Gruber Sabine
Published: January 2020

The term ‘Permaculture’ (PC) refers to a theory about diversified farming systems, based on an ethical attitude (worldview) and a practical design process, guided by 12 principles and flanked by a holistic sustainability concept. Invented in the wake of Australia’s socio-political ‘back-to-the-land’ aspirations of the 1970s, PC has since developed and grown into a diverse international grassroot movement. It can be considered a rural as well as an urban socio-cultural phenomenon that revolves around non-commercial gardening, for example urban community projects, or around farming for self-sufficiency, for instance in eco-villages. This paper intends to investigate which aspects of PC may be scalable to commercial farming whilst identifying PC aspects already implemented in commercial (organic) agriculture (OA). It analyses a current business case led by a German wholesaler of organic produce who worked in cooperation with a German supermarket chain to create the first nationwide PC label. To this end, the paper describes the degree of overlap between two organic farming certification schemes and the case study. As opposed to certified OA, PC is less prescriptive, using a deductive and inductive approach instead. It may expand scope and flexibility required for farm redesign towards improved resilience, reaching out to the landscape level. The productiveness of PC in commercial settings needs to be established further, such as best practices in soil regeneration and monitoring as well as the reduction of soil losses, or the valuation of added ecosystem services such as promotion of (agro-)biodiversity.
Low-cost activated carbon production from organic waste and its utilization for wastewater treatment
Authors: Shukla Sudheer Kumar , Al Mushaiqri Noof Rashid Said , Al Subhi Hajar Mohammed , Yoo Keunje , Al Sadeq Hafez
Published: January 2020

In the present study, organic waste materials, like coconut shell, orange peels, and banana peels were used to produce activated carbon. Chemical activation was carried out using phosphoric acid (H3PO4). The activation temperatures were selected at the range of 200–300 °C. Surface morphology of the different activated carbon derived from the different waste materials was investigated using scanning electron microscope. Pollution removal efficiency of different activated carbons was carried out by Jar test. The jar test was carried out at 120 rpm, at 20 °C temperature for 1 h. Three different sizes; 75 μm, 150 μm and 425 μm, and three concentration; 100 mg/l, 200 mg/l and 500 mg/l of the activated carbon were selected for the pollution removal experiments. Water quality parameters like pH, TSS, and COD were analyzed using standard AWWA/APHA methods to know the pollution removal efficiency. COD removal varies from 48 to 99% in different activated carbon at different size and concentration. TSS removal varies from 43 to 100% by different activated carbon. The highest adsorption was observed by 75 µm activated carbon. Among all the experimented materials activated carbon made from orange peels performed better than others possibly due to the formation of more C–O and C=O functional groups due to the presence of more carbon and oxygen elements than others. This study opens a new way of wastewater treatment in Oman by using low-cost activated carbon made from locally available organic waste and at the same time, it shall help in managing organic waste.
Novel and recurrent variants of ATP2C1 identified in patients with Hailey-Hailey disease
Authors: Sawicka J. , Kutkowska-Kaźmierczak A. , Woźniak K. , Tysarowski A. , Osipowicz K. , Poznański J. , Rygiel A. M. , Braun-Walicka N. , Niepokój K. , Bal J. , Kowalewski C. , Wertheim-Tysarowska K.
Published: January 2020

Hailey-Hailey disease (HHD) is a rare, late-onset autosomal dominant genodermatosis characterized by blisters, vesicular lesions, crusted erosions, and erythematous scaly plaques predominantly in intertriginous regions. HHD is caused byATP2C1mutations. About 180 distinct mutations have been identified so far; however, data of only few cases from Central Europe are available. The aim was to analyze theATP2C1gene in a cohort of Polish HHD patients. A group of 18 patients was enrolled in the study based on specific clinical symptoms. Mutations were detected using Sanger or next generation sequencing. In silico analysis was performed by prediction algorisms and dynamic structural modeling. In two cases, mRNA analysis was performed to confirm aberrant splicing. We detected 13 different mutations, including 8 novel, 2 recurrent (p.Gly850Ter and c.325-3 T > G), and 6 sporadic (c.423-1G > T, c.899 + 1G > A, p.Leu539Pro, p.Thr808TyrfsTer16, p.Gln855Arg and a complex allele: c.[1610C > G;1741 + 3A > G]). In silico analysis shows that all novel missense variants are pathogenic or likely pathogenic. We confirmed pathogenic status for two novel variants c.325-3 T > G and c.[1610C > G;1741 + 3A > G] by mRNA analysis. Our results broaden the knowledge about genetic heterogeneity in Central European patients withATP2C1mutations and also give further evidence that careful and multifactorial evaluation of variant pathogenicity status is essential.
Evidence for different bottom-up mechanisms in wood mouse (Apodemus sylvaticus) and bank vole (Myodes glareolus) population fluctuations in Southern Norway
Authors: Selås Vidar
Published: January 2020

Animals that feed on forest tree seeds, such asApodemusmice, increase in number after a mast year. At high latitudes, there is a similar delayed response byMyodesvoles to high seed crops of bilberry (Vaccinium myrtillus), but here the mechanism is hypothesised to be increased forage quality, caused by a trade-off between reproduction and defence in the plants. BothApodemusmice andMyodesvoles eat berries, but only the latter feed on bilberry plants. Hence, onlyMyodesvoles are predicted to respond to bilberry peak years. A second prediction is that the effect should last longer than any possible direct impacts of bilberries, because the plants would not be able to rebuild their defence until the succeeding summer. During a 21-year snap-trapping study of small rodents in Southern Norway, the spring population of bank vole (Myodes glareolus) was positively related to a bilberry seed index of the previous year, indicating increased winter survival, whereas the wood mouse (Apodemus sylvaticus) was not affected. Also the succeeding autumn population index of the bank vole was positively related to the bilberry index of the previous year, even when controlling for spring population levels. The wood mouse population responded to mast years of sessile oak (Quercus petraea), whereas seeds of Norway spruce (Picea abies) seemed to have some impact on both species. It is concluded that these rodents are mainly limited from below, but by different mechanisms for the granivorous and the herbivorous species.
A Multicenter Evaluation of Vancomycin-Associated Acute Kidney Injury in Hospitalized Patients with Acute Bacterial Skin and Skin Structure Infections
Authors: Jorgensen Sarah C. J. , Murray Kyle P. , Lagnf Abdalhamid M. , Melvin Sarah , Bhatia Sahil , Shamim Muhammad-Daniayl , Smith Jordan R. , Brade Karrine D. , Simon Samuel P. , Nagel Jerod , Williams Karen S. , Ortwine Jessica K. , Veve Michael P. , Truong James , Huang David B. , Davis Susan L. , Rybak Michael J.
Published: January 2020

Background

We sought to determine the real-world incidence of and risk factors for vancomycin-associated acute kidney injury (V-AKI) in hospitalized adults with acute bacterial skin and skin structure infections (ABSSSI).

Methods

Retrospective, observational, cohort study at ten U.S. medical centers between 2015 and 2019. Hospitalized patients treated with vancomycin (≥ 72 h) for ABSSSI and ≥ one baseline AKI risk factor were eligible. Patients with end-stage kidney disease, on renal replacement therapy or AKI at baseline, were excluded. The primary outcome was V-AKI by the vancomycin guidelines criteria.

Results

In total, 415 patients were included. V-AKI occurred in 39 (9.4%) patients. Independent risk factors for V-AKI were: chronic alcohol abuse (aOR 4.710, 95% CI 1.929–11.499), no medical insurance (aOR 3.451, 95% CI 1.310–9.090), ICU residence (aOR 4.398, 95% CI 1.676–11.541), Gram-negative coverage (aOR 2.926, 95% CI 1.158–7.392) and vancomycin duration (aOR 1.143, 95% CI 1.037–1.260). Based on infection severity and comorbidities, 34.7% of patients were candidates for oral antibiotics at baseline and 39.3% had non-purulent cellulitis which could have been more appropriately treated with a beta-lactam. Patients with V-AKI had significantly longer hospital lengths of stay (9 vs. 6 days,p = 0.001), higher 30-day readmission rates (30.8 vs. 9.0%,p < 0.001) and increased all-cause 30-day mortality (5.1 vs. 0.3%,p = 0.024)

Conclusions

V-AKI occurred in approximately one in ten ABSSSI patients and may be largely prevented by preferential use of oral antibiotics whenever possible, using beta-lactams for non-purulent cellulitis and limiting durations of vancomycin therapy.
Investigations on the occurrence of different wetting regimes in laser brazing of zinc-coated steel sheets
Authors: Mattulat Thorsten , Kügler Helge , Vollertsen Frank
Published: January 2020

In the automotive industry, the seam edge quality of laser brazed seams is a crucial factor for the required high optical quality standards of customer-visible connections of zinc-coated car body parts. The type of zinc coating is decisive for the resulting geometry of the seam edges, which are aspired to be straight. Especially brazing of hot-dip galvanised steel with conventional brazing setup is not resulting in seam edges which fulfil the required optical quality. In this study, the wetting of copper-based filler wire on electrogalvanised and hot-dip galvanised steel sheets is analysed to increase the understanding of the influence of the wetting fronts on the seam edge quality. For this, the wetting fronts are determined in high-speed camera images and the resulting seam edges are captured by microscopic pictures. The results show that two major wetting regimes occur on both types of zinc coatings but with a different occurrence probability: one with a steep wetting front and zinc evaporation in front of wetting (“steep-angle-wetting”) and one where liquid zinc connects with the wetting front and creates a flat wetting angle (“flat-angle-wetting”). It is found that the resulting seam edge quality is mainly depending on the present wetting regime. However, for flat-angle-wetting, in the regime with insufficient seam edge quality, a self-stabilising effect is identified, which is responsible for a missing process window for brazing of hot-dip galvanised steel with sufficient seam edge quality.
Herpes in Pregnancy
Authors: Guleria Kiran , Sethi Niharika
Published: January 2020

Herpes simplex virus infection (predominantly HSV2) in pregnancy can be a cause of maternal morbidity. The more serious cause of concern is perinatal transmission of infection resulting in neonatal morbidity and mortality. Genital HSV infection can be primary, non-primary first episode or recurrent infection. Clinical and laboratory diagnosis in pregnant women is similar to non-pregnant women. Direct viral testing (PCR) from lesion's and type specific serology are required to classify type of infection. Vertical transmission occurs during labor and delivery. The risk is higher in primary and non-primary first episode near the time of delivery. Antiviral treatment with Acyclovir or Valacyclovir is recommended for acute episode to reduce lesion duration and viral shedding. Acyclovir as suppressive therapy from 36 weeks onwards reduces clinical recurrences and need for caesarean delivery. Caesarean section reduces but does not eliminate the risk of vertical transmission and is recommended for a woman has an acute infection episode at the time of labor or within 6 weeks before delivery. Clinical management of preterm premature rupture of membranes in a woman with HSV infection should be individualized. All neonates born to these mothers should be carefully handled and monitored for development of neonatal herpes.
The Normative Basis of Global Governance
Authors: Breslin Shaun
Published: January 2020

How, if at all, are rising powers challenging the existing normative basis of global governance orders? This introduction establishes the overarching framework for the papers in this special issue, and outlines the questions that they collectively aim to answer.
Operational Challenges of the Bangkok Airport Rail Link
Authors: Weerawat Waressara , Samitiwantikul Lalitphan , Torpanya Ratthanan
Published: January 2020

The airport rail link (ARL) was launched in 2010 as a premium rail transit service between the inner city of Bangkok and the airport. In 2014, the express service was canceled due to its unpopularity and transformed into the commuter service. In 2017, the new extended service concept was introduced under the three airport links project. Under this new concept, both ARL and high-speed trains will run on the city line section between Don Mueang and Suvarnabhumi Airports. This paper focuses on the use of a microsimulation model to identify the challenge of mixed-service operations, with regular and express trains running on the city line section. The simulation model allows investigation of hypothetical situations and construction of feasible timetables. The model can identify sections where special attention is needed, such as speed reductions, extended dwell times, or delayed departures. During the peak hour, the results suggest that the regular ARL should run with a 10-min headway and the high-speed one line with a 20-min headway, as an alternative solution. This results in fewer train numbers and less additional running time. Simulations indicate that the high-speed train is not efficient, as it consumes 2–3 times higher energy, while offering little time saving compared with the ARL city train. In addition, the Suvarnabhumi Airport extension track layout needs to be carefully considered, since the Suvarnabhumi Station area is a bottleneck liable to disruption.
The association between paternal psychopathology and adolescent depression and anxiety: A systematic review
Authors: Wickersham Alice , Leightley Daniel , Archer Marc , Fear Nicola T.
Published: January 2020

Introduction

Paternal psychopathology is associated with various adolescent outcomes. With emotional disorders presenting a significant public health concern in the adolescent age group, the aim of this systematic review was to synthesize evidence on the relationship between paternal mental health and adolescent anxiety or depression.

Methods

PubMed, Web of Science, Embase, Ovid MEDLINE, Global Health, and PsycINFO were searched for articles which primarily aimed to investigate the relationship between paternal mental health (exposure) and adolescent anxiety or depression (outcome). Articles were assessed for risk of bias, and findings are presented in a narrative synthesis. The protocol is registered on PROSPERO (CRD42018094076).

Results

Findings from the fourteen included studies indicated that paternal depression is associated with adolescent depression and anxiety. Findings relating to other paternal mental health disorders were inconclusive. Results largely suggested that adolescent depression and anxiety is equally associated with paternal and maternal mental health. The included studies were mostly cross‐sectional, and the quality of included studies was mixed. Attempts to focus on the 11–17 year age range were hampered by the variability of age ranges included in studies.

Conclusions

Further longitudinal research is needed to clarify the association between paternal mental health disorders other than depression, and adolescent anxiety or depression. Mechanisms in this relationship should also be further explored, and could be informed by existing models on younger children.
Relationship between breastfeeding duration and undernutrition conditions among children aged 0–3 Years in Pakistan
Authors: Syeda Batool , Agho Kingsley , Wilson Leigh , Maheshwari Greesh Kumar , Raza Muhammad Qasim
Published: January 2020

Background:

The World Health Organization recommends that a child should be breastfed up to 2 years of age as it is essential for proper growth and development but population-based studies around the world have found conflicting results on the subject. Our study aims to analyze whether there is a relationship between the duration of breastfeeding and undernutrition among children aged from birth up to 3 years of age in Pakistan.

Methods:

A secondary analysis of the Pakistan Demographic and Health Survey 2013-2014 with 1072 children aged 3 years and under was conducted. The relationship between breastfeeding duration and undernutrition status was estimated through multiple logistic regression analysis.

Results:

The prevalence of stunting, wasting and underweight were 40.6%, 15.8% and 33.9% respectively, while prevalence of severe stunting is at 22.5%; severe wasting at 4.5% and severe underweight at 12.2% in children in our study. Odds of being stunted were significantly higher for children in their 3rd year of life [AOR: 4.35, CI 95% = (2.01, 9.33)] compared to children being breastfed in their 2nd year of life [AOR: 2.43, CI 95% = (1.55, 3.79) after being adjusted for maternal, child, demographic and healthcare access variables. Similarly, children being breastfed in their third year of life were more susceptible to developing severe stunting [AOR: 6.19, CI 95% = (3.31, 11.56)] in comparison to children in their second year [AOR: 2.84, CI 95% = (1.81, 4.46)]. There was no significant association between breastfeeding and wasting/severe wasting, or between breastfeeding and underweight/severe underweight.

Conclusion:

Breastfeeding in the 2nd and 3rd year of life was found to have significant relationship with stunting and severe stunting. Mothers need to be educated about the risks of prolonged breastfeeding to reduce the burden of undernutrition in the country.
Unsuspected postoperative isolated fibrinogen deficiency in a patient with lung adenocarcinoma
Authors: Son Bong Soo , Ahn Hyo Yeong , Cho Jeong Su , Jeong Hyuncheol , Kim Yeong Dae , I Hoseok
Published: January 2020

ABSTRACT

Isolated fibrinogen deficiency is a particularly rare disorder in patients with normal preoperative prothrombin time/activated partial thromboplastin time. We present a case involving a 62-year-old female patient diagnosed with isolated fibrinogen deficiency following lung cancer surgery. Her preoperative prothrombin time/activated partial thromboplastin time was normal; however, both were prolonged after the surgery. The patient had spontaneous postoperative bleeding owing to presumably congenital fibrinogen deficiency. The management of spontaneous postoperative bleeding is challenging, and the serum fibrinogen level is an important factor to consider for the treatment of this condition. The cause of postoperative isolated fibrinogen deficiency could not be ascertained; nevertheless, our findings show that it is necessary to have a countermeasure for isolated fibrinogen deficiency in order to prevent any critical complications.

Highlights:
Comorbidity and health services' usage in children with autism spectrum disorder: a nested case–control study
Authors: Dizitzer Yotam , Meiri Gal , Flusser Hagit , Michaelovski Analya , Dinstein Ilan , Menashe Idan
Published: January 2020

Aims

Children with autism spectrum disorder (ASD) tend to suffer from various medical comorbidities. We studied the comorbidity burden and health services' utilisation of children with ASD to highlight potential aetiologies and to better understand the medical needs of these children.

Methods

In this nested case–control study, ASD cases and controls – matched by age, sex and ethnicity in a 1:5 ratio – were sampled from all children born between 2009 and 2016 at a tertiary medical centre. Data were obtained from the hospital's electronic database. Comorbid diagnoses were classified according to pathophysiological aetiology and anatomical/systemic classification of disease. Standard univariate and multivariate statistics were used to demonstrate comorbidities and health services' utilisation patterns that are significantly associated with ASD.

Results

ASD children had higher rates of comorbidities according to both pathophysiological and anatomical/systemic classifications (p < 0.001). The most marked significant differences were observed for: hearing impairments (OR = 4.728; 95% CI 2.207–10.127) and other auricular conditions (OR = 5.040; 95% CI 1.759–14.438); neurological (OR = 8.198; 95% CI 5.690–11.813) and ophthalmological (OR = 3.381; 95% CI 1.617–7.068) conditions; and ADD/ADHD (OR = 3.246; 95% CI 1.811–5.818). A subgroup analysis revealed a more profound case–control difference in anaemia rates among girls than in boys (OR = 3.25; 95% CI 1.04–10.19 v. OR = 0.74; 95% CI 0.33–1.64 respectively) and an opposite trend (larger differences in males than in females in cardiovascular diseases (OR = 1.99; 95% CI 1.23–3.23 v. OR = 0.76; 95% CI 0.17–3.45, respectively)). In addition, larger case–control differences were seen among Bedouin children than in Jewish children in a number of medical comorbidities (Breslow–Day test for homogeneity of odds ratio p-value <0.05). Finally, we found that children with ASD tended to be referred to the emergency department and to be admitted to the hospital more frequently than children without ASD, even after adjusting for their comorbidity burden (aOR = 1.28; 95% CI 1.08–1.50 and aOR = 1.28; 95% CI 1.11–1.47 for >1 referrals and admissions per year, respectively).

Conclusions

The findings of this study contribute to the overall understanding of comorbid conditions and health services' utilisation for children with ASD. The higher prevalences of comorbidities and healthcare services' utilisation for children with ASD highlight the additional medical burden associated with this condition.
Experimental and Model‐Based Investigation of the Effect of the Free‐Surface Flow Regime on the Detection Threshold of Warm Water Inflows
Authors: Le Lay Hugo , Thomas Zahra , Bour Olivier , Rouault François , Pichelin Pascal , Moatar Florentina
Published: January 2020

Heat has been used as a tracer to identify and quantify groundwater inflows into streams. Over the last decade, a few methods have used fiber‐optic distributed temperature sensing to facilitate assessment of such inflows into small streams. However, these methods focused mainly on the groundwater percentage and the thermal contrast between groundwater and surface water without considering the flow regime of the surface water. In this study, artificial water inflows into a controlled flume were examined using fiber‐optic distributed temperature sensing to quantify the thermal anomalies induced as a function of the flow regime (turbulent or laminar). Computer simulations were then performed to widen the range of the parameters tested and provide insight into the physical processes involved. Experiments conducted under the turbulent regime were in accordance with results and uncertainties of previous studies. Under the laminar regime, however, the inflow‐induced thermal anomalies were always smaller than those under the turbulent regime for a given inflow percentage. Therefore, the actual inflow percentage may be underestimated when using a classic method under a laminar regime.
Shear Velocity and Radial Anisotropy beneath Southwestern Canada: Evidence for Crustal Extension and Thick‐Skinned Tectonics
Authors: Wang Jingchuan , Gu Yu Jeffrey , Chen Yunfeng
Published: January 2020

Deformation‐associated craton assembly and Cordilleran orogenesis played major roles during the crustal formation beneath the western margin of North America. To improve the understanding of the deformation history in this region, we investigate the crustal shear velocity and anisotropy by analyzing fundamental mode Rayleigh and Love waves from ambient seismic noise. Continuous recordings from 118 regional broadband stations reveal lateral variations in both velocity and anisotropy with strong spatial affinities to major geological domains. Strong variations in radial anisotropy, which dips westward and extends to at least midcrustal depths, suggest a “thick‐skinned” foreland thrust‐and‐fold belt beneath the Canadian Rocky Mountains. Our regional data also suggest increased horizontal shear velocities beneath the southern Canadian Cordillera, particularly near the Omineca Belt, which may have resulted from strong zonal deformation within the Cordilleran crust. This anisotropic anomaly migrates southward, and its spatial extent agrees well with the normal fault distribution to the west of the Rocky Mountain Trench. Our observations offer new evidence for the Eocene extension of the orogenic hinterland during the trans‐tensional motion of the Cordillera to the North American craton.
Analyzing the Synoptic‐, Meso‐ and Local‐ Scale Involved in Sea Breeze Formation and Frontal Characteristics
Authors: Arrillaga Jon A. , Jiménez Pedro , Vilà‐Guerau de Arellano Jordi , Jiménez Maria A. , Román‐Cascón Carlos , Sastre Mariano , Yagüe Carlos
Published: January 2020

Sea breeze (SB) frontal passages, the relevant factors influencing their formation and their interaction with local turbulence, are analyzed. To proceed, numerical simulations from the Weather Research and Forecasting (WRF) model are compared with a comprehensive observational database from the Cabauw Experimental Site for Atmospheric Research site, spanning a 10‐year period (January 2001 to December 2010). The fine horizontal resolution of 2 km and the replication of the observational vertical levels allow for a more precise comparison. An algorithm based on objective and strict criteria was applied to both observations and simulations to select the SB events. By carrying out a filter‐by‐filter comparison, we find that the simulated large‐scale conditions show a good rate of coincidence with the reanalysis (69%). Small biases in the large‐scale wind direction, however, induce important deviations in the surface‐wind evolution. Regarding mesoscale forcings, the land‐sea temperature gradient is overestimated in average up to 4 K, producing stronger SB fronts in WRF. The analysis of the SB characteristics and impacts is carried out by classifying the events into three boundary‐layer regimes (convective, transition, and stable) based on the value of the sensible‐heat flux at the SB onset. The stronger SB in the model leads to enhanced turbulence particularly in the convective and transition regimes: The friction velocity, for instance, is overstated by around 50% at the SB onset. In addition, the arrival of the SB front enhances the stable stratification and gives rise to faster afternoon and evening transitions compared with situations solely driven by local atmospheric turbulence.
Assimilation of Cosmic‐Ray Neutron Counts for the Estimation of Soil Ice Content on the Eastern Tibetan Plateau
Authors: Mwangi Samuel , Zeng Yijian , Montzka Carsten , Yu Lianyu , Su Zhongbo
Published: January 2020

Accurate observations and simulations of soil moisture phasal forms are crucial in cold region hydrological studies. In the seasonally frozen ground of eastern Tibetan Plateau, water vapor, liquid, and ice coexist in the frost‐susceptible silty‐loam soil during winter. Quantification of soil ice content is thus vital in the investigation and understanding of the region's freezing‐thawing processes. This study focuses on the retrieval of soil ice content utilizing the in situ soil moisture (i.e., liquid phase) and cosmic ray neutron measurements (i.e., total water including liquid and ice), with Observing System Simulation Experiments. To derive the total soil water from neutron counts, different weighting methods (revised, conventional, and uniform) for calibrating the cosmic‐ray neutron probe (CRNP) were intercompared. The comparison showed that the conventional nonlinear method performed the best. Furthermore, to assimilate fast neutrons using the particle filter, the STEMMUS‐FT (Simultaneous Transfer of Energy, Mass and Momentum in Unsaturated Soil) model was used as the physically based process model, and the COSMIC model (Cosmic‐ray Soil Moisture Interaction Code) used as the observation operator (i.e., forward neutron simulator). Other than background inputs from disturbed initializations in the STEMMUS‐FT, model uncertainties were predefined to assimilate fast neutrons. We observed that with enough spread of uncertainties, the updated states could mimic the CRNP observation. In all setups, assimilating CRNP measurements could enhance total soil water analyses, which consequently led to the improved detection of soil ice content and therefore the freezing thawing‐process at the field scale.
Characterization of the Global Sources of Atmospheric Ammonia from Agricultural Soils
Authors: Aneja Viney P. , Schlesinger William H. , Li Qi , Nahas Alberth , Battye William H.
Published: January 2020

Global ammonia (NH3) emissions to the atmosphere are projected to increase in the coming years with the increased use of synthetic nitrogen fertilizers and cultivation of nitrogen‐fixing crops. A statistical model (NH3_STAT) is developed for characterizing atmospheric NH3 emissions from agricultural soils and compared to the performance of other global and regional NH3 models (e.g., Emission Database for Global Atmospheric Research, Magnitude and Seasonality of Agricultural Emissions, MIX, and U.S. Environmental Protection Agency). The statistical model was developed from a multiple linear regression between NH3 emission and the physicochemical variables. The model was evaluated for 2012 NH3 emissions. The results indicate that, in comparison to other data sets, the model provides a lower global NH3 estimate by 58%, (NH3_STAT: 13.9 Tg N yr−1; Emission Database for Global Atmospheric Research: 33.0 Tg N yr−1). We also performed a region‐based analysis (United States, India, and China) using the NH3_STAT model. For the United States, our model produces an estimate that is a ~1.4 times higher in comparison to the Environmental Protection Agency. Meanwhile, the NH3_STAT estimate for India shows NH3 emissions between 0.8 and 1.4 times lower when compared to other data sets. A lower estimate is also seen for China, where the model estimates NH3 emissions 0.4 to 5 times lower than other data sets. The difference in the global estimates is attributed to the lower estimates in major agricultural countries like China and India. The statistical model captures the spatial distribution of global NH3 emissions by utilizing a simplified approach compared to other readily available data sets. Moreover, the NH3_STAT model provides an opportunity to predict future NH3 emissions in a changing world.
Denudation Rate Changes Along a Fast‐Eroding Mountainous River With Slate Headwaters in Taiwan From 10Be (Meteoric)/9Be Ratios
Authors: Deng Kai , Yang Shouye , von Blanckenburg Friedhelm , Wittmann Hella
Published: January 2020

The novel 10Be (meteoric)/9Be system, where 10Be is delivered by precipitation and stable 9Be is released by weathering, provides denudation rates over weathering‐erosion timescales. The new tool is applicable to quartz‐poor lithologies, for example, mafic rock and claystone, which are not readily accessible by the commonly used in situ‐produced 10Be in quartz. We provide a first application of this proxy to a tectonically active mountainous river, the Zhuoshui River in Taiwan. Taiwan Rivers supply a disproportionately high suspended and dissolved flux to the oceans and are often underlain by fine‐grained shale/slate. 10Be (meteoric)/9Be‐derived denudation rates (Dmet) from the Zhuoshui Catchment are highest in the slate‐dominated headwaters (4–8 mm/year), and much lower (1–2 mm/year) along the midlower reaches with mixed lithologies. At the basin‐wide scale, we find a poor correlation between Dmet and basin‐averaged channel steepness despite a small climatic gradient. Because large lithological heterogeneities exist in this basin, we invoke a lithological effect to explain this poor correlation. Relying on a revised stream power incision model that incorporates rock erodibility, the resulting lithology‐ and runoff‐adjusted ksn (kLrsn) can be reconciled with denudation rates with the highest erodibility predicted to prevail in the Miocene slate of low metamorphic grade and high fracture density. This model suggests that the lithological heterogeneity can alter the coupling between surface denudation and channel morphology. On a broader perspective, the successful application of the 10Be (meteoric)/9Be proxy shows its applicability as a tracer for erosion and sediment transport processes in fast‐eroding mountain belts underlain by slate lithologies.
Sediment Disposals in Estuarine Channels Alter the Eco‐Morphology of Intertidal Flats
Authors: de Vet P. L. M. , van Prooijen B. C. , Colosimo I. , Ysebaert T. , Herman P. M. J. , Wang Z. B.
Published: January 2020

Dredging of navigation channels in estuaries affects estuarine morphology and ecosystems. In the Western Scheldt, a two‐channel estuary in the Netherlands, the navigation channel is deepened and the sediment is relocated to other parts of the estuary. We analyzed the response of an intertidal flat to sediment disposals in its adjacent channel. Decades of high‐frequency monitoring data from the intertidal flat show a shift from erosion toward accretion and reveal a sequence of cascading eco‐morphological consequences. We document significant morphological changes not only at the disposal sites, but also at the nearby intertidal flats. Disposals influence channel bank migration, driving changes in the evolution of the intertidal flat hydrodynamics, morphology, and grain sizes. The analyzed disposals related to an expansion of the channel bank, an increase in bed level of the intertidal flat, a decrease in flow velocities on this higher elevated flat, and locally a decrease in grain sizes. These changes in turn affect intertidal flat benthic communities (increased in quantity in this case) and the evolution of the adjacent salt marsh (retreated less or even expanded in this case). The shifts in evolution may occur years after dredged disposal begins, especially in zones of the flats farther away from the disposal locations. The consequences of sediment disposals that we identify stress the urgency of managing such interventions with integrated strategies on a system scale.
Seasonality of Organic Matter Degradation Regulates Nutrient and Metal Net Fluxes in a High Energy Sandy Beach
Authors: Ahrens Janis , Beck Melanie , Marchant Hannah K. , Ahmerkamp Soeren , Schnetger Bernhard , Brumsack Hans‐Jürgen
Published: January 2020

During seawater circulation in permeable intertidal sands, organic matter degradation alters the composition of percolating fluids and remineralization products discharge into surficial waters. Concurrently, coastal seawater nutrient and organic matter composition change seasonally due to variations in pelagic productivity. To assess seasonal changes in organic matter degradation in the intertidal zone of a high energy beach (Spiekeroog Island, southern North Sea, Germany), we analyzed shallow pore waters for major redox constituents (oxygen [O2], manganese [Mn], and iron [Fe]) and inorganic nitrogen species (nitrite [NO2−], nitrate [NO3−], and ammonium [NH4+]) in March, August, and October. Surface water samples from a local time series station were used to monitor seasonal changes in pelagic productivity. O2 and NO3− were the dominating pore water constituents in March and October. Dissolved Mn, Fe, and NH4+ were more widely distributed in August. Seasonal changes in seawater temperature as well as organic matter and nitrate supply by seawater were assumed to affect microbial rates and degradation pathways. Pore water and seawater variability led to seasonally changing constituent effluxes to surface waters. Mn, Fe, and NH4+ effluxes are minimal in March and reached their maximum in August. Furthermore, the intertidal sands switched from a net dissolved inorganic nitrogen sink in March to a net source in August. In conclusion, seasonal effects on intertidal pore water biogeochemistry affect constituent fluxes across the sediment‐water interface. The seasonality of the beach bioreactor must be considered when fluxes are extrapolated to annual timescales.
The Central Amazon Biomass Sink Under Current and Future Atmospheric CO2: Predictions From Big‐Leaf and Demographic Vegetation Models
Authors: Holm Jennifer A. , Knox Ryan G. , Zhu Qing , Fisher Rosie A. , Koven Charles D. , Nogueira Lima Adriano J. , Riley William J. , Longo Marcos , Negrón‐Juárez Robinson I. , de Araujo Alessandro C. , Kueppers Lara M. , Moorcroft Paul R. , Higuchi Niro , Chambers Jeffrey Q.
Published: January 2020

There is large uncertainty whether Amazon forests will remain a carbon sink as atmospheric CO2 increases. Hence, we simulated an old‐growth tropical forest using six versions of four terrestrial models differing in scale of vegetation structure and representation of biogeochemical (BGC) cycling, all driven with CO2 forcing from the preindustrial period to 2100. The models were benchmarked against tree inventory and eddy covariance data from a Brazilian site for present‐day predictions. All models predicted positive vegetation growth that outpaced mortality, leading to continual increases in present‐day biomass accumulation. Notably, the two vegetation demographic models (VDMs) (ED2 and ELM‐FATES) always predicted positive stem diameter growth in all size classes. The field data, however, indicated that a quarter of canopy trees didn't grow over the 15‐year period, and while high interannual variation existed, biomass change was near neutral. With a doubling of CO2, three of the four models predicted an appreciable biomass sink (0.77 to 1.24 Mg ha−1 year−1). ELMv1‐ECA, the only model used here that includes phosphorus constraints, predicted the lowest biomass sink relative to initial biomass stocks (+21%), lower than the other BGC model, CLM5 (+48%). Models projections differed primarily through variations in nutrient constraints, then carbon allocation, initial biomass, and density‐dependent mortality. The VDM's performance was similar or better than the BGC models run in carbon‐only mode, suggesting that nutrient competition in VDMs will improve predictions. We demonstrate that VDMs are comparable to nondemographic (i.e., “big‐leaf”) models but also include finer scale demography and competition that can be evaluated against field observations.
Statistically Steady State Large‐Eddy Simulations Forced by an Idealized GCM: 1. Forcing Framework and Simulation Characteristics
Authors: Shen Zhaoyi , Pressel Kyle G. , Tan Zhihong , Schneider Tapio
Published: January 2020

Using large‐eddy simulations (LES) systematically has the potential to inform parameterizations of subgrid‐scale processes in general circulation models (GCMs), such as turbulence, convection, and clouds. Here we show how LES can be run to simulate grid columns of GCMs to generate LES across a cross section of dynamical regimes. The LES setup approximately replicates the thermodynamic and water budgets in GCM grid columns. Resolved horizontal and vertical transports of heat and water and large‐scale pressure gradients from the GCM are prescribed as forcing in the LES. The LES are forced with prescribed surface temperatures, but atmospheric temperature and moisture are free to adjust, reducing the imprinting of GCM fields on the LES. In both the GCM and LES, radiative transfer is treated in a unified but idealized manner (semigray atmosphere without water vapor feedback or cloud radiative effects). We show that the LES in this setup reaches statistically steady states without nudging to thermodynamic GCM profiles. The steady states provide training data for developing GCM parameterizations. The same LES setup also provides a good basis for studying the cloud response to global warming.
Upscaling Water Flow in Composite Nanoporous Shale Matrix Using Lattice Boltzmann Method
Authors: Zhang Tao , Javadpour Farzam , Yin Ying , Li Xiangfang
Published: January 2020

Water flow in nanoporous structures in shale strongly depends on water‐pore wall interactions; specifically, water‐pore wall interactions may influence flow more than water‐water interactions. Because of strong water‐pore wall interactions, the models that govern flow in nanoporous structures deviate from conventional continuum flow models such as the Darcy equation. We develop a novel lattice Boltzmann model to study water flow in nanoporous structures rendered from shale samples. First, we reconstruct three‐dimensional (3‐D) stochastic digital models based on composite shale samples that include hydrophobic organic matter (OM) and hydrophilic clay minerals. In the reconstructed digital models, we use pore size/shape distributions, porosity, and mineralogy from experiments. Then we use lattice Boltzmann models to model water flow through nanoporous structures (OM and clay) of the reconstructed shale sample, and we upscale the results to a microporous structure of composite shale containing OM, clay, and interpores associated to other minerals. The results show contraction/expansion effects of pore‐throat‐pore systems in nanoporous OM weaken the hydrophobicity‐induced slippage effect on total water flow. In nanoporous clay, the swelling effect predominates and diminishes water slippage effects on water flow. The work also highlights the importance of (1) the accuracy of reconstructed 3‐D pore networks in terms of pore connectivity, shape, and tortuosity in individual systems of OM and clay and (2) the role of OM nanopores in connecting isolated micropores to total water flow through the composite shale system.
A Tree‐Based Direct Sampling Method for Stochastic Surface and Subsurface Hydrological Modeling
Authors: Zuo Chen , Yin Zhen , Pan Zhibin , MacKie Emma J. , Caers Jef
Published: January 2020

Direct sampling (DS) is a versatile multiple‐point statistics method for generating spatial‐temporal geostatistical models. DS is known for being able to address a variety of training images and hence spatiotemporal stochastic modeling problems. One limitation of DS is the central processing unit (CPU) time, mostly attributed to the use of a random search for patterns in the training image. To improve CPU performance, we propose a tree‐based direct sampling (TDS) method. In our method, training patterns are grouped according to their similarities combined with a clustering tree for fast lookup. Rather than patterns, we store locations in our database. During the simulation, TDS applies a tree‐driven search approach. Two objectives, similarity and diversity, are used to rapidly retrieve patterns and prevent trapping into local optima. We also introduce a way to speed up simulation by means of pasting patterns with adaptive size. The performance of our TDS is investigated using a 2‐D benchmark training image. Moreover, we apply the proposed method to two real cases including gap filling the bedrock topography in Antarctica from radar to better understand subglacial hydrology and creating 3‐D groundwater models in the Danish aquifer system. Based on several quantitative evaluations, we find the proposed TDS is comparable to DS in terms of simulation quality, while significantly saves CPU time.
Adaptive introgression from indicine cattle into white cattle breeds from Central Italy
Authors: Barbato Mario , Hailer Frank , Upadhyay Maulik , Del Corvo Marcello , Colli Licia , Negrini Riccardo , Kim Eui-Soo , Crooijmans Richard P. M. A. , Sonstegard Tad , Ajmone-Marsan Paolo
Published: January 2020

Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.
A highly selective colorimetric fluorescence probe for Cu2+ in aqueous media: the synthesis, DFT investigation and its application in living cells
Authors: Li Dandan , Gong Lihua , Qiao Zhenyang , Zhu Congcong , Jia Qiaojuan , Kong Huajie , Jiao Shuyan
Published: January 2020

A novel highly selective colorimetric fluorescence probe, POPH, has been successfully synthesized and it shows remarkable selective and sensitive response to Cu2+ in aqueous media (HEPES buffer, pH = 7.4).
Optimizing the surface state of cobalt-iron bimetallic phosphide via regulating phosphorus vacancies
Authors: Li Shuang , Geng Zhibin , Wang Xiyang , Ren Xiaoru , Liu Jinghai , Hou Xiangyan , Sun Yu , Zhang Wei , Huang Keke , Feng Shouhua
Published: January 2020

We regulated phosphorus vacancies in Co0.68Fe0.32P by Ar-plasma treatment, leading to a unique surface state.
Enhancing the matching of acid/metal balance by engineering an extra Si–Al framework outside the Pd/HBeta catalyst towards benzene hydroalkylation
Authors: Li Zhuo-Qian , Fu Xinxin , Gao Caiyan , Huang Jinyu , Li Baojun , Yang Yongpeng , Gao Jie , Shen Yonglong , Peng Zhikun , Yang Jing-He , Liu Zhongyi
Published: January 2020

We have designed and constructed an extra Si–Al framework coating outside the Pd/HBeta catalyst, which exhibits excellent catalytic performance for benzene hydroalkylation reaction, due to the better matching relationship between metal and acid sites.