bluuebunny/crossref_metadata_2025 huggingface dataset:
Grand challenges for Smoothed Particle Hydrodynamics numerical schemes
Authors: Vacondio Renato , Altomare Corrado , De Leffe Matthieu , Hu Xiangyu , Le Touzé David , Lind Steven , Marongiu Jean-Christophe , Marrone Salvatore , Rogers Benedict D. , Souto-Iglesias Antonio
Published: September 2020

This paper presents a brief review of grand challenges of Smoothed Particle Hydrodynamics (SPH) method. As a meshless method, SPH can simulate a large range of applications from astrophysics to free-surface flows, to complex mixing problems in industry and has had notable successes. As a young computational method, the SPH method still requires development to address important elements which prevent more widespread use. This effort has been led by members of the SPH rEsearch and engineeRing International Community (SPHERIC) who have identified SPH Grand Challenges. The SPHERIC SPH Grand Challenges (GCs) have been grouped into 5 categories: (GC1) convergence, consistency and stability, (GC2) boundary conditions, (GC3) adaptivity, (GC4) coupling to other models, and (GC5) applicability to industry. The SPH Grand Challenges have been formulated to focus the attention and activities of researchers, developers, and users around the world. The status of each SPH Grand Challenge is presented in this paper with a discussion on the areas for future development.
Alterations of gut microbiota composition in post-finasteride patients: a pilot study
Authors: Borgo F. , Macandog A. D. , Diviccaro S. , Falvo E. , Giatti S. , Cavaletti G. , Melcangi R. C.
Published: September 2020

Purpose

Post-finasteride syndrome (PFS) has been reported in a subset of patients treated with finasteride (an inhibitor of the enzyme 5alpha-reductase) for androgenetic alopecia. These patients showed, despite the suspension of the treatment, a variety of persistent symptoms, like sexual dysfunction and cognitive and psychological disorders, including depression. A growing body of literature highlights the relevance of the gut microbiota-brain axis in human health and disease. For instance, alterations in gut microbiota composition have been reported in patients with major depressive disorder. Therefore, we have here analyzed the gut microbiota composition in PFS patients in comparison with a healthy cohort.

Methods

Fecal microbiota of 23 PFS patients was analyzed by 16S rRNA gene sequencing and compared with that reported in ten healthy male subjects.

Results

Sexual dysfunction, psychological and cognitive complaints, muscular problems, and physical alterations symptoms were reported in more than half of the PFS patients at the moment of sample collection. The quality sequence check revealed a low library depth for two fecal samples. Therefore, the gut microbiota analyses were conducted on 21 patients. The α-diversity was significantly lower in PFS group, showing a reduction of richness and diversity of gut microbiota structure. Moreover, when visualizing β-diversity, a clustering effect was found in the gut microbiota of a subset of PFS subjects, which was also characterized by a reduction in Faecalibacterium spp. and Ruminococcaceae UCG-005, while Alloprevotella and Odoribacter spp were increased compared to healthy control.

Conclusion

Gut microbiota population is altered in PFS patients, suggesting that it might represent a diagnostic marker and a possible therapeutic target for this syndrome.
Nanohollow Carbon for Rechargeable Batteries: Ongoing Progresses and Challenges
Authors: Jiang Jiangmin , Nie Guangdi , Nie Ping , Li Zhiwei , Pan Zhenghui , Kou Zongkui , Dou Hui , Zhang Xiaogang , Wang John
Published: September 2020

Among the various morphologies of carbon-based materials, hollow carbon nanostructures are of particular interest for energy storage. They have been widely investigated as electrode materials in different types of rechargeable batteries, owing to their high surface areas in association with the high surface-to-volume ratios, controllable pores and pore size distribution, high electrical conductivity, and excellent chemical and mechanical stability, which are beneficial for providing active sites, accelerating electrons/ions transfer, interacting with electrolytes, and giving rise to high specific capacity, rate capability, cycling ability, and overall electrochemical performance. In this overview, we look into the ongoing progresses that are being made with the nanohollow carbon materials, including nanospheres, nanopolyhedrons, and nanofibers, in relation to their applications in the main types of rechargeable batteries. The design and synthesis strategies for them and their electrochemical performance in rechargeable batteries, including lithium-ion batteries, sodium-ion batteries, potassium-ion batteries, and lithium–sulfur batteries are comprehensively reviewed and discussed, together with the challenges being faced and perspectives for them.
Covid-19: food insecurity, digital exclusion and Catholic schools
Authors: McKinney Stephen J.
Published: September 2020

Covid-19 and the subsequent worldwide lockdowns have had a major impact on families and school education. The lockdowns have highlighted and exacerbated the disadvantages experienced by those children who suffer from child poverty. This article focuses on food insecurity and the digital divide, or digital exclusion, and argues that these have emerged as very pressing issues during lockdowns for children suffering from child poverty. The article provides an outline of the response of the Catholic Church and Catholic schools, primarily in the United Kingdom. There have been some concerted efforts to address food insecurity by providing food and food vouchers for children and vulnerable families. It has proved more problematic to address digital exclusion and the article argues that for those children who experience digital exclusion, this can effectively mean exclusion from the religious education, religious life, community and the pastoral and spiritual support that is normally offered by the Catholic school.
‘Neutrality’, Muslimness and the whiteness of RE professionalism
Authors: Vince Matthew
Published: September 2020

There has been longstanding criticism of the whiteness of the professional discourses in teaching. Bariso (Race Ethn Educ 4(2):167–184,10.1080/713693054, 2001) writes that where whiteness is constructed as being professional then blackness is constructed as unprofessional, in turn excluding blackness from the construction of the teacher. Similarly, Bhopal (Br J Educ Stud, 63(2):197–211,10.1080/00071005.2015.1005045, 2015) argues that this presents a clash between embodying blackness and embodying the teacher. With the turn to research surrounding Muslim teachers, attributes of Muslimness have also been shown to be a source of marginalisation within school contexts (Shah in Education, leadership and Islam: theories, discourses and practices from an Islamic perspective, Routledge, London, 2016). Some scholarship has reflected on issues surrounding embodiment and ‘body-works’ of RE teaching’s professional discourses (Bryan and Revell in Br J Educ Stud 59(4):403–419,10.1080/00071005.2011.602328, 2011; Everington in Br J Religious Educ 36(2):155–173,10.1080/01416200.2013.820169, 2014; Vince in J Beliefs Values,10.1080/13617672.2019.1686732019, 2019). Such empirical studies have shown that embodying faith is perceived to be at odds with notions of RE teacher professionalism, particularly around notions of ‘neutrality’ (Everington in Br J Relig Educ, 38(2):177–188,10.1080/01416200.2016.1139892, 2016). Despite the concept of ‘neutrality’ being increasingly criticised (Franken and Loobuyck in Br J Relig Educ, 39(1):1–6,10.1080/01416200.2016.1218219, 2017), embodying ‘neutrality’ remains an important commitment. This has clear implications for (hyper)visible religious bodies (Jeldtoft, in: Dessing et al. (eds) Everyday Lived Islam in Europe, Routledge, London, 2016). Accordingly, in this paper I explore how ‘Muslim RE teachers’ manage their identities in relation to ‘being neutral’. For these teachers, ‘becoming neutral’ was the formative part of becoming an RE teacher. However, this was particularly challenging due to the hypervisibility of their Muslimness, particularly for female Muslim teachers. These challenges are then framed as an issue of whiteness, disproportionally affecting those who do not fit the white teacher norm. I end on arguing that there is a pressing need to change how ‘neutrality’ is understood.
Ethics education in Maltese public schools: a response to otherness or a contribution to Othering?
Authors: Mizzi Bernardette , Mercieca Duncan P.
Published: September 2020

This paper reflects on the establishment of an Ethics Education Programme for school pupils aged between five and sixteen years who opt out of Catholic Religious Education in Malta. It needs to be seen in the light of the changing demography of Malta and the increasing secularisation of the country, as well as to the growing racism, islamophobia and rejection of the Other to be found all over Europe (and of course beyond). We question if the Ethics Education Programme, in its commitment to ‘totalising’ western ideals of rationality, autonomy, and universal values, is itself rooted in discomfort with the Other and constitutes a form of ethical violence. The work of Emmanuel Levinas on Otherness, sameness and violence is central to this paper.
Past pandemics and climate variability across the Mediterranean
Authors: Luterbacher J. , Newfield T. P. , Xoplaki E. , Nowatzki E. , Luther N. , Zhang M. , Khelifi N.
Published: September 2020

The influence that meteorological, climatological and environmental factors had on historical disease outbreaks is often speculated upon, but little investigated. Here, we explore potential associations between pandemic disease and climate over the last 2,500 years in Mediterranean history, focusing on ancient disease outbreaks and the Justinianic plague in particular. We underscore variation in the quality, quantity and interpretation of written evidence and proxy information from natural archives, the comlexity of identifying and disentangling past climatological and environmental drivers, and the need to integrate diverse methodologies to discern past climate-disease linkages and leverage historical experiences to prepare for the rapid expansion of novel pathogenic diseases. Although the difficulties entailed in establishing historical climate-pandemic linkages persist to the present, this is a research area as urgent as it is complex and historical perspectives are desperately needed.
The effects of automation of a patient-centric service in primary care on the work engagement and exhaustion of nurses
Authors: Cajander Åsa , Larusdottir Marta , Hedström Gustaf
Published: September 2020

Digitalising patient-centric services to address society’s challenges with an ageing population and healthcare provision is by many seen as important. Studying the effects of the digitalisation on the work engagement of the users of the new systems is vital in this context, especially since previous research has established that the work engagement at work in healthcare is problematic. Work engagement is defined as a positive, fulfilling, affective-motivational state of work related well being, as is closely connected to the experience of resources and demands in the work context. These resources can be for example digital support, experienced demands or empowerment whereas exhaustion is connected to work demand in a workplace. This study contributes to knowledge about the effects of digitalisation on work engagement and exhaustion in the context of patient-centred services and eHealth. Contextual interviews were conducted on site for 5 h with nurses using a new chat function and using telephone for medical advice to patients. Additionally, semi-structured interviews were conducted with all the nurses participating in this digitalisation project to gather more insights into their work engagement in the two work situations. Results were analysed in different themes of areas affected by the digitalisation in the two overarching themes: job demands and job resources. The results show that the change to a chat function when communicating with advice seekers had connection to work engagement in several ways. The nurses experienced less time pressure and emotional pressure, but also a loss of job control and feedback from colleagues working from home.
Radiofrequency for benign and malign thyroid lesions
Authors: Rangel Leonardo , Volpi Leonardo M. , Stabenow Elaine , Steck Jose Higino , Volpi Erivelto , Russell Jonathon O. , Tufano Ralph P.
Published: September 2020

Background

Thermal ablation of thyroid nodules is new modality for the management of the benign and malign lesions. This minimally invasive treatment is performed as an outpatient, local anesthetic, single professional procedure that can treat neoplastic lesions without removing normal thyroid tissue and thus avoiding hypothyroidism.

Method

A comprehensive review of the most relevant literature regarding the thermal ablation of benign and malign nodules was performed in order to currently define its role on the management of the nodular thyroid disease. The data was divided into benign and malign literature.

Results

The benign nodules can be effectively treated by radiofrequency ablation (RFA) but some limitation exists regarding the nodule's size but not nodules characteristics. The RFA of primary malign tumors of the thyroid recently demonstrated positive and safe long‐term follow‐up and encouraged additional investigation and possibly a definitive role in the management of these low risk nodules.

Conclusion

RFA is a safe, cost‐effective minimally invasive procedure that avoids thyroid tissue removal while destroying neoplastic one thus, preventing hypothyroidism.
Prevalence and associated risk factors of recurrent otitis media with effusion in children in Upper Egypt
Authors: Saad Khaled , Abdelmoghny Abobakr , Abdel‐Raheem Yasser F. , Gad Eman Fathalla , Elhoufey Amira
Published: September 2020

Objective

We conducted this study to determine the associations of possible risk factors and prevalence of recurrent otitis media with effusion (OME) in a cohort of children in Upper Egypt.

Methods

This was a cross‐sectional study undertaken in two tertiary referral centers in Upper Egypt. Associations of possible risk factors with prevalence of recurrent OME were studied. Multi‐factor logistic regression analysis was done to recognize the statistically significant risk factors associated with recurrent OME.

Results

We collected the data of 2003 pediatric patients, of which 1016 were males (50.7%). A total number of 310 children have OME, including 159 males (51.3%). The prevalence rate of OME in our cohort was 15.5%. Multi‐factor logistic regression analysis of the risk factors related to recurrent OME showed it was strongly associated with adenoid hypertrophy (P < 0.0001), tonsil hypertrophy (P < 0.0001), sinusitis (P < 0.0001), posterior nostril polyps (P = 0.009), allergic rhinitis (P < 0.0001), recurrent URTIs (P = 0.029) and gastroesophageal reflux (P = 0.031).

Conclusions

Our study showed that recurrent OME in children in Upper Egypt is a common multifactorial problem, especially in young age. In our locality, allergic rhinitis, recurrent upper respiratory tract infections, gastroesophageal reflux, adenoid and tonsil hypertrophy were the most important associated factors related to the etiopathogenesis of OME.
Research on Fading Characteristics of Ultrahigh Frequency Signals in Karst Landform Around Radio Quiet Zone of FAST
Authors: Wang Jian , Shi Yafei , Yang Cheng , Ji Shengyun , Su Haibin
Published: September 2020

Ultrahigh frequency wireless signals are mainly influenced by the geomorphological environment during the transmission process, resulting in fading channels, especially in mountainous regions. The experiment was conducted in the Karst landform of Guizhou Province, China, in order to explore fading distribution characteristics for mainly analyzing electro magnetic compatibility (EMC) specialties between Five‐hundred‐meter Aperture Spherical Radio Telescope (FAST) and wireless radiation equipment around radio quiet zone of this telescope. Based on the channel variation data of six frequencies, which are mainly used by the electrical and electronic equipment of public facilities around FAST, the fading distribution was analyzed by using the Kolmogorov‐Smirnov statistic method. And finally we determined the optimal distribution model with the fading range, fading depth, and fading rate. The results show that (1) the polarization type and signal frequency have a definite influence on the fading distribution types in the Karst landform; (2) Rice distribution is the optimal and stable distribution model in the Karst landform, and the log‐normal distribution model is proposed to characterize the Rice K‐factor distribution; and (3) the line‐of‐sight (LoS) components of the normalized envelopes are 0.6837, 0.8939, 0.5963, 0.6332, 0.5516, and 0.4806. And the multipath scattered components of those are 0.2134, 0.0630, 0.2436, 0.2224, 0.2678, and 0.2880. The research results provide a potential support for the deployment and optimization of wireless communication networks in Karst landform, especially around radio quiet zone of FAST.
Imbalanced Stoichiometric Reservoir Sedimentation Regulates Methane Accumulation in China's Three Gorges Reservoir
Authors: Li Zhe , Lu Lunhui , Lv Pingyu , Zhang Zengyu , Guo Jinsong
Published: September 2020

The river‐reservoir continuum drives a separation of sedimentation along the longitudinal hydrodynamic gradients, potentially causing imbalanced stoichiometric sedimentation. However, there are still uncertainties regarding the contribution of imbalanced stoichiometric sedimentation to methane emissions along this continuum. A 2‐year field survey and in situ experiments were conducted in China's Three Gorges Reservoir (TGR), a river‐valley‐dammed reservoir. Sediments were trapped and collected to analyze for particulate carbon (C), nitrogen (N), and phosphorus (P) concentrations of different sizes in the summer flooded and winter dry seasons along the mainstem. Large amounts of sediments were deposited in the middle part of the TGR, particularly in the summer flood season. Hydrodynamic gradients structured imbalanced stoichiometric sedimentation patterns. Averaged particulate C:N:P proportions in the sediment layer along the upper, middle, and lower parts of the TGR in the first 30 years of reservoir operation were estimated to be 68:7:1, 97:8:1, and 151:13:1, respectively. The middle part of the TGR, being the “control point” of methane accumulation based on seasons, exhibited a shift in stoichiometry and stable isotope signatures, indicating that there was likely a shift in sources of POM. P, specifically in smaller size particles (<10 μm), seemed to be the potential key driver that regulates particulate C:N:P in the sediment of the TGR. Its sedimentation, primarily in the middle part of the TGR, contributed to the significant decreases in particulate C/P ratios and could possibly regulate long‐term CH4 accumulation in the reservoir.
Integrating Lateral Inflows Into a SWOT Mission River Discharge Algorithm
Authors: Nickles Cassandra , Beighley Edward , Durand Michael , Prata de Moraes Frasson Renato
Published: September 2020

Estimating river discharge from observed surface water extents and elevations is central to the Surface Water and Ocean Topography (SWOT) mission. Although near global in coverage, SWOT will only observe rivers wider than 50 to 100 m, overlooking smaller tributaries draining into observable river reaches. This is problematic for the Metropolis‐Manning (MetroMan) discharge algorithm, which assumes changes in discharge per location must be balanced by a change in cross‐sectional area, not accounting for potential flow contributions SWOT will not observe within the inversion region analyzed. Here, we quantify the effect of these lateral inflows on the performance of estimated discharges along the Muskingum River using MetroMan. Three scenarios are considered: (1) disregarding lateral inflows, (2) providing MetroMan with observed lateral inflows, and (3) providing MetroMan with uncertain model‐derived lateral inflows to assess the discharge algorithm's effectiveness. Scenarios are expanded to consider multiple lateral inflow magnitudes and distributions. Results indicate discharge retrievals were degraded once unaccounted lateral inflows exceeded 5% of average river discharge. When MetroMan is informed by observed lateral inflows, the derived discharges have a relative root‐mean‐square error (rRMSE) of 23% as compared to 360% when lateral inflows are neglected. More importantly, when MetroMan uses simulated lateral inflows, with peak flow condition percent errors as high as 93%, discharge retrieval performance is similar (rRMSE = 17%). These findings highlight the importance of accounting for lateral flows, even in the absence of perfect measurements.
Optimal Control for Precision Irrigation of a Large‐Scale Plantation
Authors: Kassing Ruud , De Schutter Bart , Abraham Edo
Published: September 2020

Distributing water optimally is a complex problem that many farmers face yearly, especially in times of drought. In this work, we propose optimization‐based feedback control to improve crop yield and water productivity in agriculture irrigation for a plantation consisting of multiple fields. The interaction between soil, water, crop (sugarcane in this work), and the atmosphere is characterized by an agrohydrological model using the crop water productivity modeling software AquaCrop‐OS. To optimally distribute water over the fields, we propose a two‐level optimal control approach. In this approach, the seasonal irrigation planner determines the optimal allocation of water over the fields for the entire growth season to maximize the crop yield, by considering an approximation of the crop productivity function. In addition, the model predictive controller takes care of the daily regulation of the soil moisture, respecting the water distribution decided on by the seasonal planner. To reduce the computational complexity of the daily controller, a mixed‐logic dynamical model is identified based on the AquaCrop‐OS model. This dynamical model incorporates saturation dynamics explicitly to improve model quality. To further improve performance, we create an evapotranspiration model by considering the expected development of the crop over the season using remote‐sensing‐based measurements of the canopy cover. The performance of the two‐level approach is evaluated through a closed‐loop simulation in AquaCrop‐OS of a real sugarcane plantation in Mozambique. Our optimal control approach boosts water productivity by up to 30% compared to local heuristics and can respect water use constraints that arise in times of drought.
Downward Migration of the Zonal‐Mean Circulation in the Tropical Atmosphere
Authors: DallaSanta Kevin , Gerber Edwin P.
Published: September 2020

The annular modes of the extratropical atmosphere have received much attention for quantifying variability of the jet streams and storm tracks, despite the fact that the midlatitude circulation itself does not vary uniformly with longitude. While tropical fluctuations in geopotential height have lower amplitude than in the extratropics, they exhibit stronger zonal coherence, or dynamical annularity. A simple index is developed to characterize zonal‐mean anomalies of the tropical circulation. It reveals that anomalies in geopotential height and zonal wind migrate downward from the upper troposphere to the surface on a time scale of about 10 days. These features are distinguishable from known modes of tropical variability, the Madden‐Julian Oscillation in particular. Evidence from reanalysis and idealized model experiments confirms that this downward migration is quite generic and driven by mechanically forced variations in the strength of the Hadley circulation on subseasonal time scales.
In Situ Observations of Light‐Absorbing Carbonaceous Aerosols at Himalaya: Analysis of the South Asian Sources and Trans‐Himalayan Valleys Transport Pathways
Authors: Yuan Qi , Wan Xin , Cong Zhiyuan , Li Mengmeng , Liu Lei , Shu Shoujuan , Liu Rui , Xu Liang , Zhang Jian , Ding Xiaokun , Li Weijun
Published: September 2020

The mountain‐valleys along the south margin of the Himalaya‐Tibetan Plateau (HTP), referred to as trans‐Himalayan valleys, are transport pathways of atmospheric pollutants from the South Asia lifting to the HTP based on atmospheric models and satellite detections. However, few field studies can be conducted to confirm the aerosol transport along these valleys due to the harsh environment and limited power supply. Individual particle collection instruments offer the unique advantage of collecting samples and tracing particle sources in remote areas due to their portability and efficiency. In this study, transmission electron microscopy was used to study individual particles collected in two trans‐Himalayan valleys. We found that 49–70% of thousands of particles were light‐absorbing carbonaceous aerosols including soot‐bearing and tarball‐bearing particles in December of 2017. The dominant sizes of soot‐bearing and tarball‐bearing particles were 151–370 and 198–255 nm, respectively. The WRF‐Chem model and wind field analyses show that the intense regional air pollution with high mass concentrations of light‐absorbing carbonaceous aerosol occurred in the South Asia and southwest wind normally prevailed along the trans‐Himalayan valleys in the afternoon of each day during wintertime. Backward trajectory and CALIPSO data further confirm that these light‐absorbing carbonaceous aerosols from the South Asia were transported to the southern HTP. These carbonaceous aerosols exhibited significantly internally mixing with secondary sulfates. Here individual particle analysis coupled with the WRF‐Chem model, the meteorological observation data, and satellite data confirm the trans‐Himalayan valleys as the direct channels for abundant carbonaceous aerosols lifting from the South Asia to the HTP.
Physical Properties of Basalt Ejecta Boulders at Lonar Crater, India: Insights Into the Target Heterogeneity and Impact Spallation Processes in Basalt With Application to Mars
Authors: Lakshmi K. Jaya Prasanna , Kumar P. Senthil
Published: September 2020

The 1.88‐km‐diameter Lonar crater emplaced in the Deccan basalt is an excellent terrestrial analog of bowl‐shaped impact craters on Mars. It contains a pristine ejecta blanket with abundant basalt boulders. We measured the density, porosity, P and S wave velocities and attenuation, magnetic susceptibility, uniaxial compressive strength, and tensile strength of 313 core specimens from 65 basalt ejecta boulders. Using these values, we quantified the gross physical properties of preimpact target and applied them in the cratering equations and estimated the spall plate dimensions and ejection distances. The impact of 35‐m‐radius projectile with 20 km/s velocity on the basaltic target with 77.2‐MPa dynamic tensile strength, 4,163 m/s P wave velocity, and 2.56 g/cm3 density gives a spall thickness range (0.2 to 9.7 m) similar to the observed boulder sizes at Lonar crater. Because aqueous weathering and vesicularity are present in the target, the Lonar impact produced smaller spall sizes than those expected from a massive basalt target. We also measured the ejecta boulder sizes and shapes around a fresh impact crater (of similar size and target to Lonar) in Arcadia Planitia on Mars and calculated the spall thicknesses. The low‐velocity impact (5.5 km/s) of 50‐m‐radius projectile on the target similar to Lonar basalt gives a spall thickness range (1 to 25 m) similar to the observed boulder sizes at the Martian impact crater. The impact craters of similar sizes and targets on Earth and Mars produced different spall boulder size distributions reflecting the distinct impact conditions on these planets.
Frost Quakes: Crack Formation by Thermal Stress
Authors: Okkonen J. , Neupauer R. M. , Kozlovskaya E. , Afonin N. , Moisio K. , Taewook K. , Muurinen E.
Published: September 2020

Fractures in frozen soils (frost quakes) can cause damage to buildings and other infrastructure, but their formation mechanisms remain poorly understood. A methodology was developed to assess thermal stress on soil due to changes in climate and weather conditions and to investigate the connection between thermal stress and frost quakes in central Finland due to brittle fracturing in uppermost soils. A hydrological model was used to simulate snow accumulation and melt, and a soil temperature model was used to simulate soil temperature at different depths beneath the snow pack. The results of modeling, together with measurements of air temperature, snow cover thickness, and soil temperature, were used to calculate temporal variations in thermal stress in soil. We show that frost quakes occur when thermal stress caused by a rapid decrease in temperature exceeds fracture toughness and strength of the soil‐ice mixture. We compared calculated thermal stress on soil, critical stress intensity factor, and a seismogram recorded in a suburban region in central Finland. Our results suggest that this methodology can be used to predict thermal stresses on soil and identify stress values that may lead to fractures of frozen soils, that is, frost quakes.
The Lability and Source of Particulate Organic Matter in the Northern Gulf of Mexico Hypoxic Zone
Authors: Liu Zhanfei , Xue Jianhong
Published: September 2020

Decomposition of particulate organic matter (POM) plays a key role in the formation of hypoxia in subsurface waters of coastal ocean, yet little is known about the lability and transformation of POM in the hypoxic zone. Suspended particles were collected from surface waters to overlying waters (~30 cm above the sediment‐water interface) along the shelf of northern Gulf of Mexico (nGOM) in late spring/early summer of 2010–2013. Total hydrolyzable amino acids (THAA) and pigments were measured in these particulate samples to trace organic matter lability. The degradation indices, derived from the THAA and chloropigments, were positively correlated with dissolved oxygen (DO) concentrations in the shelf region, suggesting that decomposition of POM contributed greatly to DO utilization. Bacterial degradation appears to be the major pathway for POM decomposition on both inner and mid shelves, while zooplankton grazing played a minor role. POM samples in the overlying water on the inner shelf were the most degraded from the THAA and pigment results, and they also had high C/N ratios (9–14) and depleted δ 13C values (−29‰ to −24‰), pointing to a source of terrestrial C3 plant material. This distinct terrestrial signal of POM in the overlying water suggests strong selective degradation of marine‐sourced organic matter, but how the terrestrial organic matter is settled to this layer and its ultimate fate remain unclear. Taken together, these data offer new angles looking into the lability and degradation pathways of POM, and mechanisms of hypoxia formation in coastal waters.
Seismotectonics at the Transition Between Opposite‐Dipping Slabs (Western Alpine Region)
Authors: Eva E. , Malusà M. G. , Solarino S.
Published: September 2020

We analyze a fully reprocessed data set of ~9,000 seismic events recorded in the western Alpine region during the past 30 yr, in order to understand how convergence between Africa and Eurasia is presently accommodated at the transition between the opposite‐dipping Alpine and Apenninic slabs. We confirm that seismicity in the Internal Zone of the Western Alps is clustered along two different arcs (Briançonnais and Piedmont arcs), clearly outlined by events in the 0–12 km depth range. The Piedmont Arc is best outlined by events in the 12–30 km depth range, forming a narrow belt that matches the shape and location of the Ivrea gravity anomaly. In the Internal Zone, σ3, is oblique to the orogen trend. Although the mountain range is spreading gravitationally at a shallow level, spreading occurs intermittently with other earthquakes that are more directly related to plate interactions. Strike‐slip solutions are predominant for events of magnitude Ml > 4, and reverse solutions are dominant along the Piedmont Arc for events of magnitude Ml < 4. Nodal planes have dominant NNW‐SSE and ENE‐WSW orientations that are common to major faults mapped in the study area. Integration with available tectonic and geodynamic constraints indicates that lithology distribution in the subduction wedge, orientation of major faults within and outside the subduction zone, and the exhumation of mantle rocks at shallow depth concurrently determine a complex seismotectonic scenario that may be expected in other subduction zones worldwide.
Nonuniform Flows in a Compound Open‐Channel: Assessment of a Hybrid RANS‐LES Approach
Authors: Chatelain M. , Proust S.
Published: September 2020

Overbank flows in rivers, also termed compound open‐channel flows, are rarely uniform in the streamwise direction. Flow nonuniformity involves transverse currents directed from the river main channel (MC) to adjacent floodplains (FPs) or vice versa. Depending on their direction and magnitude, the transverse currents can laterally displace the planform shear layer that forms at the interface between MC and FP. They can also modify the cross‐sectional distribution of the helical secondary currents (SCs). This paper reports a numerical study that focuses on assessing the ability of a hybrid RANS (Reynolds Averaged Navier‐Stokes) ‐ LES (Large Eddy Simulation) approach, namely, the Scale Adaptive Simulation (SAS), to capture the evolving structure of both depth‐uniform and nonuniform flows in a straight compound open‐channel. The simulated flows have recently been studied in an 18 m long and 3 m wide laboratory flume by Proust and Nikora (2020, https://doi.org/10.1017/jfm.2019.973). The originality of the study lies in the modeling of flows over the entire flume length and in the estimate of the length‐scales of the large Kelvin‐Helmholtz‐type coherent structures (KHCSs). The SAS approach can accurately predict the longitudinal evolution of: (i) the streamwise time‐averaged flow, including the planform shear layer width, (ii) the SC patterns, and (iii) the turbulence statistics. The emergence and development of the KHCSs are qualitatively retrieved and are confirmed to be controlled by dimensionless velocity shear irrespective of flow depth. The simulations also show that SC patterns depend on the magnitude and direction of the transverse currents and also on the development of KHCSs.
Evaluating Domestic Well Vulnerability to Contamination From Unconventional Oil and Gas Development Sites
Authors: Soriano Mario A. , Siegel Helen G. , Gutchess Kristina M. , Clark Cassandra J. , Li Yunpo , Xiong Boya , Plata Desiree L. , Deziel Nicole C. , Saiers James E.
Published: September 2020

The rapid expansion of unconventional oil and gas development (UD), made possible by horizontal drilling and hydraulic fracturing, has triggered concerns over groundwater contamination and public health risks. To improve our understanding of the risks posed by UD, we develop a physically based, spatially explicit framework for evaluating groundwater well vulnerability to aqueous phase contaminants released from surface spills and leaks at UD well pad locations. The proposed framework utilizes the concept of capture probability and incorporates decision‐relevant planning horizons and acceptable risks to support goal‐oriented modeling for groundwater protection. We illustrate the approach in northeastern Pennsylvania, where a high intensity of UD activity overlaps with local dependence on domestic groundwater wells. Using two alternative models of the bedrock aquifer and a precautionary paradigm to integrate their results, we found that most domestic wells in the domain had low vulnerability as the extent of their modeled probabilistic capture zones were smaller than distances to the nearest existing UD well pad. We also found that simulated capture probability and vulnerability were most sensitive to the model parameters of matrix hydraulic conductivity, porosity, pumping rate, and the ratio of fracture to matrix conductivity. Our analysis demonstrated the potential inadequacy of current state‐mandated setback distances that allow UD within the boundaries of delineated capture zones. The proposed framework, while limited to aqueous phase contamination, emphasizes the need to incorporate information on flow paths and transport timescales into policies aiming to protect groundwater from contamination by UD.
Reply to Comment by Wang, Che, and Ghidaoui on “Bayesian Update and Method of Distributions: Application to Leak Detection in Transmission Mains”
Authors: Alawadhi Abdulrahman , Tartakovsky Daniel M.
Published: September 2020

We thank the Comment's authors for pointing out the need for further developments of our leak detection method. We identify strategies for dealing with uncertainty in wave speed.
Single-cell genomics to understand disease pathogenesis
Authors: Nomura Seitaro
Published: September 2020

Cells are minimal functional units in biological phenomena, and therefore single-cell analysis is needed to understand the molecular behavior leading to cellular function in organisms. In addition, omics analysis technology can be used to identify essential molecular mechanisms in an unbiased manner. Recently, single-cell genomics has unveiled hidden molecular systems leading to disease pathogenesis in patients. In this review, I summarize the recent advances in single-cell genomics for the understanding of disease pathogenesis and discuss future perspectives.
Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study
Authors: St James Andrew R , Yavitt Joseph B , Zinder Stephen H , Richardson Ruth E
Published: September 2020

Ombrotrophic bogs accumulate large stores of soil carbon that eventually decompose to carbon dioxide and methane. Carbon accumulates because Sphagnum mosses slow microbial carbon decomposition processes, leading to the production of labile intermediate compounds. Acetate is a major product of Sphagnum degradation, yet rates of hydrogenotrophic methanogenesis far exceed rates of aceticlastic methanogenesis, suggesting that alternative acetate mineralization processes exist. Two possible explanations are aerobic respiration and anaerobic respiration via humic acids as electron acceptors. While these processes have been widely observed, microbial community interactions linking Sphagnum degradation and acetate mineralization remain cryptic. In this work, we use ordination and network analysis of functional genes from 110 globally distributed peatland metagenomes to identify conserved metabolic pathways in Sphagnum bogs. We then use metagenome-assembled genomes (MAGs) from McLean Bog, a Sphagnum bog in New York State, as a local case study to reconstruct pathways of Sphagnum degradation and acetate mineralization. We describe metabolically flexible Acidobacteriota MAGs that contain all genes to completely degrade Sphagnum cell wall sugars under both aerobic and anaerobic conditions. Finally, we propose a hypothetical model of acetate oxidation driven by changes in peat redox potential that explain how bogs may circumvent aceticlastic methanogenesis through aerobic and humics-driven respiration.
(+)-Clausenamide protects against drug-induced liver injury by inhibiting hepatocyte ferroptosis
Authors: Wang Min , Liu Chun-Yu , Wang Tian , Yu Hong-Min , Ouyang Shu-Hua , Wu Yan-Ping , Gong Hai-Biao , Ma Xiao-Hui , Jiao Gen-Long , Fu Lei-Lei , Wu Qiong-Shi , Kurihara Hiroshi , Li Yi-Fang , Shen Tao , He Rong-Rong
Published: September 2020

Drug-induced liver injury is the major cause of acute liver failure. However, the underlying mechanisms seem to be multifaceted and remain poorly understood, resulting in few effective therapies. Here, we report a novel mechanism that contributes to acetaminophen-induced hepatotoxicity through the induction of ferroptosis, a distinctive form of programmed cell death. We subsequently identified therapies protective against acetaminophen-induced liver damage and found that (+)-clausenamide ((+)-CLA), an active alkaloid isolated from the leaves of Clausena lansium (Lour.) Skeels, inhibited acetaminophen-induced hepatocyte ferroptosis both in vivo and in vitro. Consistently, (+)-CLA significantly alleviated acetaminophen-induced or erastin-induced hepatic pathological damages, hepatic dysfunctions and excessive production of lipid peroxidation both in cultured hepatic cell lines and mouse liver. Furthermore, treatment with (+)-CLA reduced the mRNA level of prostaglandin endoperoxide synthase 2 while it increased the protein level of glutathione peroxidase 4 in hepatocytes and mouse liver, confirming that the inhibition of ferroptosis contributes to the protective effect of (+)-CLA on drug-induced liver damage. We further revealed that (+)-CLA specifically reacted with the Cys-151 residue of Keap1, which blocked Nrf2 ubiquitylation and resulted in an increased Nrf2 stability, thereby leading to the activation of the Keap1–Nrf2 pathway to prevent drug-induced hepatocyte ferroptosis. Our studies illustrate the innovative mechanisms of acetaminophen-induced liver damage and present a novel intervention strategy to treat drug overdose by using (+)-CLA.
Immune signature driven by ADT-induced immune microenvironment remodeling in prostate cancer is correlated with recurrence-free survival and immune infiltration
Authors: Long Xingbo , Hou Huimin , Wang Xuan , Liu Shengjie , Diao Tongxiang , Lai Shicong , Hu Maolin , Zhang Shengqi , Liu Ming , Zhang Hong
Published: September 2020

Androgen deprivation therapy (ADT) is a cornerstone treatment for locally advanced or metastatic prostate cancer (PCa). However, its potential effects on the tumor immune microenvironment (TIM) of PCa patients and the underlying mechanism remain largely unclear. To explore the effects of ADT on PCa TIM, RNA sequencing was performed on six paired pre-ADT biopsy and post-ADT PCa lesions, and five paired paracancerous benign tissues from patients receiving neoadjuvant ADT with locally advanced PCa. Bioinformatics methods including ESTIMATE and ssGSEA were used to evaluate the stromal immune score and immune cell infiltration in PCa and paracancerous tissues. Weighted correlation network analysis was used to screen hub genes in the ADT-induced immune remodeling process. The results showed differences exist between PCa and paracancerous tissues in response to ADT. Compared with paracancerous tissues, the immune remodeling effect of ADT in PCa was more intense. ZFP36, JUNB, and SOCS3 served as hub genes in the ADT-induced immune remodeling process and were associated with PSA recurrent-free survival in the TCGA and our neoadjuvant ADT cohort. To investigate the joint action of the above three hub genes, an immune signature score was constructed. The results showed that immune signature score-based immune subtypes reveal the heterogeneity of the immune microenvironment of PCa and showed significant differences in patient prognosis, tumor immune infiltration, mutation burden, and landscape.
Crosstalk between cardiomyocytes and noncardiomyocytes is essential to prevent cardiomyocyte apoptosis induced by proteasome inhibition
Authors: Guo Fang , Zhang Chen-Chen , Yin Xi-Hui , Li Ting , Fang Cheng-Hu , He Xi-Biao
Published: September 2020

Heart is a multi-cellular organ made up of various cell types interacting with each other. Cardiomyocytes may benefit or suffer from crosstalk with noncardiomyocytes in response to diverse kinds of cardiac stresses. Proteasome dysfunction is a common cardiac stress which causes cardiac proteotoxicity and contributes to cardiac diseases such as heart failure and myocardial infarction. The role of crosstalk between cardiomyocytes and noncardiomyocytes in defense of cardiac proteotoxicity remains unknown. Here, we report a cardiomyocyte-specific survival upon proteasome inhibition in a heterogeneous culture consisting of cardiomyocytes and other three major cardiac cell types. Conversely, cardiomyocyte apoptosis is remarkably induced by proteasome inhibition in a homogeneous culture consisting of a majority of cardiomyocytes, demonstrating an indispensable role of noncardiomyocytes in the prevention of cardiomyocyte apoptosis resulting from proteasome inhibition. We further show that cardiomyocytes express brain natriuretic peptide (BNP) as an extracellular molecule in response to proteasome inhibition. Blockade of BNP receptor on noncardiomyocytes significantly exacerbated the cardiomyocyte apoptosis, indicating a paracrine function of cardiomyocyte-released extracellular BNP in activation of a protective feedback from noncardiomyocytes. Finally, we demonstrate that proteasome inhibition-activated transcriptional up-regulation of BNP in cardiomyocytes was associated with the dissociation of repressor element 1 silencing transcription factor (REST)/ histone deacetylase 1 (HDAC1) repressor complex from BNP gene promoter. Consistently, the induction of BNP could be further augmented by the treatment of HDAC inhibitors. We conclude that the crosstalk between cardiomyocytes and noncardiomyocytes plays a crucial role in the protection of cardiomyocytes from proteotoxicity stress, and identify cardiomyocyte-released BNP as a novel paracrine signaling molecule mediating this crosstalk. These findings provide new insights into the key regulators and cardioprotective mechanism in proteasome dysfunction-related cardiac diseases.
Nitidine chloride possesses anticancer property in lung cancer cells through activating Hippo signaling pathway
Authors: Zhang Jing , Wu Linhui , Lian Chaoqun , Lian Shuo , Bao Shimeng , Zhang Jisheng , Wang Peter , Ma Jia , Li Yuyun
Published: September 2020

Nitidine chloride (NC) has significant anti-tumor properties; however, the precise mechanism related to NC still needs further investigation. This study intends to investigate the anti-tumor functions and the feasible molecular basis of NC in NSCLC cells. Therefore, we determined the mechanism of NC-mediated anti-tumor function through various methods. Cell proliferation ability and migration and invasion were detected by CCK-8, colony formation assay and Transwell assay, respectively. Furthermore, flow cytometry was used to detect apoptosis, cell cycle and ROS. Moreover, protein expression level was measured by western blot. Our results showed that NC can inhibit the growth, motility of NSCLC cells, induce apoptosis and arrest cell cycle. Meanwhile, NC increased the level of ROS in NSCLC cells. Moreover, western blot data showed that NC suppressed the expression of Lats1, Mob1, and YAP, and enhanced the expression of p-Lats1, p-Mob1, p-YAP1 (ser127). Overall, our research reveals that NC exerts anticancer activity by activating and modulating the Hippo signaling pathway.
A reporter for noninvasively monitoring gene expression and plant transformation
Authors: He Yubing , Zhang Tao , Sun Hui , Zhan Huadong , Zhao Yunde
Published: September 2020

Reporters have been widely used to visualize gene expression, protein localization, and other cellular activities, but the commonly used reporters require special equipment, expensive chemicals, or invasive treatments. Here, we construct a new reporter RUBY that converts tyrosine to vividly red betalain, which is clearly visible to naked eyes without the need of using special equipment or chemical treatments. We show that RUBY can be used to noninvasively monitor gene expression in plants. Furthermore, we show that RUBY is an effective selection marker for transformation events in both rice and Arabidopsis. The new reporter will be especially useful for monitoring cellular activities in large crop plants such as a fruit tree under field conditions and for observing transformation and gene expression in tissue culture under sterile conditions.