bluuebunny/crossref_metadata_2025 huggingface dataset:
Stable Divisorial Gonality is in NP
Authors: Bodlaender Hans L. , van der Wegen Marieke , van der Zanden Tom C.
Published: December 2020

Divisorial gonality and stable divisorial gonality are graph parameters, which have an origin in algebraic geometry. Divisorial gonality of a connected graph G can be defined with help of a chip firing game on G. The stable divisorial gonality of G is the minimum divisorial gonality over all subdivisions of edges of G. In this paper we prove that deciding whether a given connected graph has stable divisorial gonality at most a given integer k belongs to the class NP. Combined with the result that (stable) divisorial gonality is NP-hard by Gijswijt et al., we obtain that stable divisorial gonality is NP-complete. The proof consists of a partial certificate that can be verified by solving an Integer Linear Programming instance. As a corollary, we have that the total number of subdivisions needed for minimum stable divisorial gonality of a graph with m edges is bounded by mO(mn).
COVID-19: IgG seroconversion under intensive glucocorticoid treatment in a high-risk patient with minimal change disease
Authors: Eder Michael , Strassl Robert , Kläger Johannes , Aigner Christof , Thalhammer Florian , Kikić Željko
Published: December 2020

In this case report we present a rare case of a patient with multiple risk factors for severe coronavirus disease (COVID 19) in whom intensive glucocorticoid treatment due to incipient nephrotic syndrome coincided with SARS-CoV‑2 infection. Despite this high baseline risk profile and the use of glucocorticoids the patient developed only mild disease including IgG SARS-CoV‑2 seroconversion.
Hydromorphologic Sorting of In-Stream Nitrogen Uptake Across Spatial Scales
Authors: Risse-Buhl Ute , Anlanger Christine , Noss Christian , Lorke Andreas , von Schiller Daniel , Weitere Markus
Published: December 2020

Nitrogen (N) uptake is a key process in stream ecosystems that is mediated mainly by benthic microorganisms (biofilms on different substrata) and has implications for the biogeochemical fluxes at catchment scale and beyond. Here, we focused on the drivers of assimilatory N uptake, especially the effects of hydromorphology and other environmental constraints, across three spatial scales: micro, meso and reach. In two seasons (summer and spring), we performed whole-reach15N-labelled ammonium injection experiments in two montane, gravel-bed stream reaches with riffle–pool sequences. N uptake was highest in epilithic biofilms, thallophytes and roots (min–max range 0.2–545.2 mg N m−2day−1) and lowest in leaves, wood and fine benthic organic matter (0.05–209.2 mg N m−2day−1). At the microscale, N uptake of all primary uptake compartments except wood was higher in riffles than in pools. At the mesoscale, hydromorphology determined the distribution of primary uptake compartments, with fast-flowing riffles being dominated by biologically more active compartments and pools being dominated by biologically less active compartments. Despite a lower biomass of primary uptake compartments, mesoscale N uptake was 1.7–3.0 times higher in riffles than in pools. At reach scale, N uptake ranged from 79.6 to 334.1 mg N m−2day−1. Highest reach-scale N uptake was caused by a bloom of thallopyhtes, mainly filamentous autotrophs, during stable low discharge and high light conditions. Our results reveal the important role of hydromorphologic sorting of primary uptake compartments at mesoscale as a controlling factor for reach-scale N uptake in streams.
Global tide simulations with ICON-O: testing the model performance on highly irregular meshes
Authors: Logemann Kai , Linardakis Leonidas , Korn Peter , Schrum Corinna
Published: December 2020

The global tide is simulated with the global ocean general circulation model ICON-O using a newly developed tidal module, which computes the full tidal potential. The simulated coastal M2 amplitudes, derived by a discrete Fourier transformation of the output sea level time series, are compared with the according values derived from satellite altimetry (TPXO-8 atlas). The experiments are repeated with four uniform and sixteen irregular triangular grids. The results show that the quality of the coastal tide simulation depends primarily on the coastal resolution and that the ocean interior can be resolved up to twenty times lower without causing considerable reductions in quality. The mesh transition zones between areas of different resolutions are formed by cell bisection and subsequent local spring optimisation tolerating a triangular cell’s maximum angle up to 84°. Numerical problems with these high-grade non-equiangular cells were not encountered. The results emphasise the numerical feasibility and potential efficiency of highly irregular computational meshes used by ICON-O.
Correction to: Highway to (Digital) Surveillance: When Are Clients Coerced to Share Their Data with Insurers?
Authors: Loi Michele , Hauser Christian , Christen Markus
Published: December 2020

The initial online publication contained a typesetting mistake in the author information. The original article has been corrected.
Central configurations in the spatial n-body problem for $$n=5,6$$ with equal masses
Authors: Moczurad Małgorzata , Zgliczyński Piotr
Published: December 2020

We present a computer assisted proof of the full listing of central configurations for spatialn-body problem for$$n=5$$n=5and 6, with equal masses. For each central configuration, we give a full list of its Euclidean symmetries. For all masses sufficiently close to the equal masses case, we give an exact count of configurations in the planar case for$$n=4,5,6,7$$n=4,5,6,7and in the spatial case for$$n=4,5,6$$n=4,5,6.
Pseudomonas simiae WCS417: star track of a model beneficial rhizobacterium
Authors: Pieterse Corné M. J. , Berendsen Roeland L. , de Jonge Ronnie , Stringlis Ioannis A. , Van Dijken Anja J. H. , Van Pelt Johan A. , Van Wees Saskia C. M. , Yu Ke , Zamioudis Christos , Bakker Peter A. H. M.
Published: December 2020

Background

Since the 1980s, numerous mutualisticPseudomonasspp. strains have been used in studies on the biology of plant growth-promoting rhizobacteria (PGPR) and their interactions with host plants. In 1988, a strain from thePseudomonas fluorescensgroup, WCS417, was isolated from lesions of wheat roots growing in a take-all disease-suppressive soil. In subsequent trials, WCS417 limited the build-up of take-all disease in field-grown wheat and significantly increased wheat yield. In 1991, WCS417 was featured in one of the first landmark studies on rhizobacteria-induced systemic resistance (ISR), in which it was shown to confer systemic immunity in carnation (Dianthus caryophyllus) against Fusarium wilt. The discovery that WCS417 conferred systemic immunity in the model plant speciesArabidopsis thalianain 1996 incited intensive research on the molecular mechanisms by which PGPR promote plant growth and induce broad-spectrum disease resistance in plants. Since then, the strain name appeared in over 750 studies on beneficial plant-microbe interactions.

Scope

In this review, we will highlight key discoveries in plant-microbe interactions research that have emerged from over 30 years of research featuring WCS417 as a model rhizobacterial strain. WCS417 was instrumental in improving our understanding of the microbial determinants that are involved in root colonization and the establishment of mutually beneficial interactions with the host plant. The model strain also provided novel insight into the molecular mechanisms of plant growth promotion and the onset and expression of rhizobacteria-ISR. More recently, WCS417 has been featured in studies on host immune evasion during root colonization, and chemical communication in the rhizosphere during root microbiome assembly.

Conclusions

Numerous studies on the modes of action of WCS417 have provided major conceptual advances in our understanding of how free-living mutualists colonize the rhizosphere, modulate plant immunity, and promote plant growth. The concepts may prove useful in our understanding of the molecular mechanisms involved in other binary plant-beneficial microbe interactions, and in more complex microbial community contexts, such as the root microbiome.
Levelling the playing field: The effect of including widening participation in university league tables
Authors: Hubbard Katharine , O’Neill Michael , Nattrass Stuart
Published: December 2020

Nationally and internationally, universities are ranked in university league tables (ULTs). Sustained academic criticism of the rationale and methodology of compiling ULTs has not stopped these rankings exerting considerable pressure on the decisions of university managers. The compilation of ULTs is an inherently political act, with the choice and weighting of metrics resulting in particular characteristics of individual institutions being rewarded or penalised. One aspect that is currently not considered by league tables is the diversity of the student intake, and the extent to which an institution has been successful in widening participation (WP) in higher education (HE). The need to take action is reflected in target 4.3 of the fourth United Nations Sustainable Development Goal (SDG 4), which aims to “ensure equal access for all women and men to affordable and quality technical, vocational and tertiary education, including university” by 2030. This article explores how current ULT metrics for universities in the United Kingdom (UK) relate to WP. Using publicly available data, the authors found that over 75% of UK league table metrics are negatively related to WP. This has the effect of making institutions with a diverse student body significantly more likely to be lower down in the league tables. The worst relationship with WP is for entry standards. Universities which recruit high-performing students are actively rewarded in the league tables; this fails to recognise that students with high entry grades are more likely to come from privileged backgrounds. The authors developed a ULT which includes a WP score as an explicit league table metric and found that their WP-adjusted table removed the negative relationship between WP and league table rank, resulting in a somewhat fairer comparison between universities. They conclude that ULT compilers have an ethical duty to improve their definition of a “good” university, which in the current HE environment of the UK must include WP. The authors believe this should be an urgent priority for the sector, so that universities with a commitment to widening participation can be recognised and rewarded.
Effects of Dispersant and ZDDP Additives on Fretting Wear
Authors: Kontou A. , Taylor R. I. , Spikes H. A.
Published: December 2020

This paper examines the effect of dispersant and anti-wear additives on fretting wear in lubricated bearing steel contacts. Reciprocating sliding ball-on-flat fretting tests with a stroke length of 50 μm have been carried out on steel-to-steel contacts in both dry and lubricated conditions. Wear and friction coefficient have been measured, and surface characterisation has been carried out using optical techniques to investigate fretting wear. The presence of base oil reduces fretting wear markedly compared to dry conditions, but fretting damage is still observed at low reciprocation frequencies. As frequency is increased, there is a transition from oxidative to adhesive/scuffing damage. The anti-wear additive ZDDP is effective in forming a tribofilm on the surfaces and reducing visible oxidation and wear. A succinimide dispersant also reduces the accumulation of solid debris but does not alleviate wear damage. The combination of both ZDDP anti-wear additive and dispersant in base oil appears to provide significant protection against fretting wear.
The legacy from the 50 years of acid rain research, forming present and future research and monitoring of ecosystem impact
Authors: Rosseland Bjørn Olav
Published: December 2020

Acid rain and acidification research are indeed a multidisciplinary field. This field evolved from the first attempts to mitigate acid freshwater in the 1920s, then linking acid rain to the acidification in late 1950s, to the broad project-concepts on cause and effect from the late 1960s. Three papers from 1974, 1976 and 1988 demonstrate a broad approach and comprise scientific areas from analytical chemistry, biochemistry, limnology, ecology, physiology and genetics. Few, if any, environmental problems have led to a public awareness, political decisions and binding limitations as the story of acid rain. Acid precipitation and acidification problems still exist, but at a lower pressure, and liming has been reduced accordingly. However, the biological responses in the process of recovery are slow and delayed. The need for basic science, multidisciplinary studies, long time series of high-quality data, is a legacy from the acid rain era, and must form the platform for all future environmental projects.
Mitochondrial relationships between various chamomile accessions
Authors: Ruzicka Joana , Hacek Marion , Novak Johannes
Published: December 2020

Matricaria chamomillaL. (GRIN; The Plant List 2013) is an important medicinal plant and one of the most frequently consumed tea plants. In order to assess mitochondrial genome variation of different cultivated chamomile accessions, 36 mitochondrial SNP markers were used in a HRM (high resolution melting) approach. In thirteen accessions of chamomile (n = 155), twenty mitochondrial haplotypes (genetic distances 0.028–0.693) were identified. Three of the accessions (‘Camoflora’, ‘Mat19’ and ‘Manzana’) were monomorphic. The highest genotypic variability was found for the Croatian accession ‘PG029’ with nine mitochondrial haplotypes (mitotypes) and the Argentinian ‘Argenmilla’ with seven mitotypes. However, most of the mitotypes detected in these accessions were infrequent in our sample set, thus disclosing an unusual high amount of substitutions within the mitochondrial genome of these accessions. The mitotypes with the highest frequency in the examined dataset were MT1 (n = 27), MT9 (n = 23) and MT17 (n = 20). All of the frequent mitochondrial lines are distributed not only over several accessions but also over several geographical origins. The origins often build a triplet with on average two to three concurrent lines. The most distantly related accessions were ‘Mat19’ and ‘Camoflora’ (0.539), while ‘PNOS’ and ‘Margaritar’ (0.007) showed the lowest genetic distance.
The importance of SHBG and calculated free testosterone for the diagnosis of symptomatic hypogonadism in HIV-infected men: a single-centre real-life experience
Authors: Pezzaioli Letizia Chiara , Quiros-Roldan Eugenia , Paghera Simone , Porcelli Teresa , Maffezzoni Filippo , Delbarba Andrea , Degli Antoni Melania , Cappelli Carlo , Castelli Francesco , Ferlin Alberto
Published: December 2020

Purpose

The prevalence of low testosterone and symptoms of hypogonadism in HIV-infected men is still debated. We aimed to estimate the prevalence and type of hypogonadism in HIV-infected males complaining about sexual symptoms, and to evaluate the role of calculated free testosterone (cFT) vs total testosterone (TT) for diagnosis. Furthermore, we evaluated relationship between sex hormone-binding globulin (SHBG), gonadal status and clinical and virologic parameters.

Methods

We retrospectively evaluated 169 HIV-infected men with sexual symptoms, with TT available. Among them, we selected 94 patients with TT, SHBG, cFT, and luteinizing hormone (LH) available, and classified hypogonadism into overt (low TT and/or low cFT) and compensated (high LH, normal TT and cFT). Comparison was performed by non-parametric Kruskal–Wallis test and Spearman’s correlation was calculated to verify the possible associations.

Results

Overt and compensated hypogonadism were found in 20.2% and 13.8% of patients, respectively. With reliance on TT alone, only 10.6% of patients would have met diagnosis. SHBG values were elevated in one third of patients, and higher in men with compensated hypogonadism. Significant positive correlation was found between SHBG and HIV infection duration, TT and LH.

Conclusion

Only a complete hormonal profile can properly diagnose and classify hypogonadism in HIV-infected men complaining about sexual symptoms. TT alone reliance may lead to half of diagnoses missing, while lack of gonadotropin prevents the identification of compensated hypogonadism. This largely comes from high SHBG, which seems to play a central role in the pathogenesis of hypogonadism in this population.
Keeping Up with the Trends: Analyzing the Dynamics of Online Learning and Hiring Platforms in the Software Programming Domain
Authors: Yazdanian Ramtin , West Robert , Dillenbourg Pierre
Published: December 2020

The Fourth Industrial Revolution has considerably sped up the pace of skill changes in many professional domains, with scores of new skills emerging and many old skills moving towards obsolescence. For these domains, identifying the new necessary skills in a timely manner is a difficult task, where existing methods are inadequate. Understanding the process, by which these new skills and technologies appear in and diffuse through a professional domain, could give training providers more time to identify these new skills and react. For this purpose, in the present work, we look at the dynamics between online learning platforms and online hiring platforms in the software programming profession, a rapidly evolving domain. To do so, we fuse four data sources together: Stack Overflow, an online community questions and answers (Q&A) platform; Google Trends, which provides online search trends from Google; Udemy, a platform offering skill-based Massively Open Online Courses (MOOCs) where anyone can create courses; and Stack Overflow Jobs, a job ad platform. We place these platforms along two axes: i) how much expertise it takes, on average, to create content on them, and ii) whether, in general, the decision to create content on them is made by individuals or by groups. Our results show that the topics under study have a systematic tendency to appear earlier on platforms where content creation requires (on average) less expertise and is done more individually, rather than by groups: Stack Overflow is found to be more agile than Udemy, which is itself more agile than Stack Overflow Jobs (Google Trends did not prove usable due to extreme data sparsity). However, our results also show that this tendency is not present for all new skills, and that the software programming profession as a whole is remarkably agile: there are usually only a few months between the first Stack Overflow appearance of a new topic, and its first appearance on Udemy or Stack Overflow Jobs. In addition, we find that Udemy’s agility has dramatically increased over time. Our novel methodology is able to provide valuable insights into the dynamics between online education and job ad platforms, enabling training program creators to look at said dynamics for various topics and to understand the pace of change. This allows them to maintain better awareness of the trends and to prioritize their attention, both on the right topics and on the right platforms.
Effects of dual networks on tax strategies: geography and transaction
Authors: Itoh Ryo , Li Zonghui
Published: December 2020

This study investigates how a revenue-maximizing tax strategy of local and central governments incorporates dual networks, namely, an inter-firm transaction network and an inter-country geography network. We assume a two-stage game in which governments propose discriminatory tax levels for firms, whereas each firm has an incentive to invest in a country near the foreign branch office of its transaction partner. In our model, the centrality index of the Kronecker product of the two networks describes the interplay among the location choices and tax strategies in the equilibrium. A stronger linkage within each network generally increases demand for investment and in turn raises overall tax levels to exploit the high demand. Although more central firms in the inter-firm network are likely to be levied higher taxes because of their high demand for investment, firms in the highest tax bracket differ among countries depending on their geographical location. Finally, we show that a uniform tax in which firms are not discriminated and networks do not matter is the socially optimal tax, which incorporates all inter-country externalities. We also investigate decentralized tax strategies based on the rule of non-discriminatory (uniform) taxation and show, by comparing social welfare under discriminatory and uniform tax regimes, that restricting tax discrimination improves social welfare.
Vascular Necrosis of the Upper Extremity After Self-Treatment for Peyronie's Disease
Authors: Yang David , Savage Joshua , Köhler Tobias , Helo Sevann , Trost Landon , Ziegelmann Matthew
Published: December 2020

Peyronie's disease (PD) is associated with significant psychosocial distress, including anxiety, depression, and negative effects on interpersonal relationships. We report outcomes in a patient who researched an enzymatic supplement intended for oral administration for treatment of PD and subsequently self-injected it intravascularly. The enzyme, a combination of serrapeptase and nattokinase, resulted in vascular necrosis of the upper extremity. Despite attempts to salvage the limb, he ultimately required transhumeral amputation. Although extreme, this case illustrates the potential risks of non–Food and Drug Administration–approved therapies, the significant psychosocial impact that PD can have on patients' emotional well-being, and the extent to which some may go to seek treatment.

Yang D, Savage J, Kohler T, et al. Vascular Necrosis of the Upper Extremity After Self-Treatment for Peyronie's Disease. Sex Med 2021;9:100282.
Transcriptomic Profiling of Human Pluripotent Stem Cell-Derived Retinal Pigment Epithelium over Time
Authors: Lidgerwood Grace E. , Senabouth Anne , Smith-Anttila Casey J.A. , Gnanasambandapillai Vikkitharan , Kaczorowski Dominik C. , Amann-Zalcenstein Daniela , Fletcher Erica L. , Naik Shalin H. , Hewitt Alex W. , Powell Joseph E. , Pébay Alice
Published: December 2020

Human pluripotent stem cell (hPSC)-derived progenies are immature versions of cells, presenting a potential limitation to the accurate modelling of diseases associated with maturity or age. Hence, it is important to characterise how closely cells used in culture resemble their native counterparts. In order to select appropriate time points of retinal pigment epithelium (RPE) cultures that reflect native counterparts, we characterised the transcriptomic profiles of the hPSC-derived RPE cells from 1- and 12-month cultures. We differentiated the human embryonic stem cell line H9 into RPE cells, performed single-cell RNA-sequencing of a total of 16,576 cells to assess the molecular changes of the RPE cells across these two culture time points. Our results indicate the stability of the RPE transcriptomic signature, with no evidence of an epithelial–mesenchymal transition, and with the maturing populations of the RPE observed with time in culture. Assessment of Gene Ontology pathways revealed that as the cultures age, RPE cells upregulate expression of genes involved in metal binding and antioxidant functions. This might reflect an increased ability to handle oxidative stress as cells mature. Comparison with native human RPE data confirms a maturing transcriptional profile of RPE cells in culture. These results suggest that long-term in vitro culture of RPE cells allows the modelling of specific phenotypes observed in native mature tissues. Our work highlights the transcriptional landscape of hPSC-derived RPE cells as they age in culture, which provides a reference for native and patient samples to be benchmarked against.
Novel device and technology for dynamically and hermetically sealing a rotary shaft
Authors: Fu Wei
Published: December 2020

This article proposes a novel device and technology for dynamically and hermetically sealing a rotary shaft under various rotational speeds and load capabilities for a pressurised working fluid. The author says that whilst a lot more research and development is still required, it has the potential to be applied to a range of industrial equipment. The current status of this sealing technology is set out in this article in the hope that readers will gain an understanding of what the research is aiming to achieve and be given an opportunity to respond to the author with their comments and ideas.
A Feminist Critique of Police Stops
Authors: Ross Josephine
Published: December 2020

A Feminist Critique of Police Stops examines the parallels between stop-and-frisk policing and sexual harassment. An expert whose writing, teaching and community outreach centers on the Constitution's limits on police power, Howard Law Professor Josephine Ross, argues that our constitutional rights are a mirage. In reality, we can't say no when police seek to question or search us. Building on feminist principles, Ross demonstrates why the Supreme Court got it wrong when it allowed police to stop, search, and sometimes strip-search people and call it consent. Using a wide range of sources - including her law students' experiences with police, news stories about Eric Garner, and Sandra Bland, social science and the work of James Baldwin - Ross sheds new light on policing. This book should be read by everyone interested in how Court-approved police stops sap everyone's constitutional rights and how this form of policing can be eliminated.
Probability and Consequence of Postfire Erosion for Treatability of Water in an Unfiltered Supply System
Authors: Nyman Petter , Yeates Peter , Langhans Christoph , Noske Philip J. , Peleg Nadav , Schärer Christine , Lane Patrick N. J. , Haydon Shane , Sheridan Gary J.
Published: December 2020

Forested catchments are critical to water supply in major cities. Many of these catchments face the threat of postwildfire erosion, which can contaminate reservoir water. The aim of this paper is to determine the probability and duration of disruptions to treatability due to runoff‐generated debris flows in the first year after a wildfire, before substantial vegetation recovery takes place. We combine models of reservoir hydrodynamics, postfire erosion, and stochastic rainfall to determine probability and magnitude of sediment concentration at the reservoir water offtake. Central to the paper is our technique for linking model components into a risk framework that gives probabilities to the number of days that the turbidity threshold for treatment is exceeded. The model is applied to the Upper Yarra reservoir, which is the linchpin of the water supply system for Melbourne in SE Australia. However, the framework is applicable to other unfiltered water supply systems where suspended sediment is a risk to treatability. Results show that postwildfire erosion poses a substantial threat, with a relatively high probability (annual exceedance probability = 0.1–0.3) of water being untreatable for >1 year following a high‐severity wildfire. Important factors that influence the risk include postwildfire runoff potential, reservoir temperature, and the amount of clay‐sized grains in eroding headwaters. Assumptions about spatial‐temporal rainfall attributes, reservoir hydrodynamics, and the catchment erosion potential are all important sources of error in our estimate of risk. Our approach to risk quantification will help support planning, risk management, and strategic investment to mitigate impacts.
Contribution of the Northeast Cold Vortex Index and Multiscale Synergistic Indices to Extreme Precipitation Over Northeast China
Authors: Wu Xianghua , Meng Fangxiu , Liu Peng , Zhou Jieqin , Liu Duanyang , Xie Kang , Zhu Qihao , Hu Jingbiao , Sun Haiyan , Xing Fengjuan
Published: December 2020

The northeast cold vortex (NECV) is one of the major synoptic systems affecting Northeast China. The activity of NECV is an important reason for severe convective storms. However, research on extreme precipitation over Northeast China and their associations with the northeast cold vortex index (NECVI) is limited. Based on nonstationary generalized extreme value models, we analyze and quantify the contribution of the NECVI and the multiscale synergistic indices. Then, we verify the necessity of the NECVI by the likelihood ratio test and the blank control experiment, and further verify the impact of the NECVI on the extreme precipitation over Northeast China in combination with the climate index atmospheric circulation analysis. Results suggest that the models established with East Asian summer monsoon index, Southern Oscillation Index, and NINO3.4 index as covariates the most common. The NECVI and the synergies also make significant contribution and have passed the likelihood ratio test at 80% confidence. Especially in late summer, accounting for 18.69% of the 10 selected best models and 29.41% of the nine selected best nonstationary models. Based on the blank experiments, the models with the NECVI have a maximum reduction of 4.72% than those without the NECVI in the Akaike information criterion values in late summer. In early summer and late summer, the center of the high values of the water vapor anomaly is mainly located in southwestern in the strong NECVI years. These findings help to understand the genetic mechanism of extreme precipitation over Northeast China and provide reference for risk management.
Synergies Among Environmental Science Research and Monitoring Networks: A Research Agenda
Authors: Jones J. A. , Groffman P. M. , Blair J. , Davis F. W. , Dugan H. , Euskirchen E. E. , Frey S. D. , Harms T. K. , Hinckley E. , Kosmala M. , Loberg S. , Malone S. , Novick K. , Record S. , Rocha A. V. , Ruddell B. L. , Stanley E. H. , Sturtevant C. , Thorpe A. , White T. , Wieder W. R. , Zhai L. , Zhu K.
Published: December 2020

Many research and monitoring networks in recent decades have provided publicly available data documenting environmental and ecological change, but little is known about the status of efforts to synthesize this information across networks. We convened a working group to assess ongoing and potential cross‐network synthesis research and outline opportunities and challenges for the future, focusing on the US‐based research network (the US Long‐Term Ecological Research network, LTER) and monitoring network (the National Ecological Observatory Network, NEON). LTER‐NEON cross‐network research synergies arise from the potentials for LTER measurements, experiments, models, and observational studies to provide context and mechanisms for interpreting NEON data, and for NEON measurements to provide standardization and broad scale coverage that complement LTER studies. Initial cross‐network syntheses at co‐located sites in the LTER and NEON networks are addressing six broad topics: how long‐term vegetation change influences C fluxes; how detailed remotely sensed data reveal vegetation structure and function; aquatic‐terrestrial connections of nutrient cycling; ecosystem response to soil biogeochemistry and microbial processes; population and species responses to environmental change; and disturbance, stability and resilience. This initial study offers exciting potentials for expanded cross‐network syntheses involving multiple long‐term ecosystem processes at regional or continental scales. These potential syntheses could provide a pathway for the broader scientific community, beyond LTER and NEON, to engage in cross‐network science. These examples also apply to many other research and monitoring networks in the US and globally, and can guide scientists and research administrators in promoting broad‐scale research that supports resource management and environmental policy.
Impact of Quasi‐Idealized Future Land Cover Scenarios at High Latitudes in Complex Terrain
Authors: Mooney P. A. , Lee H. , Sobolowski S.
Published: December 2020

Afforestation is gaining popularity as a climate mitigation policy in many countries, including high latitude regions such as Norway. However, the impacts of afforestation on local‐to‐regional climate is poorly understood. This study uses the Weather Research and Forecasting model to investigate the biogeophysical impacts of different forestry scenarios on the local‐to‐regional climate of Norway. The forestry scenarios considered are the conversion of open spaces to either evergreen forest by active afforestation or to mixed forest by natural succession. Results show both forestry scenarios lead to additional warming of surface temperatures in winter and spring (between 1.0°C and 1.5°C) and cooling in summer (between −1.6°C and −1.3°C). A temperature decomposition analysis shows that the warming in winter and spring is driven by surface albedo changes while summer cooling is driven by changes in sensible heat fluxes for afforestation and surface albedo for natural succession. Maximum 2 m air temperature increases considerably in spring in both forestry scenarios (∼0.8°C to 1.0°C). Analysis of precipitation, multiple climate indices and extremes, reveal little or no response to the different forestry scenarios. The largest societally relevant response to the forestry scenarios is the partial mitigation of the reduction in snow days expected from global warming by 10–20 days. This suggests that implementing current afforestation policies for climate mitigation in Norway may adversely exacerbate some effects of global warming locally while mitigating others. As such, the impacts of afforestation on the local‐to‐regional climate at high latitudes are complex and cannot support or dismiss afforestation as a climate mitigation policy.
Dynamics of Fungal and Bacterial Biomass Carbon in Natural Ecosystems: Site‐Level Applications of the CLM‐Microbe Model
Authors: He Liyuan , Lipson David A. , Mazza Rodrigues Jorge L. , Mayes Melanie , Björk Robert G. , Glaser Bruno , Thornton Peter , Xu Xiaofeng
Published: December 2020

Explicitly representing microbial processes has been recognized as a key improvement to Earth system models for the realistic projections of soil carbon (C) and climate dynamics. The CLM‐Microbe model builds upon the CLM4.5 and explicitly represents two major soil microbial groups, fungi and bacteria. Based on the compiled time‐series data of fungal (FBC) and bacterial (BBC) biomass C from nine biomes, we parameterized and validated the CLM‐Microbe model, and further conducted sensitivity and uncertainty analysis for simulating C cycling. The model performance was evaluated with mean absolute error (MAE), root mean square error (RMSE), and coefficient of determination (R2) for relative change in FBC and BBC. The CLM‐Microbe model is able to reasonably capture the seasonal dynamics of FBC and BBC across biomes, particularly for tropical/subtropical forest, temperate broadleaf forest, and grassland, with MAE <0.49 for FBC and <0.36 for BBC and RMSE <0.52 FBC and <0.39 for BBC, while R2 values are relatively smaller in some biomes (e.g., shrub) due to small sample sizes. We found good consistencies between simulated and observed FBC (R2 = 0.70, P < 0.001) and BBC (R2 = 0.26, P < 0.05) on average across biomes, but the model is not able to fully capture the large variation in observed FBC and BBC. Sensitivity analysis shows that the most critical parameters are turnover rate and carbon‐to‐nitrogen ratio of fungi and bacteria and microbial assimilation efficiency. This study confirms that the explicit representation of soil microbial mechanisms enhances model performance in simulating C variables such as heterotrophic respiration and soil organic C density. The further application of the CLM‐Microbe model would deepen our understanding of microbial contributions to global C cycle.
CRISPR/Cas9-engineered Gad1 elimination in rats leads to complex behavioral changes: implications for schizophrenia
Authors: Fujihara Kazuyuki , Yamada Kazuo , Ichitani Yukio , Kakizaki Toshikazu , Jiang Weiru , Miyata Shigeo , Suto Takashi , Kato Daiki , Saito Shigeru , Watanabe Masahiko , Kajita Yuki , Ohshiro Tomokazu , Mushiake Hajime , Miyasaka Yoshiki , Mashimo Tomoji , Yasuda Hiroki , Yanagawa Yuchio
Published: December 2020

GABAergic dysfunctions have been implicated in the pathogenesis of schizophrenia, especially the associated cognitive impairments. The GABA synthetic enzyme glutamate decarboxylase 67-kDa isoform (GAD67) encoded by the GAD1 gene is downregulated in the brains of patients with schizophrenia. Furthermore, a patient with schizophrenia harboring a homozygous mutation of GAD1 has recently been discovered. However, it remains unclear whether loss of function of GAD1 leads to the symptoms observed in schizophrenia, including cognitive impairment. One of the obstacles faced in experimental studies to address this issue is the perinatal lethality of Gad1 knockout (KO) mice, which precluded characterization at the adult stage. In the present study, we successfully generated Gad1 KO rats using CRISPR/Cas9 genome editing technology. Surprisingly, 33% of Gad1 KO rats survived to adulthood and could be subjected to further characterization. The GABA concentration in the Gad1 KO cerebrum was reduced to ~52% of the level in wild-type rats. Gad1 KO rats exhibited impairments in both spatial reference and working memory without affecting adult neurogenesis in the hippocampus. In addition, Gad1 KO rats showed a wide range of behavioral alterations, such as enhanced sensitivity to an NMDA receptor antagonist, hypoactivity in a novel environment, and decreased preference for social novelty. Taken together, the results suggest that Gad1 KO rats could provide a novel model covering not only cognitive deficits but also other aspects of the disorder. Furthermore, the present study teaches an important lesson: differences between species should be considered when developing animal models of human diseases.
Beyond chemoradiotherapy: improving treatment outcomes for patients with stage III unresectable non-small-cell lung cancer through immuno-oncology and durvalumab (Imfinzi®▼, AstraZeneca UK Limited)
Authors:   on behalf of AstraZeneca UK Limited, Patel Priyanka , Alrifai Doraid , McDonald Fiona , Forster Martin
Published: December 2020

The treatment paradigm of non-small-cell lung cancer (NSCLC) has rapidly changed in recent years following the introduction of immune-checkpoint inhibition (ICI). Pre-clinically, both chemotherapy and radiotherapy modulate the tumour microenvironment, providing the rationale for clinical trials evaluating their role in combination with immunotherapy. Standard-of-care treatment for patients with unresectable stage III disease is concurrent chemoradiotherapy (cCRT); however, only recently, the combination with ICI has been explored. The Phase 3 PACIFIC study randomised 713 patients with confirmed locally advanced, unresectable, stage III NSCLC, whose disease has not progressed following cCRT, to either the anti-programmed death-ligand 1 (PD-L1) agent durvalumab (Imfinzi®▼, AstraZeneca UK Limited) or placebo. Patients with a PD-L1 status ≥1% treated with durvalumab had a significantly longer median progression-free survival compared with placebo (17.2 vs. 5.6 months, respectively; HR: 0.51; 95% CI: 0.41–0.63), prolonged median overall survival (OS) (NR vs. 28.7 months, respectively; HR: 0.68; 99.73% CI: 0.47–0.997;P = 0.0025) and long-term clinical benefit (3-year OS HR: 0.69; 95% CI: 0.55–0.86). Grade 3 or 4 toxicity was marginally greater in the durvalumab cohort versus placebo (30.5% vs. 26.1%). Based on these results, durvalumab has been licensed in this setting, and further clinical trials are exploring the use of ICI in unresectable stage III NSCLC.
Dynamic symbioses reveal pathways to coral survival through prolonged heatwaves
Authors: Claar Danielle C. , Starko Samuel , Tietjen Kristina L. , Epstein Hannah E. , Cunning Ross , Cobb Kim M. , Baker Andrew C. , Gates Ruth D. , Baum Julia K.
Published: December 2020

Prospects for coral persistence through increasingly frequent and extended heatwaves seem bleak. Coral recovery from bleaching is only known to occur after temperatures return to normal, and mitigation of local stressors does not appear to augment coral survival. Capitalizing on a natural experiment in the equatorial Pacific, we track individual coral colonies at sites spanning a gradient of local anthropogenic disturbance through a tropical heatwave of unprecedented duration. Unexpectedly, some corals survived the event by recovering from bleaching while still at elevated temperatures. These corals initially had heat-sensitive algal symbiont communities, endured bleaching, and then recovered through proliferation of heat-tolerant symbionts. This pathway to survival only occurred in the absence of strong local stressors. In contrast, corals in highly disturbed areas were already dominated by heat-tolerant symbionts, and despite initially resisting bleaching, these corals had no survival advantage in one species and 3.3 times lower survival in the other. These unanticipated connections between disturbance, coral symbioses and heat stress resilience reveal multiple pathways to coral survival through future prolonged heatwaves.
A machine learning toolkit for genetic engineering attribution to facilitate biosecurity
Authors: Alley Ethan C. , Turpin Miles , Liu Andrew Bo , Kulp-McDowall Taylor , Swett Jacob , Edison Rey , Von Stetina Stephen E. , Church George M. , Esvelt Kevin M.
Published: December 2020

The promise of biotechnology is tempered by its potential for accidental or deliberate misuse. Reliably identifying telltale signatures characteristic to different genetic designers, termed ‘genetic engineering attribution’, would deter misuse, yet is still considered unsolved. Here, we show that recurrent neural networks trained on DNA motifs and basic phenotype data can reach 70% attribution accuracy in distinguishing between over 1,300 labs. To make these models usable in practice, we introduce a framework for weighing predictions against other investigative evidence using calibration, and bring our model to within 1.6% of perfect calibration. Additionally, we demonstrate that simple models can accurately predict both the nation-state-of-origin and ancestor labs, forming the foundation of an integrated attribution toolkit which should promote responsible innovation and international security alike.
Donkey genomes provide new insights into domestication and selection for coat color
Authors: Wang Changfa , Li Haijing , Guo Yu , Huang Jinming , Sun Yan , Min Jiumeng , Wang Jinpeng , Fang Xiaodong , Zhao Zicheng , Wang Shuai , Zhang Yanlin , Liu Qingfeng , Jiang Qiang , Wang Xiuge , Guo Yijun , Yang Chunhong , Wang Yinchao , Tian Fang , Zhuang Guilong , Fan Yanna , Gao Qican , Li Yuhua , Ju Zhihua , Li Jianbin , Li Rongling , Hou Minghai , Yang Guiwen , Liu Guiqin , Liu Wenqiang , Guo Jiao , Pan Shanshan , Fan Guangyi , Zhang Wei , Zhang Ruitao , Yu Jie , Zhang Xinhao , Yin Qi , Ji Chuanliang , Jin Yuanchun , Yue Guidong , Liu Mei , Xu Jiake , Liu Shimin , Jordana Jordi , Noce Antonia , Amills Marcel , Wu Dong Dong , Li Shuaicheng , Zhou Xiangshan , Zhong Jifeng
Published: December 2020

Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition.
An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonas
Authors: Neupert Juliane , Gallaher Sean D. , Lu Yinghong , Strenkert Daniela , Segal Na’ama , Barahimipour Rouhollah , Fitz-Gibbon Sorel T. , Schroda Michael , Merchant Sabeeha S. , Bock Ralph
Published: December 2020

Silencing of exogenous DNA can make transgene expression very inefficient. Genetic screens in the model alga Chlamydomonas have demonstrated that transgene silencing can be overcome by mutations in unknown gene(s), thus producing algal strains that stably express foreign genes to high levels. Here, we show that the silencing mechanism specifically acts on transgenic DNA. Once a permissive chromatin structure has assembled, transgene expression can persist even in the absence of mutations disrupting the silencing pathway. We have identified the gene conferring the silencing and show it to encode a sirtuin-type histone deacetylase. Loss of gene function does not appreciably affect endogenous gene expression. Our data suggest that transgenic DNA is recognized and then quickly inactivated by the assembly of a repressive chromatin structure composed of deacetylated histones. We propose that this mechanism may have evolved to provide protection from potentially harmful types of environmental DNA.
Reverse C-glycosidase reaction provides C-nucleotide building blocks of xenobiotic nucleic acids
Authors: Pfeiffer Martin , Nidetzky Bernd
Published: December 2020

C-Analogues of the canonical N-nucleosides have considerable importance in medicinal chemistry and are promising building blocks of xenobiotic nucleic acids (XNA) in synthetic biology. Although well established for synthesis of N-nucleosides, biocatalytic methods are lacking in C-nucleoside synthetic chemistry. Here, we identify pseudouridine monophosphate C-glycosidase for selective 5-β-C-glycosylation of uracil and derivatives thereof from pentose 5-phosphate (d-ribose, 2-deoxy-d-ribose, d-arabinose, d-xylose) substrates. Substrate requirements of the enzymatic reaction are consistent with a Mannich-like addition between the pyrimidine nucleobase and the iminium intermediate of enzyme (Lys166) and open-chain pentose 5-phosphate. β-Elimination of the lysine and stereoselective ring closure give the product. We demonstrate phosphorylation-glycosylation cascade reactions for efficient, one-pot synthesis of C-nucleoside phosphates (yield: 33 – 94%) from unprotected sugar and nucleobase. We show incorporation of the enzymatically synthesized C-nucleotide triphosphates into nucleic acids by RNA polymerase. Collectively, these findings implement biocatalytic methodology for C-nucleotide synthesis which can facilitate XNA engineering for synthetic biology applications.
SAMMY-seq reveals early alteration of heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford Progeria Syndrome
Authors: Sebestyén Endre , Marullo Fabrizia , Lucini Federica , Petrini Cristiano , Bianchi Andrea , Valsoni Sara , Olivieri Ilaria , Antonelli Laura , Gregoretti Francesco , Oliva Gennaro , Ferrari Francesco , Lanzuolo Chiara
Published: December 2020

Hutchinson-Gilford progeria syndrome is a genetic disease caused by an aberrant form of Lamin A resulting in chromatin structure disruption, in particular by interfering with lamina associated domains. Early molecular alterations involved in chromatin remodeling have not been identified thus far. Here, we present SAMMY-seq, a high-throughput sequencing-based method for genome-wide characterization of heterochromatin dynamics. Using SAMMY-seq, we detect early stage alterations of heterochromatin structure in progeria primary fibroblasts. These structural changes do not disrupt the distribution of H3K9me3 in early passage cells, thus suggesting that chromatin rearrangements precede H3K9me3 alterations described at later passages. On the other hand, we observe an interplay between changes in chromatin accessibility and Polycomb regulation, with site-specific H3K27me3 variations and transcriptional dysregulation of bivalent genes. We conclude that the correct assembly of lamina associated domains is functionally connected to the Polycomb repression and rapidly lost in early molecular events of progeria pathogenesis.