bluuebunny/crossref_metadata_2025 huggingface dataset:
The clustering of X-ray AGN at 0.5 < z < 4.5: host galaxies dictate dark matter halo mass
Authors: Krishnan Charutha , Almaini Omar , Hatch Nina A , Wilkinson Aaron , Maltby David T , Conselice Christopher J , Kocevski Dale , Suh Hyewon , Wild Vivienne
Published: March 2020

We present evidence that active galactic nuclei (AGN) do not reside in ‘special’ environments, but instead show large-scale clustering determined by the properties of their host galaxies. Our study is based on an angular cross-correlation analysis applied to X-ray selected AGN in the COSMOS and UDS fields, spanning redshifts from $z$ ∼ 4.5 to $z$ ∼ 0.5. Consistent with previous studies, we find that AGN at all epochs are on average hosted by galaxies in dark matter haloes of 1012–1013 M⊙, intermediate between star-forming and passive galaxies. We find, however, that the same clustering signal can be produced by inactive (i.e. non-AGN) galaxies closely matched to the AGN in spectral class, stellar mass, and redshift. We therefore argue that the inferred bias for AGN lies in between the star-forming and passive galaxy populations because AGN host galaxies are comprised of a mixture of the two populations. Although AGN hosted by higher mass galaxies are more clustered than lower mass galaxies, this stellar mass dependence disappears when passive host galaxies are removed. The strength of clustering is also largely independent of AGN X-ray luminosity. We conclude that the most important property that determines the clustering in a given AGN population is the fraction of passive host galaxies. We also infer that AGN luminosity is likely not driven by environmental triggering, and further hypothesize that AGN may be a stochastic phenomenon without a strong dependence on environment.
On the origin of magnetic driven winds and the structure of the galactic dynamo in isolated galaxies
Authors: Steinwandel Ulrich P , Dolag Klaus , Lesch Harald , Moster Benjamin P , Burkert Andreas , Prieto Almudena
Published: March 2020

We investigate the build-up of the galactic dynamo and subsequently the origin of a magnetic driven outflow. We use a set-up of an isolated disc galaxy with a realistic circum-galactic medium (CGM). We find good agreement of the galactic dynamo with theoretical and observational predictions from the radial and toroidal components of the magnetic field as function of radius and disc scale height. We find several field reversals indicating dipole structure at early times and quadrupole structure at late times. Together with the magnetic pitch angle and the dynamo control parameters Rα, Rω, and D, we present strong evidence for an α2–Ω dynamo. The formation of a bar in the centre leads to further amplification of the magnetic field via adiabatic compression which subsequently drives an outflow. Due to the Parker instability the magnetic field lines rise to the edge of the disc, break out, and expand freely in the CGM driven by the magnetic pressure. Finally, we investigate the correlation between magnetic field and star formation rate. Globally, we find that the magnetic field is increasing as function of the star formation rate surface density with a slope between 0.3 and 0.45 in good agreement with predictions from theory and observations. Locally, we find that the magnetic field can decrease while star formation increases. We find that this effect is correlated with the diffusion of magnetic field from the spiral arms to the interarm regions which we explicitly include by solving the induction equation and accounting for non-linear terms.
Hot phase generation by supernovae in ISM simulations: resolution, chemistry, and thermal conduction
Authors: Steinwandel Ulrich P , Moster Benjamin P , Naab Thorsten , Hu Chia-Yu , Walch Stefanie
Published: March 2020

Supernovae (SNe) generate hot gas in the interstellar medium (ISM), help setting the ISM structure, and support the driving of outflows. It is important to resolve the hot gas generation for galaxy formation simulations at solar mass and sub-parsec resolution that realize individual SN explosions with ambient densities varying by several orders of magnitude in a realistic multiphase ISM. We test resolution requirements by simulating SN blast waves at three metallicities (Z = 0.01, 0.1, and 1 Z⊙), six densities and their respective equilibrium chemical compositions (n = 0.001–100 cm−3), and four mass resolutions (0.1–100 M⊙), in three dimensions. We include non-equilibrium cooling and chemistry, a homogeneous interstellar radiation field, and shielding with a modern pressure–energy smoothed particle hydrodynamics method including isotropic thermal conduction and a meshless-finite-mass solver. We find stronger resolution requirements for chemistry and hot phase generation than for momentum generation. While at 10 M⊙ the radial momenta at the end of the Sedov phase start converging, the hot phase generation and chemistry require higher resolutions to represent the neutral-to-ionized hydrogen fraction at the end of the Sedov phase correctly. Thermal conduction typically reduces the hot phase by 0.2 dex and has little impact on the chemical composition. In general, our 1 and 0.1 M⊙ results agree well with previous numerical and analytic estimates. We conclude that for the thermal energy injection SN model presented here resolutions higher than 10 M⊙ are required to model the chemistry, momentum, and hot phase generation in the multiphase ISM.
A major optical and X-ray outburst from the Magellanic Bridge source RX J0209.6–7427
Authors: Coe M J , Monageng I M , Bartlett E S , Buckley D A H , Udalski A
Published: March 2020

RX J0209.6–7427 is an X-ray source in the Magellanic Bridge that was first detected in 1993, but not seen again till 2019. It has been identified as a member of the Be/X-ray binary class, a category of objects that are well established as bright, often-unpredictable transients. Such systems are rarely known in the Bridge, possibly because they lie outside the area most commonly studied by X-ray telescopes. Whatever be the reason for the sparse number of such systems in the Bridge, they can provide useful tools for trying to understand the result of the tidal dynamics of the two Magellanic Clouds. In this paper, the nature of the object is explored with the help of new data obtained during the latest outburst. In particular, the first optical spectrum of the counterpart is presented to help classify the star, plus measurements of the Balmer emission lines over several years are used to investigate changes in the size and structure of the circumstellar disc.
STRIDES: a 3.9 per cent measurement of the Hubble constant from the strong lens system DES J0408−5354
Authors: Shajib A J , Birrer S , Treu T , Agnello A , Buckley-Geer E J , Chan J H H , Christensen L , Lemon C , Lin H , Millon M , Poh J , Rusu C E , Sluse D , Spiniello C , Chen G C-F , Collett T , Courbin F , Fassnacht C D , Frieman J , Galan A , Gilman D , More A , Anguita T , Auger M W , Bonvin V , McMahon R , Meylan G , Wong K C , Abbott T M C , Annis J , Avila S , Bechtol K , Brooks D , Brout D , Burke D L , Carnero Rosell A , Carrasco Kind M , Carretero J , Castander F J , Costanzi M , da Costa L N , De Vicente J , Desai S , Dietrich J P , Doel P , Drlica-Wagner A , Evrard A E , Finley D A , Flaugher B , Fosalba P , García-Bellido J , Gerdes D W , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hollowood D L , Honscheid K , Huterer D , James D J , Jeltema T , Krause E , Kuropatkin N , Li T S , Lima M , MacCrann N , Maia M A G , Marshall J L , Melchior P , Miquel R , Ogando R L C , Palmese A , Paz-Chinchón F , Plazas A A , Romer A K , Roodman A , Sako M , Sanchez E , Santiago B , Scarpine V , Schubnell M , Scolnic D , Serrano S , Sevilla-Noarbe I , Smith M , Soares-Santos M , Suchyta E , Tarle G , Thomas D , Walker A R , Zhang Y
Published: March 2020

We present a blind time-delay cosmographic analysis for the lens system DES J0408−5354. This system is extraordinary for the presence of two sets of multiple images at different redshifts, which provide the opportunity to obtain more information at the cost of increased modelling complexity with respect to previously analysed systems. We perform detailed modelling of the mass distribution for this lens system using three band Hubble Space Telescope imaging. We combine the measured time delays, line-of-sight central velocity dispersion of the deflector, and statistically constrained external convergence with our lens models to estimate two cosmological distances. We measure the ‘effective’ time-delay distance corresponding to the redshifts of the deflector and the lensed quasar $D_{\Delta t}^{\rm eff}=$$3382_{-115}^{+146}$ Mpc and the angular diameter distance to the deflector Dd = $1711_{-280}^{+376}$ Mpc, with covariance between the two distances. From these constraints on the cosmological distances, we infer the Hubble constant H0= $74.2_{-3.0}^{+2.7}$ km s−1 Mpc−1 assuming a flat ΛCDM cosmology and a uniform prior for Ωm as $\Omega _{\rm m} \sim \mathcal {U}(0.05, 0.5)$. This measurement gives the most precise constraint on H0 to date from a single lens. Our measurement is consistent with that obtained from the previous sample of six lenses analysed by the H0 Lenses in COSMOGRAIL’s Wellspring (H0LiCOW) collaboration. It is also consistent with measurements of H0 based on the local distance ladder, reinforcing the tension with the inference from early Universe probes, for example, with 2.2σ discrepancy from the cosmic microwave background measurement.
Vasculopathy plays an important role during the development and relapse of encapsulating peritoneal sclerosis with conventional peritoneal dialysis solutions
Authors: Tawada Mitsuhiro , Ito Yasuhiko , Banshodani Masataka , Yamashita Masahiro , Shintaku Sadanori , Sun Ting , Suzuki Yasuhiro , Kinashi Hiroshi , Kubo Yoko , Ando Masahiko , Yamaguchi Makoto , Katsuno Takayuki , Mizuno Masashi , Kawanishi Hideki
Published: March 2020

Background

Encapsulating peritoneal sclerosis (EPS) is an uncommon but life-threatening complication of peritoneal dialysis (PD) therapy. The causative factors of EPS remain unclear. Pathological studies of the peritoneum affected by EPS and relationships with clinical factors including PD solutions remain lacking. The objective of this study was to examine peritoneal samples from EPS patients and to identify the associations of peritoneal pathology with different clinical factors.

Methods

Peritoneal specimens were obtained at the time of surgical enterolysis in Tsuchiya General Hospital from 1993 to 2016. A total of 223 PD patients were enrolled and analyzed. Tissues were fixed with formalin and processed with hematoxylin and eosin and Masson’s trichrome staining, as well as immunohistochemical staining for CD31 and CD68.

Results

Evaluations could be made in 174 patients who received surgical enterolysis. Conventional or pH-neutral low-glucose degradation product PD solutions were utilized during PD treatment. The conventional PD solution group showed less angiogenesis (P = 0.013) but more severe vasculopathy, in the form of a lower ratio of luminal diameter to vessel diameter (L/V ratio) (P < 0.001) in association with longer PD treatment. Multivariate Cox proportional hazard models revealed that L/V ratio (per 0.1 increase, hazard ratio = 0.88, 95% confidence interval 0.77–0.99, P = 0.047) was significantly associated with a lower incidence of EPS relapse. In contrast, most of the cases in the pH-neutral solution group showed milder vasculopathy.

Conclusions

The pathology of EPS differed between conventional and pH-neutral solution groups. Vasculopathy was related to the development and relapse of EPS in the conventional solution group.
An accurate single descriptor for ion–π interactions
Authors: Liu Zhangyun , Chen Zheng , Xi Jinyang , Xu Xin
Published: March 2020

Non-covalent interactions between ions and π systems play an important role in molecular recognition, catalysis and biology. To guide the screen and design for artificial hosts, catalysts and drug delivery, understanding the physical nature of ion–π complexes via descriptors is indispensable. However, even with multiple descriptors that contain the leading term of electrostatic and polarized interactions, the quantitative description for the binding energies (BEs) of ion–π complexes is still lacking because of the intrinsic shortcomings of the commonly used descriptors. Here, we have shown that the impartment of orbital details into the electrostatic energy (coined as OEE) makes an excellent single descriptor for BEs of not only spherical, but also multiply-shaped, ion–π systems, highlighting the importance of an accurate description of the electrostatic interactions. Our results have further demonstrated that OEEs from a low-level method could be calibrated to BEs from a high-level method, offering a powerful practical strategy for an accurate prediction of a set of ion–π interactions.
Nutrition and behavioral health disorders: depression and anxiety
Authors: Kris-Etherton Penny M , Petersen Kristina S , Hibbeln Joseph R , Hurley Daniel , Kolick Valerie , Peoples Sevetra , Rodriguez Nancy , Woodward-Lopez Gail
Published: March 2020

Suboptimal nutrition has been implicated in the underlying pathology of behavioral health disorders and may impede treatment and recovery. Thus, optimizing nutritional status should be a treatment for these disorders and is likely important for prevention. The purpose of this narrative review is to describe the global burden and features of depression and anxiety, and summarize recent evidence regarding the role of diet and nutrition in the prevention and management of depression and anxiety. Current evidence suggests that healthy eating patterns that meet food-based dietary recommendations and nutrient requirements may assist in the prevention and treatment of depression and anxiety. Randomized controlled trials are needed to better understand how diet and nutrition-related biological mechanisms affect behavioral health disorders, to assist with the development of effective evidence-based nutrition interventions, to reduce the impact of these disorders, and promote well-being for affected individuals.
The impact of polysomnograms and family-centred decision making in children with medical complexity
Authors: Jewitt Natalie , Orkin Julia , Cohen Eyal , Narang Indra , Al-Saleh Suhail , Amin Reshma
Published: March 2020

Objectives

To determine whether a change in clinical management (e.g., new tracheostomy or adenotonsillectomy) occurred following a polysomnogram (PSG) in children with medical complexity (CMC) and to explore whether families’ goals of care (regarding results and treatment implications) were discussed prior to the completion of a PSG.

Methods

All CMC enrolled in a complex care program at the Hospital for Sick Children, Canada, who underwent a baseline PSG from 2009 to 2015 were identified. Exclusion criteria included (1) PSGs for ventilation titration and (2) PSGs outside the study time frame. Health records were retrospectively reviewed to determine demographics, medical histories, families’ wishes, PSG results, and their impact on clinical care. Descriptive statistics were used to summarize results.

Results

Of 145 patients identified, 96 patients met inclusion criteria. Fifty (52%) were male. Median age was 3 years. Forty-eight (50%) were diagnosed with clinically significant (i.e., moderate to severe obstructive sleep apnea, central sleep apnea, and/or hypoventilation) sleep-related breathing disorders. Of those diagnosed, 9 (19%) had surgery, 25 (52%) underwent respiratory technology initiation, and 3 (6%) underwent both. In the remaining 11 (23%) patients, treatment was either considered too risky or did not align with the families’ wishes. Only 3 of 96 patients had clear documentation of their families’ wishes prior to PSG completion.

Conclusion

Recognizing the burden of medical tests for both the child and the health care system, a process of shared-decision making that includes clarifying a family’s wishes may be prudent prior to conducting a PSG.
Foraging optimally in social neuroscience: computations and methodological considerations
Authors: Gabay Anthony S , Apps Matthew A J
Published: March 2020

Research in social neuroscience has increasingly begun to use the tools of computational neuroscience to better understand behaviour. Such approaches have proven fruitful for probing underlying neural mechanisms. However, little attention has been paid to how the structure of experimental tasks relates to real-world decisions, and the problems that brains have evolved to solve. To go significantly beyond current understanding, we must begin to use paradigms and mathematical models from behavioural ecology, which offer insights into the decisions animals must make successfully in order to survive. One highly influential theory—marginal value theorem (MVT)—precisely characterises and provides an optimal solution to a vital foraging decision that most species must make: the patch-leaving problem. Animals must decide when to leave collecting rewards in a current patch (location) and travel somewhere else. We propose that many questions posed in social neuroscience can be approached as patch-leaving problems. A richer understanding of the neural mechanisms underlying social behaviour will be obtained by using MVT. In this ‘tools of the trade’ article, we outline the patch-leaving problem, the computations of MVT and discuss the application to social neuroscience. Furthermore, we consider the practical challenges and offer solutions for designing paradigms probing patch leaving, both behaviourally and when using neuroimaging techniques.
Neural correlates of negative expectancy and impaired social feedback processing in social anxiety
Authors: Gu Ruolei , Ao Xiang , Mo Licheng , Zhang Dandan
Published: March 2020

Social anxiety has been associated with abnormalities in cognitive processing in the literature, manifesting as various cognitive biases. To what extent these biases interrupt social interactions remains largely unclear. This study used the Social Judgment Paradigm that could separate the expectation and experience stages of social feedback processing. Event-related potentials (ERPs) in these two stages were recorded to detect the effect of social anxiety that might not be reflected by behavioral data. Participants were divided into two groups according to their social anxiety level. Participants in the high social anxiety (HSA) group were more likely to predict that they would be socially rejected by peers than did their low social anxiety (LSA) counterparts (i.e. the control group). Compared to the ERP data of the LSA group, the HSA group showed: (a) a larger P1 component to social cues (peer faces) prior to social feedback presentation, possibly indicating an attention bias; (b) a difference in feedback-related negativity amplitude between unexpected social acceptance and unexpected social rejection, possibly indicating an expectancy bias; and (c) a diminished sensitivity of the P3 amplitude to social feedback valence (be accepted/be rejected), possibly indicating an experience bias. These results could help understand the cognitive mechanisms that comprise and maintain social anxiety.
Assessing current phytase release values for calcium, phosphorus, amino acids, and energy in diets for growing-finishing pigs12
Authors: Wensley Madie R , Vier Carine M , Woodworth Jason C , DeRouchey Joel M , Tokach Mike D , Goodband Robert D , Dritz Steve S , Bergstrom Jon R
Published: March 2020

Two experiments were conducted to determine the effects of feeding 1,500 phytase units (FYT/kg; Ronozyme HiPhos 2,500; DSM Nutritional Products, Parsippany, NJ) when credited with its corresponding nutrient release values to growing-finishing pigs. The assumed phytase release values were 0.146% standardized total tract digestible (STTD) P, 0.102% STTD Ca, 8.6 kcal/kg of net energy (NE), and 0.0217%, 0.0003%, 0.0086%, 0.0224%, 0.0056%, 0.0122%, and 0.0163% standardized ileal digestible Lys, Met, Met+Cys, Thr, Trp, Ile, and Val, respectively. In Exp. 1, 1,215 pigs (PIC 359 × Camborough, initially 28.0 ± 0.46 kg) were used. Pens were assigned to one of three dietary treatments with 27 pigs per pen and 15 pens per treatment. Experimental diets consisted of a control with no added phytase or diets with 1,500 FYT fed either in the grower period (days 0–57) then switched to the control diet until market or fed throughout the entire study (day 0 to market). Diets containing added phytase were adjusted based on the supplier-provided expected nutrient release values. During the grower period, pigs fed the control diet with no added phytase had increased (P < 0.05) average daily gain (ADG) and gain-to-feed ratio (G:F) compared with pigs fed added phytase. Overall, pigs fed either the control or phytase only in the grower period had increased (P < 0.05) ADG and G:F compared with pigs fed phytase until market. In Exp. 2, 2,268 pigs (PIC 337 × 1050, initially 28.5 ± 1.96 kg) were used. There were six dietary treatments with 27 pigs per pen and 14 pens per treatment. Experimental diets consisted of a control with no added phytase or five diets with 1,500 FYT assuming nutrient release values for Ca and P; Ca, P, and Amino Acid (AA); Ca, P, AA, and half of the suggested NE; Ca, P, AA, and full NE; or no nutrient release. Overall, there was no evidence for difference in ADG or average daily feed intake among treatments; however, pigs fed the diet containing 1,500 FYT assuming that no nutrient release had improved (P < 0.05) G:F compared to pigs fed diets containing 1,500 FYT assuming either Ca and P or Ca, P, AA, and full NE release, with others intermediate. In summary, pigs fed phytase-added diets accounting for full nutrient release values in both experiments had the poorest performance. This suggests that using all of the nutrient release values attributed to this source of phytase was too aggressive and resulted in lower nutrient concentrations than needed to optimize performance.
Quantification and Distribution of the 16SrIV-D Phytoplasma in the Wild Date Palm, Phoenix sylvestris, at Different Stages of Decline Using Quantitative PCR (qPCR) Analysis
Authors: Bahder Brian W. , Soto Noemi , Mou De-Fen , Humphries Alessandra R. , Helmick Ericka E.
Published: March 2020

Lethal bronzing disease (LBD) is a fatal infection in a variety of ornamental palms in Florida caused by the 16SrIV-D phytoplasma. The disease was first found in 2006 in Florida and has since spread to 31 different counties, reaching as far north as Jacksonville and as far south as Key Largo. Stakeholders (nursery personnel, landscaping personnel, and extension agents) from across the state take and send samples for analysis. To provide better sampling recommendations and reduce the time associated with the sampling process, the distribution of the 16SrIV-D phytoplasma was examined by quantitative PCR analysis in various Phoenix sylvestris that displayed different stages of decline, including early symptoms, moderate symptoms, and late symptoms. A declining Sabal palmetto was also available for analysis and examined as well. The findings of this study revealed that regardless of the stage of decline, the highest amount of phytoplasma detected was nearest to the base of the trunk and gradually decreased further up the trunk. Also, in P. sylvestris it was found that with symptoms present, the entire trunk has a systemic infection, resulting in positive reactions for every sample taken. These data are useful to stakeholders because they provide useful sampling recommendations in that only a single sample is needed when sampling a palm suspected to be infected with phytoplasma. Also, based on these results, sampling lower on the trunk is advised.
Genome Sequence and Comparative Analysis ofColletotrichum gloeosporioidesIsolated fromLiriodendronLeaves
Authors: Fu Fang-Fang , Hao Zhaodong , Wang Pengkai , Lu Ye , Xue Liang-Jiao , Wei Guoyu , Tian Yanli , Hu Baishi , Xu Haibin , Shi Jisen , Cheng Tielong , Wang Guibin , Yi Yin , Chen Jinhui
Published: March 2020

Colletotrichum gloeosporioides is a hemibiotrophic pathogen causing significant losses to economically important crops and forest trees, including Liriodendron. To explore the interaction between C. gloeosporioides and Liriodendron and to identify the candidate genes determining the pathogenesis, we sequenced and assembled the whole genome of C. gloeosporioides Lc1 (CgLc1) using PacBio and Illumina next generation sequencing and performed a comparative genomic analysis between CgLc1 and Cg01, the latter being a described endophytic species of the C. gloeosporioides complex. Gene structure prediction identified 15,744 protein-coding genes and 837 noncoding RNAs. Species-specific genes were characterized using an ortholog analysis followed by a pathway enrichment analysis, which showed that genes specific to CgLc1 were enriched for the arginine biosynthetic process. Furthermore, genome synteny analysis revealed that most of the protein-coding genes fell into collinear blocks. However, two clusters of polyketide synthase genes were identified to be specific for CgLc1, suggesting that they might have an important role in virulence control. Transcriptional regulators coexpressed with polyketide synthase genes were detected through a Weighted Correlation Network Analysis. Taken together, this work provides new insight into the virulence- and pathogenesis-associated genes present in C. gloeosporioides and its possible lifestyle.
Dormancy dampens the microbial distance–decay relationship
Authors: Locey K. J. , Muscarella M. E. , Larsen M. L. , Bray S. R. , Jones S. E. , Lennon J. T.
Published: March 2020

Much of Earth's biodiversity has the capacity to engage in dormancy, a reversible state of reduced metabolic activity. By increasing resilience to unfavourable conditions, dormancy leads to the accumulation of ‘seed banks’. These reservoirs of genetic and phenotypic diversity should diminish the strength of environmental filtering and increase rates of dispersal. Although prevalent among single-celled organisms, evidence that dormancy influences patterns of microbial biogeography is lacking. We constructed geographical and environmental distance–decay relationships (DDRs) for the total (DNA) and active (RNA) portions of bacterial communities in a regional-scale 16S rRNA survey of forested ponds in Indiana, USA. As predicted, total communities harboured greater diversity and exhibited weaker DDRs than active communities. These observations were robust to random resampling and different community metrics. To evaluate the processes underlying the biogeographic patterns, we developed a platform of mechanistic models that used the geographical coordinates and environmental characteristics of our study system. Based on more than 106simulations, our models approximated the empirical DDRs when there was strong environmental filtering along with the presence of long-lived seed banks. By contrast, the inclusion of dispersal generally decreased model performance. Together, our findings support recent theoretical predictions that seed banks can influence the biogeographic patterns of microbial communities.

This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
Linking microbial communities to ecosystem functions: what we can learn from genotype–phenotype mapping in organisms
Authors: Morris Andrew , Meyer Kyle , Bohannan Brendan
Published: March 2020

Microbial physiological processes are intimately involved in nutrient cycling. However, it remains unclear to what extent microbial diversity or community composition is important for determining the rates of ecosystem-scale functions. There are many examples of positive correlations between microbial diversity and ecosystem function, but how microbial communities ‘map' onto ecosystem functions remain unresolved. This uncertainty limits our ability to predict and manage crucial microbially mediated processes such as nutrient losses and greenhouse gas emissions. To overcome this challenge, we propose integrating traditional biodiversity–ecosystem function research with ideas from genotype–phenotype mapping in organisms. We identify two insights from genotype–phenotype mapping that could be useful for microbial biodiversity–ecosystem function studies: the concept of searching ‘agnostically' for markers of ecosystem function and controlling for population stratification to identify microorganisms uniquely associated with ecosystem function. We illustrate the potential for these approaches to elucidate microbial biodiversity–ecosystem function relationships by analysing a subset of published data measuring methane oxidation rates from tropical soils. We assert that combining the approaches of traditional biodiversity–ecosystem function research with ideas from genotype–phenotype mapping will generate novel hypotheses about how complex microbial communities drive ecosystem function and help scientists predict and manage changes to ecosystem functions resulting from human activities.

This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
Metabolically cohesive microbial consortia and ecosystem functioning
Authors: Pascual-García Alberto , Bonhoeffer Sebastian , Bell Thomas
Published: March 2020

Recent theory and experiments have reported a reproducible tendency for the coexistence of microbial species under controlled environmental conditions. This observation has been explained in the context of competition for resources and metabolic complementarity given that, in microbial communities (MCs), many excreted by-products of metabolism may also be resources. MCs therefore play a key role in promoting their own stability and in shaping the niches of the constituent taxa. We suggest that an intermediate level of organization between the species and the community level may be pervasive, where tightly knit metabolic interactions create discrete consortia that are stably maintained. We call these units Metabolically Cohesive Consortia (MeCoCos) and we discuss the environmental context in which we expect their formation, and the ecological and evolutionary consequences of their existence. We argue that the ability to identify MeCoCos would open new avenues to link the species-, community- and ecosystem-level properties, with consequences for our understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild.

This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
Toward a dynamical understanding of microbial communities
Authors: Rainey Paul B. , Quistad Steven D.
Published: March 2020

The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry.

This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
The microbial exometabolome: ecological resource and architect of microbial communities
Authors: Douglas Angela E.
Published: March 2020

All microorganisms release many metabolites, collectively known as the exometabolome. The resultant multi-way cross-feeding of metabolites among microorganisms distributes resources, thereby increasing total biomass of the microbial community, and promotes the recruitment and persistence of phylogenetically and functionally diverse taxa in microbial communities. Metabolite transfer can also select for evolutionary diversification, yielding multiple closely related but functionally distinct strains. Depending on starting conditions, the evolved strains may be auxotrophs requiring metabolic outputs from producer cells or, alternatively, display loss of complementary reactions in metabolic pathways, with increased metabolic efficiency. Metabolite cross-feeding is widespread in many microbial communities associated with animals and plants, including the animal gut microbiome, and these metabolic interactions can yield products valuable to the host. However, metabolite exchange between pairs of intracellular microbial taxa that share the same host cell or organ can be very limited compared to pairs of free-living microorganisms, perhaps as a consequence of host controls over the metabolic function of intracellular microorganisms. Priorities for future research include the development of tools for improved quantification of metabolite exchange in complex communities and greater integration of the roles of metabolic cross-feeding and other ecological processes, including priority effects and antagonistic interactions, in shaping microbial communities.

This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
Understanding the evolution of interspecies interactions in microbial communities
Authors: Gorter Florien A. , Manhart Michael , Ackermann Martin
Published: March 2020

Microbial communities are complex multi-species assemblages that are characterized by a multitude of interspecies interactions, which can range from mutualism to competition. The overall sign and strength of interspecies interactions have important consequences for emergent community-level properties such as productivity and stability. It is not well understood how interspecies interactions change over evolutionary timescales. Here, we review the empirical evidence that evolution is an important driver of microbial community properties and dynamics on timescales that have traditionally been regarded as purely ecological. Next, we briefly discuss different modelling approaches to study evolution of communities, emphasizing the similarities and differences between evolutionary and ecological perspectives. We then propose a simple conceptual model for the evolution of interspecies interactions in communities. Specifically, we propose that to understand the evolution of interspecies interactions, it is important to distinguish between direct and indirect fitness effects of a mutation. We predict that in well-mixed environments, traits will be selected exclusively for their direct fitness effects, while in spatially structured environments, traits may also be selected for their indirect fitness effects. Selection of indirectly beneficial traits should result in an increase in interaction strength over time, while selection of directly beneficial traits should not have such a systematic effect. We tested our intuitions using a simple quantitative model and found support for our hypotheses. The next step will be to test these hypotheses experimentally and provide input for a more refined version of the model in turn, thus closing the scientific cycle of models and experiments.

This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
Chitinasiproducens palmae gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from leaf tissues of oil palm (Elaeis guineensis Jacq.)
Authors: Madhaiyan Munusamy , See-Too Wah-Seng , Ee Robson , Saravanan Venkatakrishnan Sivaraj , Wirth Joseph S. , Alex Tan Hian Hwee , Lin Cai , Kim Soo-Jin , Weon Hang-Yeon , Kwon Soon-Wo , Whitman William B. , Ji Lianghui
Published: March 2020

A Gram-stain-negative, aerobic, rod-shaped, leaf-associated bacterium, designated JS23T, was isolated from surface-sterilized leaf tissue of an oil palm grown in Singapore and was investigated by polyphasic taxonomy. Phylogenetic analyses based on 16S rRNA gene sequences and 180 conserved genes in the genome of several members of

Burkholderiaceae

revealed that strain JS23T formed a distinct evolutionary lineage independent of other taxa within the family

Burkholderiaceae

. The predominant ubiquinone was Q-8. The primary polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminophospholipid. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1
 ω7c /C16 : 1
 ω6c) and summed feature 8 (C18 : 1
 ω7c /C18 : 1
 ω6c). The size of the genome is 5.36 Mbp with a DNA G+C content of 66.2 mol%. Genomic relatedness measurements such as average nucleotide identity, genome-to-genome distance and digital DNA–DNA hybridization clearly distinguished strain JS23T from the closely related genera

Burkholderia

,

Caballeronia

,

Mycetohabitans

,

Mycoavidus

,

Pandoraea

,

Paraburkholderia

,

Robbsia

and

Trinickia

. Furthermore, average amino acid identity values and the percentages of conserved proteins, 56.0–68.4 and 28.2–45.5, respectively, were well below threshold values for genus delineation and supported the assignment of JS23T to a novel genus. On the basis of the phylogenetic, biochemical, chemotaxonomic and phylogenomic evidence, strain JS23T is proposed to represent a novel species of a new genus within the family

Burkholderiaceae

, for which the name Chitinasiproducens palmae gen. nov., sp. nov., is proposed with the type strain of JS23T (= DSM 27307T=KACC 17592T).
Preprint server use in kidney disease research: a rapid review
Authors: Vlasschaert Caitlyn , Giles Cameron , Hiremath Swapnil , Lanktree Matthew B.
Published: March 2020

Purpose of review

Preprint servers including arXiv and bioRxiv have disrupted the scientific communication landscape by providing rapid access to pre--peer reviewed research. MedRxiv is a recently launched free online repository for preprints in the health sciences. We sought to summarize potential benefits and risks to preprint server use, from both the researcher and end--user perspective, and evaluate the uptake of preprint servers in the nephrology community.

Sources of Information

We performed a rapid review of articles describing preprint servers and their use. We approached the 20 highest impact nephrology journals regarding their policy towards the use of preprint servers. We evaluated the average time from study completion to publication of impactful articles in nephrology. Finally, we evaluated the number of nephrology articles submitted to preprint servers.

Findings

To date over 600 kidney--related articles have been uploaded to bioRxiv and medRxiv. The average time from study completion to publication was over 10 months. 16 of the top 20 nephrology journals currently accept research submitted to a preprint server. Transparency and collaboration, visibility and recognition, and rapid dissemination of results were identified as benefits of preprint servers. Concerns exist regarding the potential risk of non--peer reviewed medical research being publicly available.

Limitations

Preprint servers remain a recent phenomenon in health sciences and their long-- term impact on the medical literature remains to be seen.

Implications

The quantity of research submitted to preprint servers is likely to continue to grow. The model for dissemination of research results will need to adapt to incorporate preprint servers.
High incidence of asymptomatic SARS-CoV-2 infection, Chongqing, China
Authors: Tao Yang , Cheng Panke , Chen Wen , Wan Peng , Chen Yaokai , Yuan Guodan , Chen Junjie , Huo Da , Guan Ge , Sun Dayu , Tan Ju , Yang Guanyuan , Zeng Wen , Zhu Chuhong
Published: March 2020

Background

SARS-CoV-2 has been a global pandemic, but the emergence of asymptomatic patients has caused difficulties in the prevention of the epidemic. Therefore, it is significant to understand the epidemiological characteristics of asymptomatic patients with SARS-CoV-2 infection.

Methods

In this single-center, retrospective and observational study, we collected data from 167 patients with SARS-CoV-2 infection treated in Chongqing Public Health Medical Center (Chongqing, China) from January to March 2020. The epidemiological characteristics and variable of these patients were collected and analyzed.

Findings

82.04% of the SARS-CoV-2 infected patients had a travel history in Wuhan or a history of contact with returnees from Wuhan, showing typical characteristics of imported cases, and the proportion of severe Covid-19 patients was 13.2%, of which 59% were imported from Wuhan. For the patients who was returnees from Wuhan, 18.1% was asymptomatic patients. In different infection periods, compared with the proportion after 1/31/2020, the proportion of asymptomatic patient among SARS-CoV-2 infected patient was higher(19% VS 1.5%). In different age groups, the proportion of asymptomatic patient was the highest(28.6%) in children group under 14, next in elder group over 70 (27.3%). Compared with mild and common Covid-19 patients, the mean latency of asymptomatic was longer (11.25 days VS 8.86 days), but the hospital length of stay was shorter (14.3 days VS 16.96 days).

Conclusion

The SARS-CoV-2 prevention needs to focus on the screening of asymptomatic patients in the community with a history of contact with the imported population, especially for children and the elderly population.
ACE-2 Expression in the Small Airway Epithelia of Smokers and COPD Patients: Implications for COVID-19
Authors: Leung Janice M. , Yang Chen X. , Tam Anthony , Shaipanich Tawimas , Hackett Tillie-Louise , Singhera Gurpreet K. , Dorscheid Delbert R. , Sin Don D.
Published: March 2020

Introduction

Coronavirus disease 2019 (COVID-19) is a respiratory infection caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This virus uses the angiotensin converting enzyme II (ACE-2) as the cellular entry receptor to infect the lower respiratory tract. Because individuals with chronic obstructive pulmonary disease (COPD) are at increased risk of severe COVID-19, we determined whether ACE-2 expression in the lower airways was related to COPD and cigarette smoking.

Methods

Using RNA-seq, we determined gene expression levels in bronchial epithelia obtained from cytologic brushings of 6th to 8th generation airways in individuals with and without COPD. We eternally validated these results from two additional independent cohorts, which used microarray technologies to measure gene expression levels from 6th to 12th generation airways.

Results

In the discovery cohort (n=42 participants), we found that ACE-2 expression levels were increased by 48% in the airways of COPD compared with non-COPD subjects (COPD=2.52±0.66 log2 counts per million reads (CPM) versus non-COPD= 1.70±0.51 CPM, p=7.62×10−4). There was a significant inverse relationship between ACE-2 gene expression and FEV1% of predicted (r=-0.24; p=0.035). Current smoking also significantly increased ACE-2 expression levels compared with never smokers (never current smokers=2.77±0.91 CPM versus smokers=1.78±0.39 CPM, p=0.024). These findings were replicated in the two eternal cohorts.

Conclusions

ACE-2 expression in lower airways is increased in patients with COPD and with current smoking. These data suggest that these two subgroups are at increased risk of serious COVID-19 infection and highlight the importance of smoking cessation in reducing the risk.
Effectiveness and safety of antiviral or antibody treatments for coronavirus
Authors: Rios Patricia , Radhakrishnan Amruta , Antony Jesmin , Thomas Sonia , Muller Matthew , Straus Sharon E. , Tricco Andrea C.
Published: March 2020

Background

To identify safe and effective medical countermeasures (e.g., antivirals/antibodies) to address the current outbreak of a novel coronavirus (COVID-19)

Methods

Comprehensive literature searches were developed by an experienced librarian for MEDLINE, EMBASE, the Cochrane Library, and biorxiv.org/medrxiv.org; additional searches for ongoing trials and unpublished studies were conducted in clinicaltrials.gov and the Global Infectious Diseases and Epidemiology Network (GIDEON). Title/abstract and full-text screening, data abstraction, and risk of bias appraisal were carried out by single reviewers.

Results

54 studies were included in the review: three controlled trials, 10 cohort studies, seven retrospective medical record/database studies, and 34 case reports or series. These studies included patients with severe acute respiratory syndrome (SARs, n=33), middle east respiratory syndrome (MERS, n=16), COVID-19 (n=3), and unspecified coronavirus (n=2). The most common treatment was ribavirin (n=41), followed by oseltamivir (n=10) and the combination of lopinavir/ritonavir (n=7). Additional therapies included broad spectrum antibiotics (n=30), steroids (n=39) or various interferons (n=12). No eligible studies examining monoclonal antibodies for COVID-19 were identified. One trial found that ribavirin prophylactic treatment statistically significantly reduced risk of MERS infection in people who had been exposed to the virus. Of the 21 studies reporting rates of ICU admission in hospitalized SARS or MERS patients, none reported statistically significant results in favour of or against antiviral therapies. Of the 40 studies reporting mortality rates in hospitalized SARS or MERS patients, one cohort study (MERS) and one retrospective study (SARS) found a statistically significant increase in the mortality rate for patients treated with ribavirin. Eighteen studies reported potential drug-related adverse effects including gastrointestinal symptoms, anemia, and altered liver function in patients receiving ribavirin.

Conclusion

The current evidence for the effectiveness and safety of antiviral therapies for coronavirus is inconclusive and suffers from a lack of well-designed prospective trials or observational studies, preventing any treatment recommendations from being made. However, it is clear that the existing body of evidence is weighted heavily towards ribavirin (41/54 studies), which has not shown conclusive evidence of effectiveness and may cause harmful adverse events so future investigations may consider focusing on other candidates for antiviral therapy.
Role of meteorological temperature and relative humidity in the January-February 2020 propagation of 2019-nCoV in Wuhan, China
Authors: Alvarez-Ramirez Jose , Meraz Monica
Published: March 2020

Identified in December 2019, the 2019-nCoV emerged in Wuhan, China, and its spread increased rapidly, with cases arising across Mainland China and several other countries. By January 2020, the potential risks imposed by 2019-nCoV in human health and economical activity were promptly highlighted. Considerable efforts have been devoted for understanding the transmission mechanisms aimed to pursue public policies oriented to mitigate the number of infected and deaths. An important question requiring some attention is the role of meteorological variables (e.g., temperature and humidity) in the 2019-nCoV transmission. Correlations between meteorological temperature and relative humidity with the number of daily confirmed cases were explored in this work for the epicenter city of Wuhan, China for the period from 29 January to March 6, 2020. Long-term trend of temperature and relative humidity was obtained with a 14-days adjacent-averaging filter, and lagged correlations of the number of daily confirmed cases were explored. The analysis showed negative correlations between temperatures with the number of daily confirmed cases. Maximum correlations were found for 6-day lagged temperatures, which is likely reflecting the incubation period of the virus. It was postulated that the indoor crowding effect is responsible of the high incidence of 2019-nCoV cases, where low absolute humidity and close human contact facilitate the transport of aerosol droplets.