bluuebunny/crossref_metadata_2025 huggingface dataset:
High-redshift star formation in the Atacama large millimetre/submillimetre array era
Authors: Hodge J. A. , da Cunha E.
Published: December 2020

The Atacama Large Millimetre/submillimetre Array (ALMA) is currently in the process of transforming our view of star-forming galaxies in the distant (z≳1) universe. Before ALMA, most of what we knew about dust-obscured star formation in distant galaxies was limited to the brightest submillimetre sources—the so-called submillimetre galaxies (SMGs)—and even the information on those sources was sparse, with resolved (i.e. sub-galactic) observations of the obscured star formation and gas reservoirs typically restricted to the most extreme and/or strongly lensed sources. Starting with the beginning of early science operations in 2011, the last 9 years of ALMA observations have ushered in a new era for studies of high-redshift star formation. With its long baselines, ALMA has allowed observations of distant dust-obscured star formation with angular resolutions comparable to—or even far surpassing—the best current optical telescopes. With its bandwidth and frequency coverage, it has provided an unprecedented look at the associated molecular and atomic gas in these distant galaxies through targeted follow-up and serendipitous detections/blind line scans. Finally, with its leap in sensitivity compared to previous (sub-)millimetre arrays, it has enabled the detection of these powerful dust/gas tracers much further down the luminosity function through both statistical studies of colour/mass-selected galaxy populations and dedicated deep fields. We review the main advances ALMA has helped bring about in our understanding of the dust and gas properties of high-redshift (z≳1) star-forming galaxies during these first 9 years of its science operations, and we highlight the interesting questions that may be answered by ALMA in the years to come.
Linear parameter-varying model for a refuellable zinc–air battery
Authors: Lao-atiman Woranunt , Olaru Sorin , Diop Sette , Skogestad Sigurd , Arpornwichanop Amornchai , Cheacharoen Rongrong , Kheawhom Soorathep
Published: December 2020

Due to the increasing trend of using renewable energy, the development of an energy storage system (ESS) attracts great research interest. A zinc–air battery (ZAB) is a promising ESS due to its high capacity, low cost and high potential to support circular economy principles. However, despite ZABs' technological advancements, a generic dynamic model for a ZAB, which is a key component for effective battery management and monitoring, is still lacking. ZABs show nonlinear behaviour where the steady-state gain is strongly dependent on operating conditions. The present study aims to develop a dynamic model, being capable of predicting the nonlinear dynamic behaviour of a refuellable ZAB, using a linear parameter-varying (LPV) technique. The LPV model is constructed from a family of linear time-invariant models, where the discharge current level is used as a scheduling parameter. The developed LPV model is benchmarked against linear and nonlinear model counterparts. Herein, the LPV model performs remarkably well in capturing the nonlinear behaviour of a ZAB. It significantly outperforms the linear model. Overall, the LPV approach provides a systematic way to construct a robust dynamic model which well represents the nonlinear behaviour of a ZAB.
Virtual body ownership and its consequences for implicit racial bias are dependent on social context
Authors: Banakou Domna , Beacco Alejandro , Neyret Solène , Blasco-Oliver Marta , Seinfeld Sofia , Slater Mel
Published: December 2020

When people hold implicit biases against a group they typically engage in discriminatory behaviour against group members. In the context of the implicit racial bias of ‘White' against ‘Black' people, it has been shown several times that implicit bias is reduced after a short exposure of embodiment in a dark-skinned body in virtual reality. Embodiment usually leads to the illusion of ownership over the virtual body, irrespective of its skin colour. Previous studies have been carried out in virtual scenarios that are affectively neutral or positive. Here, we show that when the scenario is affectively negative the illusion of body ownership of White participants over a White body is lessened, and implicit bias is higher for White participants in a Black virtual body. The study was carried out with 92 White female participants, in a between-groups design with two factors: BodyType (their virtual body was White or Black) and a surrounding Crowd was Negative, Neutral or Positive towards the participant. We argue that negative affect prevents the formation of new positive associations with Black and distress leads to disownership of the virtual body. Although virtual reality is often thought of as an ‘empathy machine' our results suggest caution, that this may not be universally the case.
Dynamics of a waveboard simplified
Authors: DasGupta Anirvan
Published: December 2020

A study of dynamics of a waveboard is presented. The equations of motion are derived and analysed to understand the intriguing propulsion mechanism. A reduced order model is obtained, and the contributions of different terms are clearly brought out. The geometry of the castor wheels is found to play a key role in the conversion of the twisting oscillatory motion of the rider to the forward translational motion. The process of periodic gain in potential energy and its subsequent conversion to kinetic energy aids the propulsion. Interestingly, the dynamic analysis reveals that the efficacy of this propulsion mechanism tapers off as the speed increases. Rolling resistance in the wheels ultimately limits the speed of the device. The effect of various geometric and dynamic parameters on the motion and forces are studied, and optimality of design is indicated.
A revisit of the tonal noise of small rotors
Authors: Zhong Siyang , Zhou Peng , Fattah Ryu , Zhang Xin
Published: December 2020

In this study, asymptotic analysis of the frequency-domain formulation to compute the tonal noise of the small rotors in the now ubiquitously multi-rotor powered drones is conducted. Simple scaling laws are proposed to evaluate the impacts of the influential parameters such as blade number, flow speed, rotation speed, unsteady motion, thrust and observer angle on the tonal noise. The rate of noise increment with thrust (or rotational speed) is determined by orders of blade passing frequency harmonics and the unsteady motion. The axial mean flow influence can be approximated by quadratic functions. At given thrust, the sound decreases rapidly with the radius and blade number as the surface pressure becomes less intensive. The higher tonal harmonics are significantly increased if unsteady motions, although of small-amplitude, are existed, as indicated by the defined sensitivity function, emphasizing that the unsteady motions should be avoided for quiet rotor designs. The scaling laws are examined by comparing with the full computations of the rotor noise using the frequency-domain method, the implementation of which has been validated by comparing with experiments. Good data collapse is obtained when the proposed scaling laws, which highlights the dominant influence of the design parameters, are incorporated.
Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae)
Authors: Chan Kin Onn , Hutter Carl R. , Wood Perry L. , Grismer L. Lee , Brown Rafe M.
Published: December 2020

Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to use traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention has been given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World treefrogs (Family: Rhacophoridae)—a group that is fraught with conflicting and poorly supported topologies among major clades. Additionally, a suite of data filtering strategies and analytical methods were applied to assess their impact on phylogenetic inference. We showed that incomplete lineage sorting was detected at all nodes that exhibited high levels of discordance. Those nodes were also associated with extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology and, hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that phylogenetic discordances in Old World treefrogs resulted from incomplete lineage sorting and that species tree inference can be improved using a multi-faceted, total-evidence approach, which uses the most amount of data and considers results from different analytical methods and datasets.
Towards a taxonomically unbiased European Union biodiversity strategy for 2030
Authors: Mammola Stefano , Riccardi Nicoletta , Prié Vincent , Correia Ricardo , Cardoso Pedro , Lopes-Lima Manuel , Sousa Ronaldo
Published: December 2020

Through the Habitats Directive (92/43/EEC) and the financial investments of the LIFE projects, Europe has become an experimental arena for biological conservation. With an estimated annual budget of €20 billion, the EU Biodiversity Strategy for 2030 has set an ambitious goal of classifying 30% of its land and sea territory as Protected Areas and ensuring no deterioration in conservation trends and the status of protected species. We analysed LIFE projects focused on animals from 1992 to 2018 and found that investment in vertebrates was six times higher than that for invertebrates (€970 versus €150 million), with birds and mammals alone accounting for 72% of species and 75% of the total budget. In relative terms, investment per species towards vertebrates has been 468 times higher than that for invertebrates. Using a trait-based approach, we show that conservation effort is primarily explained by species' popularity rather than extinction risk or body size. Therefore, we propose a roadmap to achieve unbiased conservation targets for 2030 and beyond.
Environmental DNA metabarcoding reveals winners and losers of global change in coastal waters
Authors: Gallego Ramón , Jacobs-Palmer Emily , Cribari Kelly , Kelly Ryan P.
Published: December 2020

Studies of the ecological effects of global change often focus on one or a few species at a time. Consequently, we know relatively little about the changes underway at real-world scales of biological communities, which typically have hundreds or thousands of interacting species. Here, we use COI mtDNA amplicons from monthly samples of environmental DNA to survey 221 planktonic taxa along a gradient of temperature, salinity, dissolved oxygen and carbonate chemistry in nearshore marine habitat. The result is a high-resolution picture of changes in ecological communities using a technique replicable across a wide variety of ecosystems. We estimate community-level differences associated with time, space and environmental variables, and use these results to forecast near-term community changes due to warming and ocean acidification. We find distinct communities in warmer and more acidified conditions, with overall reduced richness in diatom assemblages and increased richness in dinoflagellates. Individual taxa finding more suitable habitat in near-future waters are more taxonomically varied and include the ubiquitous coccolithophore
Emiliania huxleyi
and the harmful dinoflagellate
Alexandrium
sp. These results suggest foundational changes for nearshore food webs under near-future conditions.
Infectious disease and sickness behaviour: tumour progression affects interaction patterns and social network structure in wild Tasmanian devils
Authors: Hamilton David G. , Jones Menna E. , Cameron Elissa Z. , Kerlin Douglas H. , McCallum Hamish , Storfer Andrew , Hohenlohe Paul A. , Hamede Rodrigo K.
Published: December 2020

Infectious diseases, including transmissible cancers, can have a broad range of impacts on host behaviour, particularly in the latter stages of disease progression. However, the difficulty of early diagnoses makes the study of behavioural influences of disease in wild animals a challenging task. Tasmanian devils (
Sarcophilus harrisii
) are affected by a transmissible cancer, devil facial tumour disease (DFTD), in which tumours are externally visible as they progress. Using telemetry and mark–recapture datasets, we quantify the impacts of cancer progression on the behaviour of wild devils by assessing how interaction patterns within the social network of a population change with increasing tumour load. The progression of DFTD negatively influences devils' likelihood of interaction within their network. Infected devils were more active within their network late in the mating season, a pattern with repercussions for DFTD transmission. Our study provides a rare opportunity to quantify and understand the behavioural feedbacks of disease in wildlife and how they may affect transmission and population dynamics in general.
Leuconostoc falkenbergense sp. nov., isolated from a lactic culture, fermentating string beans and traditional yogurt
Authors: Wu Yan , Gu Chun Tao
Published: December 2020

In the present study, the taxonomic positions of five strains (C, 17-2, LMG 10779T, LMG 18969 and LMG 11483) of

Leuconostoc pseudomesenteroides

were re-evaluated by a polyphasic approach, including the analyses of 16S rRNA, pheS and rpoA gene sequences, cellular fatty acids, average nucleotide and amino acid identities (ANI and AAI), digital DNA–DNA hybridization (dDDH), and phenotypic features. Based on rpoA sequence analysis, the five strains and

L. pseudomesenteroides

LMG 11482T were divided into two groups: strains C, LMG 10779T and LMG 18969; strains 17-2, LMG 11483 and LMG 11482T. Each of the two groups had almost identical rpoA sequences. The rpoA sequence similarity between strain LMG 10779T and

L. pseudomesenteroides

LMG 11482T was 95.6 %. Strains LMG 11483 and 17-2 had 98.1 and 97.2 % ANI values, 83.5 and 73.2 % dDDH values, and a 97.0 % AAI value with

L. pseudomesenteroides

LMG 11482T, greater than the threshold for species demarcation, indicating that strains LMG 11483 and 17-2 belong to

L. pseudomesenteroides

. Strains LMG 18969 and C shared 97.1 and 98.2 % ANI values, 73.4 and 83.2 % dDDH values, and 96.9 and 96.6 % AAI values with strain LMG 10779T, greater than the threshold for species demarcation, indicating that strains LMG 10779T, LMG 18969 and C represent the same species. The ANI, dDDH and AAI values between strain LMG 10779T and the type strains of phylogenetically related species were 75.2–92.5, 20.0–48.2 and 75.3–93.9 %, respectively, below the thresholds for species demarcation, indicating that strain LMG 10779T represents a novel species within the genus

Leuconostoc

. On the basis of the results presented here, (i) strains 17-2 and LMG 11483 belong to

L. pseudomesenteroides

, and (ii) strains LMG 10779T, LMG 18969 and C are considered to represent a novel species within the genus

Leuconostoc

, for which the name Leuconostoc falkenbergense sp. nov. is proposed with the type strain LMG 10779T (=CCUG 27119T).
Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies
Authors: Choo Siew Woh , Rishik Shusruto , Wee Wei Yee
Published: December 2020

Mycobacteroides immunogenumis an emerging opportunistic pathogen implicated in nosocomial infections. Comparative genome analyses may provide better insights into its genomic structure, functions and evolution. The present analysis showed thatM. immunogenumhas an open pan-genome. Approximately 36.8% of putative virulence genes were identified in the accessory regions ofM. immunogenum. Phylogenetic analyses revealed two potential novel subspecies ofM. immunogenum, supported by evidence from ANIb (average nucleotide identity usingblast) and GGDC (Genome to Genome Distance Calculator) analyses. We identified 74 genomic islands (GIs) in Subspecies 1 and 23 GIs in Subspecies 2. All Subspecies 2-harboured GIs were not found in Subspecies 1, indicating that they might have been acquired by Subspecies 2 after their divergence. Subspecies 2 has more defence genes than Subspecies 1, suggesting that it might be more resistant to the insertion of foreign DNA and probably explaining why Subspecies 2 has fewer GIs. Positive selection analysis suggest thatM. immunogenumhas a lower selection pressure compared to non-pathogenic mycobacteria. Thirteen genes were positively selected and many were involved in virulence.
carP, encoding a Ca2+-regulated putative phytase, is evolutionarily conserved in Pseudomonas aeruginosa and has potential as a biomarker
Authors: Mares Sergio E. , King Michelle M. , Kubo Aya , Khanov Anna A. , Lutter Erika I. , Youssef Noha , Patrauchan Marianna A.
Published: December 2020

Pseudomonas aeruginosa

infects patients with cystic fibrosis, burns, wounds and implants. Previously, our group showed that elevated Ca2+ positively regulates the production of several virulence factors in

P. aeruginosa

, such as biofilm formation, production of pyocyanin and secreted proteases. We have identified a Ca2+-regulated β-propeller putative phytase, CarP, which is required for Ca2+ tolerance, regulation of the intracellular Ca2+ levels, and plays a role in Ca2+ regulation of

P. aeruginosa

virulence. Here, we studied the conservation of carP sequence and its occurrence in diverse phylogenetic groups of bacteria. In silico analysis revealed that carP and its two paralogues PA2017 and PA0319 are primarily present in

P. aeruginosa

and belong to the core genome of the species. We identified 155 single nucleotide alterations within carP, 42 of which lead to missense mutations with only three that affected the predicted 3D structure of the protein. PCR analyses with carP-specific primers detected

P. aeruginosa

specifically in 70 clinical and environmental samples. Sequence comparison demonstrated that carP is overall highly conserved in

P. aeruginosa

isolated from diverse environments. Such evolutionary preservation of carP illustrates its importance for

P. aeruginosa

adaptations to diverse environments and demonstrates its potential as a biomarker.
The Impact of Extracorporeal Shockwave Therapy on the Reported Pain Levels of Chronic Patients in a Clinical Setting
Authors: Cremata Edward J. , Cremata Edward E , Bidkaram Ulyss , Brown Bryce , Radman Allan
Published: December 2020

Background

A review of literature for in-office, low to medium energy (.04mj/mm2 to .4mj/mm2) Extracorporeal Shockwave Therapy (ESWT) shows a substantial body of evidence suggesting strong efficacy and safety for the use of this form of Acoustic Compression Therapy. Much of this evidence is focused on the treatment of a specific region of the body, such as lateral epicondylitis, plantar fasciitis, and shoulder tendinopathies. This evaluation is designed to address the clinical utility of low to medium energy ESWT in an outpatient health care office setting, including delivery to multiple regions of the body, and for patients considered good candidates based on the failure of at least six months of prior conservative care.

Methods

Ordinary least squares (OLS) models with errors clustered at the patient level estimate the association between shockwave treatments and patient-reported pain levels. Additional models utilizing polynomial treatment indicators test for a non-linear relationship between treatment number and reported pain level.

Results

For the sixty-one patients represented in this analysis, the mean reduction in pain was 2.3 points on a 10 point scale, representing a 47% reduction in average reported pain levels. Results suggest that each treatment is associated with a 0.33 point reduction in reported pain levels (on a 10 point scale), controlling for patient demographics and treatment intensity. Additional models utilizing polynomial treatment indicators suggest a non-linear relationship between treatment number and reported pain level, indicating that the initial benefit of treatment is a 0.67 point reduction in pain for the first treatment, and falling slightly with each subsequent treatment. A subset of patients responded to follow up requests to ascertain reported pain levels at least three months after the final treatment. All patients were contacted, out of which 24 responded, reporting average pain levels of 2.9 out of 10, a substantial improvement from initial reported pain levels following final treatment (4.0), representing a decrease of 28%.

Conclusion

The results suggest the use of Acoustic Compression at these doses on properly selected cases can improve clinical outcomes for conservatively treated patients who may otherwise end up requiring more aggressive measures in the absence of ESWT. Evidence reviewed suggests that continued healing time leads to further improvement.
Effect of COVID-19 response policies on walking behavior in US cities
Authors: Hunter Ruth F. , Garcia Leandro , de Sa Thiago Herick , Zapata-Diomedi Belen , Millet Christopher , Woodcock James , Pentland Alex ’Sandy’ , Moro Esteban
Published: December 2020

The COVID-19 pandemic has caused mass disruption to our daily lives. Mobility restrictions implemented to reduce the spread of COVID-19 have impacted walking behavior, but the magnitude and spatio-temporal aspects of these changes have yet to be explored. Walking is the most common form of physical activity and non-motorized transport, and so has an important role in our health and economy. Understanding how COVID-19 response measures have affected walking behavior of populations and distinct subgroups is paramount to help devise strategies to prevent the potential health and societal impacts of declining walking levels. In this study, we integrated mobility data from mobile devices and area-level data to study the walking patterns of 1.62 million anonymous users in 10 metropolitan areas in the United States (US). The data covers the period from mid-February 2020 (pre-lockdown) to late June 2020 (easing of lockdown restrictions). We detected when users were walking, measured distance walked and time of the walk, and classified each walk as recreational or utilitarian. Our results revealed dramatic declines in walking, especially utilitarian walking, while recreational walking has recovered and even surpassed the levels before the pandemic. However, our findings demonstrated important social patterns, widening existing inequalities in walking behavior across socio-demographic groups. COVID-19 response measures had a larger impact on walking behavior for those from low-income areas, of low education, and high use of public transportation. Provision of equal opportunities to support walking could be key to opening up our society and the economy.
Gut microbiome profiles and associated metabolic pathways in HIV-infected treatment-naïve patients
Authors: do Nascimento Wellinton M. , Machiavelli Aline , Ferreira Luiz G. E. , Silveira Luisa Cruz , de Azevedo Suwellen S. D. , Bello Gonzalo , Smith Daniel P. , Mezzari Melissa P. , Petrosino Joseph , Duarte Rubens Tadeu Delgado , Zaráte-Bládes Carlos R. , Pinto Aguinaldo R.
Published: December 2020

The normal composition of the intestinal microbiota is a key factor for maintaining health homeostasis and, accordingly, dysbiosis is well known to be present in HIV-1 patients. Here, we investigate the gut microbiota profile of HIV-1 positive patients without antiretroviral therapy and healthy donors living in Latin America. We enrolled 13 HIV positive patients (six elite controllers, EC and seven non-controllers, NC) and nine healthy donors (HD). Microbiota compositions in stool samples were determined by sequencing the V3-V4 region of the bacterial 16S rRNA and functional prediction was inferred using PICRUSt. Several taxa were enriched in EC compared to NC or HD groups, including Acidaminococcus, Clostridium methylpentosum, Barnesiella, Eubacterium coprostanoligenes and Lachnospiraceae UCG-004. Importantly, we confirmed that the route of infection is a strong factor associated with changes in gut microbiome composition and we extended these results by identifying several metabolic pathways associated with each route of infection. Moreover, we observed several bacterial taxa associated with different viral subtypes such as Succinivibrio which were more abundant in patients infected by HIV subtype B, and Streptococcus enrichment in patients infected by subtype C. In conclusion, our data brings a significant contribution to our understanding of dysbiosis-associated changes in HIV infection and describes, for the first time, differences in microbiota composition according to HIV subtypes.
Spinal cord associative plasticity improves forelimb sensorimotor function after cervical injury
Authors: Pal Ajay , Park HongGeun , Ramamurthy Aditya , Asan Ahmet S. , Bethea Thelma , Johnkutty Meenu , Carmel Jason B.
Published: December 2020

Associative plasticity occurs when two stimuli converge on a common neural target. Previous efforts to promote associative plasticity have targeted cortex, with variable and moderate effects. In addition, the targeted circuits are inferred, rather than tested directly. In contrast, we sought to target the strong convergence between motor and sensory systems in the spinal cord.

We developed spinal cord associative plasticity (SCAP), precisely timed pairing of motor cortex and dorsal spinal cord stimulations, to target this interaction. We tested the hypothesis that properly timed paired stimulation would strengthen the sensorimotor connections in the spinal cord and improve recovery after spinal cord injury (SCI). We tested physiological effects of paired stimulation, the pathways that mediate it, and its function in a preclinical trial.

Subthreshold spinal cord stimulation strongly augmented motor cortex evoked muscle potentials at the time they were paired, but only when they arrived synchronously in the spinal cord. This paired stimulation effect depended on both cortical descending motor and spinal cord proprioceptive afferents; selective inactivation of either of these pathways fully abrogated the paired stimulation effect. SCAP, repetitive pairing of these pathways for 5 or 30 minutes in awake rats, increased spinal excitability for hours after pairing ended. To apply SCAP as therapy, we optimized the parameters to promote strong and long-lasting effects. This effect was just as strong in rats with cervical SCI as in uninjured rats, demonstrating that spared connections after moderate SCI were sufficient to support plasticity. In a blinded trial, rats received a moderate C4 contusive SCI. Ten days after injury, they were randomized to 30 minutes of SCAP each day for 10 days or sham stimulation. Rats with SCAP had significantly improved function on the primary outcome measure, a test of dexterity during manipulation of food, at 50 days after SCI. In addition, rats with SCAP had persistently stronger responses to cortical and spinal stimulation than sham stimulation rats, indicating a spinal locus of plasticity. SCAP rats had lasting improvements in H-reflex modulation. The groups had no difference in the rat grimace scale, a measure of pain.

We conclude that SCAP strengthens sensorimotor connections within the spinal cord, resulting in improved reflex modulation and forelimb function after moderate SCI. Since both motor cortex and spinal cord stimulation are performed routinely in humans, this approach can be trialed in people with SCI or other disorders that damage sensorimotor connections and impair dexterity.
Improvements to strip-based digital image registration for robust eye-tracking and to minimize distortions in images from scanned ophthalmic imaging systems
Authors: Zhang Min , Gofas-Salas Elena , Leonard Bianca T. , Rui Yuhua , Snyder Valerie , Reecher Hope , Mecê Pedro , Rossi Ethan A.
Published: December 2020

Retinal image-based eye tracking from scanned ophthalmic imaging systems, such as scanning laser ophthalmoscopy, has allowed for precise real-time eye tracking at sub-micron resolution. To achieve real-time processing rates, strip-based image registration methods for real-time applications have several constraints that limit their performance. This trade-off is acceptable for many imaging and psychophysical applications but when the objective is precise eye motion measurement over time, a high error tolerance can be consequential. Dropped strips in these applications can complicate FEMs quantification. Some light starved imaging applications, such as autofluorescence retinal imaging, also require the retention and registration of as much of the data as possible to increase the signal to noise ratio in the final integrated or averaged image. We show here that eye motion can be extracted from image sequences from scanned imaging systems more consistently when the constraints of real-time processing are lifted, and all data is available at the time of registration. This is enabled with additional image processing steps to achieve a more robust solution. Our iterative approach identifies and discards distorted frames, detects coarse motion to generate a synthetic reference frame and then uses it for fine scale motion tracking with improved sensitivity over a larger area. We demonstrate its application here to tracking scanning laser ophthalmoscopy (TSLO) and adaptive optics scanning light ophthalmoscopy (AOSLO). We show that it can successfully capture most of the eye motion across each image sequence, leaving only between 0.04-3.39% of non-blink frames untracked, even with low quality images, while simultaneously minimizing image distortions induced from eye motion. These improvements will facilitate precise FEMs measurement in TSLO and longitudinal tracking of individual cells in AOSLO.
Applications of the indole-alkaloid gramine modulate the assembly of individual members of the barley rhizosphere microbiota
Authors: Maver Mauro , Escudero-Martinez Carmen , Abbott James , Morris Jenny , Hedley Pete E. , Mimmo Tanja , Bulgarelli Davide
Published: December 2020

Microbial communities proliferating at the root-soil interface, collectively referred to as the rhizosphere microbiota, represent an untapped beneficial resource for plant growth, development and health. Integral to a rational manipulation of the microbiota for sustainable agriculture is the identification of the molecular determinants of these communities. In plants, biosynthesis of allelochemicals is centre stage in defining inter-organismal relationships in the environment. Intriguingly, this process has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgareL.) is widespread among wild genotypes but has been counter selected in several modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how exogenous applications of gramine impacted on the rhizosphere microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. High throughput 16S rRNA gene amplicon sequencing revealed that applications of gramine interfere with the proliferation of a subset of soil microbes with a relatively broad phylogenetic assignment. Strikingly, growth of these bacteria appeared to be rescued by barley plants in a genotype- and dosage-independent manner. In parallel, we discovered that host recruitment cues can interfere with the impact of gramine application in a host genotype-dependent manner. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the prokaryotic communities inhabiting the root-soil interface.
A holobiont view of island biogeography: unraveling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates
Authors: Armstrong Ellie E. , Perez-Lamarque Benoît , Bi Ke , Chen Cerise , Becking Leontine E. , Lim Jun Ying , Linderoth Tyler , Krehenwinkel Henrik , Gillespie Rosemary
Published: December 2020

The diversification of a host lineage can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, distributed along a chronologically arranged series of volcanic mountains, to determine the parallels between the evolutionary histories of the host spiders and their associated microbial communities, together forming the “holobiont”. Using the stick spiderAriamnes waikula(Araneae, Theridiidae) on the island of Hawaiʻi, and outgroup taxa on older islands, we tested whether each component of the holobiont (the spider hosts, the intracellular endosymbionts, and the gut microbial communities) showed correlated signatures of diversity due to sequential colonization from older to younger volcanoes. In order to investigate this, we generated ddRAD data for the host spiders and 16S rRNA gene amplicon data from their microbiota. We expected sequential colonizations to result in a (phylo)genetic structuring of the host spiders and in a diversity gradient in microbial communities. Results showed that the hostA. waikulais indeed structured by geographic isolation, suggesting sequential colonization from older to younger volcanoes. Similarly, the endosymbiont communities were markedly different betweenAriamnesspecies on different islands, but more homogeneous amongA. waikulapopulations on the island of Hawaiʻi. Conversely, the gut microbiota was largely conserved across all populations and species, which we suspect are generally environmentally derived. Our results highlight that the different components of the holobiont have responded in distinct ways to the dynamic environment of the volcanic archipelago, showing the necessity of understanding the interplay between components to better characterize holobiont evolution.
Rapid selection response to ethanol inS. eubayanusemulates the domestication process under brewing conditions
Authors: Mardones Wladimir , Villarroel Carlos A. , Abarca Valentina , Urbina Kamila , Peña Tomás A. , Molinet Jennifer , Nespolo Roberto F. , Cubillos Francisco A.
Published: December 2020

Although the typical genomic and phenotypic changes that characterize the evolution of organisms under the human domestication syndrome represent textbook examples of rapid evolution, the molecular processes that underpin such changes are still poorly understood. Domesticated yeasts for brewing, where short generation times and large phenotypic and genomic plasticity were attained in a few generations under selection, are prime examples. To experimentally emulate the lager yeast domestication process, we created a genetically complex (panmictic) artificial population of multipleSaccharomyces eubayanusgenotypes, one of the parents of lager yeast. Then we imposed a constant selection regime under a high ethanol concentration in 10 replicated populations during 260 generations (six months) and compared them with evolved controls exposed solely to glucose. Evolved populations exhibited a selection differential of 60% in growth rate in ethanol, mostly explained by the proliferation of a single lineage (CL248.1) that competitively displaced all other clones. Interestingly, the outcome does not require the entire time course of adaptation, as four lineages monopolized the culture at generation 120. Sequencing demonstrated thatde novogenetic variants were produced in all evolved lines, including SNPs, aneuploidies, INDELs, and translocations. In addition, the evolved populations showed correlated responses resembling the domestication syndrome: genomic rearrangements, faster fermentation rates, lower production of phenolic-off flavors and lower volatile compound complexity. Expression profiling in beer wort revealed altered expression levels of genes related to methionine metabolism, flocculation, stress tolerance and diauxic shift, likely contributing to higher ethanol and fermentation stress tolerance in the evolved populations. Our study shows that experimental evolution can rebuild the brewing domestication process in “fast motion” in wild yeast, and also provides a powerful tool for studying the genetics of the adaptation process in complex populations.
Genetic Encoding of Three Distinct Noncanonical Amino Acids Using Reprogrammed Initiator and Nonsense Codons
Authors: Tharp Jeffery M. , Vargas-Rodriguez Oscar , Schepartz Alanna , Söll Dieter
Published: December 2020

We recently described an orthogonal initiator tRNA (itRNATy2) that can initiate protein synthesis with noncanonical amino acids (ncAAs) in response to the UAG nonsense codon. Here we report that a mutant ofitRNATy2(itRNATy2AUA) can efficiently initiate translation in response to the UAU tyrosine codon, giving rise to proteins with an ncAA at their N-terminus. We show that, in cells expressingitRNATy2AUA, UAU can function as a dual-use codon that selectively encodes ncAAs at the initiating position and tyrosine at elongating positions. UsingitRNATy2AUA, in conjunction with its cognate tyrosyl-tRNA synthetase and two mutually orthogonal pyrrolysyl-tRNA synthetases, we demonstrate that UAU can be reassigned along with UAG or UAA to encode two distinct ncAAs in the same protein. Furthermore, by engineering the substrate specificity of one of the pyrrolysyl-tRNA synthetases, we developed a triply orthogonal system that enables simultaneous reassignment of UAU, UAG, and UAA to produce proteins containing three distinct ncAAs at precisely defined sites. To showcase the utility of this system, we produced proteins containing two or three ncAAs, with unique bioorthogonal functional groups, and demonstrate that these proteins can be separately modified with multiple fluorescent probes.

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Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study
Authors: Kim Ashley E. , Brandstetter Elisabeth , Wilcox Naomi , Heimonen Jessica , Graham Chelsey , Han Peter D. , Starita Lea M. , McCulloch Denise J. , Casto Amanda M. , Nickerson Deborah A. , Van de Loo Margaret M. , Mooney Jennifer , Ilcisin Misja , Fay Kairsten A. , Lee Jover , Sibley Thomas R. , Lyon Victoria , Geyer Rachel E. , Thompson Matthew , Lutz Barry R. , Rieder Mark J. , Bedford Trevor , Boeckh Michael , Englund Janet A. , Chu Helen Y.
Published: December 2020

Introduction

While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure.

Methods

From October 2019 to March 2020, we conducted a home-based cross-sectional study in the greater Seattle area, utilizing electronic consent and data collection instruments. Participants received nasal swab collection kits via rapid delivery within 24 hours of self-reporting respiratory symptoms. Samples were returned to the laboratory and were screened for 26 respiratory pathogens and a human marker. Participant data were recorded via online survey at the time of sample collection and one week later.

Results

Of the 4,572 consented participants, 4,359 (95.3%) received a home swab kit, and 3,648 (83.7%) returned a nasal specimen for respiratory pathogen screening. The 3,638 testable samples had a mean RNase P CRT value of 19.0 (SD: 3.4) and 1,232 (33.9%) samples had positive results for one or more pathogens, including 645 (17.7%) influenza-positive specimens. Among the testable samples, the median time between shipment of the home swab kit and completion of laboratory testing was 8 days [IQR: 7.0-14.0].

Discussion

Home-based surveillance using online participant enrollment and specimen self-collection is a feasible method for community-level monitoring of influenza and other respiratory pathogens, which can readily be adapted for use during pandemics.
Extendedin vitroinactivation of SARS-CoV-2 by titanium dioxide surface coating
Authors: Mlcochova P , Chadha A , Hesselhoj T , Fraternali F , Ramsden JJ , Gupta RK
Published: December 2020

SARS-CoV-2 transmission occurs via airborne droplets and surface contamination. We show tiles coated with TiO2120 days previously can inactivate SARS-CoV-2 under ambient indoor lighting with 87% reduction in titres at 1h and complete loss by 5h exposure. TiO2coatings could be an important tool in containing SARS-CoV-2.
Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism
Authors: Rao Qinhui , Wang Yue , Chai Pengxin , Han Long , Kuo Yin-Wei , Yang Renbin , Hu Fangheng , Yang Yuchen , Howard Jonathon , Zhang Kai
Published: December 2020

Thousands of outer-arm dyneins (OADs) are arrayed in the axoneme to drive a rhythmic ciliary beat. Coordination among multiple OADs is essential for generating mechanical forces to bend microtubule doublets (MTDs). Using electron microscopy, we determined high-resolution structures of OAD arrays bound to MTD in two different states. OAD preferentially binds to MTD protofilaments with a pattern resembling the native tracks for its distinct microtubule-binding domains. Upon MTD binding, free OADs are induced to adopt a stable parallel conformation, primed for array formation. Extensive tail-to-head (TTH) interactions between OADs are observed, which need to be broken for ATP turnover by the dynein motor. We propose that OADs in an array sequentially hydrolyze ATP to slide MTDs. ATP-hydrolysis in turn relaxes the TTH interfaces to effectuate free nucleotide cycles of downstream OADs. These findings lead to a model explaining how conformational changes in the axoneme produce coordinated action of dyneins.
Multiple clones of colistin-resistantSalmonella entericacarryingmcr-1plasmids in meat products and patients in Northern Thailand
Authors: Patchanee Prapas , Chokesajjawatee Nipa , Santiyanont Pannita , Chuammitri Phongsakorn , Deeudom Manu , Monteith William , Sheppard Samuel K. , Pascoe Ben , Prasertsee Teerarat
Published: December 2020

Salmonellaspp. is an important foodborne pathogen associated with consumption of contaminated food, especially livestock products. Antimicrobial resistance (AMR) inSalmonellahas been reported globally and increasing AMR in food production is a major public health issue worldwide. The objective of this study was to describe the genetic relatedness amongSalmonella entericaisolates, which displayed identical DNA fingerprint profiles. TenS. entericaisolates were selected from meat and human cases with an identical rep-PCR profile of serovars Rissen (n=4), Weltevreden (n=4), and Stanley (n=2). We used long-read whole genome sequencing (WGS) on the MinION sequencing platform to type isolates and investigatein silicothe presence of specific AMR genes. Antimicrobial susceptibility testing was tested by disk diffusion and gradient diffusion method to corroborate the AMR phenotype. Multidrug resistance and resistance to more than one antimicrobial agent were observed in eight and nine isolates, respectively. Resistance to colistin with an accompanyingmcr-1 gene was observed among theSalmonellaisolates. The analysis of core genome and whole genome MLST revealed that theSalmonellafrom meat and human salmonellosis were closely genetic related. Hence, it could be concluded that meat is one of the important sources forSalmonellainfection in human.

Highlights

Colistin resistance detected in 2 clones from 2 differentSalmonella entericaserovars (Rissen and Weltevreden) with accompanying plasmid-bornemcr-1 gene from the food production chain and human clinical salmonellosis.

High prevalence of multidrug resistant isolates and resistance to more than one antimicrobial agent.

MinION has potential for mobile, rapid and accurate application in veterinary genomic epidemiology studies.
Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces
Authors: Prévost Chantal , Sacquin-Mora Sophie
Published: December 2020

The modeling of protein assemblies at the atomic level remains a central issue in structural biology, as protein interactions play a key role in numerous cellular processes. This problem is traditionally addressed using docking tools, where the quality of the models is based on their similarity to a single reference experimental structure. However, using a static reference does not take into account the dynamic quality of the protein interface. Here, we used all-atom classical Molecular Dynamics simulations to investigate the stability of the reference interface for three complexes that previously served as targets in the CAPRI competition. For each one of these targets, we also ran MD simulations for ten models that are distributed over the High, Medium and Acceptable accuracy categories. To assess the quality of these models from a dynamic perspective, we set up new criteria which take into account the stability of the reference experimental protein interface. We show that, when the protein interfaces are allowed to evolve along time, the original ranking based on the static CAPRI criteria no longer holds as over 50% of the docking models undergo a category change (which can be either toward a better or a lower accuracy group) when reassessing their quality using dynamic information.
Large- and multi-scale networks in the rodent brain during novelty exploration
Authors: Cohen Michael X , Englitz Bernhard , França Arthur S C
Published: December 2020

Neural activity is coordinated across multiple spatial and temporal scales, and these patterns of coordination are implicated in both healthy and impaired cognitive operations. However, empirical cross-scale investigations are relatively infrequent, due to limited data availability and to the difficulty of analyzing rich multivariate datasets. Here we applied frequency-resolved multivariate source-separation analyses to characterize a large-scale dataset comprising spiking and local field potential activity recorded simultaneously in three brain regions (prefrontal cortex, parietal cortex, hippocampus) in freely-moving mice. We identified a constellation of multidimensional, inter-regional networks across a range of frequencies (2-200 Hz). These networks were reproducible within animals across different recording sessions, but varied across different animals, suggesting individual variability in network architecture. The theta band (~4-10 Hz) networks had several prominent features, including roughly equal contribution from all regions and strong inter-network synchronization. Overall, these findings demonstrate a multidimensional landscape of large-scale functional activations of cortical networks operating across multiple spatial, spectral, and temporal scales during open-field exploration.

Significance statement

Neural activity is synchronized over space, time, and frequency. To characterize the dynamics of large-scale networks spanning multiple brain regions, we recorded data from the prefrontal cortex, parietal cortex, and hippocampus in awake behaving mice, and pooled data from spiking activity and local field potentials into one data matrix. Frequency-specific multivariate decomposition methods revealed a cornucopia of neural networks defined by coherent spatiotemporal patterns over time. These findings reveal a rich, dynamic, and multivariate landscape of large-scale neural activity patterns during foraging behavior.