bluuebunny/crossref_metadata_2025 huggingface dataset:
Diurnal variation of the surface temperature of Mars with the Emirates Mars Mission: a comparison with Curiosity and Perseverance rover measurements
Authors: Atri Dimitra , Abdelmoneim Nour , Dhuri Dattaraj B , Simoni Mathilde
Published: October 2022

For the first time, the Emirates Mars Infrared Spectrometer (EMIRS) instrument on board the Emirates Mars Mission (EMM) ‘Hope’, is providing us with the temperature measurements of Mars at all local times covering most of the planet. As a result, it is now possible to compare surface temperature measurements made from orbit with those from the surface by rovers during the same time period. We use data of diurnal temperature variation from the Rover Environmental Monitoring Station (REMS) suite on board the Mars Science Laboratory (MSL) ‘Curiosity’ rover, and the Mars Environmental Dynamics Analyzer (MEDA) suite on board the Mars 2020 ‘Perseverance’ rover, between June and August 2021 and compare them with EMIRS observations and estimates of the Mars Climate Database (MCD) model. We show that although the overall trend of temperature variation is in excellent agreement across missions, EMIRS measurements are systematically lower at night compared to Mars 2020. The lower spatial resolution of EMIRS compared to the rovers and consequently lower average thermal inertia of the observed regions in this particular case primarily contributed to this discrepancy, among other factors. We discuss the implications of these results in improving our understanding of the Martian climate which would lead to better modeling of local weather prediction, useful for future robotic and crewed missions.
Pericyclases for cycloaddition
Authors: Zhang Bo , Ge Hui Ming
Published: October 2022

Focusing on the cycloadditions, which have been widely utilized in total synthesis, this perspective reviews the flourish research of pericyclase for cycloaddition and discusses existing challenges.
Clinical Impact of Ceftriaxone Resistance in Escherichia coli Bloodstream Infections: A Multicenter Prospective Cohort Study
Authors: Tamma Pranita D , Komarow Lauren , Ge Lizhao , Garcia-Diaz Julia , Herc Erica S , Doi Yohei , Arias Cesar A , Albin Owen , Saade Elie , Miller Loren G , Jacob Jesse T , Satlin Michael J , Krsak Martin , Huskins W Charles , Dhar Sorabh , Shelburne Samuel A , Hill Carol , Baum Keri R , Bhojani Minal , Greenwood-Quaintance Kerryl E , Schmidt-Malan Suzannah M , Patel Robin , Evans Scott R , Chambers Henry F , Fowler Vance G , van Duin David ,   for the Antibacterial Resistance Leadership Group
Published: October 2022

Background

Ceftriaxone-resistant (CRO-R) Escherichia coli bloodstream infections (BSIs) are common.

Methods

This is a prospective cohort of patients with E coli BSI at 14 United States hospitals between November 2020 and April 2021. For each patient with a CRO-R E coli BSI enrolled, the next consecutive patient with a ceftriaxone-susceptible (CRO-S) E coli BSI was included. Primary outcome was desirability of outcome ranking (DOOR) at day 30, with 50% probability of worse outcomes in the CRO-R group as the null hypothesis. Inverse probability weighting (IPW) was used to reduce confounding.

Results

Notable differences between patients infected with CRO-R and CRO-S E coli BSI included the proportion with Pitt bacteremia score ≥4 (23% vs 15%, P = .079) and the median time to active antibiotic therapy (12 hours [interquartile range {IQR}, 1–35 hours] vs 1 hour [IQR, 0–6 hours]; P < .001). Unadjusted DOOR analyses indicated a 58% probability (95% confidence interval [CI], 52%–63%) for a worse clinical outcome in CRO-R versus CRO-S BSI. In the IPW-adjusted cohort, no difference was observed (54% [95% CI, 47%–61%]). Secondary outcomes included unadjusted and adjusted differences in the proportion of 30-day mortality between CRO-R and CRO-S BSIs (−5.3% [95% CI, −10.3% to −.4%] and −1.8 [95% CI, −6.7% to 3.2%], respectively), postculture median length of stay (8 days [IQR, 5–13 days] vs 6 days [IQR, 4–9 days]; P < .001), and incident admission to a long-term care facility (22% vs 12%, P = .045).

Conclusions

Patients with CRO-R E coli BSI generally have poorer outcomes compared to patients infected with CRO-S E coli BSI, even after adjusting for important confounders.
Areas of Law: Three Questions in Special Jurisprudence
Authors: Khaitan Tarunabh , Steel Sandy
Published: October 2022

This article addresses three fundamental questions about a key phenomenon in special jurisprudence, ‘areas of law’: (i) what is an area of law; (ii) what are the consequences of dividing law into distinct areas; and (iii) what constitutes the foundations of an area of law. It claims that (i) ‘an area of law’ is a set of legal norms that are intersubjectively recognised by the legal complex as a subset of legal norms in a given jurisdiction; (ii) the sub-division of law into multiple areas matters to the content and scope of legal doctrine, to law’s perceived legitimacy and possibly to its effectiveness; and (iii) the search for the normative foundations of an area of law is typically an inquiry into its ‘aims’ or ‘functions’. This article systematically articulates, explains and answers these three questions generally, ie in relation to areas of law as such.
Bird associations with floristics and physiognomy differ across five biogeographic subregions of the Great Basin, USA
Authors: Zillig Martha W , Fogarty Frank A , Fleishman Erica
Published: October 2022

The majority of management plans for birds on public lands across the western United States do not recognize the geographic variation in a given species’ habitat. We examined associations of plant species and functional groups with occupancy of 19 bird species across 5 biogeographic subregions of the Great Basin (central, western, Sierra Nevada, northern, and eastern), USA. We hypothesized that occupancy was associated with floristics (individual plant species) within subregions, and with physiognomy (characterized by functional groups) across the Great Basin. We used two methods to evaluate bird-vegetation associations within and across subregions. First, we examined which covariates of floristics and physiognomy were significantly associated with occupancy in each subregion. Second, for each bird species, we compared covariate estimates between each of the 10 pairs of subregions. We classified the effects of covariates on occupancy in 2 subregions as significantly different if <5% of their posterior distributions overlapped. The plant species and functional groups that were associated significantly with occupancy varied considerably among subregions. Twenty-four percent of bird-plant associations that were significant at the Great Basin level were not significant in any subregion. Associations between occupancy and floristics differed the most between the Sierra Nevada and central or western subregions, and the least between the eastern and western subregions. Associations between occupancy and physiognomy differed the most between the Sierra Nevada and western and central subregions, and the least between the northern and western subregions. These differences and similarities may reflect variations in climate or bird communities or differences in sampling effort. In addition, the number and strength of associations between occupancy and floristic or physiognomic covariates varied substantially among bird species and subregions. We recommend that the management of birds across the Great Basin or other large ecoregions evaluate and account for geographic variation in environmental attributes associated with occupancy, and not assume bird-plant relations are consistent across the Great Basin.
A rallid ballad: Communal signaling is correlated with year-round territoriality in the most duet-rich family of birds (Gruiformes: Rallidae)
Authors: Goldberg Daniel L , Sadd Ben M , Capparella Angelo P
Published: October 2022

Duetting, in which 2 or more individuals call in coordinated unison, is common in birds, yet most research investigating the function of avian duets has focused only on oscine passerines. However, we have discovered that duetting occurs in 61 species (59%) in the family Rallidae (rails), one of the highest known rates in any bird clade, and that rail duets are also significantly associated with year-round territoriality and habitat type. We applied a comparative approach to study the occurrence of duetting relative to socio-ecological traits and call properties in 103 rail species, with the prediction that duetting rails produce low-frequency calls that spread well over short distances in densely vegetated habitats. Using a model correcting for phylogenetic signal, we found that duetting is the ancestral state in Rallidae, and that duetting rails show a trending effect for being sedentary and nonmigratory. Contrary to our predictions, there was no significant correlation between rail duetting and social bond length, breeding system, breeding latitude from the equator, or sexual dimorphism, as year-round territoriality and forest or heterogeneous habitats were the strongest predictors of duets. Despite the prevalence of duetting in Rallidae, few studies have tested duet functions such as territory defense in this family, and our comparative phylogenetic study lays the groundwork for future research, as little remains known about the behavioral ecology and vocal interactions of many rails.
The power few missing persons: A 10-year follow-up study of over 2,000 youth missing persons
Authors: Thomas Stuart D M , Ferguson Lorna
Published: October 2022

Youths going missing continues to be a matter of great concern for the police. This group has been consistently found to comprise most police missing person reports, be more likely to go repeatedly missing, and experience victimization and vulnerability related to these incidents. This study thus sought to examine single versus repeat versus habitual/chronic missing youth cases to extract differentiated insights to initiate discussions on proactive policing efforts for reducing and preventing missing youth cases. Data employed tracked 2,126 young people reported missing for the first time in 2005, for 10 years using their police records. Over a third went missing more than once. There was evidence of the power few hypothesis, with the habitual/chronic cases constituting 17% of the cases and over 60% of the missing person reports across the study period, and clear differences emerged between single, repeat, and habitual/chronic cases in terms of their demographics, mental health concerns, and justice involvement.
Professional policing and the role of autonomy and discretion in decision-making: A qualitative study from a virtue ethical perspective
Authors: Maile Andrew , Ritzenthaler Sarah , Thompson Aidan , Kristjánsson Kristján
Published: October 2022

Within an overarching identified construct of ‘autonomy and discretion’, this paper uses four themes to discuss how 30 interviewed UK police officers respond to challenging, ethically charged situations and what frameworks guide and structure their decision-making. These themes, elicited through qualitative thematic analysis, are personal judgement, doing the right thing, effective and adaptive communication, and emotional regulation. The relevance of these themes is discussed in the context of police professionalization and the Code of Ethics in England and Wales. The findings illustrate that the professional autonomy of police officers, when grounded in virtue ethics rather than more formulaic deontology, supports morally good policing and safeguards police legitimacy.
Nutrient digestibility, rumen parameters, and (cannabinoid) residues in sheep fed a pelleted diet containing green hemp (Cannabis sativa L.) biomass
Authors: Stevens S A , Krebs G L , Scrivener C J , Noble G K , Blake B L , Dods K C , May C D , Tai Z X , Clayton E H , Lynch E E , Johnson K N
Published: October 2022

The feeding value for ruminants of green hemp biomass, from the low Δ9-tetrahydrocannabinol (Δ9-THC) variety of Cannabis sativa L., is unknown. Twelve Merino ewes were individually penned and randomly allocated on a stratified liveweight basis to one of two pelleted dietary treatments, control (0% hemp, n = 6) or hemp (42% green hemp biomass, n = 6) that delivered a diet meeting the nutrient requirements of the animals. The experimental period consisted of 17 d dietary and housing adaptation, followed by 7 d total urine and feces collection for determination of apparent nutrient digestibility. A ruminal fluid sample was collected on day 27 and assessed for pH, ammonia, volatile fatty acid (VFA), and cannabinoid concentrations. A blood sample from the jugular vein and incisional subcutaneous fat biopsy from an area around the base of the tail were collected on day 28 with additional fat biopsies taken 35 d and 140 d post-feeding to measure cannabinoids. The dry matter (DM), organic matter (OM), and crude protein (CP) digestibilities, along with total VFA concentration did not differ (P = 0.713) between the two diets; however, acid detergent fiber (ADF) and neutral detergent fiber (NDF) digestibilities (P < 0.001), water intake (P = 0.023), and fecal water output (P < 0.001) were significantly lower for the sheep-fed Hemp. Rumen pH did not vary (P = 0.256) between diets, but ruminal ammonia concentration was significantly lower (P = 0.024) for sheep consuming Hemp. Sheep-fed Hemp had significantly greater molar proportions of butyric (P = 0.039) and hexanoic (P = 0.012) acids and lower molar proportions of propionic acid (P = 0.003). There were no differences between diets for N intake (P = 0.175), fecal N output (P = 0.253), and N balance (P = 0.695), with all sheep in positive N balance; however, there was significantly lower (P = 0.001) urinary N output for sheep-fed Hemp. Cannabidiolic acid (CBDA) and tetrahydrocannabinolic acid (THCA) were detected in plasma of all sheep-fed Hemp. ∆9-tetrahydrocannabinol was present in the subcutaneous fat of four of the six sheep on the final day of being fed Hemp, and in all (six) sheep 35 d post-feeding and one sheep 140 d post-feeding Hemp. No cannabinoids were detected in the corresponding samples taken from the sheep-fed Control. Thus, despite green hemp biomass being nutritionally a suitable feed for ruminants, under current Food Standards in Australia, the presence of these cannabinoid residues restricts its use in ruminant diets.
Guilt by Association: DNA Barcoding-Based Identification of Potential Plant Hosts of Phytoplasmas from Their Insect Carriers
Authors: Inaba Junichi , Shao Jonathan , Trivellone Valeria , Zhao Yan , Dietrich Christopher H. , Bottner-Parker Kristi D. , Ivanauskas Algirdas , Wei Wei
Published: October 2022

Phytoplasmas are small phloem-restricted and insect-transmissible bacteria that infect many plant species, including important crops and ornamental plants, causing severe economic losses. Our previous studies screened phytoplasmas in hundreds of leafhoppers collected from natural habitats worldwide and identified multiple genetically different phytoplasmas in seven leafhopper species (potential insect vectors). As an initial step toward determining the impact of these phytoplasmas on the ecosystem, ribulose 1,5-biphosphate carboxylase large subunit ( rbcL), a commonly used plant DNA barcoding marker, was employed to identify the plant species that the phytoplasma-harboring leafhoppers feed on. The DNA of 17 individual leafhoppers was PCR amplified using universal rbcL primers. PCR products were cloned, and five clones per amplicon were randomly chosen for Sanger sequencing. Moreover, Illumina high-throughput sequencing on selected PCR products was conducted and confirmed no missing targets in Sanger sequencing. The nucleotide BLAST results revealed 14 plant species, including six well-known plant hosts of phytoplasmas such as tomato, alfalfa, and maize. The remaining species have not been documented as phytoplasma hosts, expanding our knowledge of potential plant hosts. Notably, the DNA of tomato and maize (apparently cultivated in well-managed croplands) was detected in some phytoplasma-harboring leafhopper species sampled in non-crop lands, suggesting the spillover/spillback risk of phytoplasma strains between crop and non-crop areas. Furthermore, our results indicate that barcoding (or metabarcoding) is a valuable tool to study the three-way interactions among phytoplasmas, plant hosts, and vectors. The findings contribute to a better understanding of phytoplasma host range, host shift, and disease epidemiology.
Screening and testing for latent tuberculosis infection among patients who are immunocompromised
Authors: Sierra Carmen Josefa , Downs Charles A.
Published: October 2022

It is critical to detect latent tuberculosis infection through screening and testing individuals at high risk of progression to active tuberculosis, including patients who are immunocompromised. NPs should be familiar with available testing for accurate diagnosis in order to expedite treatment.
Spontaneous Coronary Artery Dissection: Review of Possible Pathophysiological Risk Factors
Authors: Kim Chan W. , Frishman William H. , Aronow Wilbert S.
Published: October 2022

Spontaneous coronary artery dissection (SCAD) is a rare cause of acute coronary syndrome (ACS) that typically affects the younger and healthier female population without the typical ACS risk factors such as hypertension, diabetes, or hyperlipidemia. The clinical presentation of SCAD can be diverse and the diagnosis is typically by coronary angiography but also can require advanced imaging such as intravascular ultrasound or optical coherence tomography. Past studies have shown the atypical patient characteristics of SCAD patients among ACS patients. The main challenge is that the exact pathophysiology of SCAD is unknown. Potential pathophysiological risk factors are discussed including fibromuscular dysplasia, other arteriopathies, pregnancy and female sex hormone changes, migraines, inflammatory conditions, and stress. The current understanding of these risk factors along with potential pathophysiological mechanisms are discussed. There still remain many areas of additional investigation in understanding this rare cause of ACS.
Impact of Peripheral and Corneal Neuropathy on Markers of Ocular Surface Discomfort in Diabetic Chronic Kidney Disease
Authors: Asiedu Kofi , Dhanapalaratnam Roshan , Krishnan Arun V. , Kwai Natalie , Poynten Ann , Markoulli Maria
Published: October 2022

SIGNIFICANCE

There is a reduction in corneal nerve fiber density and length in type 2 diabetes mellitus with chronic kidney disease compared with type 2 diabetes mellitus alone; however, this difference does not result in worse ocular surface discomfort or dry eye disease.

PURPOSE

This study aimed to determine the clinical impact of corneal nerve loss on ocular surface discomfort and markers of ocular surface homeostasis in people with type 2 diabetes mellitus without chronic kidney disease (T2DM–no CKD) and those with type 2 diabetes mellitus with concurrent chronic kidney disease (T2DM-CKD).

METHODS

Participants were classified based on estimated glomerular filtration rates into two groups: T2DM-CKD (n = 27) and T2DM–no CKD (n = 28).

RESULTS

There was a significant difference between the T2DM-CKD and T2DM–no CKD groups in corneal nerve fiber density (14.9 ± 8.6 and 21.1 ± 7.1 no./mm2, respectively; P = .005) and corneal nerve fiber length (10.0 ± 4.6 and 12.3 ± 3.7 mm/mm2, respectively; P = .04). Fluorescein tear breakup time was significantly reduced in T2DM-CKD compared with T2DM–no CKD (8.1 ± 4.4 and 10.7 ± 3.8 seconds, respectively; P = .01), whereas ocular surface staining was not significantly different (3.5 ± 1.7 and 2.7 ± 2.3 scores, respectively;P = .12). In terms of ocular surface discomfort, there were no significant differences in the ocular discomfort score scores (12.5 ± 11.1 and 13.6 ± 12.1, respectively; P = .81) and Ocular Pain Assessment Survey scores (3.3 ± 5.4 and 4.3 ± 6.1, respectively; P = .37) between the T2DM-CKD and T2DM–no CKD.

CONCLUSIONS

The current study demonstrated that corneal nerve loss is greater in T2DM-CKD than in T2DM–no CKD. However, these changes do not impact ocular surface discomfort or markers of ocular surface homeostasis.
The General Movements Motor Optimality Score in High-Risk Infants: A Systematic Scoping Review
Authors: Crowle Cathryn , Jackman Michelle , Morgan Catherine
Published: October 2022

Purpose:

The aim of this systematic scoping review was to explore the use of the motor optimality score in the fidgety movement period in clinical practice, and to investigate evidence for the motor optimality score in predicting neurodevelopmental outcomes.

Summary of Key Points:

Thirty-seven studies, with 3662 infants, were included. Studies were conceptualized and charted into 4 categories based on the motor optimality score: prediction, outcome measure, descriptive, or psychometric properties. The most represented populations were preterm or low-birth-weight infants (16 studies), infants with cerebral palsy or neurological concerns (5 studies), and healthy or term-born infants (4 studies).

Conclusion:

The motor optimality score has the potential to add value to existing tools used to predict risk of adverse neurodevelopmental outcomes. Further research is needed regarding the reliability and validity of the motor optimality score to support increased use of this tool in clinical practice. What this adds to the evidence: The motor optimality score has potential to improve the prediction of adverse neurodevelopmental outcomes. Further research on validity and reliability of the motor optimality score is needed; however, a revised version, the motor optimality score-R (with accompanying manual) will likely contribute to more consistency in the reporting of the motor optimality score in future.
PSMA-PET Detection of Unusual Metastases in Castrate-Sensitive Prostate Carcinoma
Authors: Harris Nathanial , Tan Mun Yee , Ng Michael , Blakey David , Guerrieri Mario , Joon Daryl Lim , Lau Eddie , Foroudi Farshad , Armstrong Alexander , Chao Michael
Published: October 2022

Prostate cancer (PCa) is a multifaceted, heterogeneous disease (with 7 molecular subtypes), which can metastasize to common sites, such as bone, lymph nodes, liver, and lungs. However, with PSMA PET imaging, rare sites of metastasis are increasingly discovered. We report 5 cases of unusual metastases in patients with castrate-sensitive PCa: solitary right inguinal nodal metastasis, solitary abdominal wall metastasis, penile shaft metastases, solitary perineum metastasis, and pleural metastases. These cases further support the use of PSMA-PET imaging in PCa monitoring, with the ability to detect solitary, small volume, and rare sites of metastases, which may not be apparent on conventional imaging.
Locally correlated kinetics of post-replication DNA methylation reveals processivity and region specificity in DNA methylation maintenance
Authors: Ren Honglei , Taylor Robert B. , Downing Timothy L. , Read Elizabeth L.
Published: October 2022

DNA methylation occurs predominantly on cytosine-phosphate-guanine (CpG) dinucleotides in the mammalian genome, and the methylation landscape is maintained over mitotic cell division. It has been posited that coupling of maintenance methylation activity among neighbouring CpGs is critical to stability over cellular generations; however, the mechanism is unclear. We used mathematical models and stochastic simulation to analyse data from experiments that probe genome-wide methylation of nascent DNA post-replication in cells. We find that DNA methylation maintenance rates on individual CpGs are locally correlated, and the degree of this correlation varies by genomic regional context. By using theory of protein diffusion along DNA, we show that exponential decay of methylation rate correlation with genomic distance is consistent with enzyme processivity. Our results provide quantitative evidence of genome-wide methyltransferase processivity
in vivo
. We further developed a method to disentangle different mechanistic sources of kinetic correlations. From the experimental data, we estimate that an individual methyltransferase methylates neighbour CpGs processively if they are 36 basepairs apart, on average. But other mechanisms of coupling dominate for longer inter-CpG distances. Our study demonstrates that quantitative insights into enzymatic mechanisms can be obtained from replication-associated, cell-based genome-wide measurements, by combining data-driven statistical analyses with hypothesis-driven mathematical modelling.
A model for the collective synchronization of flashing in
Photinus carolinus
Authors: McCrea Madeline , Ermentrout Bard , Rubin Jonathan E.
Published: October 2022

Recent empirical investigations have characterized the synchronized flashing behaviours of male
Photinus carolinus
fireflies in their natural habitat in Great Smoky Mountain National Park as well as in controlled environments. We develop a model for the flash dynamics of an individual firefly based on a canonical elliptic burster, a slow-fast dynamical system that produces a repeating pattern of multiple flashes followed by a quiescent period. We show that a small amount of noise renders that oscillation very irregular, but when multiple model fireflies interact through their flashes, the behaviour becomes much more periodic. We show that the aggregate behaviour is qualitatively similar to the experimental findings. We next distribute the fireflies in a two-dimensional spatial domain and vary the interaction range. In addition to synchronization, various spatio-temporal patterns involving propagation of activity emerge spontaneously. Finally, we allow a certain number of fireflies to move and demonstrate how their speed affects the rate and degree of synchronization.
Emerging roles of centrosome cohesion
Authors: Dang Hairuo , Schiebel Elmar
Published: October 2022

The centrosome, consisting of centrioles and the associated pericentriolar material, is the main microtubule-organizing centre (MTOC) in animal cells. During most of interphase, the two centrosomes of a cell are joined together by centrosome cohesion into one MTOC. The most dominant element of centrosome cohesion is the centrosome linker, an interdigitating, fibrous network formed by the protein C-Nap1 anchoring a number of coiled-coil proteins including rootletin to the proximal end of centrioles. Alternatively, centrosomes can be kept together by the action of the minus end directed kinesin motor protein KIFC3 that works on interdigitating microtubules organized by both centrosomes and probably by the actin network. Although cells connect the two interphase centrosomes by several mechanisms into one MTOC, the general importance of centrosome cohesion, particularly for an organism, is still largely unclear. In this article, we review the functions of the centrosome linker and discuss how centrosome cohesion defects can lead to diseases.
Individual differences in decision-making: evidence for the scarcity hypothesis from the English Longitudinal Study of Ageing
Authors: Tunney Richard J. , James Richard J. E.
Published: October 2022

We report the results of a pre-registered analysis of data from the English Longitudinal Study of Ageing that was designed to test the hypothesis that economic scarcity is associated with individual differences in decision-making. We tested this hypothesis by comparing time preferences for different socio-economic groups and in geographical areas ranging from the most deprived to the least deprived in England using the English indices of multiple deprivation. The data supported this hypothesis: people in the most deprived areas were more likely to prefer smaller-sooner rewards than people from the least deprived areas. Similarly, people in technical or routine occupations tended to prefer smaller-sooner rewards than people in professional or intermediate occupations. In addition, we found that gender, cognitive function and subjective social status also predicted time preferences. We discuss these results in the context of theoretical models of scarcity-based models of choice behaviour and decision-making.
Ternary network models for disturbed ecosystems
Authors: Peel Kieran , Evans Darren , Emary Clive
Published: October 2022

The complex network of interactions between species makes understanding the response of ecosystems to disturbances an enduring challenge. One commonplace way to deal with this complexity is to reduce the description of a species to a binary presence–absence variable. Though convenient, this limits the patterns of behaviours representable within such models. We address these shortcomings by considering discrete population models that expand species descriptions beyond the binary setting. Specifically, we focus on ternary (three-state) models which, alongside presence and absence, additionally permit species to become overabundant. We apply this ternary framework to the robustness analysis of model ecosystems and show that this expanded description permits the modelling of top-down extinction cascades emerging from consumer pressure or mesopredator release. Results therefore differ significantly from those seen in binary models, where such effects are absent. We also illustrate how this method opens up the modelling of ecosystem disturbances outside the scope of binary models, namely those in which species are externally raised to overabundance. Our method therefore has the potential to provide a richer description of ecosystem dynamics and their disturbances, while at the same time preserving the conceptual simplicity of familiar binary approaches.
Correlated evolution between colour conspicuousness and drum speed in woodpeckers
Authors: Cárdenas-Posada Ghislaine , Fuxjager Matthew J.
Published: October 2022

Sexual selection drives the evolution of many spectacular animal displays that we see in nature. Yet, how selection combines and elaborates different signal traits remains unclear. Here, we investigate this issue by testing for correlated evolution between head plumage colour and drumming behaviour in woodpeckers. These signals function in the context of mate choice and male–male competition, and they may appear to a receiver as a single multimodal display. We test for such correlations in males of 132 species using phylogenetic linear models, while considering the effect of habitat. We find that the plumage chromatic contrast is positively correlated with the speed of the drum, supporting the idea that species evolving more conspicuous plumage on their head also evolve faster drum displays. By contrast, we do not find evidence of correlated evolution between drum speed and head colour diversity, size of the head's red patch, or extent of the plumage achromatic contrast. Drum length was not correlated with any of the plumage coloration metrics. Lastly, we find no evidence that habitat acts as a strong selective force driving the evolution of head coloration or drumming elaboration. Coevolution between different signal modalities is therefore complex, and probably depends on the display components in question.
Regulation of stem cell dynamics through volume exclusion
Authors: García-Tejera Rodrigo , Schumacher Linus , Grima Ramon
Published: October 2022

The maintenance and regeneration of adult tissues rely on the self-renewal of stem cells. Regeneration without over-proliferation requires precise regulation of the stem cell proliferation and differentiation rates. The nature of such regulatory mechanisms in different tissues, and how to incorporate them in models of stem cell population dynamics, is incompletely understood. The critical birth-death (CBD) process is widely used to model stem cell populations, capturing key phenomena, such as scaling laws in clone size distributions. However, the CBD process neglects regulatory mechanisms. Here, we propose the birth-death process with volume exclusion (vBD), a variation of the birth-death process that considers crowding effects, such as may arise due to limited space in a stem cell niche. While the deterministic rate equations predict a single non-trivial attracting steady state, the master equation predicts extinction and transient distributions of stem cell numbers with three possible behaviours: long-lived quasi-steady state (QSS), and short-lived bimodal or unimodal distributions. In all cases, we approximate solutions to the vBD master equation using a renormalized system-size expansion, QSS approximation and the Wentzel–Kramers–Brillouin method. Our study suggests that the size distribution of a stem cell population bears signatures that are useful to detect negative feedback mediated via volume exclusion.
Local adaptation to hosts and parasitoids shapeHamiltonella defensagenotypes across aphid species
Authors: Wu Taoping , Monnin David , Lee Rene A. R. , Henry Lee M.
Published: October 2022

Facultative symbionts are common in insects and can provide their hosts with significant adaptations. Yet we still have a limited understanding of what shapes their distributions, such as why particular symbiont strains are common in some host species yet absent in others. To address this question, we genotyped the defensive symbiontHamiltonella defensain 26 aphid species that commonly carry this microbe. We found thatHamiltonellastrains were strongly associated with specific aphid species and that strains found in one host species rarely occurred in others. To explain these associations, we reciprocally transferred theHamiltonellastrains of three aphid species,Acyrthosiphon pisum,Macrosiphoniella artemisiaeandMacrosiphum euphorbiae, and assessed the impact ofHamiltonellastrain on: the stability of the symbiosis, aphid fecundity and parasitoid resistance. We demonstrate that theHamiltonellastrains found in nature are locally adapted to specific aphid hosts, and their ecology: aphids tend to carryHamiltonellastrains that are efficiently transmitted to their offspring, non-lethal, and that provide strong protection against their dominant parasitoid species. Our results suggest that facultative symbiont distributions are shaped by selection from natural enemies, and the host itself, resulting in locally adapted symbioses that provide significant benefits against prevailing natural enemies.
Disentangling the developmental origins of a novel phenotype: enhancement versus reversal of environmentally induced gene expression
Authors: Levis Nicholas A. , McKay Daniel J. , Pfennig David W.
Published: October 2022

Increasing evidence suggests that many novel traits might have originated via plasticity-led evolution (PLE). Yet, little is known of the developmental processes that underpin PLE, especially in its early stages. One such process is ‘phenotypic accommodation’, which occurs when, in response to a change in the environment, an organism experiences adjustments across variable parts of its phenotype that improve its fitness. Here, we asked if environmentally induced changes in gene expression are enhanced or reversed during phenotypic accommodation of a novel, complex phenotype in spadefoot toad tadpoles (
Spea multiplicata
). More genes than expected were affected by both the environment and phenotypic accommodation in the liver and brain. However, although phenotypic accommodation primarily reversed environmentally induced changes in gene expression in liver tissue, it enhanced these changes in brain tissue. Thus, depending on the tissue, phenotypic accommodation may either minimize functional disruption via reversal of gene expression patterns or promote novelty via enhancement of existing expression patterns. Our study thereby provides insights into the developmental origins of a novel phenotype and the incipient stages of PLE.
Hybridization order is not the driving factor behind biases in duplicate gene losses among the hexaploid Solanaceae
Authors: McRae Logan , Beric Aleksandra , Conant Gavin C.
Published: October 2022

We model the post-hexaploidy evolution of four genomes from the Solanaceae, a group of flowering plants comprising tomatoes, potatoes and their relatives. The hexaploidy that these genomes descend from occurred through two sequential allopolyploidy events and was marked by the unequal losses of duplicated genes from the different progenitor subgenomes. In contrast with the hexaploid Brassiceae (broccoli and its relatives), where the subgenome with the most surviving genes arrived last in the hexaploidy, among the Solanaceae the most preserved subgenome descends from one of the original two tetraploid progenitors. In fact, the last-arriving subgenome in these plants actually has the fewest surviving genes in the modern genomes. We explore whether the distribution of repetitive elements (REs) in these genomes can explain the biases in gene losses, but while the signals we find are broadly consistent with a role for high RE density in driving gene losses, the REs turn over so quickly that little signal of the RE condition at the time of paleopolyploidy is extant in the modern genomes.
20S-ginsenoside Rg3 inhibits the biofilm formation and haemolytic activity of Staphylococcus aureus by inhibiting the SaeR/SaeS two-component system
Authors: Chen Junwen , Chen Jinlian , Wang Zhanwen , Chen Chengchun , Zheng Jinxin , Yu Zhijian , Deng Qiwen , Zhao Yuxi , Wen Zewen
Published: October 2022

Introduction.

Staphylococcus aureus

is a major cause of chronic diseases and biofilm formation is a contributing factor. 20S-ginsenoside Rg3 (Rg3) is a natural product extracted from the traditional Chinese medicine red ginseng.

Gap statement. The effects of Rg3 on biofilm formation and haemolytic activity as well as its antibacterial mechanism against

S. aureus

have not been reported.

Aim. This study aimed to investigate the effects of Rg3 on biofilm formation and haemolytic activity as well as its antibacterial action against clinical

S. aureus

isolates.

Methodology. The effect of Rg3 on biofilm formation of clinical

S. aureus

isolates was studied by crystal violet staining. Haemolytic activity analysis was carried out. Furthermore, the influence of Rg3 on the proteome profile of

S. aureus

was studied by quantitative proteomics to clarify the mechanism underlying its antibacterial action and further verified by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR).

Results. Rg3 significantly inhibited biofilm formation and haemolytic activity in clinical

S. aureus

isolates. A total of 63 with >1.5-fold changes in expression were identified, including 34 upregulated proteins and 29 downregulated proteins. Based on bioinformatics analysis, the expression of several virulence factors and biofilm-related proteins, containing CopZ, CspA, SasG, SaeR/SaeS two-component system and SaeR/SaeS-regulated proteins, including leukocidin-like protein 2, immunoglobulin-binding protein G (Sbi) and fibrinogen-binding protein, in the

S. aureu

s of the Rg3-treated group was downregulated. RT-qPCR confirmed that Rg3 inhibited the regulation of SaeR/SaeS and decreased the transcriptional levels of the biofilm-related genes CopZ, CspA and SasG.

Conclusions. Rg3 reduces the formation of biofilm by reducing cell adhesion and aggregation. Further, Rg3 can inhibit the SaeR/SaeS two-component system, which acts as a crucial signal transduction system for the anti-virulence activity of Rg3 against clinical

S. aureus

isolates.
Phenotypic and genotypic profiling reveals a high prevalence of methicillin-resistant Staphylococcus aureus isolated from hospitals, houseflies and adjacent informal food retailers in Botswana
Authors: Seetswane Eunicah , Loeto Daniel , Muzila Mbaki , Tshekiso Kgomotso , Gomba Annancietar , Baruti Kabo , Jongman Mosimanegape
Published: October 2022

The increasing occurrence of methicillin-resistant

Staphylococcus aureus

(MRSA) in the environment, food and healthcare systems is a global public health concern. MRSA is reported to cause food poisoning, osteomyelitis and pyogenic infections of the skin, and consequently has been categorized as a high-priority pathogen by the World Health Organization. Here, we determined the presence of MRSA in clinical (n=56), food (n=150) and housefly samples (n=970) collected from two hospitals in Botswana. Characterization based on phenotypic (antimicrobial resistance, biofilm production) and genotypic (antimicrobial resistance genes and integrons) profiles were performed on all isolates. Of the total samples tested, 64 were positive for MRSA following conventional culture methods and PCR amplification of the mecA and mecC genes for confirmation of presumptive MRSA isolates. The confirmed isolates included 71 % (95 % CI 83.2–59.6) from clinical, 9 % (95 % CI 14­–4.8) from food, and 1 % (95 % CI 1.6–0.4) collected from housefly samples. In total 89 % (n=57) isolates in the current study showed a multidrug resistance phenotype, among these, resistance to β-lactams and glycoside antibiotic classes were predominant. Genotypic characterization showed the domination of the blatem gene (95 %) followed by fox (63 %) and tetO (19 %) whilst vanA was only reported in 13 % of the isolates. Integrons were detected in 50 % (32/64) of the total MRSA isolates, and we report a high prevalence of etd gene, detected in 67 % (43/64) of the isolates followed by eta 38 % (24/64) whilst tsst-1 (3%) was the least detected genetic determinant. The genes etb and PVL were not detected in a ll the tested MRSA isolates. We provide the first report on the prevalence of MRSA isolated from the clinical-food-vector nexus harbouring biofilm and blatem genes, and antibiotic resistance profiles in Botswana. These results are significant for risk-assessment analysis and the development of improved MRSA infection prevention and control strategies.
Enhanced donor antigen presentation by B-cells predicts acute cellular rejection and late outcomes after transplantation
Authors: Ashokkumar Chethan , Ningappa Mylarappa , Raghu Vikram , Mazariegos George , Higgs Brandon W. , Morgan Paul , Remaley Lisa , Fazzolare Tamara , Holzer Pamela , Trostle Kevin , Xu Qingyong , Zeevi Adriana , Squires James , Soltys Kyle , Horslen Simon , Khanna Ajai , Ganoza Armando , Sindhi Rakesh
Published: October 2022

Purpose

Enhanced B-cell presentation of donor alloantigen relative to presentation of HLA-mismatched reference alloantigen is associated with acute cellular rejection (ACR), when expressed as a ratio called the antigen presenting index (API) in an exploratory cohort of liver and intestine transplant (LT, IT) recipients.

Methods

To test clinical performance, we measured the API using the previously described 6-hour assay in 84 LT and 54 IT with median age 3.3 years (0.05-23.96). Recipients experiencing ACR within 60 days after testing were termed rejectors.

Results

We first confirmed that B-cell uptake and presentation of alloantigen induced and thus reflected the alloresponse of T-helper cells, which were incubated without and with cytochalasin and primaquine to inhibit antigen uptake and presentation, respectively. Transplant recipients included 76 males and 62 females. Rejectors were tested at median 3.6 days before diagnosis. The API was higher among rejectors compared with non-rejectors (2.2 ± 0.2 vs 0.6 ± 0.04, p-value=1.7E-09). In logistic regression and ROC analysis, API ≥ 1.1 achieved sensitivity, specificity, positive and negative predictive values for predicting ACR in 99 training set samples. Corresponding metrics ranged from 80-88% in 32 independent post-transplant samples, and 73-100% in 20 independent pre-transplant samples. In time-to-event analysis, API ≥ 1,1 predicted higher incidence of late DSA after API measurements in LT (p=0.011) and graft loss in IT recipients (p=0.008), compared with recipients with API<1.1, respectively.

Conclusion

Enhanced donor antigen presentation by circulating B-cells predicts rejection after liver or intestine transplantation as well as higher incidence of DSA and graft loss late after transplantation
Evidences of a component Allee effect for an invasive pathogen:Hymenoscyphus fraxineus, the ash dieback agent
Authors: Laubray Simon , Buée Marc , Marçais Benoît
Published: October 2022

Invasive pathogens are a major threat to forest health especially in managed forest with low diversity. The die-back of EuropeanFraxinus spp. caused by the fungusHymenoscyphus fraxineusis the latest example of pathogen invasion causing widespread damage. Host resistance and environment, in particular stand factors were shown to strongly impact disease severity on European ash. The fact thatH. fraxineusreproduce mostly through heterothallic sexual reproduction suggest that an Allee effect could limit the mating success at low host densities, thus limiting inoculum production and disease development. Populations ofH. fraxineuswere monitored during the fruiting period in a network of stands across a host density gradient in forest and non-forest environment. Ash dieback, basal area of ash, density of infected ash leaf debris (rachis) and apothecia in the litter and ascospores load in the air were determined in the different environments during two years. We showed significant differences between forest and non-forest environment with ash dieback, infection rate and inoculum production higher in forest settings. Host density significantly affected disease development, with crown dieback, density of infected rachis in the litter and inoculum production increasing with host density. We also demonstrated that fruiting rate, i.e. the number of apothecia per infected rachis dry weight, is strongly dependent on infected rachis density. Inoculum production is therefore limited at low host densities. Such a component Allee effect could be important inH. fraxineusepidemiology and invasion dynamic.
EPIGENETIC LANDSCAPE OF HEAT STRESS INTERGENERATIONAL INHERITANCE IN A TELEOST FISH
Authors: Brionne Aurélien , Goupil Anne-Sophie , Kica Stéphanie , Lareyre Jean-Jacques , Labbé Catherine , Laurent Audrey
Published: October 2022

Epigenetic information is transmitted from cell to cell, and even generation to generation. The question of epigenetic inheritance in fish has become of crucial interest in the recent years, when the mammalian model of methylome erasure in germ cells and embryos was found not to be conserved. Fish, which are particularly exposed to environmental variations might thus be prone to transmit epigenetic alterations to their offspring, driving rapid environmental acclimation. Here, by sequencing spermatozoa and muscle methylomes, we characterized the methylation landscape of paternal gametes in rainbow trout and demonstrated its sensitivity to a 4°C increased rearing temperature during spermatogenesis. We found that spermatozoa methylome primes housekeeping and developmental genes for activation and might be instrumental to early development. Most of these methylation-free promoters were not affected by temperature, attesting the robustness of the epigenetic programming of early development. However, the increase of temperature triggered the differential methylation of 5,359 regions, among which 560 gene promoters control spermiogenesis and lipid metabolism. We therefore report, for the first time in fish, that sperm epigenetic landscape carries marks of parental environmental conditions. In the context of a 4°C temperature increase during spermatogenesis, we describe how rainbow trout sperm DNA methylation might be a molecular basis of intergenerational inheritance and question its role in controlling next generation’s performances and acclimation to climate change.