bluuebunny/crossref_metadata_2025 huggingface dataset:
Operative Volumes and Postoperative Outcomes After Elective Resection of Congenital Lung Malformations in Infants
Authors: Engwall-Gill Abigail J. , Weller Jennine H. , Salvi Pooja S. , Sescleifer Anne M. , Penikis Annalise B. , Sferra Shelby R. , Halbert-Elliott Kyra M. , Rhee Daniel S. , Solomon Daniel G. , Kunisaki Shaun M.
Published: March 2024

Objective:

To determine whether hospital- and surgeon-level operative volumes are associated with differences in postoperative outcomes among infants undergoing elective lung surgery for a congenital lung malformation (CLM).

Summary Background Data:

Infant lung surgery is a relatively uncommon procedure performed by pediatric surgeons nationwide. The relationship between surgical volume and postoperative outcomes remains unknown.

Methods:

A retrospective cohort study of asymptomatic infants who underwent elective lung resection of a CLM was conducted using the Pediatric Health Information System database (2016-2020). Multivariable linear and poisson regressions were performed based on annual lung resection tertiles.

Results:

There were 1420 infants managed by 48 hospitals and 309 primary surgeons. Institutions that performed seven or fewer CLM resections per year (56%) were associated with significantly higher postoperative complication rates compared to medium- and high-volume hospitals (low: 134 [34%], medium: 110 [21%], high: 144 [29%]; P<0.001). Surgeons who performed one or fewer CLM resections per year (82%) were associated with significantly higher complication rates compared to medium- and high-volume surgeons (low: 171 [31%], medium: 75 [26%], high: 119 [24%]; P=0.02). Multivariable analyses confirmed that low-volume hospitals were associated with higher complications (OR 1.81, CI 1.38-2.37; P<0.001), and low-volume surgeons had an increased risk of complications (overall: OR 1.37, CI 1.01-1.84; P=0.04).

Conclusions:

In this cohort study of infants undergoing elective lung resection for a CLM, lower volume providers were associated with higher postoperative patient morbidity. These findings represent an opportunity to inform quality improvement initiatives on pediatric lung resection and the debate on surgical subspecialization for this unique patient population.
Modulation of cell-mediated immunity during pregnancy in wild bonobos
Authors: Behringer Verena , Deimel Caroline , Ostner Julia , Fruth Barbara , Sonnweber Ruth
Published: March 2024

During pregnancy, the mammalian immune system must simultaneously protect against pathogens while being accommodating to the foreign fetal tissues. Our current understanding of this immune modulation derives predominantly from industrialized human populations and laboratory animals. However, their environments differ considerably from the pathogen-rich, resource-scarce environments in which pregnancy and the immune system co-evolved. For a better understanding of immune modulation during pregnancy in challenging environments, we measured urinary neopterin, a biomarker of cell-mediated immune responses, in 10 wild female bonobos (
Pan paniscus
) before, during and after pregnancy. Bonobos, sharing evolutionary roots and pregnancy characteristics with humans, serve as an ideal model for such investigation. Despite distinct environments, we hypothesized that cell-mediated immune modulation during pregnancy is similar between bonobos and humans. As predicted, neopterin levels were higher during than outside of pregnancy, and highest in the third trimester, with a significant decline post-partum. Our findings suggest shared mechanisms of cell-mediated immune modulation during pregnancy in bonobos and humans that are robust despite distinct environmental conditions. We propose that these patterns indicate shared immunological processes during pregnancy among hominins, and possibly other primates. This finding enhances our understanding of reproductive immunology.
Sir Derek Harry Roberts. 28 March 1932—17 February 2021
Authors: Pepper FRS Michael , Kelly FRS Michael
Published: March 2024

Derek Roberts was one of the most influential figures in British industrial technology and subsequently in the academic world. The word most frequently used to describe him is ‘visionary’. From a humble background, his abilities in science and the hard work characterizing his later career resulted in academic success in Physics at Manchester University. He joined the Plessey Company Ltd just as the silicon revolution, which was to change the face of electronics, began and quickly established his outstanding abilities in research and management. His most important scientific achievements involved the transition from component to all-semiconductor electronics, to which he made numerous original contributions in an industrial context. After rising to the top of the ranks at Plessey, he moved to GEC, where his outstanding managerial skills brought together the many different companies within the GEC portfolio. His final career move as Provost of University College London (UCL) was due in part to his strong contacts with the academic world, particularly his active presence as a Visiting Professor at UCL. There, his remarkable ability to make change was successfully deployed across all areas of the university's activity, particular successes being in the areas of health and medicine.
Shrinking Alpine chamois: higher spring temperatures over the last 27 years in Switzerland are linked to a 3 kg reduction in body mass of yearlings
Authors: Masoero Giulia , Gencheva Kristina Georgieva , Ioset Noémie , Bersier Louis-Félix , Tettamanti Federico , Bize Pierre
Published: March 2024

Although climate change is considered to be partly responsible for the size change observed in numerous species, the relevance of this hypothesis for ungulates remains debated. We used body mass measurements of 5635 yearlings (i.e. 1.5 years old) of Alpine chamois (
Rupicapra rupicapra
) harvested in September in the Swiss Alps (Ticino canton) from 1992 to 2018. In our study area, during this period, yearlings shrank by
ca
3 kg while temperatures between May and July rose by 1.7°C. We identified that warmer temperatures during birth and the early suckling period (9 May to 2 July in the year of birth) had the strongest impact on yearling mass. Further analyses of year-detrended mass and temperature data indicate that this result was not simply due to changes in both variables over years, but that increases in temperature during this particularly sensitive time window for development and growth are responsible for the decrease in body mass of yearling chamois. Altogether, our results suggest that rising temperatures in the Alpine regions could significantly affect the ecology and evolution of this wild ungulate.
Soundscape enrichment increases larval settlement rates for the brooding coral
Porites astreoides
Authors: Aoki Nadège , Weiss Benjamin , Jézéquel Youenn , Zhang Weifeng Gordon , Apprill Amy , Mooney T. Aran
Published: March 2024

Coral reefs, hubs of global biodiversity, are among the world’s most imperilled habitats. Healthy coral reefs are characterized by distinctive soundscapes; these environments are rich with sounds produced by fishes and marine invertebrates. Emerging evidence suggests these sounds can be used as orientation and settlement cues for larvae of reef animals. On degraded reefs, these cues may be reduced or absent, impeding the success of larval settlement, which is an essential process for the maintenance and replenishment of reef populations. Here, in a field-based study, we evaluated the effects of enriching the soundscape of a degraded coral reef to increase coral settlement rates.
Porites astreoides
larvae were exposed to reef sounds using a custom solar-powered acoustic playback system.
Porites astreoides
settled at significantly higher rates at the acoustically enriched sites, averaging 1.7 times (up to maximum of seven times) more settlement compared with control reef sites without acoustic enrichment. Settlement rates decreased with distance from the speaker but remained higher than control levels at least 30 m from the sound source. These results reveal that acoustic enrichment can facilitate coral larval settlement at reasonable distances, offering a promising new method for scientists, managers and restoration practitioners to rebuild coral reefs.
Metabolic reprogramming and signalling cross-talks in tumour–immune interaction: a system-level exploration
Authors: Shukla Mudita , Bhowmick Rupa , Ganguli Piyali , Sarkar Ram Rup
Published: March 2024

Tumour-immune microenvironment (TIME) is pivotal in tumour progression and immunoediting. Within TIME, immune cells undergo metabolic adjustments impacting nutrient supply and the anti-tumour immune response. Metabolic reprogramming emerges as a promising approach to revert the immune response towards a pro-inflammatory state and conquer tumour dominance. This study proposes immunomodulatory mechanisms based on metabolic reprogramming and employs the regulatory flux balance analysis modelling approach, which integrates signalling, metabolism and regulatory processes. For the first time, a comprehensive system-level model is constructed to capture signalling and metabolic cross-talks during tumour–immune interaction and regulatory constraints are incorporated by considering the time lag between them. The model analysis identifies novel features to enhance the immune response while suppressing tumour activity. Particularly, altering the exchange of succinate and oxaloacetate between glioma and macrophage enhances the pro-inflammatory response of immune cells. Inhibition of glutamate uptake in T-cells disrupts the antioxidant mechanism of glioma and reprograms metabolism. Metabolic reprogramming through adenosine monophosphate (AMP)-activated protein kinase (AMPK), coupled with glutamate uptake inhibition, was identified as the most impactful combination to restore T-cell function. A comprehensive understanding of metabolism and gene regulation represents a favourable approach to promote immune cell recovery from tumour dominance.
Caller identification and characterization of individual humpback whale acoustic behaviour
Authors: Zeh Julia M. , Perez-Marrufo Valeria , Adcock Dana L. , Jensen Frants H. , Knapp Kaitlyn J. , Robbins Jooke , Tackaberry Jennifer E. , Weinrich Mason , Friedlaender Ari S. , Wiley David N. , Parks Susan E.
Published: March 2024

Acoustic recording tags provide fine-scale data linking acoustic signalling with individual behaviour; however, when an animal is in a group, it is challenging to tease apart calls of conspecifics and identify which individuals produce each call. This, in turn, prohibits a robust assessment of individual acoustic behaviour including call rates and silent periods, call bout production within and between individuals, and caller location. To overcome this challenge, we simultaneously instrumented small groups of humpback whales on a western North Atlantic feeding ground with sound and movement recording tags. This approach enabled a comparison of the relative amplitude of each call across individuals to infer caller identity for 97% of calls. We recorded variable call rates across individuals (mean = 23 calls/h) and groups (mean = 55 calls/h). Calls were produced throughout dives, and most calls were produced in bouts with short inter-call intervals of 2.2 s. Most calls received a likely response from a conspecific within 100 s. This caller identification (ID) method facilitates studying both individual- and group-level acoustic behaviour, yielding novel results about the nature of sequence production and vocal exchanges in humpback whale social calls. Future studies can expand on these caller ID methods for understanding intra-group communication across taxa.
Design and optimization of a high-performance multi-barrier IPMS motor for an electric scooter and bicycle
Authors: Gör Halil , Dalcalı Adem
Published: March 2024

Acknowledging the growing importance of electric vehicles (EVs) in the face of environmental concerns and increasing mobility needs, this study focuses on enhancing the performance of the electric motor, a critical component in EVs. The electric motor of these battery-powered vehicles is expected to have optimal characteristics and efficiency. This paper presents a comprehensive investigation into the design and optimization of a multi-barrier interior permanent magnet synchronous motor tailored for e-scooters and electric bicycles. A multi-barrier rotor structure is proposed and analysed through finite element method simulations to optimize key design parameters. The parametric analysis examines the influence of geometric variables on key motor performance criteria, including efficiency, cogging torque and weight. A correlation analysis of the variables was conducted. A very high positive correlation (0.999) was revealed, especially between the ‘magnet duct dimension parameter’ and efficiency. A very high negative correlation (−1) was found between ‘distance from duct bottom to shaft surface’ and efficiency. The optimized motor design achieves a theoretical improvement of around 7% in efficiency, reaching an overall efficiency of 89.86%. This study highlights the consideration of multiple factors such as efficiency, cogging torque and weight in the design process for the development of sustainable and high-performance EV motor designs.
Zig-zag dynamics in a Stern–Gerlach spin measurement
Authors: Krekels Simon , Maes Christian , Meerts Kasper , Struyve Ward
Published: March 2024

The century-old Stern–Gerlach setup is paradigmatic for a quantum measurement. We visualize the electron trajectories following the Bohmian zig-zag dynamics. This dynamics was developed in order to deal with the fundamentally massless nature of particles (with mass emerging from the Brout–Englert–Higgs mechanism). The corresponding trajectories exhibit a stochastic zig-zagging, as the result of the coupling between left- and right-handed chiral Weyl states. This zig-zagging persists in the non-relativistic limit, which will be considered here, and which is described by the Pauli equation for a non-uniform external magnetic field. Our results clarify the different meanings of ‘spin’ as a property of the wave function and as a random variable in the Stern–Gerlach setup, and they illustrate the notion of effective collapse. We also examine the case of an EPR-pair. By letting one of the entangled particles pass through a Stern–Gerlach device, the non-local influence (action-at-a-distance) on the other particle is manifest in its trajectory, e.g. by initiating its zig-zagging.
Variational construction of tubular and toroidal streamsurfaces for flow visualization
Authors: Li Mingwu , Kaszás Bálint , Haller George
Published: March 2024

Approximate streamsurfaces of a three-dimensional velocity field have recently been constructed as isosurfaces of the closest first integral of the velocity field. Such approximate streamsurfaces enable effective and efficient visualization of vortical regions in three-dimensional flows. Here we propose a variational construction of these approximate streamsurfaces to remove the limitation of Fourier series representation of the first integral in earlier work. Specifically, we use finite-element methods to solve a partial differential equation that describes the best approximate first integral for a given velocity field. We use several examples to demonstrate the power of our approach for three-dimensional flows in domains with arbitrary geometries and boundary conditions. These include generalized axisymmetric flows in the domains of a sphere (spherical vortex), a cylinder (cylindrical vortex) and a hollow cylinder (Taylor–Couette flow) as benchmark studies for various computational domains, non-integrable periodic flows (ABC and Euler flows) and Rayleigh–Bénard convection flows. We also illustrate the use of the variational construction in extracting momentum barriers in Rayleigh–Bénard convection.
The use of social information in vulture flight decisions
Authors: Sassi Yohan , Nouzières Basile , Scacco Martina , Tremblay Yann , Duriez Olivier , Robira Benjamin
Published: March 2024

Animals rely on a balance of personal and social information to decide when and where to move next in order to access a desired resource. The benefits from cueing on conspecifics to reduce uncertainty about resource availability can be rapidly overcome by the risks of within-group competition, often exacerbated toward low-ranked individuals. Being obligate soarers, relying on thermal updraughts to search for carcasses around which competition can be fierce, vultures represent ideal models to investigate the balance between personal and social information during foraging movements. Linking dominance hierarchy, social affinities and meteorological conditions to movement decisions of eight captive vultures,
Gyps spp
., released for free flights in natural soaring conditions, we found that they relied on social information (i.e. other vultures using/having used the thermals) to find the next thermal updraught, especially in unfavourable flight conditions. Low-ranked individuals were more likely to disregard social cues when deciding where to go next, possibly to minimize the competitive risk of social aggregation. These results exemplify the architecture of decision-making during flight in social birds. It suggests that the environmental context, the context of risk and the social system as a whole calibrate the balance between personal and social information use.
Advances in remote sensing of emperor penguins: first multi-year time series documenting trends in the global population
Authors: LaRue Michelle , Iles David , Labrousse Sara , Fretwell Peter , Ortega David , Devane Eileen , Horstmann Isabella , Viollat Lise , Foster-Dyer Rose , Le Bohec Céline , Zitterbart Daniel , Houstin Aymeric , Richter Sebastian , Winterl Alexander , Wienecke Barbara , Salas Leo , Nixon Monique , Barbraud Christophe , Kooyman Gerald , Ponganis Paul , Ainley David , Trathan Philip , Jenouvrier Stephanie
Published: March 2024

Like many polar animals, emperor penguin populations are challenging to monitor because of the species' life history and remoteness. Consequently, it has been difficult to establish its global status, a subject important to resolve as polar environments change. To advance our understanding of emperor penguins, we combined remote sensing, validation surveys and using Bayesian modelling, we estimated a comprehensive population trajectory over a recent 10-year period, encompassing the entirety of the species’ range. Reported as indices of abundance, our study indicates with 81% probability that there were fewer adult emperor penguins in 2018 than in 2009, with a posterior median decrease of 9.6% (95% credible interval (CI) −26.4% to +9.4%). The global population trend was −1.3% per year over this period (95% CI = −3.3% to +1.0%) and declines probably occurred in four of eight fast ice regions, irrespective of habitat conditions. Thus far, explanations have yet to be identified regarding trends, especially as we observed an apparent population uptick toward the end of time series. Our work potentially establishes a framework for monitoring other Antarctic coastal species detectable by satellite, while promoting a need for research to better understand factors driving biotic changes in the Southern Ocean ecosystem.
Land-use change interacts with island biogeography to alter bird community assembly
Authors: Zhao Yuhao , Mendenhall Chase D. , Matthews Thomas J. , Wang Duorun , Li Wande , Liu Xiangxu , Tang Shupei , Han Peng , Wei Guangpeng , Kang Yi , Wu Chenxiao , Wang Rui , Zeng Di , Frishkoff Luke O. , Si Xingfeng
Published: March 2024

Anthropogenic activities have reshaped biodiversity on islands worldwide. However, it remains unclear how island attributes and land-use change interactively shape multiple facets of island biodiversity through community assembly processes. To answer this, we conducted bird surveys in various land-use types (mainly forest and farmland) using transects on 34 oceanic land-bridge islands in the largest archipelago of China. We found that bird species richness increased with island area and decreased with isolation, regardless of the intensity of land-use change. However, forest-dominated habitats exhibited lower richness than farmland-dominated habitats. Island bird assemblages generally comprised species that share more similar traits or evolutionary histories (i.e. functional and/or phylogenetic clustering) than expected if assemblages were randomly assembled. Contrary to our expectations, we observed that bird assemblages in forest-dominated habitats were more clustered on large and close islands, whereas assemblages in farmland-dominated habitats were more clustered on small islands. These contrasting results indicate that land-use change interacts with island biogeography to alter the community assembly of birds on inhabited islands. Our findings emphasize the importance of incorporating human-modified habitats when examining the community assembly of island biota, and further suggest that agricultural landscapes on large islands may play essential roles in protecting countryside island biodiversity.
Pollen chemical and mechanical defences restrict host-plant use by bees
Authors: Rivest Sébastien , Muralidhar Madhupreeta , Forrest Jessica R. K.
Published: March 2024

Plants produce an array of chemical and mechanical defences that provide protection against many herbivores and pathogens. Putatively defensive compounds and structures can even occur in floral rewards: for example, the pollen of some plant taxa contains toxic compounds or possesses conspicuous spines. Yet little is known about whether pollen defences restrict host-plant use by bees. In other words, do bees, like other insect herbivores, tolerate the defences of their specific host plants while being harmed by non-host defences? To answer this question, we compared the effects of a chemical defence from
Lupinus
(Fabaceae) pollen and a putative mechanical defence (pollen spines) from Asteraceae pollen on larval survival of nine bee species in the tribe Osmiini (Megachilidae) varying in their pollen-host use. We found that both types of pollen defences reduce larval survival rate in some bee species. These detrimental effects were, however, mediated by host-plant associations, with bees being more tolerant of the pollen defences of their hosts, relative to the defences of plant taxa exploited by other species. This pattern strongly suggests that bees are adapted to the pollen defences of their hosts, and that host-plant use by bees is constrained by their ability to tolerate such defences.
Newly identified nematodes from the Great Salt Lake are associated with microbialites and specially adapted to hypersaline conditions
Authors: Jung Julie , Loschko Tobias , Reich Shelley , Rassoul-Agha Maxim , Werner Michael S.
Published: March 2024

Extreme environments enable the study of simplified food-webs and serve as models for evolutionary bottlenecks and early Earth ecology. We investigated the biodiversity of invertebrate meiofauna in the benthic zone of the Great Salt Lake (GSL), Utah, USA, one of the most hypersaline lake systems in the world. The hypersaline bays within the GSL are currently thought to support only two multicellular animals: brine fly larvae and brine shrimp. Here, we report the presence, habitat, and microbial interactions of novel free-living nematodes. Nematode diversity drops dramatically along a salinity gradient from a freshwater river into the south arm of the lake. In Gilbert Bay, nematodes primarily inhabit reef-like organosedimentary structures built by bacteria called microbialites. These structures likely provide a protective barrier to UV and aridity, and bacterial associations within them may support life in hypersaline environments. Notably, sampling from Owens Lake, another terminal lake in the Great Basin that lacks microbialites, did not recover nematodes from similar salinities. Phylogenetic divergence suggests that GSL nematodes represent previously undescribed members of the family Monhysteridae—one of the dominant fauna of the abyssal zone and deep-sea hydrothermal vents. These findings update our understanding of halophile ecosystems and the habitable limit of animals.
Heatwaves are detrimental to fertility in the viviparous tsetse fly
Authors: Weaving Hester , Terblanche John S. , English Sinead
Published: March 2024

Heatwaves are increasing in frequency and intensity due to climate change, pushing animals beyond physiological limits. While most studies focus on survival limits, sublethal effects on fertility tend to occur below lethal thresholds, and consequently can be as important for population viability. Typically, male fertility is more heat-sensitive than female fertility, yet direct comparisons are limited. Here, we measured the effect of experimental heatwaves on tsetse flies,Glossina pallidipes, disease vectors and unusual live-bearing insects of sub-Saharan Africa. We exposed males or females to a 3-day heatwave peaking at 36, 38 or 40°C for 2 h, and a 25°C control, monitoring mortality and reproduction over six weeks. For a heatwave peaking at 40°C, mortality was 100%, while a 38°C peak resulted in only 8% acute mortality. Females exposed to the 38°C heatwave experienced a one-week delay in producing offspring, whereas no such delay occurred in males. Over six weeks, heatwaves resulted in equivalent fertility loss in both sexes. Combined with mortality, this lead to a 10% population decline over six weeks compared to the control. Furthermore, parental heatwave exposure gave rise to a female-biased offspring sex ratio. Ultimately, thermal limits of both survival and fertility should be considered when assessing climate change vulnerability.
Social network shrinking is explained by active and passive effects but not increasing selectivity with age in wild macaques
Authors: Sadoughi Baptiste , Mundry Roger , Schülke Oliver , Ostner Julia
Published: March 2024

Evidence of social disengagement, network narrowing and social selectivity with advancing age in several non-human animals challenges our understanding of the causes of social ageing. Natural animal populations are needed to test whether social ageing and selectivity occur under natural predation and extrinsic mortality pressures, and longitudinal studies are particularly valuable to disentangle the contribution of within-individual ageing from the demographic processes that shape social ageing at the population level. Data on wild Assamese macaques (
Macaca assamensis
) were collected between 2013 and 2020 at the Phu Khieo Wildlife Sanctuary, Thailand. We investigated the social behaviour of 61 adult females observed for 13 270 h to test several mechanistic hypotheses of social ageing and evaluated the consistency between patterns from mixed-longitudinal and within-individual analyses. With advancing age, females reduced the size of their social network, which could not be explained by an overall increase in the time spent alone, but by an age-related decline in mostly active, but also passive, behaviour, best demonstrated by within-individual analyses. A selective tendency to approach preferred partners was maintained into old age but did not increase. Our results contribute to our understanding of the driver of social ageing in natural animal populations and suggest that social disengagement and selectivity follow independent trajectories during ageing.
The environmental conditions of endemism hotspots shape the functional traits of mammalian assemblages
Authors: Shipley Benjamin R. , McGuire Jenny L.
Published: March 2024

Endemic (small-ranged) species are distributed non-randomly across the globe. Regions of high topography and stable climates have higher endemism than flat, climatically unstable regions. However, it is unclear how these environmental conditions interact with and filter mammalian traits. Here, we characterize the functional traits of highly endemic mammalian assemblages in multiple ways, testing the hypothesis that these assemblages are trait-filtered (less functionally diverse) and dominated by species with traits associated with small range sizes. Compiling trait data for more than 5000 mammal species, we calculated assemblage means and multidimensional functional metrics to evaluate the distribution of traits across each assemblage. We then related these metrics to the endemism of global World Wildlife Fund ecoregions using linear models and phylogenetic fourth-corner regression. Highly endemic mammalian assemblages had small average body masses, low fecundity, short lifespans and specialized habitats. These traits relate to the stable climate and rough topography of endemism hotspots and to mammals' ability to expand their ranges, suggesting that the environmental conditions of endemism hotspots allowed their survival. Furthermore, species living in endemism hotspots clustered near the edges of their communities’ functional spaces, indicating that abiotic trait filtering and biotic interactions act in tandem to shape these communities.
Dominance reversals: the resolution of genetic conflict and maintenance of genetic variation
Authors: Grieshop Karl , Ho Eddie K. H. , Kasimatis Katja R.
Published: March 2024

Beneficial reversals of dominance reduce the costs of genetic trade-offs and can enable selection to maintain genetic variation for fitness. Beneficial dominance reversals are characterized by the beneficial allele for a given context (e.g. habitat, developmental stage, trait or sex) being dominant in that context but recessive where deleterious. This context dependence at least partially mitigates the fitness consequence of heterozygotes carrying one non-beneficial allele for their context and can result in balancing selection that maintains alternative alleles. Dominance reversals are theoretically plausible and are supported by mounting empirical evidence. Here, we highlight the importance of beneficial dominance reversals as a mechanism for the mitigation of genetic conflict and review the theory and empirical evidence for them. We identify some areas in need of further research and development and outline three methods that could facilitate the identification of antagonistic genetic variation (dominance ordination, allele-specific expression and allele-specific ATAC-Seq (assay for transposase-accessible chromatin with sequencing)). There is ample scope for the development of new empirical methods as well as reanalysis of existing data through the lens of dominance reversals. A greater focus on this topic will expand our understanding of the mechanisms that resolve genetic conflict and whether they maintain genetic variation.
Academic publishing requires linguistically inclusive policies
Authors: Arenas-Castro Henry , Berdejo-Espinola Violeta , Chowdhury Shawan , Rodríguez-Contreras Argelia , James Aubrie R. M. , Raja Nussaïbah B. , Dunne Emma M. , Bertolino Sandro , Emidio Nayara Braga , Derez Chantelle M. , Drobniak Szymon M. , Fulton Graham R. , Henao-Diaz L. Francisco , Kaur Avneet , Kim Catherine J. S. , Lagisz Malgorzata , Medina Iliana , Mikula Peter , Narayan Vikram P. , O'Bryan Christopher J. , Oh Rachel Rui Ying , Ovsyanikova Ekaterina , Pérez-Hämmerle Katharina-Victoria , Pottier Patrice , Powers Jennifer Sarah , Rodriguez-Acevedo Astrid J. , Rozak Andes Hamuraby , Sena Pedro H. A. , Sockhill Nicola J. , Tedesco Anazélia M. , Tiapa-Blanco Francisco , Tsai Jo-Szu , Villarreal-Rosas Jaramar , Wadgymar Susana M. , Yamamichi Masato , Amano Tatsuya
Published: March 2024

Scientific knowledge is produced in multiple languages but is predominantly published in English. This practice creates a language barrier to generate and transfer scientific knowledge between communities with diverse linguistic backgrounds, hindering the ability of scholars and communities to address global challenges and achieve diversity and equity in science, technology, engineering and mathematics (STEM). To overcome those barriers, publishers and journals should provide a fair system that supports non-native English speakers and disseminates knowledge across the globe. We surveyed policies of 736 journals in biological sciences to assess their linguistic inclusivity, identify predictors of inclusivity, and propose actions to overcome language barriers in academic publishing. Our assessment revealed a grim landscape where most journals were making minimal efforts to overcome language barriers. The impact factor of journals was negatively associated with adopting a number of inclusive policies whereas ownership by a scientific society tended to have a positive association. Contrary to our expectations, the proportion of both open access articles and editors based in non-English speaking countries did not have a major positive association with the adoption of linguistically inclusive policies. We proposed a set of actions to overcome language barriers in academic publishing, including the renegotiation of power dynamics between publishers and editorial boards.
Disentangling genetic, plastic and social learning drivers of sex-specific foraging behaviour in Trinidadian guppies (
Poecilia reticulata
)
Authors: Earl Shayna R. , Johnson Lauren E. , Grant Elly , Kasubhai Avika , López-Sepulcre Andrés , Yang Yusan , Gordon Swanne
Published: March 2024

Evolutionary biologists have long been interested in parsing out the roles of genetics, plasticity and their interaction on adaptive trait divergence. Since males and females often have different ecological and reproductive roles, separating how their traits are shaped by interactions between their genes and environment is necessary and important. Here, we disentangle the sex-specific effects of genetic divergence, developmental plasticity, social learning and contextual plasticity on foraging behaviour in Trinidadian guppies (
Poecilia reticulata
) adapted to high- or low-predation habitats. We reared second-generation siblings from both predation regimes with or without predator chemical cues, and with adult conspecifics from either high- or low-predation habitats. We then quantified their foraging behaviour in water with and without predator chemical cues. We found that high-predation guppies forage more efficiently than low-predation guppies, but this behavioural difference is context-dependent and shaped by different mechanisms in males and females. Higher foraging efficiency in high-predation females is largely genetically determined, and to a smaller extent socially learned from conspecifics. However, in high-predation males, higher foraging efficiency is plastically induced by predator cues during development. Our study demonstrates sex-specific differences in genetic versus plastic responses in foraging behaviour, a trait of significance in organismal fitness and ecosystem dynamics.
Disentangling the influence of entanglement on recruitment in North Atlantic right whales
Authors: Reed Joshua , New Leslie , Corkeron Peter , Harcourt Robert
Published: March 2024

North Atlantic right whales are Critically Endangered and declining, with entanglements in fishing gear a key contributor to their decline. Entanglement events can result in lethal and sub-lethal (i.e. increased energetic demands and reduced foraging ability) impacts, with the latter influencing critical life-history states, such as reproduction. Using a multi-event framework, we developed a Bayesian mark-recapture model to investigate the influence of entanglement severity on survival and recruitment for female right whales. We used information from 199 known-aged females sighted between 1977 and 2018, combined with known entanglements of varying severity that were classified as minor, moderate or severe. Severe entanglements resulted in an average decline in survival of 27% for experienced non-breeders, 9% for breeders and 26% for pre-breeding females compared with other entanglements and unentangled individuals. Surviving individuals with severe entanglements had low transitional probabilities to breeders, but surprisingly, individuals with minor entanglements had the lowest transitional probabilities, contrary to expectations underpinning current management actions. Management actions are needed to address the lethal and sub-lethal impacts of entanglements, regardless of severity classification.
Transcriptional Regulation of Protein Synthesis by Mediator Kinase in MYC-driven Medulloblastoma
Authors: Wang Dong , Ritz Caitlin , Pierce Angela , Brunt Breauna , Luo Yuhuan , Dahl Nathan , Venkataraman Sujatha , Danis Etienne , Kuś Kamil , Mazan Milena , Rzymski Tomasz , Veo Bethany , Vibhakar Rajeev
Published: March 2024

MYC-driven medulloblastoma (MB) is a highly aggressive cancer type with poor prognosis and limited treatment options. Through CRISPR-Cas9 screening across MB cell lines, we identified the Mediator-associated kinase CDK8 as the top dependence for MYC-driven MB. Loss of CDK8 markedly reduces MYC expression and impedes MB growth. Mechanistically, we demonstrate that CDK8 depletion suppresses ribosome biogenesis and mRNA translation. CDK8 regulates occupancy of phospho-Polymerase II at specific chromatin loci facilitating an epigenetic alteration that promotes transcriptional regulation of ribosome biogenesis. Additionally, CDK8-mediated phosphorylation of 4EBP1 plays a crucial role in initiating eIF4E-dependent translation. Targeting CDK8 effectively suppresses cancer stem and progenitor cells, characterized by increased ribosome biogenesis activity. We also report the synergistic inhibition of CDK8 and mTORin vivoandin vitro. Overall, our findings establish a connection between transcription and translation regulation, suggesting a promising therapeutic approach targets multiple points in the protein synthesis network for MYC-driven MB.
De novogenome assembly ofMyricaria laxifloraprovides insights into its molecular mechanisms under flooding stress
Authors: Weibo Xiang , Linbao Li , Guiyun Huang , Bicheng Dun , Huiyuan Chen , Xiaobo Ma , Haibo Zhang , Zhiqiang Xiao , Jihong Liu , Zhen Yang , Di Wu
Published: March 2024

M. laxiflorais an endangered plant distributed in the Yangtze River floodplain of China, which often suffers from flood hazards during its growth and development. Due to the lack of a reference genome forM. laxiflora, the molecular regulatory mechanism of its waterlogging stress remains unclear. Here, we report for the first time the high-quality reference genome ofM. laxifloraby using HiFi sequencing and Hi-C. The total assembly size of theM. laxifloragenome was 1.29 Gb with a scaffold N50 size of 29.5 Mb. A total of 23,666 genes encoding proteins and 5,457 ncRNA were predicted in this reference genome. In theM. laxifloragenome, a total of 101 MylAP2/ERF genes were identified and divided into 5 subgroups. Many MeJA responsive elements, ABA responsive elements, and hypoxia responsive elements were found in the promoter regions of these MylAP2/ERF genes. Based on transcriptome data analysis, a total of 74 MylAP2/ERF genes can respond to flooding stress. Meanwhile, it was found that three genes (MylAP2/ERF49/78/91) which belong to the same branch with RAP2.2 gene exhibited different expression trends under flooding stress. Our results provide valuable information on the molecular regulatory mechanism of flooding stress inM. laxiflora.
Influence of frailty on cardiovascular events and mortality in patients with Chronic Obstructive Pulmonary Disease (COPD): Study Protocol for a multicentre European observational study
Authors: Verduri A , Clini E , Carter B , Hewitt J
Published: March 2024

Background

Frailty is a clinical state that increases susceptibility to minor stressor events. The risk of frailty is higher in chronic conditions, such as Chronic Obstructive Pulmonary Disease (COPD). Recent studies on COPD have shown that patients living with frailty have an increased risk of mortality. The presence of cardiovascular diseases or conditions are common in COPD and may increase the risk of death.

Methods

This protocol describes a European prospective cohort study of community-based people, in a stable condition with diagnosis of COPD (as defined by GOLD guidelines) across hospitals in Italy and UK. Frailty prevalence will be assessed using the Clinical Frailty Scale. At 1- and 2-year follow up, primary outcome will be the impact of frailty on the number of cardiovascular events; secondary outcomes: the influence of frailty on cardiovascular mortality, all-cause mortality, and deaths due to COPD. For the primary outcome a zero-inflated Poisson regression will compare the number of cardiovascular events at 1 year. Secondary outcomes will be analysed using the time to mortality.

Discussion

This multicentre study will assess the association between frailty and cardiovascular events and mortality in population with COPD. Data collection is prospective and includes routine clinical data. This research will have important implications for the management of patients with COPD to improve their quality of care, and potentially prognosis.

Trial registration number

NCT05922202 (www.clinicaltrials.gov).
Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History
Authors: Wu Chih Hao , Joshi Suraj , Robinson Welles , Robbins Paul F. , Schwartz Russell , Sahinalp S. Cenk , Malikić Salem
Published: March 2024

Intratumoral heterogeneity arises as a result of genetically distinct subclones emerging during tumor progression. These subclones are characterized by various types of somatic genomic aberrations, with single nucleotide variants (SNVs) and copy number aberrations (CNAs) being the most prominent. While single-cell sequencing provides powerful data for studying tumor progression, most existing and newly generated sequencing datasets are obtained through conventional bulk sequencing. Most of the available methods for studying tumor progression from multi-sample bulk sequencing data are either based on the use of SNVs from genomic loci not impacted by CNAs or designed to handle a small number of SNVs via enumerating their possible copy number trees. In this paper, we introduceDETOPT, a combinatorial optimization method for accurate tumor progression tree inference that places SNVs impacted by CNAs on trees of tumor progression with minimal distortion on their variant allele frequencies observed across available samples of a tumor. We show that on simulated dataDETOPTprovides more accurate tree placement of SNVs impacted by CNAs than the available alternatives. When applied to a set of multi-sample bulk exome-sequenced tumor metastases from a treatment-refractory, triple-positive metastatic breast cancer,DETOPTreports biologically plausible trees of tumor progression, identifying the tree placement of copy number state gains and losses impacting SNVs, including those in clinically significant genes.
PREVALENCE, INCIDENCE AND DETERMINANTS OF QUANTIFERON-POSITIVITY IN SOUTH AFRICAN SCHOOLCHILDREN
Authors: Stewart Justine , Walker Neil , Jennings Karen , Delport Carmen , Nuttall James , Coussens Anna K , Dyers Robin , Jolliffe David A , Tang Jonathan C. Y. , Fraser William D , Wilkinson Robert J , Bekker Linda-Gail , Martineau Adrian R , Middelkoop Keren
Published: March 2024

Background

Tuberculosis (TB) control requires the understanding and disruption of TB transmission. We describe prevalence, incidence and risk factors associated with childhood TB infection in Cape Town.

Methods

We report cross-sectional baseline and prospective incidence data from a large trial among primary school children living in high TB-burden communities. Prevalent infection was defined as QuantiFERON-TB Gold Plus (QFT-Plus) positivity as assessed at baseline. Subsequent conversion to QFT-Plus positivity was measured 3 years later among those QFT-Plus-negative at baseline. Multivariable logistic regression models examined factors associated with TB infection.

Results

QuantiFERON-positivity at baseline (prevalence: 22.6%, 95% Confidence Interval [CI]: 20.9 – 24.4), was independently associated with increasing age (adjusted odds ratio [aOR] 1.24 per additional year, 95% CI: 1.15 – 1.34) and household exposure to TB during the participant’s lifetime (aOR 1.87, 95% CI: 1.46 – 2.40). QFT-Plus conversion at year 3 (12.2%, 95% CI: 10.5-14.0; annual infection rate: 3.95%) was associated with household exposure to an index TB case (aOR 2.74, 95% CI: 1.05 to 7.18).

Conclusion

Rates of QFT-diagnosed TB infection remain high in this population. The strong association with household TB exposure reinforces the importance of contact tracing, preventative treatment and early treatment of infectious disease to reduce community transmission.
Burden and Determinants of Self-Reported High Blood Pressure Among Women of Reproductive Age In Tanzania: Evidence from 2022 Tanzania Demographic and Health Survey
Authors: Musilanga Nelson , Nasib Hussein , Mwakibolwa Ambokile , Jackson Given , Shayo Frank , Kijusya Keneth , Henry Samson , Nhanga Clarkson , Girukwigomba Saleh , Keshi Joseph , Luwumba Mussa
Published: March 2024

Background

High blood pressure, commonly referred to as hypertension, remains a prevalent global health concern characterized by elevated arterial pressure. Its multifactorial etiology involves genetic predisposition, lifestyle factors, and comorbidities, posing significant risks such as cardiovascular diseases, stroke, and kidney diseases. Therefore, the aim of this study was to assess the burden and determinants of self-reported high blood pressure among women of reproductive age in Tanzania.

Methods

We utilized population-based cross-sectional data obtained from the Tanzania Demographic and Health Survey (TDHS) 2022, specifically phase VIII. The analysis involved a weighted sample of 15,254 women aged 15-49 years. The outcome variable was self-reported high blood pressure. Multivariable logistic regression models were employed to examine the independent variables associated with self-reported high blood pressure, and the results were presented as adjusted odds ratios (aOR) with a 95% confidence interval (CI). The significance level was set at p < 0.05 for all analyses.

Results

Overall, the mean age of study participants was 29.3 ± 9.8 years, with a self-reported high blood pressure burden of 6.6% among women of reproductive age in Tanzania. Moreover, increased age correlated with higher odds of high blood pressure compared to women aged 15-19 years. Those with a secondary level of education exhibited a higher likelihood of high blood pressure (aOR: 1.76, 95% CI: 1.36-2.28, p < 0.001) in contrast to women with no education. Married (aOR: 1.57, 95% CI: 1.19-2.08, p=0.002) and widowed (aOR: 1.54, 95% CI: 1.11-2.12, p=0.009) individuals were more prone to high blood pressure than those who were never married. Additionally, women in higher wealth brackets showed a significantly elevated risk of high blood pressure compared to those in the poorest wealth group. Giving birth once or twice in the last 5 years reduced the odds by 20% (aOR: 0.80, 95% CI: 0.67-0.96, p < 0.001). Conversely, self-reported poor health status and recent visits to health facilities were associated with significantly higher odds of high blood pressure (aOR: 2.87, 95% CI: 1.76-4.67, p < 0.001) and (aOR: 1.38, 95% CI: 1.20-1.60, p < 0.001), respectively.

Conclusion

This study highlights the substantial burden of high blood pressure among reproductive-age women, urging heightened awareness and proactive screening measures. It unveils intricate factors contributing to elevated blood pressure, suggesting tailored strategies involving lifestyle changes, education, and improved healthcare access. These findings prompt targeted interventions, emphasizing the need for collaborative efforts among stakeholders to effectively curb this health burden.