bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of behavioural sampling methods on local and global social network metrics: a case-study of three macaque species
Authors: Kaburu Stefano S. K. , Balasubramaniam Krishna N. , Marty Pascal R. , Beisner Brianne , Fuji Kevin , Bliss-Moreau Eliza , McCowan Brenda
Published: December 2023

Social network analysis (SNA) is a powerful, quantitative tool to measure animals' direct and indirect social connectedness in the context of social groups. However, the extent to which behavioural sampling methods influence SNA metrics remains unclear. To fill this gap, here we compare network indices of grooming, huddling, and aggression calculated from data collected from three macaque species through two sampling methods: focal animal sampling (FAS) and all-occurrences behaviour sampling (ABS). We found that measures of direct connectedness (degree centrality, and network density) were correlated between FAS and ABS for all social behaviours. Eigenvector and betweenness centralities were correlated for grooming and aggression networks across all species. By contrast, for huddling, we found a correlation only for betweenness centrality while eigenvector centralities were correlated only for the tolerant bonnet macaque but not so for the despotic rhesus macaque. Grooming and huddling network modularity and centralization were correlated between FAS and ABS for all but three of the eight groups. By contrast, for aggression network, we found a correlation for network centralization but not modularity between the sampling methodologies. We discuss how our findings provide researchers with new guidelines regarding choosing the appropriate sampling method to estimate social network metrics.
The first articulated skeletons of enigmatic Late Cretaceous billfish-like actinopterygians
Authors: El Hossny Tamara , Cavin Lionel , Kaplan Ulrich , Schwermann Achim H. , Samankassou Elias , Friedman Matt
Published: December 2023

Only few candidates of Mesozoic fishes with a similar body plan and ecological niche to the modern billfishes are suggested as their analogues. Several specimens were recovered from Cenomanian deposits in Germany and Lebanon and display a billfish-like fusiform body with elongated premaxillae. They are found close to the plethodids and show a unique combination of characters (rostrum pointed and extremely elongated, double articular head of the quadrate, anteroposteriorly elongated abdominal centra indicating a slender body and different types of scales on the body) allowing their inclusion in a new genus. Two ‘
Protosphyraena
’ species are also assigned to this new genus. This fish can be considered as an ecological analogue to the extant xiphioids sharing their feeding habits. This fish was abundant and roamed, as an apex predator, the Central Tethys and the Boreal realms during the Cenomanian.
A novel approach to seabird posture estimation: finding roll and yaw angles of dynamic soaring albatrosses using tri-axial magnetometers
Authors: Schoombie Stefan , Wilson R. P. , Ryan P. G.
Published: December 2023

With advances in bio-logging technology, the posture of animals is now commonly described by inertial measurement units, which include tri-axial accelerometers to estimate pitch and roll angles. Many large seabirds use dynamic soaring flight to travel long distances, but this low-cost flight mode results in high centripetal acceleration, which obscures posture derived from accelerometers. Tri-axial magnetometers are not influenced by acceleration and might provide a way to estimate the posture of animals that experience high centripetal acceleration. We propose a new method to estimate the posture of dynamic soaring seabirds using tri-axial magnetometer data, with the assumption that they do not have large pitch angles during routine flight. This method was field-tested by deploying a combination of bio-logging devices on three albatross species breeding on Marion Island, using bird-borne video loggers to validate the roll angles. Validated data showed that the method worked well in most instances, but accuracy decreased when the heading was close to magnetic north or south. Accurate, fine-scale posture estimates may provide insight into dynamic soaring flight and allow estimates of fine-scale tracks using dead-reckoning, not only for seabirds, but potentially for other species where centripetal acceleration limits the use of accelerometers to estimate posture.
Applying collective motion models to study discordant individual behaviours within a school of fish
Authors: Trucco Andrea
Published: December 2023

Computational models of collective motion successfully reproduce the most common behaviours of a school of fish, using only a few elementary interactions between individuals. However, their ability to also reproduce individual behaviours that are discordant from those of the group has not yet been adequately investigated. In this paper, a self-propelled particle model using three interaction zones is considered in relation to the counter-rotation of an individual: a phenomenon observable in real schools of fish milling in a torus, when an individual moves in the same torus but in the opposite direction for a certain period of time. This study shows that the interactions of repulsion, orientation and attraction between individuals moving at constant speed in a three-dimensional space, with asynchronous updating, can generate temporary counter-rotations. The analysis of such events sheds light on the mechanisms that start the counter-rotation and those that end it. Although the contribution of the repulsion interaction is often significant to start and terminate the counter-rotation, it does not prove to be decisive. Indeed, it is observed that even when interactions between individuals are limited to attraction alone, temporary counter-rotations of individuals occur, provided the fish density along the circumference is not uniform. Some of these conclusions, deduced from the simulations performed, are visually consistent with what is observed in some underwater video recordings of milling schools of fish.
Use of connecting vowels after stems ending in the same vowel: a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes
Authors: Pallen Mark J.
Published: December 2023

The International Code of Nomenclature of Prokaryotes (ICNP) provides guidance on the formation of names from compound words. This includes recommendations on the use of connecting vowels, which are meant to make names easier to pronounce. However, deployment of a connecting vowel when the preceding word element ends in the same vowel can make a name harder to spell or say, bringing us into conflict with the recommendations that we should avoid names that are disagreeable and difficult to pronounce. Given that there are many precedents where connecting vowels are not used in this context, particularly in names formed from the term ‘alkali’, I hereby propose an emendation to the ICNP to drop the connecting vowel when the preceding word element ends in the same vowel.
Strong cascading impacts of micropollutants on planktonic food web in urban river
Authors: Adyari Bob , Zhang Lanping , Nascimento Francisco J.A. , Zhang Yiqing , Cao Meixian , Wang Jianjun , Li Hongjun , Sun Qian , Yu Changping , Hu Anyi
Published: December 2023

Urban rivers rely on intricate multitrophic interactions in food webs, which are vital for ecological functions. Human-induced pollutant discharge, notably micropollutants, poses a threat to these interactions. To study the impact of micropollutants on the microbial food web, we sampled downstream areas of the Jiulong River’s north tributary (lower urbanization, ∼25% built land) and west tributary (higher urbanization, ∼65% built land) for eleven consecutive days in both dry and wet seasons in Fujian, China. We constructed a conceptualized planktonic food web model by employing DNA metabarcoding targeting bacteria, micro-eukaryotes (algae and protozoa), and microzooplankton. Our results revealed that the more urbanized west tributary exhibited significantly higher micropollutant concentrations. Structural equation modeling (SEM) incorporating micropollutants and all food web elements indicated a significantly stronger impact of micropollutants on the planktonic food web in the west tributary than in the north tributary. Micropollutants exhibited both direct and indirect (cascade) effects on high trophic levels (protozoa and microzooplankton), with algal communities mediating the cascade effects instead of bacterial communities, likely due to the increased eutrophication in the urbanized tributary. Overall, our study underscores the potential ecological disruptions caused by micropollutants in shaping planktonic food web interactions in urban rivers.

Synopsis

Urban rivers face ecological threats from micropollutants. This study shows elevated micropollutants significantly affected the planktonic food webs. Algal, rather than bacterial, food web pathway mediated micropollutants cascading effects on high trophic levels, emphasizing micropollutant-induced disruptions in urban rivers.
Identification and Analysis of SARS-CoV-2 Mutation and Subtype using 2x tiled Primer Set with Oxford Nanopore Technologies Sequencing for Enhanced Variant Detection and Surveillance in Seoul, Korea
Authors: Han Giyoun , Lee Sojung , Kwon YaeEun , Lyu Jaemyun , Kim Hyunsoo , Yoon Kang-Jun , Kim Minlee
Published: December 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a respiratory virus that contains RNA as its genetic material and has caused a global pandemic since its outbreak in 2020. This virus has many mutations, some of which can reduce the effectiveness of existing vaccines. Therefore, next-generation sequencing (NGS) is necessary to accurately identify new mutations. Current NGS analysis of SARS-CoV-2 uses the amplicon analysis method through a multiplex polymerase chain reaction. This study collected and validated RNA samples from patients who tested positive for SARS-CoV-2 from April to July 2022, and selected 613 samples for sequencing. The findings demonstrate the importance of long-read-based NGS analysis and 2x tiled primer set for identifying full SARS-CoV-2 genome sequence with new mutations and understanding the correlation between viral genotypes and patient characteristics for the effective management of SARS-CoV-2.
Liver discard rate due to conservative estimations of steatosis: an inference-based approach
Authors: Guo Hao , Gala-Lopez Boris L. , Alwayn Ian P.J. , Hewitt Kevin C.
Published: December 2023

Background

On-site conservative estimations of steatosis could result in the unnecessary discard of donor livers. This study applied the body mass index (BMI) as an independent statistical indicator to determine the extent of this problem. We explored two hypotheses: (I) that because of varying levels of expertise and protocols (reputational risk for pathologists), biopsies at transplant centers overestimate hepatic steatosis (HS), and (ii) that non-biopsy donor liver assessments are more conservative than biopsy-based evaluations.

Methods

The study processed cross-database and intra-database comparisons using data from the National Health and Nutrition Examination Survey (NHANES) and Organ Procurement and Transplantation Network (OPTN) spanning January 2017 to March 2020 in the United States. Post-matching BMI was applied as an independent indicator of statistical risk of HS.

Results

Contrary to our first hypothesis, biopsies at transplant centers didnotoverestimate HS - biopsy-classified donor livers were found in similar or lower risk categories.Consistent with our second hypothesis, absent biopsies, evaluations before and during organ procurementwereobserved to be more conservative, leading to the discard of 11.9% (373) of potential donor livers.

Conclusions

The study concludes that there was a significant (11.9%) disparity caused by on-site non-biopsy assessments of HS, leading to the unnecessary discard of potential donor livers. The findings emphasize the need to develop more accurate intraoperative techniques for assessing HS to optimize donor liver procurement.
From the third to the seventh generation of selection for muscle fat content in rainbow trout: Consequences for flesh quality
Authors: Lefevre Florence , Bugeon Jérôme , Goardon Lionel , Kerneis Thierry , Labbe Laurent , Panserat Stéphane , Medale Françoise , Quillet Edwige
Published: December 2023

Muscle lipid content was shown to affect many quality features in salmonids in both raw and processed fillets. The objective of the present work was to assess the consequences of 7 generations of divergent selection for muscle adiposity on some rainbow trout flesh quality and muscle parameters. Fish from Lean (L) and Fat (F) lines had a similar body weight but L fish were longer and had consequently lower condition factor values. Carcass yield was not affected by selective breeding, but L fish had lower hepato- and gonado-somatic indexes, a bigger head, and lower fillet yield than F fish. A difference of more than 15 points in mean fat-meter®values (genetic selection criteria) was measured between the two lines. Mean muscle lipid content was 5.0±1.0% for L line vs 13.5±2.2% for F line. An absolute difference of more than 6% was measured in fillet dry matter content between the two lines, for raw, cooked, and smoked fillets. Raw fillets from F fish were lighter (L*>) and more colorful (a* and b*>), but softer than those from the L line. Quality parameters of cooked fillets were very similar between the two lines, whereas smoked fillets exhibited, between the two lines, similar differences than raw fillets. A large difference in white muscle fiber size was observed, fish from F line having higher fiber mean diameter, a lower proportion of small fibers, and a higher proportion of large fibers. Sex effects were observed on these immature fish, on classically sex-related traits (GSI and head development), but also on muscle fiber size. Moreover, these effects were more marked in F line. Correlation analysis showed that raw fillet color was positively related to muscle adiposity whereas mechanical resistance was negatively related. Raw fillet mechanical resistance was also negatively correlated to white muscle fiber size. Moreover, smoked fillet quality parameters were correlated to raw fillet ones. The relationships between muscle adiposity, but also muscle cellularity, and fillet quality were discussed.

Highlights

7 generations of adiposity divergent selection affect raw and smoked fillet quality.

Selective breeding led to a noteworthy response in white muscle cellularity.

Some differences between male and female was measured in immature pan-size trout.

Graphical abstract
Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics
Authors: Fang Shuangsang , Xu Mengyang , Cao Lei , Liu Xiaobin , Bezulj Marija , Tan Liwei , Yuan Zhiyuan , Li Yao , Xia Tianyi , Guo Longyu , Kovacevic Vladimir , Hui Junhou , Guo Lidong , Liu Chao , Cheng Mengnan , Lin Li’ang , Wen Zhenbin , Josic Bojana , Milicevic Nikola , Qiu Ping , Lu Qin , Li Yumei , Wang Leying , Hu Luni , Zhang Chao , Kang Qiang , Chen Fengzhen , Deng Ziqing , Li Junhua , Li Mei , Li Shengkang , Zhao Yi , Fan Guangyi , Zhang Yong , Chen Ao , Li Yuxiang , Xu Xun
Published: December 2023

Tracing cellular dynamic changes across conditions, time, and space is crucial for understanding the molecular mechanisms underlying complex biological systems. However, integrating multi-sample data in a unified and flexible way to explore cellular heterogeneity remains a major challenge. Here, we present Stereopy, a flexible and versatile framework for modeling and dissecting comparative and spatiotemporal patterns in multi-sample spatial transcriptomics with interactive data visualization. To optimize this flexible framework, we have developed three key components: a multi-sample tailored data container, a scope controller, and an analysis transformer. Furthermore, Stereopy showcases three transformative applications supported by pivotal algorithms. Firstly, the multi-sample cell community detection (CCD) algorithm introduces an innovative capability to detect specific cell communities and identify genes responsible for pathological changes in comparable datasets. Secondly, the spatially resolved temporal gene pattern inference (TGPI) algorithm represents a notable advancement in detecting important spatiotemporal gene patterns while concurrently considering spatial and temporal features, which enhances the identification of important genes, domains and regulatory factors closely associated with temporal datasets. Finally, the 3D niche-based regulation inference tool, named NicheReg3D, reconstructs the 3D cell niches to enable the inference of cell-gene interaction network within the spatial texture, thus bridging intercellular communications and intracellular regulations to unravel the intricate regulatory mechanisms that govern cellular behavior. Overall, Stereopy serves as both a bioinformatics toolbox and an extensible framework that provides researchers with enhanced data interpretation abilities and new perspectives for mining multi-sample spatial transcriptomics data.
fastDFE: fast and flexible inference of the distribution of fitness effects
Authors: Sendrowski Janek , Bataillon Thomas
Published: December 2023

Estimating the distribution of fitness effects (DFE) of new mutations is of fundamental importance in evolutionary biology, ecology, and conservation. However, existing methods for DFE estimation suffer from limitations, such as slow computation speed and limited scalability. To address these issues, we introduce fastDFE, a Python-based software package, offering fast and flexible DFE inference from site-frequency spectrum (SFS) data. Apart from providing efficient joint inference of multiple DFEs that share parameters, it offers the feature of introducing genomic covariates that influence the DFEs, and testing their significance. To further simplify usage, fastDFE is equipped with comprehensive VCF-to-SFS parsing utilities. These include options for site filtering and stratification, as well as site-degeneracy annotation and probabilistic 11 ancestral-allele inference. fastDFE thereby covers the entire workflow of DFE inference from the moment of acquiring a raw VCF file. Despite its Python foundation, fastDFE comprises a full R interface, including native R visualization capabilities. The package is comprehensively tested, and documented atfastdfe.readthedocs.io.
Adenosinergic modulation of layer 6 microcircuitry in the medial prefrontal cortex is specific to presynaptic cell type
Authors: Ding Chao , Yang Danqing , Feldmeyer Dirk
Published: December 2023

Adenosinergic modulation in the PFC is recognised for its involvement in various behavioural aspects including sleep homoeostasis, decision-making, spatial working memory and anxiety. While the principal cells of layer 6 (L6) exhibit significant morphological diversity, the detailed cell-specific regulatory mechanisms of adenosine in L6 remain unexplored. Here, we quantitatively analysed the morphological and electrophysiological parameters of L6 neurons in the rat medial prefrontal cortex (mPFC) using whole-cell recordings combined with morphological reconstructions. We were able to identify two different morphological categories of excitatory neurons, those with a leading dendrite that was oriented either upright (towards the dial surface) or inverted (towards the white matter). These two excitatory neuron subtypes exhibited different electrophysiological and synaptic properties. Adenosine at a concentration of 30 µM indiscriminately suppressed connections with either an upright or an inverted presynaptic excitatory neuron. However, using lower concentrations of adenosine (10 µM) revealed that synapses originating from L6 upright neurons have a higher sensitivity to adenosine-induced inhibition of synaptic release. Adenosine receptor activation causes a reduction in the probability of presynaptic neurotransmitter release that could be abolished by specifically blocking A1adenosine receptors (A1ARs) using 8-cyclopentyltheophylline (CPT). Our results demonstrate a differential expression level of A1ARs at presynaptic sites of two functionally and morphologically distinct subpopulations of L6 principal neurons, suggesting that they may play distinct roles in the maintenance of sleep homoeostasis by adenosine.
KGRACDA: A Model Based on Knowledge Graph from Recursion and Attention Aggregation for CircRNA-disease Association Prediction
Authors: Wang Ying , Ma Maoyuan , Xie Yanxin , Peng Qinke , Lyu Hongqiang , Sun Hequan , Fu Laiyi
Published: December 2023

CircRNA has been found to exhibit with human diseases, rendering the investigation of the circRNA-disease association (CDA) of significant importance. Deep learning provides a novel avenue for predicting CDA, however, due to the limited availability of comprehensive CDA datasets, most existing methods operate by directly reasoning over triplets of embedded entities and relations, neglecting the explicit capture local depth information. In this study, we propose a novel approach called Knowledge Graph-Enhanced Recursive Aggregation for CDA (KGRACDA), which enables the querying of explicit local structures surrounding triplets, thereby serving as crucial evidence for predicting CDA. First, we construct a comprehensive CDA knowledge graph utilizing a large-scale, multi-source heterogeneous dataset. Subsequently, we develop a graph neural network using recursive techniques and employ attention aggregation to generate CDA prediction scores. Experimental results demonstrate that KGRACDA surpasses other state-of-the-art methods by explicitly capturing local depth information related to CDA. To improve the convenience of CDA prediction, we have updated an interactive web platform named HNRBase v2.0, which provides rich visualization of circRNA data, and allows users to easily download data and predict CDA using KGRACDA. The code and datasets are publicly available athttps://github.com/maoyuanma/KGRACDA.
ANDROMEDA by Prosilico and log D outperform human hepatocytes for the prediction of intrinsic hepatic metabolic clearance of carboxylic acids
Authors: Fagerholm Urban
Published: December 2023

Introduction

Extrahepatic metabolism/conjugation, deconjugation of their metabolites, and low and varying unbound fraction in plasma (fu), is characteristic for carboxylic drugs. Thus, it is comparably difficult to estimate theirin vivointrinsic hepatic metabolic clearance (CLint) and hepatic CL (CLH) and to predict theirin vivoCLint, CLHand CL. One objective was to investigate the laboratory variability of fuand CLintfor carboxylic acids. Another objective was to compare human hepatocytes, measured log D and the software ANDROMEDA with regards to prediction of humanin vivoCLintof carboxylic acids.

Materials and Methods

Measured unbound hepatocyte CLint, non-renal CL (surrogate for CLH), non-renal CLint(surrogate for hepatic metabolic CLint), log D and fudata were taken from studies in the literature. ANDROMEDA (by Prosilico; version 1.0) prediction software was used forin silicopredictions of CLintfor carboxylic acids not used in the training set of its CLint-model.

Results and Discussion

Mean and maximum differences between highest and lowest reportedin vivoCLintpredicted from hepatocyte CLintwere 210- and 1,476-fold (n=8), respectively. Corresponding estimates forin vitrofuwere 19- and 50-fold, respectively. The data set with the apparently highest number of carboxylic acids contains 39 carboxylic acids within vitroCLintand log D (both measured at the same laboratory),in vivoCLintandin vitrofu. 18 carboxylic acids were excluded as theirin vitroCLintwas below the limit of quantification. The correlation coefficient (R2) for log hepatocyte predictedin vivoCLintvslogin vivoCLintwas 0.34. The corresponding R2for log Dvslogin vivoCLintwas 0.40 (0.47 for 64 carboxylic acids). The Q2(forward-looking R2) forin silico(ANDROMEDA) predicted and measured login vivoCLintfor 12 carboxylic acids was 0.86. The corresponding R2for hepatocytes and log D were 0.67 and 0.66, respectively. ANDROMEDA produced a lower maximum prediction error compared to hepatocytes and also predicted thein vivoCLintfor all carboxylic acids out of reach for the hepatocyte assay.

Conclusion

Very large interlaboratory variability was demonstrated for plasma protein binding and hepatocyte assays. Log D, and especially ANDROMEDA, outperformed the hepatocyte assay for the prediction of CLintof carboxylic acidsin vivoin man.
Motor unit discharge rate modulation during isometric contractions to failure is intensity and task dependent
Authors: Valenčič Tamara , Ansdell Paul , Brownstein Callum G , Spillane Padraig M , Holobar Aleš , Škarabot Jakob
Published: December 2023

The nature of neuromuscular decrements associated with contractions to task failure is known to dependent on task demands. Task-specificity of the associated adjustments in motor unit discharge rate (MUDR) behaviour, however, remains unclear. This study examined MUDR adjustments during different submaximal isometric knee-extension tasks to failure. Participants performed a sustained and an intermittent task at 20 and 50% of maximal voluntary torque (MVT), respectively (Experiment 1). High-density surface electromyography signals were recorded from vastus lateralis (VL) and medialis (VM) and decomposed into individual MU discharge timings, with the identified MUs tracked from recruitment to task failure. MUDR was quantified and normalised to intervals of 10% of contraction time (CT). MUDR of both muscles exhibited distinct modulation patterns in each task. During 20% MVT sustained task, MUDR decreased until ∼50% CT, after which it gradually returned to baseline. Conversely, during the 50% MVT intermittent task, MUDR remained stable until ∼40-50% CT, after which it started to continually increase until task failure. To explore the effect of contraction intensity on the observed patterns, VL and VM MUDR was quantified during sustained contractions at 30 and 50% MVT (Experiment 2). During the 30% MVT sustained task, MUDR remained stable until ∼80-90% CT in both muscles, after which it continually increased until task failure. During the 50% MVT sustained task the increase in MUDR occurred earlier, after ∼70-80% CT. Our results suggest that adjustments in MUDR during submaximal isometric contractions to failure are task- and intensity-dependent.
Extracellular symbiont colonizes insect during embryo development
Authors: Porras Miguel Ángel González , Pons Inès , García-Lozano Marleny , Jagdale Shounak , Emmerich Christiane , Weiss Benjamin , Salem Hassan
Published: December 2023

Insects typically acquire their beneficial microbes early in development. Endosymbionts housed intracellularly are commonly integrated during oogenesis or embryogenesis, whereas extracellular microbes are only known to be acquired after hatching by immature instars such as larvae or nymphs. Here, however, we report on an extracellular symbiont that colonises its host during embryo development. Tortoise leaf beetles (Chrysomelidae: Cassidinae) host their digestive bacterial symbiontStammeraextracellularly within foregut symbiotic organs, and in ovary-associated glands to ensure its vertical transmission. We outline the initial stages of symbiont colonization and observe that while the foregut symbiotic organs develop three days prior to larval emergence, they remain empty until the final 24 hours of embryo development. Infection byStammeraoccurs during that timeframe, and prior to hatching. By experimentally manipulating symbiont availability to embryos in the egg, we describe a 12-hour developmental window governing colonization byStammera. Symbiotic organs form normally in aposymbiotic larvae, demonstrating that theseStammera-bearing structures develop autonomously. In adults, the foregut symbiotic organs are already colonized following metamorphosis and host a stableStammerapopulation to facilitate folivory. The ovary-associated glands, however, initially lackStammera. Symbiont abundance subsequently increases within these transmission organs, thereby ensuring sufficient titers at the onset of oviposition ∼29 days following metamorphosis. Collectively, our findings reveal thatStammeracolonization precedes larval emergence, where its proliferation is eventually decoupled in adult beetles to match the nutritional and reproductive requirements of its host.
Common types of microdebris affect the physiology of reef-building corals
Authors: Reichert Jessica , Tirpitz Vanessa , Plaza Katherine , Wörner Elisabeth , Bösser Luisa , Kühn Susanne , Primpke Sebastian , Schubert Patrick , Ziegler Maren , Wilke Thomas
Published: December 2023

Marine debris, particularly microdebris (< 1 mm) poses a potential threat to marine life, including reef-building corals. While previous research has mainly focused on the impact of single polymer microplastics, the effects of natural microdebris, composed of a mixture of materials, have not been explored. Therefore, this study aimed to assess the effects of different microdebris, originating from major sources of pollution, on reef-building corals. For this, we exposed two scleractinian coral species,Pocillopora verrucosaandStylophora pistillata, known to frequently ingest microplastics, to four types of microdebris in an 8-week laboratory experiment: fragmented environmental plastic debris, artificial fibers from clothing, residues from the automobile sector consisting of tire wear, brake abrasion, and varnish flakes, a single polymer microplastic treatment consisting of polyethylene particles, and a microdebris-free control treatment. Specifically, we (I) compared the effects of the different microdebris on coral growth, necrosis, and photosynthesis, (II) investigated the difference between the microdebris mixtures and the exposure to the single polymer treatment, and (III) identified potential mechanisms causing species-specific effects by contrasting the feeding responses of the two coral species on microdebris and natural food. We show that the fibers and tire wear had the strongest effects on coral physiology, withP. verrucosabeing more affected thanS. pistillata. Both species showed increased volume growth in response to the microdebris treatments, accompanied by decreased calcification inP. verrucosa. Photosynthetic efficiency of the symbionts was enhanced in both species. The species-specific physiological responses might be attributed to feeding reactions, withP. verrucosaresponding significantly more often to microdebris thanS. pistillata. These findings highlight the effect of different microdebris on coral physiology and the need for future studies to use particle mixtures to better mimic naturally occurring microdebris and assess its effect on corals in more detail.

Highlights

The effects of major sources of microdebris pollution on coral physiology were compared.

Overall, microdebris had only minor impacts on coral physiology.

Artificial fibers and tire wear caused the strongest effect on coral physiology.

Single polymer and complex microdebris caused similar, yet species-specific effects.

Species-specific effects might be due to different feeding behaviors.

Graphical abstract
Rapid host switching of Wolbachia and even more rapid turnover of their phages and incompatibility-causing loci
Authors: Shropshire Dylan , Conner William R. , Vanderpool Daniel , Hoffmann Ary A. , Turelli Michael , Cooper Brandon S.
Published: December 2023

About half of all insect species carry maternally inherited Wolbachia alphaproteobacteria, making Wolbachia the most common endosymbionts known in nature. Often Wolbachia spread to high frequencies within populations due to cytoplasmic incompatibility (CI), a Wolbachia-induced sperm modification caused by prophage-associated genes (cifs) that kill embryos without Wolbachia. Several Wolbachia variants also block viruses, including wMel from Drosophila melanogaster when transinfected into the mosquito Aedes aegypti. CI enables the establishment and stable maintenance of pathogen-blocking wMel in natural Ae. aegypti populations. These transinfections are reducing dengue disease incidence on multiple continents. While it has long been known that closely related Wolbachia occupy distantly related hosts, the timing of Wolbachia host switching and molecular evolution has not been widely quantified. We provide a new, conservative calibration for Wolbachia chronograms based on examples of co-divergence of Wolbachia and their insect hosts. Synthesizing publicly available and new genomic data, we use our calibration to demonstrate that wMel-like variants separated by only about 370,000 years have naturally colonized holometabolous dipteran and hymenopteran insects that diverged approximately 350 million years ago. Data from Wolbachia variants closely related to those currently dominant in D. melanogaster and D. simulans illustrate that cifs are rapidly acquired and lost among Wolbachia genomes, on a time scale of 10^4 - 10^5 years. This turnover occurs with and without the Wovirus prophages that contain them, with closely related cifs found in distantly related phages and distantly related cifs found in closely related phages. We present evidence for purifying selection on CI rescue function and on particular Cif protein domains. Our results quantify the tempo and mode of rapid host switching and horizontal gene transfer that underlie the spread and diversity of Wolbachia sampled from diverse host species. The wMel variants we highlight from hosts in different climates may offer new options for broadening Wolbachia-based biocontrol of diseases and pests.
Influenza infected macrophages release viral ribonucleoproteins that shape the local host response
Authors: Fritzlar Svenja , Lakdawala Seema S. , Roberts Jason A. , Coin Lachlan J. M. , Deng Yi-Mo , Moselen Jean , Le Sage Valerie M. , Mackenzie Jason M. , Labzin Larisa I. , Brooks Andrew G. , Reading Patrick C. , Londrigan Sarah L.
Published: December 2023

Airway epithelial cells and macrophages (MΦ) represent cellular targets of infection by influenza A virus (IAV). Epithelial cells support IAV infection and replication by enabling the generation and release of new viral particles (productive replication). In contrast, MΦ are susceptible to initial IAV infection but the release of infectious viral particles is inhibited through abortive replication. Despite the lack of infectious virions released from infected MΦ, we detected newly synthesised viral RNA and nucleoprotein (NP) in MΦ supernatants. We show that viral RNA is released from infected MΦ as viral ribonucleoprotein (vRNP) complexes which elicits potent inflammatory responses when exposed to uninfected cells. These vRNPs specifically induced IL-1β, CXCL13, IL-32, CCL4 and CXCL10 in uninfected cells and were at least partially sensed through the RIG-I/MDA5 pathway. While MΦ represent a dead-end for IAV infection through abortive replication, the release of vRNPs shapes immune repsonses of uninfected cells in the local microenvironment.
Fecal bacterial communities of the platypus (Ornithorhynchus anatinus) reflect captivity status – implications for conservation and management
Authors: Dungan Ashley M. , Thomas Jessica L.
Published: December 2023

The duck-billed platypus (Ornithorhynchusanatinus) is currently listed as ‘Near-Threatened’ under the International Union for Conservation of Nature (IUCN) Red List based on observed population declines and local extinctions. A key part of the conservation strategy for this species is its captive maintenance; however, captive animals often undergo significant changes in their gut microbiome. The study of the gut microbiome in threatened wildlife species has enormous potential to improve conservation efforts and gain insights into host-microbe coevolution. Here, for the first time, we characterize the gut microbiome of wild platypus via fecal samples using high-throughput sequencing of the bacterial 16S rRNA gene and identify microbial biomarkers of captivity in this species. At the phylum level, Firmicutes (50.4%) predominated among all platypuses, followed by Proteobacteria (28.7%), Fusobacteria (13.4%), and Bacteroidota (6.9%), with twenty-one ‘core’ bacteria identified. Captive individuals did not differ in their microbial α-diversity compared to wild platypus but had significantly different community composition (β-diversity) and exhibited higher abundances ofEnterococcus, which are potential pathogenic bacteria. Four taxa were identified as biomarkers of wild platypus, includingRickettsiella, Epulopiscium, Clostridium, and Cetobacterium. This contrast in gut microbiome composition between wild and captive platypus is an essential insight for guiding conservation management as the rewilding of captive animal microbiomes is a new and emerging tool to improve captive animal health, maximize captive breeding efforts, and give reintroduced or translocated animals the best chance of survival.
Tardigrade secretory proteins protect biological structures from desiccation
Authors: Lim Samuel , Reilly Charles B. , Barghouti Zeina , Marelli Benedetto , Way Jeffrey C. , Silver Pamela A.
Published: December 2023

Tardigrades, microscopic animals that survive a broad range of environmental stresses, express a unique set of proteins termed tardigrade-specific intrinsically disordered proteins (TDPs). TDPs are often expressed at high levels in tardigrades upon desiccation, and appear to mediate stress adaptation. Here, we focused on the proteins belonging to the secretory family of tardigrade proteins termed secreted-abundant heat soluble (“SAHS”) proteins, and investigated their ability to protect diverse biological structures. Recombinantly expressed SAHS proteins prevented desiccated liposomes from fusion, and enhanced desiccation tolerance ofE. coliandRhizobium tropiciupon extracellular application. Molecular dynamics simulation and comparative structural analysis suggest a model by which SAHS proteins may undergo a structural transition upon desiccation, in which removal of water and solutes from a large internal cavity in SAHS proteins destabilizes the beta-sheet structure. These results highlight the potential application of SAHS proteins as stabilizing molecules for preservation of cells.
Dorsal hippocampal oxytocin receptor regulates adult peer bonding in rats
Authors: Hu Yufei , Li Wensi , Zhao Yinji , Liu Yuying , Sun Wenyu , Yan Yi , Liu Laixin , Deng Bowen , Fan Pu
Published: December 2023

Healthy social relationships are beneficial whereas their breakdown is often linked to psychiatric disorders. Parental care and bonding between sexual partners have been well studied both at the level of behavioral analysis and underlying neuronal mechanisms. By contrast, little is known about the neural and molecular basis of peer bonding, defined as social bonds formed between unrelated individuals of the same sex, due to the lack of a suitable experimental paradigm. We found that adult Sprague Dawley (SD) rats of the same sex form strong peer bonds with each other following co-housing. Peer bonded rats exhibit affiliative displays toward their cagemates who are distressed whereas they exhibit agonistic behaviors toward strangers in these situations. Using innovative, genetic strategies in rats, we show that both oxytocin receptor (OXTR) bearing neurons andOxtrsignaling in the dorsal hippocampus are essential for peer bonds to form. Together, we have developed a new platform for studying peer bonding and demonstrate a neural pathway that governs this behavior.
AI-algorithm training and validation for endometrial CD138+ cells in infertility-associated conditions; polycystic ovary syndrome (PCOS) and recurrent implantation failure (RIF)
Authors: Lee Seungbaek , Arffman Riikka K. , Komsi Elina K. , Lindgren Outi , Kemppainen Janette A. , Metsola Hanna , Ahtikoski Anne , Kask Keiu , Saare Merli , Salumets Andres , Piltonen Terhi T.
Published: December 2023

Immunohistochemical analysis of CD138+ plasma cells has been applied for detecting endometrial inflammation, especially chronic endometritis (CE). In this study, we developed for the first time an artificial intelligence (AI) algorithm, AITAH, to identify CD138+ plasma cells within endometrial tissue, focusing on two infertility-related conditions: polycystic ovary syndrome (PCOS) and recurrent implantation failure (RIF). We obtained 193 endometrial tissues from healthy controls (n=73), women with PCOS (n=91), and RIF patients (n=29) and compared CD138+ cell percentages across cycle phases, ovulation status, and endometrial receptivity. We trained AITAH with CD138 stained tissue images, and experienced pathologists validated the training and performance of AITAH. AITAH, with high accuracy in detecting CD138+ cells (88.57%), revealed higher CD138+ cell percentages in the proliferative phase than in the secretory phase or in the anovulatory PCOS endometrium, irrespective of PCOS diagnosis. Interestingly, CD138+ percentages differed according to PCOS phenotype in the proliferative phase (p=0.01). Different receptivity statuses had no impact on the cell percentages in RIF samples. In summary, the AI-enabled analysis is a rapid and accurate tool to examine endometrial tissues, potentially aiding clinical decision-making. Here, the AI analysis demonstrated cycle-phase differences in CD138+ aggregations pattern, but no major alterations in PCOS or RIF samples.
A Video Intervention to Improve Patient Understanding of Tumor Genomic Testing in Patients with Cancer
Authors: Veney Deloris , Wei Lai , Toland Amanda E. , Presley Carolyn J. , Hampel Heather , Padamsee Tasleem J. , Lee Clara N. , Irvin William J. , Bishop Michael , Kim James , Hovick Shelly R. , Senter Leigha , Stover Daniel G.
Published: December 2023

Background

Tumor genomic testing (TGT) has become standard-of-care for most patients with advanced/metastatic cancer. Despite established guidelines, patient education prior to TGT is variable or frequently omitted. The purpose of this study was to evaluate the impact of a concise (3-4 minute) video for patient education prior to TGT.

Methods

Based on a quality improvement cycle, an animated video was created to be applicable to any cancer type, incorporating culturally diverse images, available in English and Spanish. Patients undergoing standard-of care TGT were enrolled at a tertiary academic institution and completed validated survey instruments immediately prior to video viewing (T1) and immediately post-viewing (T2). Instruments included: 1) 10-question objective genomic knowledge/understanding; 2) 10-question video message-specific knowledge/recall; 3) 11-question Trust in Physician/Provider; 4) attitudes regarding TGT. The primary objective was change in outcomes from before to after the video was assessed with Wilcoxon signed rank test.

Results

From April 2022 to May 2023, a total of 150 participants were enrolled (MBC n=53, LC n=38, OC n=59). For the primary endpoint, there was a significant increase in video message-specific knowledge (median 10 point increase; p<0.0001) with no significant change in genomic knowledge/understanding (p=0.89) or Trust in Physician/Provider (p=0.59). Results for five questions significantly improved, including the likelihood of TGT impact on treatment decision, incidental germline findings, and cost of testing. Improvement in video message-specific knowledge was consistent across demographic groups, including age, income, and education. Individuals with less educational attainment had had greater improvement from before to after video viewing.

Conclusions

A concise, 3-4 minute, broadly applicable video incorporating culturally diverse images administered prior to TGT significantly improved video message-specific knowledge across all demographic groups. This resource is publicly available athttp://www.tumor-testing.com, with a goal to efficiently educate and empower patients regarding TGT while addressing guidelines within the flow of clinical practice.

Clinical Trial Registration

ClinicalTrials.govNCT05215769
Higher loss of livelihood and impoverishment in households affected by tuberculosis compared to non-tuberculosis affected households in Zimbabwe: a cross-sectional study
Authors: Timire Collins , Houben Rein MGJ , Pedrazzoli Debora , Ferrand Rashida Abbas , Calderwood Claire J , Bond Virginia , Mbiba Fredrick , Kranzer Katharina
Published: December 2023

Introduction

Tuberculosis (TB) disproportionally affects poor people, leading to income and non-income losses. Measures of socioeconomic impact of TB, e.g. impoverishment and patient costs are inadequate to capture non-income losses. We applied impoverishment and a multidimensional measure on TB and non-TB affected households in Zimbabwe.

Methods

We conducted a cross-sectional study in 270 households: 90 non-TB; 90 drug-susceptible TB (DS-TB), 90 drug-resistant TB (DR-TB) during the COVID-19 pandemic (2020-2021). Household data included ownership of assets, number of household members, income and indicators on five capital assets: financial, human, social, natural and physical. We determined proportions of impoverished households for periods 12 months prior and at the time of the interview. Households with incomes below US$1.90/day were considered to be impoverished. We used principal component analysis on five capital asset indicators to create a binary outcome variable indicating loss of livelihood. Log-binomial regression was used to determine associations between loss of livelihood and type of household.

Results

TB-affected households reported higher previous episodes of TB and household members requiring care than non-TB households. Households that were impoverished 12 months prior to the study were: 21 non-TB (23%); 40 DS-TB (45%); 37 DR-TB (41%). The proportions increased to 81%, 88% and 94%, respectively by the time of interview. Overall, 56% (152/270) of households sold assets: 44% (40/90) non-TB, 58% (52/90) DS-TB and 67% (60/90) DR-TB. Children’s education was affected in 31% (56/180) of TB-affected compared to 13% (12/90) non-TB households. Overall, 133(50%) households experienced loss of livelihood, with TB-affected households twice as likely to experience loss of livelihood; adjusted prevalence ratio (aPR=2.02 (95%CI:1.35-3.03)). The effect of TB on livelihood was most pronounced in poorest households (aPR=2.64, (95%CI:1.29-5.41)).

Conclusions

TB-affected households experienced greater socioeconomic losses compared to non-TB households. Multidimensional measures of TB are crucial to inform multisectoral approaches to mitigate impacts of TB and other shocks.