bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing energy and entropy formulations for cosmic ray hydrodynamics
Authors: Weber Matthias , Thomas Timon , Pfrommer Christoph
Published: December 2022

Cosmic rays (CRs) play an important role in many astrophysical systems. Acting on plasma scales to galactic environments, CRs are usually modelled as a fluid, using the CR energy density as the evolving quantity. This method comes with the flaw that the corresponding CR evolution equation is not in conservative form as it contains an adiabatic source term that couples CRs to the thermal gas. In the absence of non-adiabatic changes, instead evolving the CR entropy density is a physically equivalent option that avoids this potential numerical inconsistency. In this work, we study both approaches for evolving CRs in the context of magnetohydrodynamic (MHD) simulations using the massively parallel moving-mesh code Arepo. We investigate the performance of both methods in a sequence of shock-tube tests with various resolutions and shock Mach numbers. We find that the entropy-conserving scheme performs best for the idealized case of purely adiabatic CRs across the shock while both approaches yield similar results at lower resolution. In this set-up, both schemes operate well and almost independently of the shock Mach number. Taking active CR acceleration at the shock into account, the energy-based method proves to be numerically much more stable and significantly more accurate in determining the shock velocity, in particular at low resolution, which is more typical for astrophysical large-scale simulations. For a more realistic application, we simulate the formation of several isolated galaxies at different halo masses and find that both numerical methods yield almost identical results with differences far below common astrophysical uncertainties.
Orbits of the TOI-1338 and TIC-172900988 systems
Authors: Gakis Dionysios , Gourgouliatos Konstantinos N
Published: December 2022

Recent observations by TESS revealed the existence of circumbinary planets in the systems of TOI-1338 and TIC-172900988. The purpose of this work is to model the planetary orbits in these two systems and study them under the perspective of previous theoretical models. Each planet’s distance from the barycentre through time is simulated using N-body integrations and is compared with outcomes from a semi-analytic, a geometric and a Keplerian-based approach. Furthermore, we infer the most prominent frequencies of both planets’ orbits induced by the central binaries. We confirm that both systems appear to be stable. Lastly, we examine the implications of an additional candidate planet in TOI-1338 system finding that an extra, 48 M⊕ planet that has been hinted from observations could be located at 0.8 au without generating any radical changes to the orbits of the other members of the system.
Nature of the galaxies on top of quasars producing Mg ii absorption
Authors: Guha Labanya Kumar , Srianand Raghunathan
Published: December 2022

Quasar–galaxy pairs at small separations are important probes of gas flows in the disc–halo interface in galaxies. We study host galaxies of 198 Mg ii absorbers at 0.39 ≤ zabs ≤ 1.05 that show detectable nebular emission lines in the Sloan Digital Sky Survey (SDSS) spectra. We report measurements of impact parameter (5.9 ≤ D [kpc] ≤ 16.9) and absolute B-band magnitude (−18.7 ≤ MB ≤ −22.3 mag) of host galaxies of 74 of these absorbers using multiband images from the Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Survey, more than doubling the number of known host galaxies with D ≤ 17 kpc. This has allowed us to quantify the relationship between Mg ii rest equivalent width (W2796) and D, with best-fitting parameters of W2796 (D = 0) = 3.44 ± 0.20 Å and an exponential scale length of 21.6$^{+2.41}_{-1.97}\, \mathrm{ kpc}$. We find a significant anticorrelation between MB and D, and MB and W2796, consistent with the brighter galaxies producing stronger Mg ii absorption. We use stacked images to detect average emissions from galaxies in the full sample. Using these images and stacked spectra, we derive the mean stellar mass (9.4 ≤ log(M*/M⊙) ≤ 9.8), star formation rate (2.3 ≤ SFR [M⊙ yr−1] ≤ 4.5), age (2.5–4 Gyr), metallicity (12 + log(O/H) ∼ 8.3), and ionization parameter (log q [cm s−1] ∼ 7.7) for these galaxies. The average M* found is less than that of Mg ii absorbers studied in the literature. The average SFR and metallicity inferred are consistent with that expected in the main sequence and the known stellar mass–metallicity relation, respectively. High spatial resolution follow-up spectroscopic and imaging observations of this sample are imperative for probing gas flows close to the star-forming regions of high-z galaxies.
Impact of a binary black hole on its outer circumbinary disc
Authors: Mignon-Risse Raphaël , Varniere Peggy , Casse Fabien
Published: December 2022

Accreting supermassive binary black holes (SMBBHs) are potential targets for multimessenger astronomy as they emit gravitational waves (GW) while their environment emits electromagnetic (EM) waves. In order to get the most out of a joint GW–EM detection we first need to obtain theoretically predicted EM signals unambiguously linked to BBHs. In that respect, this is the first of a series of papers dedicated to accreting pre-merger BBHs and their associated EM observables. Here, we extend our Numerical Observatory of Violent Accreting systems, e-NOVAs, to any space–time. Unlike previous studies, almost exclusively focused on the inner regions, we investigated the impact of the BBH on its outer circumbinary disc, located in the radiation (or wave) zone, after implementing an approximate analytical space–time of spinning, inspiralling BBHs in e-NOVAs. We follow the formation of a weak spiral structure in disc density arising from the retardation effects in the radiation zone metric. Simulation data are then post-processed with a general-relativistic ray-tracing code incorporating the same BBH space–time, assuming SMBBH sources. The density spiral creates a small $({\lt }1{{\ \rm per\ cent}})$ but unambiguous modulation of the light curve at the semi-orbital period. This signal, although weak, is fundamentally different from that of an axisymmetric disc around a single BH providing a lower limit on the impact of a BBH on its outer disc. This potential difference being found, we study how binary parameters impact this modulation in order to find the optimal case which is a high source inclination of any binary mass ratio (from 0.1 to 1).
From X-rays to physical parameters: a comprehensive analysis of thermal tidal disruption event X-ray spectra
Authors: Mummery Andrew , Wevers Thomas , Saxton Richard , Pasham Dheeraj
Published: December 2022

We perform a comprehensive analysis of a population of 19 X-ray bright tidal disruption events (TDEs), fitting their X-ray spectra with a new, physically self-consistent, relativistic accretion disc model. Not all of the TDEs inhabit regions of parameter space where the model is valid, or have sufficient data for a detailed analysis, and physically interpretable parameters for a subsample of 11 TDEs are determined. These sources have thermal (power-law free) X-ray spectra. The radial sizes measured from these spectra lie at values consistent with the innermost stable circular orbit of black holes with masses given by the MBH–σ relationship, and can be used as an independent measurement of MBH. The bolometric disc luminosity can also be inferred from X-ray data. All of the TDEs have luminosities that are sub-Eddington (Lbol, disc ≲ Ledd), and larger than the typical hard-state transitional luminosity of X-ray binary discs (Lbol, disc ≳ 0.01Ledd). The peak bolometric luminosity is found to be linearly correlated with the MBH–σ mass. The TDE X-ray-to-bolometric correction can reach values up to ∼100, and grows exponentially at late times, resolving the missing energy problem. We show that the peak disc luminosities of some TDEs are smaller than their observed optical luminosities, implying that not all of the early time optical emission can be sourced from reprocessed disc emission. Our results are supportive of the hypothesis that thermal X-ray bright TDEs are in accretion states analogous to the ‘soft’ accretion state of X-ray binaries, and that black hole accretion processes are scale (mass) invariant.
Investigation of the dependence of angular momentum transport on spatial scales for construction of differential rotation
Authors: Mori K , Hotta H
Published: December 2022

We investigate the dependence of the angular momentum transport (AMT) on the spatial scales with numerical simulation of solar-like stars. It is thought that turbulence has an essential role in constructing solar differential rotation (DR). In a widely used method to analyse the construction mechanism of DR, the flow is divided into two components, ‘mean flow’ and ‘turbulence’, where ‘turbulence’ includes a broad spectrum of spatial scales. The features of the AMT are expected to depend on the scale. In this study, we decompose the angular momentum flux (AMF) to investigate the dependence of the AMF on the spatial scale. We compare the results with anti-solar (fast pole) and solar-type (fast equator) DR. Our conclusions are summarized as (1) Radially outward AMT is seen on a large scale (60 Mm ≤ L < 120 Mm) in rotationally constrained systems. (2) Even when the scale-integrated AMF is negative, we sometimes observe positive AMF on certain scales. (3) Small-scale turbulence tends to transport the angular momentum radially inward and causes the anti-solar DR, indicating that high-resolution simulation is a negative factor for solar-like DR. Our method to decompose the AMF provides a deep understanding of the angular momentum and construction mechanism of DR.
Teak plantations are complementary habitat for the Green Peafowl movement within the fragmented Bago Yoma range, south-central Myanmar
Authors: Win Lay , Sukumal Niti , Shwe Nay Myo , Savini Tommaso
Published: December 2022

Habitat loss, degradation, and fragmentation following intensive agricultural expansion, and both legal and illegal logging, have contributed to the rapid decline of the Green Peafowl (Pavo muticus) over mainland Southeast Asia. Dry forest habitat in the Bago Yoma range (Myanmar) is considered one of the region’s last remaining strongholds for the species. However, the area has been fragmented over the past years, mostly due to large-scale teak (Tectona grandis) plantations. This study aimed to estimate the Green Peafowl population in the Bago Yoma range with a particular focus on the use of large-scale teak plantations as possible complementary habitat for the species. The survey was conducted over 47 line transects located in the natural forest and teak plantations. The average estimated density, using distance sampling, was 0.800 calling males km–2 across the whole survey area. Estimated densities were similar within the natural forest and teak plantations (0.825 and 0.866 calling males km–2, respectively), suggesting an extensive use of this crop by Green Peafowl. The remaining suitable habitat covered an area of 8,554 km2 divided into 8 large forest patches (>40 km2). When including large-scale teak plantations in the landscape matrix, more suitable habitat fragments could be connected to each other, with the remaining suitable habitat grouped into 6 large forest patches. These results suggest teak plantations could be used for connecting remaining forest patches and improving fragmented natural habitats for Green Peafowl.
Magneto-structural phase transition in exfoliated pyrrhotite (Fe7S8) ultra-thin sheets
Authors: Puthirath Balan Aravind , Oliveira Eliezer F , Costin Gelu , Gray Tia , Chakingal Nithya , Biswas Abhijit , Puthirath Anand B
Published: December 2022

Non-van der Waals (n-vdW) 2D materials are gaining popularity due to their exciting confinement-enhanced properties for magnetic, catalytic and optoelectronic applications. The recent discovery of mechanical and liquid exfoliation of n-vdW materials along the cleavage planes, owing to the very low scission energies, is encouraging and opens the avenue for further exploration of n-vdW materials having exceptional properties. Herein, we successfully isolated a few layers of pyrrhotite (Fe7S8) nanosheets from bulk mineral ore by means of liquid phase exfoliation in organic solvent and studied the magnetic ordering at bulk and exfoliated samples. Both experimental and first principle theoretical investigations point out confinement-induced magneto-structural phase transition from ferromagnetic monoclinic (4M) to antiferromagnetic hexagonal (3T) characterized by the suppression of Besnus transition.
Quantifying resilience and the risk of regime shifts under strong correlated noise
Authors: Heßler Martin , Kamps Oliver
Published: December 2022

Early warning indicators often suffer from the shortness and coarse-graining of real-world time series. Furthermore, the typically strong and correlated noise contributions in real applications are severe drawbacks for statistical measures. Even under favourable simulation conditions the measures are of limited capacity due to their qualitative nature and sometimes ambiguous trend-to-noise ratio. In order to solve these shortcomings, we analyze the stability of the system via the slope of the deterministic term of a Langevin equation, which is hypothesized to underlie the system dynamics close to the fixed point. The open-source available method is applied to a previously studied seasonal ecological model under noise levels and correlation scenarios commonly observed in real world data. We compare the results to autocorrelation, standard deviation, skewness, and kurtosis as leading indicator candidates by a Bayesian model comparison with a linear and a constant model. We show that the slope of the deterministic term is a promising alternative due to its quantitative nature and high robustness against noise levels and types. The commonly computed indicators apart from the autocorrelation with deseasonalization fail to provide reliable insights into the stability of the system in contrast to a previously performed study in which the standard deviation was found to perform best. In addition, we discuss the significant influence of the seasonal nature of the data to the robust computation of the various indicators, before we determine approximately the minimal amount of data per time window that leads to significant trends for the drift slope estimations.
Model of inverse bleb growth explains giant vacuole dynamics during cell mechanoadaptation
Authors: Cairoli Andrea , Spenlehauer Alice , Overby Darryl R , Lee Chiu Fan
Published: December 2022

Cells can withstand hostile environmental conditions manifest as large mechanical forces such as pressure gradients and/or shear stresses by dynamically changing their shape. Such conditions are realized in the Schlemm’s canal of the eye where endothelial cells that cover the inner vessel wall are subjected to the hydrodynamic pressure gradients exerted by the aqueous humor outflow. These cells form fluid-filled dynamic outpouchings of their basal membrane called giant vacuoles. The inverses of giant vacuoles are reminiscent of cellular blebs, extracellular cytoplasmic protrusions triggered by local temporary disruption of the contractile actomyosin cortex. Inverse blebbing has also been first observed experimentally during sprouting angiogenesis, but its underlying physical mechanisms are poorly understood. Here, we hypothesize that giant vacuole formation can be described as inverse blebbing and formulate a biophysical model of this process. Our model elucidates how cell membrane mechanical properties affect the morphology and dynamics of giant vacuoles and predicts coarsening akin to Ostwald ripening between multiple invaginating vacuoles. Our results are in qualitative agreement with observations from the formation of giant vacuoles during perfusion experiments. Our model not only elucidates the biophysical mechanisms driving inverse blebbing and giant vacuole dynamics, but also identifies universal features of the cellular response to pressure loads that are relevant to many experimental contexts.
Reprogramming of ovarian aging epigenome by resveratrol
Authors: Gou Mo , Li Jie , Yi Lizhi , Li Huiyu , Ye Xiaoying , Wang Huasong , Liu Linlin , Sun Baofa , Zhang Song , Zhu Zhengmao , Liu Jiang , Liu Lin
Published: December 2022

Resveratrol is an antiaging, antioxidant, and anti-inflammatory natural polyphenolic compound. Growing evidence indicates that resveratrol has potential therapeutic effects for improving aging ovarian function. However, the mechanisms underlying prolonged reproductive longevity remain elusive. We found that resveratrol ameliorates ovarian aging transcriptome, some of which are associated with specific changes in methylome. In addition to known aging transcriptome of oocytes and granulosa cells such as decline in oxidoreductase activity, metabolism and mitochondria function, and elevated DNA damage and apoptosis, actin cytoskeleton are notably downregulated with age, and these defects are mostly rescued by resveratrol. Moreover, the aging-associated hypermethylation of actin cytoskeleton is decreased by resveratrol. In contrast, deletion of Tet2, involved in DNA demethylation, abrogates resveratrol-reprogrammed ovarian aging transcriptome. Consistently, Tet2 deficiency results in additional altered pathways as shown by increased mTOR and Wnt signaling, as well as reduced DNA repair and actin cytoskeleton with mouse age. Moreover, genes associated with oxidoreductase activity and oxidation–reduction process were hypermethylated in Tet2-deficient oocytes from middle-age mice treated with resveratrol, indicating that loss of Tet2 abolishes the antioxidant effect of resveratrol. Taking together, our finding provides a comprehensive landscape of transcriptome and epigenetic changes associated with ovarian aging that can be reprogrammed by resveratrol administration, and suggests that aberrantly increased DNA methylation by Tet2 deficiency promotes additional aging epigenome that cannot be effectively restored to younger state by resveratrol.
Efficient delivery ofFMR1across the blood brain barrier using AAVphp construct in adultFMR1KO mice demonstrates the feasibility of gene therapy for fragile X syndrome
Authors: Chadman Kathryn K. , Adayev Tatyana , Udayan Aishwarya , Ahmed Rida , Dai Chun-Ling , Goodman Jeffrey H. , Meeker Harry , Dolzhanskaya Natalia , Velinov Milen
Published: December 2022

Background

Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability and autism. Gene therapy may offer an efficient method to ameliorate symptoms of the disorder.

Methods

An AAVphp.eb-hSyn-mFMR1IOS7 vector and an empty control were injected in the tail vein ofFmr1knock out (KO) mouse and wildtype (WT) controls. KO mice were injected with 2 × 1013vg/kg of the construct. Control KO and WT mice were injected with empty vector. After treatment the animals underwent a battery of tests: open field, marble burying, rotarod, and fear conditioning. Mouse brains were studied for levels of theFmr1product, FMRP.

Results

Significant levels of FMRP were not found outside the CNS in treated animals. The gene delivery was highly efficient, where it exceeded the control FMRP levels in all tested brain regions. There was also improved performance in the rotarod test and partial improvements on other tests in the treated KO animals.

Conclusion

These experiments demonstrate efficient, brain-specific delivery ofFmr1via peripheral administration in adult mice. The gene delivery led to partial alleviation of the Fmr1 KO phenotypical behaviors. FMRP oversupply may explain why not all behaviors were significantly affected. Since AAV.php vectors are less efficient in humans than the mice used in the current experiment, studies to determine the optimal dose and using human suitable vectors will be necessary to further demonstrate feasibility.
Development of a shortwave infrared (SWIR) sinuscope for the detection of cerebrospinal fluid (CSF) leaks
Authors: Klein Tjadina-W. , Yang Stella , Tusty Mahbuba A. , Nayak Jayakar V. , Chang Michael T. , Bruns Oliver T. , Bischof Thomas S. , Valdez Tulio A.
Published: December 2022

Significance

CSF rhinorrhea (leakage of brain fluid from the nose) can be difficult to identify and currently requires invasive procedures such as intrathecal fluorescein which requires a lumbar drain placement. Fluorescein is also known to have rare but significant side effects including seizures and death. As the number of endonasal skull base cases increase, the number of CSF leaks have also increased for which an alternative diagnostic method would be highly advantageous to patients.

Aim

To develop an instrument to identify CSF leaks based on water absorption in the SWIR without the need of intrathecal contrast agents. This device needed to be adapted to the anatomy of the human nasal cavity while maintaining low weight and ergonomic characteristics of current surgical instruments.

Approach

Absorption spectra of CSF and artificial CSF were obtained to characterize the absorption peaks that could be targeted with SWIR light. Different illumination systems were tested and refined prior to adapting them into a portable endoscope for testing in 3D printed models and cadavers for feasibility.

Results

We identified CSF to have an identical absorption profile as water. In our testing, a narrow band laser source at 1480nm proved superior to using a broad 1450 nm LED. Using a SWIR enabling endoscope set up, we tested the ability to detect artificial CSF in a cadaver model.

Conclusions

An endoscopic system based on SWIR narrow band imaging can provide an alternative in the future to invasive methods of CSF leak detection.
The phylogenetic history of theGorteria diffusaradiation sheds light on the origins of plant sexual deception
Authors: Delahaie Boris , Mellers Gregory , Kellenberger Roman T. , Fernández-Mazuecos Mario , Fattorini Róisín , Brockington Samuel F. , Ellis Allan G. , Glover Beverley J.
Published: December 2022

The morphologically diverse daisy speciesGorteria diffusaemploys varying levels of sexually deceptive pollination. The species comprises at least fifteen spatially and phenotypically discrete floral morphotypes that are associated with a range of pollination strategies, from generalism to highly specialised sexual deception involving visual mimicry of females of the bee-flyMegapalpus capensis. However, the pattern of evolution of the unique floral traits in this lineage remains unknown because the phylogenetic history of the closely related floral morphotypes has proved unresolvable using traditional approaches. Here we apply genotyping-by-sequencing (GBS), a reduced representation sequencing technology that has significantly increased the tractability of phylogenetic problems involving recent radiations, to the recalcitrant phylogenetic problem ofGorteriaacross its South African distribution. Population genomic analyses show that individuals group according to morphotype, irrespective of geographic proximity, highlighting the distinctiveness of the morphotypes at the genetic level. We resolve the phylogenetic history of the closely related morphotypes, demonstrating that they are mostly well supported monophyletic entities that are grouped into at least three distinct geographically separated clades. Our results suggest that both incomplete lineage sorting and introgression across geographical clades have previously hindered reconstruction of the phylogeny of this species complex that has diversified rapidly during the Quaternary. Sexual deception is a phylogenetically derived pollination strategy within the complex that evolved at least twice, and was likely achieved by sequential evolution of a set of floral traits that in combination elicit sexual responses from the bee-fly pollinator. While insight into the evolution of sexual deception has been limited by strong phylogenetic conservatism of this strategy in other plant lineages, our results both provide the framework, and confirm the utility ofG. diffusa, for further understanding the genetic pathways and selective pressures underlying the complex phenotypes required to exploit insect mating behaviour for pollination.
Transcutaneous electrical nerve stimulation acutely impacts motor unit firing activity during isometric contractions
Authors: Avrillon Simon , Hernandez-Pavon Julio C. , Kurukuti Nish M. , Hoo Grace W. , Pons José L.
Published: December 2022

A low intensity electrical current delivered transcutaneously at a high frequency over a muscle can acutely recruit motor units in a physiological order by activating peripheral sensory pathways. This method has been used in patients to reduce tremor or supplement motor function, leading to the development of therapies and products.

We aimed to better understand how the stimulation of the median nerve, the contralateral first dorsal interosseus muscle (FDI), and the combination of these two paradigms impact the motor unit activity from the FDI muscle. We identified and tracked the same motor units across the conditions and compared the electromyographic amplitude, motor unit discharge rates, and the degree of correlation between fast and slow oscillations of motor unit discharge rates.

We found that the stimulation of the FDI muscle can acutely increase the electromyographic amplitude of the homonymous muscle on the contralateral side (F = 20.4; p < 0.001) while the discharge rate of motor units did not differ between the control and the stimulation condition (F = 0.2; p = 0.806). We did not observe any significant effect of the stimulation on the ratio of pairs of motor units with a significant correlation, showing that the stimulation barely impacted the distribution of correlated inputs to the pool of motor units. We did not observe short-term effects of the stimulation once it was discontinued. Overall, these results showed that the specific stimulation of peripheral sensory pathways can acutely impact motor unit firing activity without disturbing the neural control of force.

New & Noteworthy

We identified and tracked the same motor units across stimulation and control conditions using high-density electromyography. We found that the specific stimulation of peripherial sensory pathways can acutely impact motor unit firing activity, likely due to the recruitment of additional motor units. At the same time, the degree of correlation between fast and slow oscillations of motor unit discharge rates was stable, limiting the disturbance of the neural control of force.
Impact of cannabis use on immune cell populations and the viral reservoir in people with HIV on suppressive antiretroviral therapy
Authors: Falcinelli Shane D. , Cooper-Volkheimer Alicia D , Semenova Lesia , Wu Ethan , Richardson Alexander , Ashokkumar Manickam , Margolis David M , Archin Nancie M. , Rudin Cynthia D , Murdoch David , Browne Edward P
Published: December 2022

HIV infection remains incurable due to the persistence of a viral reservoir during antiretroviral therapy. Cannabis (CB) use is prevalent amongst people with HIV (PWH), but the impact of CB on the latent HIV reservoir has not been investigated. Peripheral CD4 and CD8 T cells from a cohort of CB-using PWH and a matched cohort of non-users on antiretroviral therapy were evaluated for expression of maturation/activation markers, HIV-specific T cell responses, and the frequency of intact proviral DNA. CB use was associated with increased abundance of naïve T cells, reduced effector T cells, and reduced expression of activation markers. CB users also exhibited reduced levels of exhausted and senescent T cells compared to non-using controls. HIV-specific CD8 T cell responses were unaffected by CB use. While the abundance of intact proviruses was not significantly affected by CB use across the whole cohort, we observed that, for participants with high frequency of NKG2A or CD16 expression in NK cells, CB use was associated with a smaller intact HIV reservoir. This analysis is consistent with the hypothesis that CB use reduces activation, exhaustion and senescence in the T cells of PWH and may influence the size of the HIV reservoir.
Guided-topic modelling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes
Authors: Swapna Lakshmipuram Seshadri , Huang Michael , Li Yue
Published: December 2022

Cell-type composition is an important indicator of health. We present Guided Topic Model for deconvolution (GTM-decon) to automatically infer cell-type-specific gene topic distributions from single-cell RNA-seq data for deconvolving bulk transcriptomes. GTM-decon performs competitively on deconvolving simulated and real bulk data compared with the state-of-the-art methods. Moreover, as demonstrated in deconvolving disease transcriptomes, GTM-decon can infer multiple cell-type-specific gene topic distributions per cell type, which captures sub-cell-type variations. GTM-decon can also use phenotype labels from single-cell or bulk data as a guide to infer phenotype-specific gene distributions. In a nested-guided design, GTM-decon identified cell-type-specific differentially expressed genes from bulk breast cancer transcriptomes.
Uncovering Changes in Microbiome Profiles Across Commercial and Backyard Poultry Farming Systems
Authors: Muyyarikkandy Muhammed Shafeekh , Parzygnat Jessica , Thakur Siddhartha
Published: December 2022

Environmental health and microbiome can affect poultry production in a variety of ways. Poor environmental conditions can lead to increased stress, disease, and mortality in poultry, resulting in reduced production. Poor environmental conditions can also reduce the diversity of microbial populations in the poultry microbiome, which can lead to an increased risk of disease and reduced production. Finally, microorganisms in the environment can be introduced to the poultry microbiome, which can increase the risk of disease and reduce production. Additionally, poultry production can have significant impacts on the environmental microbiome. Poultry farming can alter soil and water microbiomes through pollution from manure and other agricultural runoff. These changes can lead to increased concentrations of certain microbes as well as an altered balance between beneficial microorganisms. In this study, we investigated the changes in the microbiome profiles of commercial and backyard broiler farming systems at different time points. To explore the microbiome profiles, fecal, soil, litter samples, and swabs from feeders and waterers were collected three times over the production period from a single flock. Each backyard farm was sampled at three time points: 10, 31, and 52 days of production and days 10, 24, and 38 of production in commercial farms. Statistical and network analyses were performed using DADA2 and MicrobiomeAnalyst platforms. Our results show marked differences in alpha diversity, beta diversity, and relative abundance of taxa between commercial and backyard farms over time. The observed species index significantly differed between the backyard and commercial farms for the soil, litter, and waterer samples. In addition, the fecal samples from backyard farms were found to have more Firmicutes, Bacteriodota, Desulfobacteria, Synergitota, Fusobacteriota, and Campilobacterota. Moreover, clustering showed different patterns in commercial and backyard farms with distinct marker taxa for each production system. Furthermore, the microbiome profiles of commercial and backyard farms evolved differently over time.
Context-dependent effects of temperature and community complexity on trophic interaction strength in a mite community
Authors: Torres-Campos Inmaculada , Magalhães Sara , Moya-Laraño Jordi , Montserrat Marta
Published: December 2022

Both temperature and community complexity are known to affect trophic interaction strength (TIS), but whether their effect is additive or not is as yet an open question. Here we used a 2-predator/3-prey system consistently occurring in avocado orchards to explore the effects of increasing warming and community complexity on the strength of predator:prey trophic interactions. The two predator species differed in their diet breath (acarnivoreand anomnivore) and the prey types included a herbivore, heterospecific juvenile predators, and/or pollen. Overall, analyses revealed multiplicative effects of community complexity and both temperature and predator diet breath on the net predator:prey(s) TIS. Indeed, warming led to increased TIS in the community with omnivore as top predator, but only in absence of its preferred food source. When the carnivore was the top predator, in contrast, higher temperatures led to TIS being more negative, but only for the IGprey. We conclude that sources of context dependence in specific systems need to be identified to unveil effects of warming on communities.
Effects of food supplementation and helminth removal on space use and spatial overlap in wild rodent populations
Authors: Mistrick Janine , Veitch Jasmine S.M. , Kitchen Shannon M. , Clague Samuel , Newman Brent C. , Hall Richard J. , Budischak Sarah A. , Forbes Kristian M. , Craft Meggan E.
Published: December 2022

1. Animal space use and spatial overlap can have important consequences for population-level processes such as social interactions and pathogen transmission. Identifying how environmental variability and inter-individual variation affect spatial patterns and in turn influence interactions in animal populations is a priority for the study of animal behavior and disease ecology. Environmental food availability and macroparasite infection are common drivers of variation, but there are few experimental studies investigating how they affect spatial patterns of wildlife.

2. Bank voles (Clethrionomys glareolus) are a tractable study system to investigate spatial patterns of wildlife and are amenable to experimental manipulations. We conducted a replicated, factorial field experiment in which we provided supplementary food and removed helminths in vole populations in natural forest habitat and monitored vole space use and spatial overlap using capture-mark-recapture methods.

3. Using network analysis, we quantified vole space use and spatial overlap. We compared the effects of food supplementation and helminth removal and investigated the impact of season, sex, and reproductive status on space use and spatial overlap.

4. We found that food supplementation decreased vole space use while helminth removal increased space use. Space use also varied by sex, reproductive status, and season. Spatial overlap was similar between treatments despite up to three-fold differences in population size.

5. By quantifying the spatial effects of food availability and macroparasite infection on wildlife populations, we demonstrate the potential for space use and population density to trade off and maintain consistent spatial overlap in wildlife populations. This has important implications for spatial processes in wildlife including pathogen transmission.
Uncovering context-specific genetic-regulation of gene expression from single-cell RNA-sequencing using latent-factor models
Authors: Strober Benjamin J. , Tayeb Karl , Popp Joshua , Qi Guanghao , Gordon M. Grace , Perez Richard , Ye Chun Jimmie , Battle Alexis
Published: December 2022

Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-specific expression quantitative trait loci (eQTLs) from single-cell transcriptomic data. This allows discovery of the contexts or cell types modulating genetic regulation without prior knowledge. Applied to peripheral blood single-cell eQTL data, SURGE contexts capture continuous representations of distinct cell types and groupings of biologically related cell types. We demonstrate the disease-relevance of SURGE context-specific eQTLs using colocalization analysis and stratified LD-score regression.
voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues
Authors: Schneider Arthur L. , Martins-Silva Rita , Kaizeler Alexandre , Saraiva-Agostinho Nuno , Barbosa-Morais Nuno L.
Published: December 2022

We herein introduce voyAGEr, an online graphical interface to explore age-related gene expression alterations in 49 human tissues. voyAGEr offers a visualisation and statistical toolkit for the finding and functional exploration of sex– and tissue-specific transcriptomic changes with age. In its conception, we developed a novel bioinformatics pipeline leveraging RNA sequencing data, from the GTEx project, encompassing more than 900 individuals. voyAGEr reveals transcriptomic signatures of the known asynchronous ageing between tissues, allowing the observation of tissue-specific age-periods of major transcriptional changes, associated with alterations in different biological pathways, cellular composition, and disease conditions.

Notably, voyAGEr was created to assist researchers with no expertise in bioinformatics, providing a supportive framework for elaborating, testing and refining their hypotheses on the molecular nature of human ageing and its association with pathologies, thereby also aiding in the discovery of novel therapeutic targets. voyAGEr is freely available athttps://compbio.imm.medicina.ulisboa.pt/app/voyAGEr.
A cornichon protein controls polar localization of the PINA auxin transporter inPhyscomitrium patens
Authors: Yáñez-Domínguez C. , Lagunas-Gómez D. , Torres-Cifuentes D.M. , Bezanilla M. , Pantoja O.
Published: December 2022

Newly synthesized membrane proteins pass through the secretory pathway starting at the endoplasmic reticulum and packaged into COPII vesicles to continue to the Golgi apparatus before reaching their membrane of residence. It is known that cargo receptor proteins form part of the COPII complex and play a role in the recruitment of cargo proteins for their subsequent transport through the secretory pathway. The role of cornichon proteins is conserved from yeast to vertebrates, but it is poorly characterized in plants. To study the role of this protein in cellular traffic mechanisms in plants, the mossPhyscomitrium patenshas been selected since it can be studied at the single-cell level. Here, we studied the role of the two moss cornichon homologs in the secretory pathway. Mutant analyzes revealed that cornichon genes regulate different growth processes during the moss life cycle, by controlling auxin transport; with CNIH2 functioning as a specific cargo receptor for the auxin efflux carrier PINA, with the C-terminus of the receptor regulating the interaction and trafficking of PINA.
Gap-free nuclear and mitochondrial genomes ofFusarium verticillioidesstrain HN2
Authors: Yang Wei , Zhai Haoyu , Yang Lei , Yang Qun , Song Le , Wu Jianyu , Lai Zhibing , Li Guotian
Published: December 2022

Fusarium ear rot (FER) and Fusarium stalk rot (FSR) caused by the filamentous fungusFusarium verticillioideshave become increasingly serious around the world. Additionally, fumonisins produced byF. verticillioidesthreaten food and feed security. By adding the contribution of genomic resources to better understand the pathosystem including the mechanisms ofF. verticillioides–maize interactions, and further improving the quality of theF. verticillioidesgenome, the gap-free nuclear genome and mitochondrial genome ofF. verticillioidesstrain HN2 were sequenced and assembled. Using Oxford Nanopore long reads and next-generation sequencing short reads, the final 42.81-Mb genome was assembled into 12 contigs (N50 = 4.16-Mb). A total of 13,466 protein-coding genes were annotated, including 1,076 secreted proteins that contain 342 candidate effectors. In addition, we assembled the complete 53,764 bp mitochondrial genome.F. verticillioidesstrain 7600 genome assemblies are fragmented and high-quality reference genomes were needed. The genomes presented here will serve as an important resource forF. verticillioidesresearch.
Neural substrates in Parkinson’s Disease psychosis: A systematic review
Authors: Pisani Sara , Gunasekera Brandon , Lu Yining , Vignando Miriam , ffytche Dominic , Aarsland Dag , Chaudhuri K. Ray , Ballard Clive , Lee Jee-Young , Kim Yu Kyeong , Velayudhan Latha , Bhattacharyya Sagnik
Published: December 2022

Neural underpinnings of Parkinson’s Disease psychosis (PDP) remain unclear to this day with relatively few studies and reviews available. Using a systematic review approach, here we aimed to qualitatively synthesize evidence from studies investigating PD psychosis-specific alterations in brain structure, function or chemistry using different neuroimaging modalities. PubMed, Web of Science and Embase databases were searched for fMRI, rsfMRI, DTI, PET, and SPECT studies comparing PDP patients with PD patients without psychosis (PDnP). We report findings from 18 studies (291 PDP patients, mean age ± SD = 68.65 ± 3.76 years; 48.5% males; 433 PDnP patients, mean age ± SD = 66.97 ± 3.80 years; 52% males). Qualitative synthesis revealed widespread patterns of altered brain function across task-based and resting-state fMRI studies in PDP compared to PDnP patients. Similarly, white matter abnormalities were reported in parietal, temporal, and occipital regions. Hypometabolism and reduced dopamine transporter binding were also reported whole brain and in subcortical areas. This suggests extensive alterations affecting regions involved in high order visual processing and attentional networks.
A combined DTI-fMRI approach for optimizing the delineation of posteromedial vs. anterolateral entorhinal cortex
Authors: Syversen Ingrid Framås , Reznik Daniel , Witter Menno P. , Kobro-Flatmoen Asgeir , Schröder Tobias Navarro , Doeller Christian F.
Published: December 2022

In the entorhinal cortex (EC), attempts have been made to identify the human homologue regions of the medial (MEC) and lateral (LEC) subdivision using either functional magnetic resonance imaging (fMRI) or diffusion tensor imaging (DTI). However, there are still discrepancies between entorhinal subdivisions depending on the choice of connectivity seed regions and the imaging modality used. While DTI can be used to follow the white matter tracts of the brain, fMRI can identify functionally connected brain regions. In this study, we used both DTI and resting-state fMRI in 103 healthy adults to investigate both structural and functional connectivity between the EC and associated cortical brain regions. Differential connectivity with these regions was then used to predict the locations of the human homologues of MEC and LEC. Our results from combining DTI and fMRI support a subdivision into posteromedial (pmEC) and anterolateral (alEC) EC and reveal a confined border between the pmEC and alEC. Furthermore, the EC subregions obtained by either imaging modality showed similar distinct connectivity patterns: While pmEC showed increased connectivity preferentially with the default mode network, the alEC exhibited increased connectivity with regions in the dorsal attention and salience networks. Optimizing the delineation of the human homologues of MEC and LEC with a combined, cross-validated DTI-fMRI approach allows to define a likely border between the two subdivisions and has implications for both cognitive and translational neuroscience research.
Intracellular fraction of zona pellucida protein 3 is required for the oocyte to embryo transition in mice
Authors: Israel Steffen , Seyfarth Julia , Nolte Thomas , Drexler Hannes C.A. , Fuellen Georg , Boiani Michele
Published: December 2022

In oocyte biology the zona pellucida has long been known to operate three extracellular functions, namely, encasing the oocytes in ovarian follicles, mediating sperm-oocyte interaction and preventing premature embryo contact with maternal epithelia. The present study uncovers a fourth function that is fundamentally distinct from the other three, being critical for embryonic cell survival. Intriguingly, the three proteins of the mouse zona pellucida (ZP1, ZP2, ZP3) were found abundantly present also inside the embryo four days after fertilization, as shown by mass spectrometry, immunoblotting and immunofluorescence.Trim-away-mediated knockdown of ZPs in fertilized oocytes resulted in various grades of embryopathy: knockdown of ZP1 impeded blastocyst expansion, knockdown of ZP2 hampered the 2ndzygotic cleavage, while knockdown of ZP3 hampered the 1stzygotic cleavage - unlike the overexpression. Transcriptome analysis of ZP3-knockdown embryos pointed at defects of cytoplasmic translation in the context of embryonic genome activation. This conclusion was supported by reduced protein synthesis in the ZP3-knockdown and by the lack of cleavage arrest when knockdown was postponed from the 1-cell to the late 2-cell stage. These data place constraints on the long-standing notion that the zona pellucida proteins only operate in the extracellular space. We postulate that such noncanonical localization of ZP3 reflect novel roles in the embryo’s interior during the oocyte-to-embryo transition in mice.

Graphical abstract
ROS signaling-induced mitochondrial Sgk1 regulates epithelial cell plasticity
Authors: Li Yingxiang , Liu Chengdong , Rolling Luke , Sikora Veronica , Chen Zhimin , Gurwin Jack , Barabell Caroline , Lin Jiandie , Duan Cunming
Published: December 2022

Many types of differentiated cells can reenter the cell cycle upon injury or stress. The mechanisms underlying this cell plasticity are still poorly understood. Here we investigated cell plasticity regulation using a zebrafish model, in which a population of differentiated epithelial cells are reactivated under a physiological context. We observed a robust and sustained increase in mitochondrial membrane potential in reactivated cells. Genetic and pharmacological perturbations show that elevated mitochondrial metabolism and ATP synthesis are critical for cell reactivation. Elevated mitochondrial metabolism increases mitochondrial ROS levels, which induces Sgk1 expression in the mitochondria. Deletion and inhibition of Sgk1 in zebrafish abolished cell reactivation. Similarly, ROS-dependent mitochondrial expression of SGK1 promotes S phase entry in human breast cancer cells. Mechanistically, Sgk1 coordinates mitochondrial activity with ATP synthesis by modulating F1Fo-ATP synthase phosphorylation. These findings suggest a conserved intramitochondrial signaling loop regulating epithelial cell renewal.

One sentence highlight

This study reports a new intramitochondrial signaling loop regulating epithelial cell renewal.