bluuebunny/crossref_metadata_2025 huggingface dataset:
PSIII-3 Late-Breaking: Diisobutyl Phthalate (DIBP) at Low Doses Alters Gene Expression of Epigenetic Regulators in Bovine Granulosa Cells
Authors: Pena Bello Camilo P , Batalha Isadora M , Archilia Evandro C , Wulstein Katarina , Schütz Luis F F
Published: October 2022

Phthalates are ubiquitous environmental contaminants and impact reproduction and epigenetic mechanisms. The use of diisobutyl phthalate (DIBP) has increased in the last decade. However, studies about DIBP's effects on female reproductive physiology are limited. Methylation of DNA and RNA are epigenetic processes that regulate gene expression, cell biology, and reproductive functions. How DIBP exposure regulates these epigenetic mechanisms in ovarian follicular cells remains to be unveiled. We hypothesize that DIBP at low doses alters the expression of RNA and DNA methylation regulators in bovine granulosa cells (GC). Bovine GC was isolated from small antral follicles (1-5 mm on surface diameter) from ovaries obtained at a slaughterhouse. Cells were cultured in vitro until reaching an average 70% confluence and treated with DIBP at levels detected in human blood (0 ng/mL, 1 ng/mL, 10 ng/mL, 100 ng/mL) combined with hormones that regulate ovarian folliculogenesis: FSH or FSH+IGF1. Cells were cultured for 24h for total RNA isolation (n = 5 pools) or for 48h for cell counting (n=5 pools). Relative mRNA abundance of RNA N6 methyladenine (m6A) methylation machinery (m6A writers: METTL3, METTL14; m6A erasers: ALKBH5, FTO), RNA 5-methylcytosine (m5C) methylation regulators (NSUN2, TRDMT1), and DNA methylation players (DNA methyltransferases: DNMT1, DNMT3A, DNMT3B; DNA demethylases: TET1, TET2, TET3) was determined via qPCR using 18S as housekeeping gene and expressed as 2-ΔΔCt. Cell proliferation was analyzed by cell counting using a MUSE cell analyzer. Data were analyzed via one-way ANOVA with GLM procedures of SAS for Windows. Normality was tested using Shapiro-Wilk test procedures and data considered not normal were transformed to log2 (Y + 0.6). Data sets that showed non-gaussian distribution after log-transformation was analyzed via the Kruskal-Wallis test using GraphPad Prism 9.2.0. Cell proliferation was not affected by DIBP treatments in combination with FSH or with FSH+IGF1. In GC treated with FSH in combination with DIBP, there was no significant effect on relative mRNA abundance of RNA or DNA methylation players. In combination with FSH+IGF1, GC treated with DIBP had lower (P < 0.05) METTL14 relative mRNA abundance at 1 ng/mL and 10 ng/mL than at 0 ng/mL and 100 ng/mL. TRDMT1 relative mRNA abundance was lower (P < 0.05) in the DIBP group at 10 ng/mL in comparison to groups 0 ng/mL and 1 ng/mL, but no 100 ng/mL. In addition, there was no significant effect on the relative mRNA abundance of DNA methylation regulators. In summary, GC treated with FSH+IGF1 and DIBP at low doses alters the gene expression of RNA methylation players in m6A and m5C RNA modifications in a non-monotonic dose-response, but does not alter mRNA abundance of DNA methylation regulators.
PSIII-5 Late-Breaking: Genetic Evaluation of Energy Efficiency in Bos taurus Cows Classified by Residual Feed Intake
Authors: Schaff Nathan , Dafoe Julia , Boss Darrin L , Thomson Jennifer M , Boles Jane A
Published: October 2022

Genetic selection for efficiency traits is essential to improve the profitability and sustainability of livestock operations. Inefficient metabolism and energy production in animal physiology leads to excess feed consumption, resulting in higher feed costs. The objective of this study was to investigate hepatic gene expression in mature Angus-influenced cows that were classified as low or high RFI as heifers and had either a low or high ratio of calf weaning weight to mature body weight at weaning. Eleven cows were selected from the Northern Agricultural Research Center (NARC) research herd. Cows were ranked as efficient (n = 5) or inefficient (n = 6) based on their low or high residual feed intake (RFI) measured as a growing heifer and then by the ratio of calf weaning weight by mature body weight. Animals were partitioned from the bottom quartile with low RFI as a heifer and weaned with a higher proportion of the calf were classified as efficient, and animals from the top quartile with a high RFI as a heifer and a lower ratio of the calf to body weight were classified as inefficient. Liver samples were collected by needle biopsy approximately one week after weaning and snap frozen. The liver gene expression profile was measured using RNAseq. Two cows' data were not reported, one from each group, as RNA quality prevented sequencing (Efficient n = 4 and Inefficient n = 5). Over 5 million reads were mapped for each sample and were aligned to BTau 4.6.1 reference sequence using HISAT2. Differentially expressed genes were determined using the DEseq2 R package using a model based on the negative binomial distribution, and p-values were adjusted using the Benjamini-Hochberg approach. A corrected P-value of less than 0.05 defined a differentially expressed gene. Gene lists were used for gene ontology and KEGG pathway enrichment using clusterProfiler software. One novel gene was significantly differentially expressed with higher expression in the efficient group. However, no annotation currently exists for this gene. Additionally, the KEGG pathway biosynthesis of unsaturated fatty acids was significantly enriched (P < 0.05) with the following differentially expressed genes SCD, FADS1/2, ELOVL6, and HACD2, all being down-regulated in inefficient cows. The enrichment of this pathway is most functionally relevant, as it indicates that local liver changes could directly affect the efficient metabolism and biosynthesis of fatty acids. With encouraging, but limited results, this study provides the groundwork for future study of the heritable mechanisms contributing to the generation of more energy-efficient cows.
A novel bio-inspired approach with multi-resolution mapping for the path planning of multi-robot system in complex environments
Authors: Yi Xin , Zhu Anmin , Li Chaofan , Yang Simon X
Published: October 2022

For multi-robot systems (MRSs), conventional path planning with single resolution mapping is challenging to balance information and computation. Regarding path planning of MRS, the previous research lacked systematic definition, quantitative evaluation, and the consideration of complex environmental factors. In this paper, a new systematic formulation is proposed to redefine the multi-robot path planning problem in complex environments, and evaluate the related solutions of this problem. To solve this problem, a novel bio-inspired approach based on reaction-diffusion system is given to deal with the path planning of MRS in complex environments, such as electromagnetic interference, ocean currents, and so on. Furthermore, a multi-layer neural dynamic network is proposed to describe environments with multiple resolutions, which can improve time performance while ensuring the integrity of environmental information. Comparative experimental results indicate that the proposed approach shows the excellent path planning performance of MRS in complex environments. The stability of the proposed method is determined by the mathematical basis.
Public Versus Secret Voting in Committees
Authors: Mattozzi Andrea , Nakaguma Marcos Y
Published: October 2022

We study the effect of transparency of individual votes in committees where members are heterogeneous in competence and bias, they are career-concerned, and they can abstain. We show that public voting attenuates the biases of competent members and secret voting attenuates the biases of incompetent members. Public voting leads to better decisions when the magnitude of the bias is large, while secret voting performs better otherwise. We present novel experimental evidence consistent with our theory.
Patterns and Ecological Mechanisms of Tick-Borne Disease Exposure Risk in Acadia National Park, Mount Desert Island, Maine, United States
Authors: McBride Sara E , Lieberthal Brandon A , Buttke Danielle E , Cronk Brittany D , De Urioste-Stone Sandra M , Goodman Laura B , Guarnieri Lucy D , Rounsville Thomas F , Gardner Allison M
Published: October 2022

National parks are unique and significant vector-borne pathogen transmission settings, engaging over 300 million people in outdoor recreation per year. In this study, we integrated vector surveys and ecological habitat feature data in spatial models to characterize tick-borne disease exposure risk in Acadia National Park (ANP), Maine. To determine the broad-scale patterns of blacklegged tick Ixodes scapularis Say (Acari: Ixodidae) densities in ANP, we conducted host-seeking tick collections at 114 sites across the park over two years. Using these tick survey data and geospatial landscape feature data (i.e., land cover, elevation, forest patch size, and aspect) we developed a random forest model of nymphal tick density. We found that host-seeking tick density varies significantly across the park and is particularly high in areas characterized by deciduous forest cover and relatively low elevation. To explore potential fine-scale ecological drivers of tick density spatial patterns, we quantified microclimate conditions, host activity, and vegetation characteristics at a subset of 19 sites. We identified significant differences in microclimate conditions but not host activity or vegetation metrics across broad-scale landscape feature classes. Mean temperature and mean humidity were correlated to nymphal densities and therefore may provide a mechanistic link between landscape features and blacklegged tick densities. Finally, we detected multiple tick-borne pathogens in both ticks and small mammals sampled in ANP, including Borrelia burgdorferi, Babesia microti, and Anaplasma phagocytophilum. Our findings demonstrate the value of using ecological metrics to estimate vector-borne disease exposure risk and provide insight into habitat characteristics that may drive tick-borne disease exposure risk.
Populist attitudes and politicians’ disinformation accusations: effects on perceptions of media and politicians
Authors: Egelhofer Jana Laura , Boyer Ming , Lecheler Sophie , Aaldering Loes
Published: October 2022

Populist politicians increasingly accuse opposing media of spreading disinformation or “fake news.” However, empirical research on the effects of these accusations is scarce. This survey experiment (N = 1,330) shows that disinformation accusations reduce audience members’ trust in the accused news outlet and perceived accuracy of the news message, while trust in the accusing politician is largely unaffected. However, only individuals with strong populist attitudes generalize disinformation accusations to the media as an institution and reduce their general media trust. The phrase “fake news” does not amplify any of these effects. These findings suggest that politicians can undermine the credibility of journalism without much repercussion—a mechanism that might also threaten other authoritative information sources in democracies such as scientists and health authorities.
Discovery and study of abrasion behavior in granular shear flow
Authors: Hsiau Shu-San , Hutter Kolumban , Lu Li-Shin , Teufel Andreas , Chou Shih-Hao , Sheng Li-Tsung
Published: October 2022

Experiments were performed in an Couette ring shear cell with particles from the food industry of nearly spherical geometry and nominal diameters between 2.0 and 6.7 mm and with quartz grains with 2.1 to 3.3 mm diameter to examine whether rapid shear flow would give rise to an appreciable change in the granular properties. In particular, it was suspected that surface roughness would change during shearing and lead to changes in the values of the internal and wall friction angles. Measuring these angles corroborated the supposition that abrasion of the particles reduced their frictional resistance, both via the internal and wall friction angles. This demonstrates that roughness changes may occur in granular flows and should in those situations not be ignored in the theoretical descriptions.
Dissatisfied, but not discouraged: the effects of French female lawyers perceiving gender discrimination
Authors: Insarauto Valeria , Boni-Le Goff Isabel , Mallard Grégoire , Lépinard Eléonore , Le Feuvre Nicky
Published: October 2022

Previous research has suggested not only that gender discrimination is widespread in law firms, conditioning women’s career paths and full integration into the legal profession, but also that female lawyers are more likely than their male counterparts to perceive unfair treatment. However, little research exists on how female lawyers’ perceptions of gender discrimination may affect their individual work experiences, in particular their attitudes toward their job and their career. This article aims to fill this gap by examining how perceived gender discrimination affects female lawyers’ job satisfaction with their career prospects and work–life balance, as well as their intentions to leave the legal profession. With a focus on the under-researched French case, it draws on the quantitative analysis of the data collected from an online survey administered to 663 female Parisian lawyers. Results show that perceptions of discrimination negatively affect women’s satisfaction with regard to their career prospects and work–life balance, but do not have any influence on their quitting intentions. By adopting a ‘view from below’ on the individual work experiences of female lawyers, the article sheds new light on the dynamics of women’s disadvantage in legal careers.
Immunogenicity of a single fractional intradermal dose of Japanese encephalitis live attenuated chimeric vaccine
Authors: Furuya-Kanamori Luis , Gyawali Narayan , Mills Deborah J , Mills Christine , Hugo Leon E , Devine Gregor J , Lau Colleen L
Published: October 2022

Background

Japanese encephalitis (JE) is endemic in Asia and the western Pacific. Vaccination is recommended for travellers to endemic regions, but the high cost of the vaccine is a major barrier to uptake.

Methods

A quasi-experimental, pre-post intervention clinical trial without a control group was conducted to assess the immunogenicity and safety of intradermal (ID) JE vaccine. Healthy adults (18–45 years) received one dose of 0.1 mL (20% of standard dose) ID Imojev® (JE live attenuated chimeric vaccine, Sanofi-Aventis). Adverse events following immunization (AEFIs) were recorded 10 days post-vaccination. Blood samples were collected at baseline, 4 and 8 weeks post-vaccination. Neutralizing antibodies were measured using 50% plaque reduction neutralization test (PRNT50). Seroconversion was defined as PRNT50 titre ≥10. An in vitro study was also conducted to quantify the rate of decay of vaccine potency after reconstitution.

Results

In total, 51 participants (72.6% females, median age 31 years), all non-reactive to JE virus at baseline were enrolled. Mild and moderate AEFIs were reported by 19.6% of participants; none required medical attention or interfered with normal daily activities. All participants seroconverted at 4 weeks (GMT 249.3; 95%CI:192.8–322.5) and remained seropositive at 8 weeks (GMT 135.5; 95%CI:104.5–175.6). Vaccine potency declined at a rate of 0.14 log plaque-forming units/0.5 mL per hour.

Conclusions

In healthy adults, a single 0.1 mL ID dose of Imojev was safe and immunogenic, at least in the short term. Reconstituted vials of Imojev vaccine may not retain their potency after 6 hours. Fractional JE ID vaccination could be a cheaper yet effective alternative for short-term travellers. Further studies need to investigate the immune response in a wider age range of individuals and the long-term immunogenicity of fractional JE ID vaccines.

Clinical trials registration

ACTRN12621000024842.
Air travel and SARS-CoV-2: many remaining knowledge gaps
Authors: Freedman David O
Published: October 2022

COVID-19 is with us indefinitely and air travel is a necessity. Needed research has lagged due to pandemic disruption but must not stall due to COVID indifference. A US government report proposes that national aviation authorities, not health agencies, take the lead. Research priorities and study designs are proposed.
Exposure to past immigration waves and attitudes toward newcomers
Authors: Gihleb Rania , Giuntella Osea , Stella Luca
Published: October 2022

How does previous exposure to massive immigrant inflows affect concerns about current immigration and the integration of refugees? To answer this question, we investigate attitudes toward newcomers among natives and previous immigrants. In areas that in the 1990s received higher inflows of immigrants of German origin—the so-called ethnic Germans—native Germans are more likely to believe that refugees are a resource for the economy and the culture, viewing them as an opportunity rather than a risk. Refugees living in these areas report better health and feel less exposed to xenophobia.
Leptocline as a shallow substructure of near-surface shear layer in 3D radiative hydrodynamic simulations
Authors: Kitiashvili Irina N , Kosovichev A G , Wray A A , Sadykov V M , Guerrero G
Published: October 2022

Understanding the effects driven by rotation in the solar convection zone is essential for many problems related to solar activity, such as the formation of differential rotation, meridional circulation, and others. We analyse realistic 3D radiative hydrodynamics simulations of solar subsurface dynamics in the presence of rotation in a local domain 80 Mm wide and 25 Mm deep, located at 30° latitude. The simulation results reveal the development of a shallow 10 Mm deep substructure of the near-surface shear layer (NSSL), characterized by a strong radial rotational gradient and self-organized meridional flows. This shallow layer (‘leptocline’) is located in the hydrogen ionization zone associated with enhanced anisotropic overshooting-type flows into a less unstable layer between the H and He ii ionization zones. We discuss current observational evidence of the presence of the leptocline and show that the radial variations of the differential rotation and meridional flow profiles obtained from the simulations in this layer qualitatively agree with helioseismic observations.
Stellar feedback impact on the ionized gas kinematics in the dwarf galaxy Sextans A
Authors: Gerasimov Ivan S , Egorov Oleg V , Lozinskaya Tatiana A , Moiseev Alexei V , Oparin Dmitry V
Published: October 2022

Feedback from massive stars shapes the interstellar medium (ISM) and affects the evolution of galaxies, but its mechanisms acting at the small scales (∼10 pc) are still not well constrained observationally, especially in the low-metallicity environments. We present the analysis of the ionized gas (focusing on its kinematics, which were never studied before) and its connection to the massive stars in the nearby (D ∼ 1.4 Mpc) star-forming very metal poor ($Z\sim 0.07 \, \mathrm{Z}_\odot$) galaxy Sextans A. The analysis is based on the observations with a scanning Fabry–Perot interferometer, long-slit spectroscopy, and imaging in emission lines with narrow-band tunable filters. We found 10 expanding superbubbles of ionized gas with ages of 1–3 Myr. We argue that three of them are probable supernova remnants, while the pre-supernova feedback is an important source of energy for blowing out the remaining superbubbles. The two brightest sites of star formation exhibit signs of outflowing ionized gas, which is traced by its ionized and atomic gas kinematics and (in one case) by its emission line flux ratios. Overall, the ionized gas kinematics in Sextans A is highly affected by the feedback from several generations of massive stars and inconsistent with the mere solid-body rotation observed in atomic hydrogen.
The density distribution and physical origins of intermittency in supersonic, highly magnetized turbulence with diverse modes of driving
Authors: Beattie James R , Mocz Philip , Federrath Christoph , Klessen Ralf S
Published: October 2022

The probability density function (PDF) of the logarithmic density contrast, s = ln (ρ/ρ0), with gas density ρ and mean density ρ0, for hydrodynamical supersonic turbulence is well known to have significant non-Gaussian (intermittent) features that monotonically increase with the turbulent Mach number, $\mathcal {M}$. By studying the mass- and volume-weighted s-PDF for an ensemble of 36 sub-to-trans-Alfv́enic mean-field, supersonic, isothermal turbulence simulations with different modes of driving, relevant to molecular gas in the cool interstellar medium, we show that a more intricate picture emerges for the non-Gaussian nature of s. Using four independent measures of the non-Gaussian components, we find hydrodynamical-like structure in the highly magnetized plasma for $\mathcal {M} \lesssim 4$. However, for $\mathcal {M} \gtrsim 4$, the non-Gaussian signatures disappear, leaving approximately Gaussian s-statistics – exactly the opposite of hydrodynamical turbulence in the high-$\mathcal {M}$ limit. We also find that the non-Gaussian components of the PDF increase monotonically with more compressive driving modes. To understand the $\mathcal {M} \lesssim 4$ non-Gaussian features, we use one-dimensional pencil beams to explore the dynamics along and across the large-scale magnetic field, $\mathrm{{\boldsymbol {\mathit {B}}}}_0$. We discuss kinetic, density, and magnetic field fluctuations from the pencil beams, and identify physical sources of non-Gaussian components to the PDF as single, strong shocks coupled to fast magnetosonic compressions that form along $\mathrm{{\boldsymbol {\mathit {B}}}}_0$. We discuss the Gaussianization of the $\mathcal {M} \gtrsim 4$s-fields through the lens of two phenomenologies: the self-similarity of the s-field and homogenization of the dynamical time-scales between the over- and underdense regions in the compressible gas.
ΛCDM with baryons versus MOND: The time evolution of the universal acceleration scale in the Magneticum simulations
Authors: Mayer Alexander C , Teklu Adelheid F , Dolag Klaus , Remus Rhea-Silvia
Published: October 2022

MOdified Newtonian Dynamics (MOND) is an alternative to the standard Cold Dark Matter (CDM) paradigm which proposes an alteration of Newton’s laws of motion at low accelerations, characterized by a universal acceleration scale a0. It attempts to explain observations of galactic rotation curves and predicts a specific scaling relation of the baryonic and total acceleration in galaxies, referred to as the Rotational Acceleration Relation (RAR), which can be equivalently formulated as a Mass Discrepancy Acceleration Relation (MDAR). The appearance of these relations in observational data such as SPARC has lead to investigations into the existence of similar relations in cosmological simulations using the standard ΛCDM model. Here, we report the existence of an RAR and MDAR similar to that predicted by MOND in ΛCDM using a large sample of galaxies extracted from a cosmological, hydrodynamical simulation (Magneticum). Furthermore, by using galaxies in Magneticum at different redshifts, a prediction for the evolution of the inferred acceleration parameter a0 with cosmic time is derived by fitting a MOND force law to these galaxies. In Magneticum, the best fit for a0 is found to increase by a factor ≃3 from redshift z = 0 to z = 2.3. This offers a powerful test from cosmological simulations to distinguish between MOND and ΛCDM observationally.
Probing particle acceleration at trans-relativistic shocks with off-axis gamma-ray burst afterglows
Authors: Takahashi Kazuya , Ioka Kunihito , Ohira Yutaka , van Eerten Hendrik J
Published: October 2022

Particle acceleration is expected to be different between relativistic and non-relativistic collisionless shocks. We show that electromagnetic counterparts to gravitational waves (GWs), gamma-ray burst (GRB) afterglows, are ideal targets for observing trans-relativistic evolution of accelerated electron distribution because the GWs spot nearby GRBs with off-axis jets, otherwise missed in gamma-ray observations. We find that the relativistic spectral slope begins to change steeply near the peak time of the light curve and approaches the non-relativistic limit in about 10 times the peak time. The trans-relativistic evolution of the afterglow synchrotron spectrum is consistent with GRB 170817A observations within errors, and will be measurable in similar but more distant events at a GW horizon ∼200 Mpc in a denser environment. We roughly estimate that such events represent a fraction of 10–50 per cent of the GRB 170817A-like off-axis short GRBs. We also find that the spectral evolution does not depend on the jet structure if their light curves are similar to each other.
CS-ROMER: a novel compressed sensing framework for Faraday depth reconstruction
Authors: Cárcamo Miguel , Scaife Anna M M , Alexander Emma L , Leahy J Patrick
Published: October 2022

The reconstruction of Faraday depth structure from incomplete spectral polarization radio measurements using the RM synthesis technique is an underconstrained problem requiring additional regularization. In this paper, we present cs-romer: a novel object-oriented compressed sensing framework to reconstruct Faraday depth signals from spectropolarization radio data. Unlike previous compressed sensing applications, this framework is designed to work directly with data that are irregularly sampled in wavelength-squared space and to incorporate multiple forms of compressed sensing regularization. We demonstrate the framework using simulated data for the VLA telescope under a variety of observing conditions, and we introduce a methodology for identifying the optimal basis function for reconstruction of these data, using an approach that can also be applied to data sets from other telescopes and over different frequency ranges. In this work, we show that the delta basis function provides optimal reconstruction for VLA L-band data and we use this basis with observations of the low-mass galaxy cluster Abell 1314 in order to reconstruct the Faraday depth of its constituent cluster galaxies. We use the cs-romer framework to de-rotate the Galactic Faraday depth contribution directly from the wavelength-squared data and to handle the spectral behaviour of different radio sources in a direction-dependent manner. The results of this analysis show that individual galaxies within Abell 1314 deviate from the behaviour expected for a Faraday-thin screen such as the intra-cluster medium and instead suggest that the Faraday rotation exhibited by these galaxies is dominated by their local environments.
Accurate dark-matter halo elongation from weak-lensing stacking analysis
Authors: Gonzalez Elizabeth J , Hoffmann Kai , Gaztañaga Enrique , García Lambas Diego R , Fosalba Pablo , Crocce Martin , Castander Francisco J , Makler Martín
Published: October 2022

Shape estimates that quantifying the halo anisotropic mass distribution are valuable parameters that provide information on their assembly process and evolution. Measurements of the mean shape estimates for a sample of cluster-sized haloes can be used to test halo formation scenarios, as well as improving the modelling of potential biases in constraining cosmological parameters using these systems. In this work, we test the recovery of halo cluster shapes and masses applying weak-lensing stacking techniques. To this end, we use lensing shear and a new dark-matter halo catalogue, derived from the light-cone output of the cosmological simulation MICE-GC. We perform this study by combining the lensing signals obtained for several samples of haloes, selected according to their mass and redshift, taking into account the main directions of the dark-matter distributions. In the analysis, we test the impact of several potential introduced systematics, such as the adopted modelling, the contribution of the neighbouring mass distribution, miscentring, and misalignment effects. Our results show that when some considerations regarding the halo relaxation state are taken into account, the lensing semi-axial ratio estimates are in agreement within a 5 per cent with the mean shapes of the projected dark-matter particle distribution of the stacked haloes. The presented methodology provides a useful tool to derive reliable shapes of galaxy clusters and to contrast them with those expected from numerical simulations. Furthermore, our proposed modelling, that takes into account the contribution of neighbouring haloes, allows to constraint the elongation of the surrounding mass distribution.
Properties of atomic hydrogen gas in the Galactic plane from THOR 21-cm absorption spectra: a comparison with the high latitude gas
Authors: Basu Arghyadeep , Roy Nirupam , Beuther Henrik , Syed Jonas , Ott Jürgen , Soler Juan D , Stil Jeroen , Rugel Michael R
Published: October 2022

The neutral hydrogen 21-cm line is an excellent tracer of the atomic interstellar medium in the cold and the warm phases. Combined 21-cm emission and absorption observations are very useful to study the properties of the gas over a wide range of density and temperature. In this work, we have used 21-cm absorption spectra from recent interferometric surveys, along with the corresponding emission spectra from earlier single dish surveys to study the properties of the atomic gas in the Milky Way. In particular, we focus on a comparison of properties between lines of sight through the gas disc in the Galactic plane and high Galactic latitude lines of sight through more diffuse gas. As expected, the analysis shows a lower average temperature for the gas in the Galactic plane compared to that along the high latitude lines of sight. The gas in the plane also has a higher molecular fraction, showing a sharp transition and flattening in the dust–gas correlation. On the other hand, the observed correlation between 21-cm brightness temperature and optical depth indicates some intrinsic difference in spin temperature distribution and a fraction of gas in the Galactic plane having intermediate optical depth (for 0.02 < τ < 0.2) but higher spin temperature, compared to that of the diffuse gas at high latitude with the same optical depth. This may be due to a small fraction of cold gas with slightly higher temperature and lower density present on the Galactic plane.
Zonal winds in the gas planets driven by convection above a stably stratified layer
Authors: Wulff Paula N , Dietrich W , Christensen U R , Wicht J
Published: October 2022

The analysis of the recent gravity measurements of Jupiter and Saturn reveal that the zonal winds observed on their surfaces reach several thousand kilometres deep into their atmospheres. However, it remains unclear which mechanism prevents them from penetrating deeper. Recent models suggest that a stably stratified region would yield the desired effect. In this numerical study we systematically explore the dynamics of flow in a rotating spherical shell where the lower third is stably stratified while convection in the outer region drives multiple zonal winds, similar to those observed on Jupiter or Saturn. When using a rigid lower boundary condition, only an equatorial jet pair is formed without an underlying stable layer. When including a stable layer, fierce multiple jets also develop at mid to high latitudes, once the stable stratification is strong enough to effectively decouple the jet dynamics from the lower boundary. We find that the decay of the jet amplitude near the stable layer boundary is controlled by Ω/N, where Ω is the rotation rate and N the Brunt-Väisälä frequency that quantifies the degree of stable stratification. Furthermore, the penetration distance of the jets is proportional to the jet width. In the convective region, the winds are invariant along the axis of rotation, whereas their extension in the stable layer tends to become radially aligned.
Infrared variability of young solar analogues in the Lagoon Nebula
Authors: Ordenes-Huanca C , Zoccali M , Bayo A , Cuadra J , Contreras Ramos R , Hillenbrand L A , Lacerna I , Abarzua S , Avendaño C , Diaz P , Fernandez I , Lara G
Published: October 2022

T Tauri stars are low-mass pre-main sequence stars that are intrinsically variable. Due to the intense magnetic fields they possess, they develop dark spots on their surface that, because of rotation, introduce a periodic variation of brightness. In addition, the presence of surrounding discs could generate flux variations by variable extinction or accretion. Both can lead to a brightness decrease or increase, respectively. Here, we have compiled a catalogue of light curves for 379 T Tauri stars in the Lagoon Nebula (M8) region, using VVVX survey data in the Ks-band. All these stars were already classified as pre-MS stars based on other indicators. The data presented here are spread over a period of about eight years, which gives us a unique follow-up time for these sources at this wavelength. The light curves were classified according to their degree of periodicity and asymmetry, to constrain the physical processes responsible for their variation. Periods were compared with the ones found in literature, on a much shorter baseline. This allowed us to prove that for 126 stars, the magnetically active regions remain stable for several years. Besides, our near-IR data were compared with the optical Kepler/K2 light curves, when available, giving us a better understanding of the mechanisms responsible for the brightness variations observed and how they manifest at different bands. We found that the periodicity in both bands is in fairly good agreement, but the asymmetry will depend on the amplitude of the bursts or dips events and the observation cadence.
The eccentricity distribution of wide binaries
Authors: Benisty David , Evans N Wyn , Davis Anne-Christine
Published: October 2022

Future Gaia and Legacy Survey of Space and Time data releases, together with wide area spectroscopic surveys, will deliver large samples of resolved binary stars with phase space coordinates, albeit with low-cadence. Given an eccentricity law f(ϵ), we derive properties of (i) the velocity distribution $v/\sqrt{G M/r}$ normalized by the value for a circular orbit at the measured separation r; (ii) the astrometric acceleration distributions a/(GM/r2) again normalized to the circular orbit value. Our formulation yields analytic predictions for the full statistical distribution for some commonly used eccentricity laws, if the time-scale of data sampling is comparable to or exceeds the binary period. In particular, the velocity distribution for the linear eccentricity law is surprisingly simple. With Bayesian analysis, we suggest a method to infer the eccentricity distribution based on the measured velocity distribution.
Functional Attenuation of UCP1 as the Potential Mechanism for a Thickened Blubber Layer in Cetaceans
Authors: Zhou Ming , Wu Tianzhen , Chen Yue , Xu Shixia , Yang Guang
Published: October 2022

Uncoupling protein 1 (UCP1) is an essential protein in the mitochondrial inner membrane that mediates nonshivering thermogenesis (NST) and plays an important role in thermoregulation and fat deposition. However, the relationship between the evolution of UCP1 and fat deposition in the blubber layer in cetaceans remains unclear. Here, frameshift mutations, premature termination, and relaxed selection pressure (ω = 0.9557, P < 0.05) were detected in UCP1 in cetaceans, suggesting that UCP1 was inactivated during cetacean evolution. By time estimation, it was found that the inactivation of UCP1 in cetaceans occurred between 53.1 and 50.2 Ma. However, combined with findings from immunohistochemical analysis of the blubber layer of the Yangtze finless porpoise and in vitro functional assays, a premature termination of cetacean UCP1 resulted in a reduction of UCP1-mediated NST capacity (about 50%) and lipolytic capacity (about 40%), both of which were beneficial to maintain blubber layer and body temperature without excessive fat consumption. This study provides new insights into the molecular mechanisms of the blubber thickening in cetaceans and highlights the importance of UCP1 attenuation in cetaceans for secondary aquatic adaptation.
Prokaryotic Pangenomes Act as Evolving Ecosystems
Authors: McInerney James O
Published: October 2022

Understanding adaptation to the local environment is a central tenet and a major focus of evolutionary biology. But this is only part of the adaptionist story. In addition to the external environment, one of the main drivers of genome composition is genetic background. In this perspective, I argue that there is a growing body of evidence that intra-genomic selective pressures play a significant part in the composition of prokaryotic genomes and play a significant role in the origin, maintenance and structuring of prokaryotic pangenomes.
Single-cell and bulk ICP–MS investigation of accumulation patterns of Pt-based metallodrugs in cisplatin-sensitive and -resistant cell models
Authors: Lim Si Ying , Low Zhi En , Tan Regina Pei Woon , Lim Zhi Chiaw , Ang Wee Han , Kubota Tetsuo , Yamanaka Michiko , Pang Steven , Simsek Erhan , Li Sam Fong Yau
Published: October 2022

In research enabling preclinical development and attaining a deeper understanding of the behavior of metallodrugs in cancer cells with acquired resistance, intracellular Pt accumulation could be considered an important biomarker and analytical focus. In this work, Pt accumulation patterns in terms of the number of cells and Pt mass in single cells were precisely defined by using inductively coupled plasma-mass spectrometry (ICP–MS) operating in a fast time-resolved analysis mode. This technique is otherwise known as single-cell (SC)–ICP–MS. By applying the nascent and validated SC–ICP–MS technique, comparisons across three Pt drugs (cisplatin, carboplatin, and oxaliplatin) in the A2780 and A2780cis ovarian cancer cell models could be made. Additional roles of transporters on top of passive diffusion and the drugs’ bioactivity could be postulated. The SC–ICP–MS-based observations also served as a cross-validation point to augment preexisting research findings on Pt-resistance mechanisms. Conjectures regarding S and Fe metabolism were also derived based on an additional and direct ICP–MS analysis of endogenous elements. Overall, our work not only confirms the utility of SC–ICP–MS in chemotherapeutic research, but also provided insights into further ICP–MS-based analytical capacities to be developed.
Molecular basis for lethal cross-talk between two unrelated bacterial transcription factors - the regulatory protein of a restriction-modification system and the repressor of a defective prophage
Authors: Wisniewska Aleksandra , Wons Ewa , Potrykus Katarzyna , Hinrichs Rebecca , Gucwa Katarzyna , Graumann Peter L , Mruk Iwona
Published: October 2022

Bacterial gene expression depends on the efficient functioning of global transcriptional networks, however their interconnectivity and orchestration rely mainly on the action of individual DNA binding proteins called transcription factors (TFs). TFs interact not only with their specific target sites, but also with secondary (off-target) sites, and vary in their promiscuity. It is not clear yet what mechanisms govern the interactions with secondary sites, and how such rewiring affects the overall regulatory network, but this could clearly constrain horizontal gene transfer. Here, we show the molecular mechanism of one such off-target interaction between two unrelated TFs in Escherichia coli: the C regulatory protein of a Type II restriction-modification system, and the RacR repressor of a defective prophage. We reveal that the C protein interferes with RacR repressor expression, resulting in derepression of the toxic YdaT protein. These results also provide novel insights into regulation of the racR-ydaST operon. We mapped the C regulator interaction to a specific off-target site, and also visualized C protein dynamics, revealing intriguing differences in single molecule dynamics in different genetic contexts. Our results demonstrate an apparent example of horizontal gene transfer leading to adventitious TF cross-talk with negative effects on the recipient's viability. More broadly, this study represents an experimentally-accessible model of a regulatory constraint on horizontal gene transfer.
PlantExp: a platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples
Authors: Liu Jinding , Zhang Yaru , Zheng Yiqing , Zhu Yali , Shi Yapin , Guan Zhuoran , Lang Kun , Shen Danyu , Huang Wen , Dou Daolong
Published: October 2022

Over the last decade, RNA-seq has produced a massive amount of plant transcriptomic sequencing data deposited in public databases. Reanalysis of these public datasets can generate additional novel hypotheses not included in original studies. However, the large data volume and the requirement for specialized computational resources and expertise present a barrier for experimental biologists to explore public repositories. Here, we introduce PlantExp (https://biotec.njau.edu.cn/plantExp), a database platform for exploration of plant gene expression and alternative splicing profiles based on 131 423 uniformly processed publicly available RNA-seq samples from 85 species in 24 plant orders. In addition to two common retrieval accesses to gene expression and alternative splicing profiles by functional terms and sequence similarity, PlantExp is equipped with four online analysis tools, including differential expression analysis, specific expression analysis, co-expression network analysis and cross-species expression conservation analysis. With these online analysis tools, users can flexibly customize sample groups to reanalyze public RNA-seq datasets and obtain new insights. Furthermore, it offers a wide range of visualization tools to help users intuitively understand analysis results. In conclusion, PlantExp provides a valuable data resource and analysis platform for plant biologists to utilize public RNA-seq. datasets.
Molecular basis of cyclic tetra-oligoadenylate processing by small standalone CRISPR-Cas ring nucleases
Authors: Molina Rafael , Garcia-Martin Ricardo , López-Méndez Blanca , Jensen Anne Louise Grøn , Ciges-Tomas J Rafael , Marchena-Hurtado Javier , Stella Stefano , Montoya Guillermo
Published: October 2022

Standalone ring nucleases are CRISPR ancillary proteins, which downregulate the immune response of Type III CRISPR-Cas systems by cleaving cyclic oligoadenylates (cA) second messengers. Two genes with this function have been found within the Sulfolobus islandicus (Sis) genome. They code for a long polypeptide composed by a CARF domain fused to an HTH domain and a short polypeptide constituted by a CARF domain with a 40 residue C-terminal insertion. Here, we determine the structure of the apo and substrate bound states of the Sis0455 enzyme, revealing an insertion at the C-terminal region of the CARF domain, which plays a key role closing the catalytic site upon substrate binding. Our analysis reveals the key residues of Sis0455 during cleavage and the coupling of the active site closing with their positioning to proceed with cA4 phosphodiester hydrolysis. A time course comparison of cA4 cleavage between the short, Sis0455, and long ring nucleases, Sis0811, shows the slower cleavage kinetics of the former, suggesting that the combination of these two types of enzymes with the same function in a genome could be an evolutionary strategy to regulate the levels of the second messenger in different infection scenarios.
Fungal names: a comprehensive nomenclatural repository and knowledge base for fungal taxonomy
Authors: Wang Fang , Wang Ke , Cai Lei , Zhao Mingjun , Kirk Paul M , Fan Guomei , Sun Qinglan , Li Bo , Wang Shuai , Yu Zhengfei , Han Dong , Ma Juncai , Wu Linhuan , Yao Yijian
Published: October 2022

Fungal taxonomy is a complex and rapidly changing subject, which makes proper naming of fungi challenging for taxonomists. A registration platform with a standardized and information-integrated database is a powerful tool for efficient research on fungal taxonomy. Fungal Names (FN, https://nmdc.cn/fungalnames/; launched in 2011) is one of the three official fungal nomenclatural repositories authorized by the International Nomenclature Committee for Fungi (NCF). Currently, FN includes >567 000 taxon names from >10 000 related journals and books published since 1596 and covers >147 000 collection records of type specimens/illustrations from >5000 preserving agencies. FN is also a knowledge base that integrates nomenclature information with specimens, culture collections and herbaria/fungaria, publications and taxonomists, and represents a summary of the history and recent advances in fungal taxonomy. Published fungal names are categorized based on well-accepted nomenclature rules and can be readily searched with different keywords and strategies. In combination with a standardized name checking tool and a sequence alignment-based identification package, FN makes the registration and typification of nomenclatural novelties of fungi convenient and accurate.
OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids
Authors: Ma Qinfeng , Tao Haodong , Li Qiang , Zhai Zhaoyu , Zhang Xuelu , Lin Zhewei , Kuang Ni , Pan Jianbo
Published: October 2022

Organoids, three-dimensional in vitro tissue cultures derived from pluripotent (embryonic or induced) or adult stem cells, are promising models for the study of human processes and structures, disease onset and preclinical drug development. An increasing amount of omics data has been generated for organoid studies. Here, we introduce OrganoidDB (http://www.inbirg.com/organoid_db/), a comprehensive resource for the multi-perspective exploration of the transcriptomes of organoids. The current release of OrganoidDB includes curated bulk and single-cell transcriptome profiles of 16 218 organoid samples from both human and mouse. Other types of samples, such as primary tissue and cell line samples, are also integrated to enable comparisons with organoids. OrganoidDB enables queries of gene expression under different modes, e.g. across different organoid types, between different organoids from different sources or protocols, between organoids and other sample types, across different development stages, and via correlation analysis. Datasets and organoid samples can also be browsed for detailed information, including organoid information, differentially expressed genes, enriched pathways and single-cell clustering. OrganoidDB will facilitate a better understanding of organoids and help improve organoid culture protocols to yield organoids that are highly similar to living organs in terms of composition, architecture and function.