bluuebunny/crossref_metadata_2025 huggingface dataset:
JWST’s PEARLS: TN J1338–1942 – I. Extreme jet-triggered star formation in a z = 4.11 luminous radio galaxy
Authors: Duncan Kenneth J , Windhorst Rogier A , Koekemoer Anton M , Röttgering Huub J A , Cohen Seth H , Jansen Rolf A , Summers Jake , Tompkins Scott , Hutchison Taylor A , Conselice Christopher J , Driver Simon P , Yan Haojing , Adams Nathan J , Cheng Cheng , Coe Dan , Diego Jose M , Dole Hervé , Frye Brenda , Gim Hansung B , Grogin Norman A , Holwerda Benne W , Lim Jeremy , Marshall Madeline A , Nonino Mario , Pirzkal Nor , Robotham Aaron , Ryan Russell E , Willmer Christopher N A
Published: April 2023

We present the first JWST observations of the z  = 4.11 luminous radio galaxy TN J1338–1942, obtained as part of the ‘Prime Extragalactic Areas for Reionization and Lensing Science’ (‘PEARLS’) project. Our NIRCam observations, designed to probe the key rest-frame optical continuum and emission line features at this redshift, enable resolved spectral energy distribution modelling that incorporates both a range of stellar population assumptions and radiative shock models. With an estimated stellar mass of log10(M/M⊙) ∼ 10.9, TN J1338–1942 is confirmed to be one of the most massive galaxies known at this epoch. Our observations also reveal extremely high equivalent-width nebular emission coincident with the luminous AGN jets that is best fit by radiative shocks surrounded by extensive recent star formation. We estimate the total star-formation rate (SFR) could be as high as $\sim 1600\, \text{M}_{\odot }\, \text{yr}^{-1}$ , with the SFR that we attribute to the jet induced burst conservatively $\gtrsim 500\, \text{M}_{\odot }\, \text{yr}^{-1}$ . The mass-weighted age of the star-formation, tmass < 4 Myr, is consistent with the likely age of the jets responsible for the triggered activity and significantly younger than that measured in the core of the host galaxy. The extreme scale of the potential jet-triggered star-formation activity indicates the potential importance of positive AGN feedback in the earliest stages of massive galaxy formation, with our observations also illustrating the extraordinary prospects for detailed studies of high-redshift galaxies with JWST.
Discovery of extraordinary X-ray emission from magnetospheric interaction in the unique binary stellar system ϵ Lupi
Authors: Das B , Petit V , Nazé Y , Corcoran M F , Cohen D H , Biswas A , Chandra P , David-Uraz A , Leutenegger M A , Neiner C , Pablo H , Paunzen E , Shultz M E , ud-Doula A , Wade G A
Published: April 2023

We report detailed X-ray observations of the unique binary system ϵ Lupi, the only known short-period binary consisting of two magnetic early-type stars. The components have comparably strong, but anti-aligned magnetic fields. The orbital and magnetic properties of the system imply that the magnetospheres overlap at all orbital phases, suggesting the possibility of variable inter-star magnetospheric interaction due to the non-negligible eccentricity of the orbit. To investigate this effect, we observed the X-ray emission from ϵ Lupi, both near and away from periastron passage, using the Neutron Star Interior Composition Explorer mission (NICER) X-ray Telescope. We find that the system produces excess X-ray emission at the periastron phase, suggesting the presence of variable inter-star magnetospheric interaction. We also discover that the enhancement at periastron is confined to a very narrow orbital phase range ($\approx 5~{{\ \rm per\ cent}}$ of the orbital period), but the X-ray properties close to periastron phase are similar to those observed away from periastron. From these observations, we infer that the underlying cause is magnetic reconnection heating the stellar wind plasma, rather than shocks produced by wind–wind collision. Finally, by comparing the behavior of ϵ Lupi with that observed for cooler magnetic binary systems, we propose that elevated X-ray flux at periastron phase is likely a general characteristic of interacting magnetospheres irrespective of the spectral types of the constituent stars.
Ammonia masers towards G 358.931−0.030
Authors: McCarthy T P , Breen S L , Kaczmarek J F , Chen X , Parfenov S , Sobolev A M , Ellingsen S P , Burns R A , MacLeod G C , Sugiyama K , Brierley A L , van den Heever S P
Published: April 2023

We report the detection of ammonia masers in the non-metastable (6, 3), (7, 5), and (6, 5) transitions; the latter being the first unambiguous maser detection of that transition ever made. Our observations include the first very long baseline interferometry detection of ammonia maser emission, which allowed effective constraining of the (6, 5) maser brightness temperature. The masers were detected towards G 358.931−0.030, a site of 6.7-GHz class II methanol maser emission that was recently reported to be undergoing a period of flaring activity. These ammonia masers appear to be flaring contemporaneously with the class II methanol masers during the accretion burst event of G 358.931−0.030. This newly detected site of ammonia maser emission is only the 12th such site discovered in the Milky Way. We also report the results of an investigation into the maser pumping conditions, for all three detected masing transitions, through radiative transfer calculations constrained by our observational data. These calculations support the hypothesis that the ammonia (6, 5) maser transition is excited through high colour temperature infrared emission, with the (6, 5) and (7, 5) transition line ratio implying dust temperatures >400 K. Additionally, we detect significant linearly polarized emission from the ammonia (6, 3) maser line. Alongside our observational and radiative transfer calculation results, we also report newly derived rest frequencies for the ammonia (6, 3) and (6, 5) transitions.
Magnetic field line separation by random ballistic decorrelation in transverse magnetic turbulence
Authors: Yannawa C , Pongkitiwanichakul P , Ruffolo D , Chuychai P , Sonsrettee W
Published: April 2023

The statistics of the magnetic field line separation provide insight into how a bundle of field lines spreads out and the dispersion of non-thermal particles in a turbulent environment, which underlies various astrophysical phenomena. Its diffusive character depends on the distance along the field line, the initial separation, and the characteristics of the magnetic turbulence. This work considers the separation of two magnetic field lines in general transverse turbulence in terms of the magnetic power spectrum in three-dimensional wavenumber space. We apply non-perturbative methods using Corrsin’s hypothesis and assume random ballistic decorrelation to calculate the ensemble average field line separation for general transverse magnetic turbulence. For 2D + slab power spectra, our analytical formulae and computer simulations give similar results, especially at low slab fraction. Our analytical expression also demonstrates several features of field line separation that are verified by computer simulations.
MaNGA DynPop – I. Quality-assessed stellar dynamical modelling from integral-field spectroscopy of 10K nearby galaxies: a catalogue of masses, mass-to-light ratios, density profiles, and dark matter
Authors: Zhu Kai , Lu Shengdong , Cappellari Michele , Li Ran , Mao Shude , Gao Liang
Published: April 2023

This is the first paper in our series on the combined analysis of the Dynamics and stellar Population (DynPop) for the MaNGA survey in the final SDSS Data Release 17 (DR17). Here, we present a catalogue of dynamically determined quantities for over 10 000 nearby galaxies based on integral-field stellar kinematics from the MaNGA survey. The dynamical properties are extracted using the axisymmetric Jeans Anisotropic Modelling (JAM) method, which was previously shown to be the most accurate for this kind of study. We assess systematic uncertainties using eight dynamical models with different assumptions. We use two orientations of the velocity ellipsoid: either cylindrically aligned JAMcyl or spherically aligned JAMsph. We also make four assumptions for the models’ dark versus luminous matter distributions: (1) mass-follows-light, (2) free NFW dark halo, (3) cosmologically constrained NFW halo, (4) generalized NFW dark halo, i.e. with free inner slope. In this catalogue, we provide the quantities related to the mass distributions (e.g. the density slopes and enclosed mass within a sphere of a given radius for total mass, stellar mass, and dark matter mass components). We also provide the complete models which can be used to compute the full luminous and mass distribution of each galaxy. Additionally, we visually assess the qualities of the models to help with model selections. We estimate the observed scatter in the measured quantities which decreases as expected with improvements in quality. For the best data quality, we find a remarkable consistency of measured quantities between different models, highlighting the robustness of the results.
The LOFAR Two-metre Sky Survey: Deep Fields data release 1. V. Survey description, source classifications, and host galaxy properties
Authors: Best P N , Kondapally R , Williams W L , Cochrane R K , Duncan K J , Hale C L , Haskell P , Małek K , McCheyne I , Smith D J B , Wang L , Botteon A , Bonato M , Bondi M , Rivera G Calistro , Gao F , Gürkan G , Hardcastle M J , Jarvis M J , Mingo B , Miraghaei H , Morabito L K , Nisbet D , Prandoni I , Röttgering H J A , Sabater J , Shimwell T , Tasse C , van Weeren R
Published: April 2023

Source classifications, stellar masses, and star-formation rates are presented for ≈80 000 radio sources from the first data release of the Low Frequency Array Two-metre Sky Survey (LoTSS) Deep Fields, which represents the widest deep radio survey ever undertaken. Using deep multi-wavelength data spanning from the ultraviolet to the far-infrared, spectral energy distribution (SED) fitting is carried out for all of the LoTSS Deep host galaxies using four different SED codes, two of which include modelling of the contributions from an active galactic nucleus (AGN). Comparing the results of the four codes, galaxies that host a radiative AGN are identified, and an optimized consensus estimate of the stellar mass and star-formation rate for each galaxy is derived. Those galaxies with an excess of radio emission over that expected from star formation are then identified, and the LoTSS Deep sources are divided into four classes: star-forming galaxies, radio-quiet AGN, and radio-loud high-excitation and low-excitation AGN. Ninety-five per cent of the sources can be reliably classified, of which more than two-thirds are star-forming galaxies, ranging from normal galaxies in the nearby Universe to highly-starbursting systems at z > 4. Star-forming galaxies become the dominant population below 150-MHz flux densities of ≈1 mJy, accounting for 90 per cent of sources at S150MHz ∼ 100 μJy. Radio-quiet AGN comprise ≈10 per cent of the overall population. Results are compared against the predictions of the SKADS and T-RECS radio sky simulations, and improvements to the simulations are suggested.
New constraints on the Bray conservation-of-momentum natal kick model from multiple distinct observations
Authors: Richards S M , Eldridge J J , Briel M M , Stevance H F , Willcox R
Published: April 2023

Natal supernova kicks, the linear momentum compact remnants receive during their formation, are an essential part of binary population synthesis (BPS) models. Although these kicks are well supported by evidence, their underlying distributions and incorporation into BPS models are uncertain. In this work, we investigate the nature of natal kicks using a previously proposed analytical prescription where the strength of the kick is given by $v_\text{k}=\alpha \frac{m_\text{ejecta}}{m_\text{remnant}}+\beta \, \mathrm{km\, s}^{-1}$ , for free parameters α and β. We vary the free parameters over large ranges of possible values, comparing these synthetic populations simultaneously against four constraints: the merger rate of compact binary neutron star (BNS) systems, the period–eccentricity distribution of Galactic BNSs, the velocity distribution of single-star pulsars, and the likelihood for low ejecta mass supernovae to produce low-velocity kicks. We find that different samples of the parameter space satisfy each test, and only 1 per cent of the models satisfy all four constraints simultaneously. Although we cannot identify a single best kick model, we report $\alpha =115^{+40}_{-55}\, \mathrm{km\, s}^{-1}, \beta =15^{+10}_{-15}\, \mathrm{km\, s}^{-1}$ as the centre of the region of the parameter space that fulfils all of our constraints, and expect $\beta \ge 0\, \mathrm{km\, s}^{-1}$ as a further constraint. We also suggest further observations that will enable future refinement of the kick model. A sensitive test for the kick model will be the redshift evolution of the BNS merger rate since this is effectively a direct measure of the delay-time distribution for mergers. For our best-fitting values, we find that the peak of the BNS merger rate is the present day.
Gravitational lensing modification of the high-redshift galaxy luminosity function
Authors: Ferrami G , Wyithe J Stuart B
Published: April 2023

The bright end of the rest-frame ultraviolet luminosity function (UVLF) of high-redshift galaxies is modified by gravitational lensing magnification bias. Motivated by recent discoveries of very high-z galaxies with JWST, we study the dependence of magnification bias on the finite size of sources at 6 < z < 14. We calculate the magnification probability distributions and use these to calculate the magnification bias assuming a rest-frame Schechter UVLF for galaxies at redshift 6 < z < 14. We find that the finite size of bright high-redshift galaxies together with lens ellipticity significantly suppresses magnification bias, producing an observed bright end which declines more sharply than the power law resulting from assumption of point sources. By assuming a luminosity–size relation for the source population and comparing with the observed z  = 6 galaxy luminosity function from Harikane et al. (2022), we show that the UVLF can be used to set mild constraints on the galaxies intrinsic size, favouring smaller galaxies compared to the fiducial luminosity–size relation. In the future, wide surveys using Euclid and Roman Space Telescope will place stronger constraints. We also tabulate the maximum magnification possible as a function of source size and lens ellipticity.
Advances in the construction of diverse SuFEx linkers
Authors: Zeng Daming , Deng Wei-Ping , Jiang Xuefeng
Published: April 2023

Sulfur fluoride exchange (SuFEx), a new generation of click chemistry, was first presented by Sharpless, Dong and co-workers in 2014. Owing to the high stability and yet efficient reactivity of the SVI–F bond, SuFEx has found widespread applications in organic synthesis, materials science, chemical biology and drug discovery. A diverse collection of SuFEx linkers has emerged, involving gaseous SO2F2 and SOF4 hubs; SOF4-derived iminosulfur oxydifluorides; O-, N- and C-attached sulfonyl fluorides and sulfonimidoyl fluorides; and novel sulfondiimidoyl fluorides. This review summarizes the progress of these SuFEx connectors, with an emphasis on analysing the advantages and disadvantages of synthetic strategies of these connectors based on the SuFEx concept, and it is expected to be beneficial to researchers to rapidly and correctly understand this field, thus inspiring further development in SuFEx chemistry.
Patterns of Diagnostic Evaluation and Determinants of Treatment in Older Patients With Non-transfusion Dependent Myelodysplastic Syndromes
Authors: Mukherjee Sudipto , Dong Weichuan , Schiltz Nicholas K , Stange Kurt C , Cullen Jennifer , Gerds Aaron T , Carraway Hetty E , Singh Abhay , Advani Anjali S , Sekeres Mikkael A , Koroukian Siran M
Published: April 2023

Background

Older patients with myelodysplastic syndromes (MDS), particularly those with no or one cytopenia and no transfusion dependence, typically have an indolent course. Approximately, half of these receive the recommended diagnostic evaluation (DE) for MDS. We explored factors determining DE in these patients and its impact on subsequent treatment and outcomes.

Patients and Methods

We used 2011-2014 Medicare data to identify patients ≥66 years of age diagnosed with MDS. We used Classification and Regression Tree (CART) analysis to identify combinations of factors associated with DE and its impact on subsequent treatment. Variables examined included demographics, comorbidities, nursing home status, and investigative procedures performed. We conducted a logistic regression analysis to identify correlates associated with receipt of DE and treatment.

Results

Of 16 851 patients with MDS, 51% underwent DE. patients with MDS with no cytopenia (n = 3908) had the lowest uptake of DE (34.7%). Compared to patients with no cytopenia, those with any cytopenia had nearly 3 times higher odds of receiving DE [adjusted odds ratio (AOR), 2.81: 95% CI, 2.60-3.04] and the odds were higher for men than for women [AOR, 1.39: 95%CI, 1.30-1.48] and for Non-Hispanic Whites [vs. everyone else (AOR, 1.17: 95% CI, 1.06-1.29)]. The CART showed DE as the principal discriminating node, followed by the presence of any cytopenia for receiving MDS treatment. The lowest percentage of treatment was observed in patients without DE, at 14.6%.

Conclusion

In this select older patients with MDS, we identified disparities in accurate diagnosis by demographic and clinical factors. Receipt of DE influenced subsequent treatment but not survival.
Dramatic Response to Pyrotinib and T-DM1 in HER2-Negative Metastatic Breast Cancer With 2 Activating HER2 Mutations
Authors: Tian Hao , Qu Man , Zhang Guozhi , Yuan Long , Shi Qiyun , Wang Yinhuan , Yang Ying , Zhang Yi , Qi Xiaowei
Published: April 2023

HER2 signaling is activated in response to somatic HER2 mutations, which are often found in invasive lobular breast cancer (ILC) and are associated with poor prognosis. Tyrosine kinase inhibitors (TKIs) have demonstrated considerable antitumor activity in patients with HER2-mutated advanced breast cancer (BC). Further, several clinical trials have indicated that HER2-targeted antibody-drug conjugates (ADCs) exhibit promising efficacy in lung cancer with HER2 mutations, and the efficacy of ADCs against HER2-mutated BC is currently being evaluated. Several preclinical studies have demonstrated that the therapeutic efficacy of ADCs in HER2-mutated cancer can be enhanced by the addition of irreversible TKIs, but the potential of such a combined treatment regimen for the treatment of HER2-mutated BC has not been reported. Herein, we describe a case in which a patient with estrogen receptor-positive/HER2-negative metastatic ILC with 2 activating HER2 mutations (D769H and V777L) exhibited a significant and durable response to anti-HER2 treatment with pyrotinib (an irreversible TKI) in combination with ado-trastuzumab emtansine, which was administered after multiple lines of therapy that had resulted in disease progression. Further, based on the evidence from the present case, TKI plus ADC seems to be a promising combination anti-HER2 regimen for patients with HER2-negative/HER2-mutated advanced BC, although further rigorous studies are warranted to confirm these findings.
Bacterial colony size growth estimation by deep learning
Authors: Nagy Sára Ágnes , Makrai László , Csabai István , Tőzsér Dóra , Szita Géza , Solymosi Norbert
Published: April 2023

The bacterial growth rate is important for pathogenicity and food safety. Therefore, the study of bacterial growth rate over time can provide important data from a medical and veterinary point of view. We trained convolutional neural networks (CNNs) on manually annotated solid medium cultures to detect bacterial colonies as accurately as possible. Predictions of bacterial colony size and growth rate were estimated from image sequences of independentStaphylococcus aureuscultures using trained CNNs. A simple linear model for control cultures with less than 150 colonies estimated that the mean growth rate was 60.3μm/hfor the first 24 h. Analyzing with a mixed effect model that also takes into account the effect of culture, smaller values of change in colony size were obtained (control: 51.0μm/h, rifampicin pretreated: 36.5μm/h). An increase in the number of neighboring colonies clearly reduces the colony growth rate in the control group but less typically in the rifampicin-pretreated group. Based on our results, CNN-based bacterial colony detection and the subsequent analysis of bacterial colony growth dynamics might become an accurate and efficient tool for bacteriological work and research.
Zooarchaeological investigation of the Hoabinhian exploitation of reptiles and amphibians in Thailand and Cambodia with a focus on the Yellow-headed Tortoise (Indotestudo elongata(Blyth, 1854))
Authors: Bochaton Corentin , Chantasri Sirikanya , Maneechote Melada , Claude Julien , Griggo Christophe , Naksri Wilailuck , Forestier Hubert , Sophady Heng , Auertrakulvit Prasit , Bowonsachoti Jutinach , Zeitoun Valéry
Published: April 2023

While non-marine turtles are almost ubiquitous in the archaeological record of Southeast Asia, their zooarchaeological examination has been inadequately pursued within this tropical region. This gap in research hinders a complete comprehension of past human subsistence strategies and economies, as only a limited number of comprehensive studies encompassing all the taxa found in archaeological sites have been conducted thus far. This constraint becomes particularly significant in relation to prehistoric hunter-gatherer populations, who might have extensively utilized inland chelonian taxa. In order to initiate a new approach to the study of past human-turtle interactions in Southeast Asia, we propose an in-depth zooarchaeological analysis of turtle bone remains recovered from four Hoabinhian Hunter-gatherer archaeological assemblages located in Thailand and Cambodia, dating from the Late Pleistocene to the first half of the Holocene. Our study focuses on the bone remains attributed to the Yellow-headed Tortoise (Indotestudo elongata) as it is the most represented taxon in archaeological assemblages in the region of study. For this species, we developed osteometric equations enabling the estimation of the carapace size of the archaeological individuals. This allowed us to study the size structure of the archaeological populations at different sites and to reveal the human exploitation strategies of these animals. We observed a significant taphonomic homogeneity among the studied assemblages, along with similarities in the diversity of hunted reptile and amphibian taxa as well as the size of the exploited tortoises. These findings suggest consistent subsistence behaviors across distinct sites, despite their varying environmental conditions, and raise the possibility of cultural similarities across different periods and regions. Additionally, we provide a baseline for future zooarchaeological studies and a methodological framework for the detailed analysis of archaeological turtle bones in continental Southeast Asia.
Vessel normalization and maturation promotes nanoparticle delivery to solid tumors while minimizing metastases
Authors: Izci Mukaddes , Maksoudian Christy , Gonçalves Filipa , Chu Tianjiao , Luci Carla Rios , Bolea-Fernandez Eduardo , Vanhaecke Frank , Manshian Bella B. , Soenen Stefaan J.
Published: April 2023

Nanoparticle delivery to solid tumors is known to be an inefficient process and various studies have tried to increase efficacy, but mechanistic and comparative studies remain scarce. Here, we use pharmacological agents to study the effect of vessel normalization or vessel disintegration on nanoparticle delivery to solid tumors. Using a multiparametric approach, we find that vessel disintegration fails to improve nanoparticle delivery and instead seems to have a limiting effect. Vessel normalization, however, improves delivery efficacy for nanoparticles ranging from 20 to 60 nm diameter. The normalization of the tumor blood vessels results in reduced hypoxia, reduced necrosis and an increase inPlvap+CD276+endothelial cells, which have been linked with nanoparticle delivery. Interestingly, where vessel disintegration stimulated cancer cell intravasation and associated metastases, vessel normalization impeded these processes. Together, these data reveal that, vessel normalization may be a safer and more suited approach for improving nanoparticle delivery to solid tumors, but its efficacy is limited by nanoparticle diameter and tumor parameters.

Graphical abstract
The dynamic interaction between predator and prey drives mesopredator movement and foraging ecology
Authors: Florko Katie R.N. , Ross Tyler R. , Ferguson Steven H. , Northrup Joseph M. , Obbard Martyn E. , Thiemann Gregory W. , Yurkowski David J. , Auger-Méthé Marie
Published: April 2023

Prey availability is a fundamental driver of animal distribution, movement, and foraging ecology. The perceived risk of predation also influences these aspects of animal ecology. Our paper explores how animals balance these tradeoffs, which are seldom analyzed together. Such understanding becomes increasingly important as species that face anthropogenic-caused ecosystem change. In the Arctic, there has been substantial research on consequences of sea ice loss, however our understanding of top-down and bottom-up processes is limited. Ringed seals (Pusa hispida) and polar bears (Ursus maritimus), form a strong predator-prey relationship but limited information is available explaining how fear of polar bears affects ringed seal ecology. Using a large tracking dataset from 26 ringed seals with >70,000 dives and >10,000 locations, we explored the influence of top-down (polar bear space use based on >18,000 locations) and bottom-up (modeled fish distribution) processes on the movement, habitat selection, and foraging behavior of this mesopredator. Our results suggest that polar bears spatially restrict seal movements and reduce the amount of time they spend in area-restricted search and at depth, which likely decreases the seals’ foraging success. However, we found tradeoffs between predation risk and foraging, where ringed seals were more likely to be present and dive for a long duration in high-risk areas when prey diversity was high. Prey habitat use models that excluded predators overestimated core space use. These findings illustrate the dynamic tradeoffs that mesopredators are forced to make when balancing the risk of predation and need to forage.

Significance Statement

Our paper explores how animals balance finding food and avoiding predators. This balancing act is often poorly understood, particularly in Arctic ecosystems, but is necessary for understanding and conserving species. Our results show that interactions between polar bear presence and prey diversity explain the foraging behavior, habitat selection, and activity budgets of ringed seals. Seals constrained their movements to areas with low predation risk, but entered high-risk areas if prey diversity was high. Additionally, our inference on the relationship between ringed seals and their prey would be overlooked if the potential risk of polar bear predation was not included. Our study advances our understanding of the complex dynamics in predator-prey ecology, which is essential to incorporate when identifying critical habitat.
Stromule geometry allows optimal spatial regulation of organelle interactions in the quasi-2D cytoplasm
Authors: Erickson Jessica Lee , Prautsch Jennifer , Reynvoet Frisine , Niemeyer Frederik , Hause Gerd , Johnston Iain G. , Schattat Martin
Published: April 2023

In plant cells, plastids form elongated extensions called stromules, the regulation and purposes of which remain unclear. Here we quantitatively explore how different stromule structures serve to enhance the ability of a plastid to interact with other organelles: increasing the effective space for interaction and biomolecular exchange between organelles. Strikingly, electron microscopy and confocal imaging showed that the cytoplasm inArabidopsis thalianaandNicotiana benthamianaepidermal cells is extremely thin (around 100 nm in regions without organelles), meaning that inter-organelle interactions effectively take place in 2D. We combine these imaging modalities with mathematical modelling and newin plantaexperiments to demonstrate how different the elongation of stromules (single or multiple, linear or branching) could be employed to optimise different aspects of inter-organelle interaction capacity in this 2D space. Stromule formation and branching is shown to provide a proportionally higher benefit to interaction capacity in 2D than in 3D. Additionally we find this benefit depends on optimal plastid spacing. We hypothesize that cells can promote the formation of different stromule architectures in the quasi-2D cytoplasm to optimise their interaction interface to meet specific requirements. These results provide new insight into the mechanisms underlying the transition from low to high stromule numbers during biotic stress, the consequences for interaction with smaller organelles, how plastid access and plastid to nucleus signalling is balanced, as well as the impact of plastid density on organelle interaction.
Being a tree crop increases the odds of experiencing yield declines irrespective of pollinator dependence
Authors: Aizen Marcelo A. , Gleiser Gabriela , Kitzberger Thomas , Milla Rubén
Published: April 2023

Crop yields,i.e., harvestable production per unit of cropland area, are in decline for a number of crops and regions, but the drivers of this process are poorly known. Global decreases in pollinator abundance and diversity have been proposed as a major driver of yield declines in crops that depend on animals, mostly bees, to produce fruits and seeds. Alternatively, widespread tree mortality has been directly and indirectly related to global climate change, which could also explain yield decreases in tree crops. As tree crops are expected to be more dependent on pollinators than other crop types, disentangling the relative influence of growth form and pollinator dependence is relevant to identify the ultimate factors driving yield declines. Yield decline, defined here as a negative average annual yearly change in yield from 1961 to 2020, was measured in 4270 time series, involving 136 crops and 163 countries and territories. About one-fourth of all time series showed declines in crop yield, a characteristic associated with both high pollinator dependence and a tree growth form. Because pollinator dependence and plant growth form were partially correlated, we disentangled the effect of each of these two predictors using a series of generalized linear mixed models that evaluated direct and indirect associations. Our analyses revealed a stronger association of yield decline with growth form than with pollinator dependence, a relationship that persisted after partialling out the effect of pollinator dependence. In particular, yield declines were more common among tree than herbaceous and shrub crops in all major regions but in Africa, a continent showing a high incidence of yield declines irrespective of growth form. These results suggest that pollinator decline is not the main reason behind crop productivity loss, but that other factors such as climate change could be already affecting crop yield.
Multiscale Model for Ion Transport in Cellular Media and Applications in Smooth Muscle Cells
Authors: Xiao Chun , Sun Yishui , Huang Huaxiong , Song Zilong , Yue Xingye , David Tim , Xu Shixin
Published: April 2023

Ion transport in biological tissues is crucial in the study of many biological and pathological problems. Some multi-cellular structures, like the smooth muscles on vessel walls, can be treated as periodic bi-domain structures consisting of the intracellular space (ICS) and extracellular space (ECS) with semipermeable membranes in between. In this work, we first use a multi-scale asymptotic method to derive a macroscopic homogenized bidomain model from the microscopic electro-neutral (EN) model with different diffusion coefficients and nonlinear interface conditions. Then, the obtained homogenized model is applied to study ion transportation and micro-circulation in multi-celluar tissues under the impact of agonists, an internal calcium source, and extracellular potassium. Our model serves as a useful bridge between existing ordinary differential equation models and partial differential models that take into consideration spatial variation. On the one hand, numerical results show that ECS variables are almost invariant in the first two scenarios and confirm the validity of existing single-domain models, which treat variables in the ECS as constants. On the other hand, only the bidomain model is applicable to consider the effect of local extracellular potassium. Finally, the membrane potential of syncytia formed by connected cells is found to play an important role in the propagation of oscillation from the stimulus region to the non-stimulus region.

Author summary

Smooth muscle cells (SMCs) play a vital role in neurovascular coupling, which is the mechanism by which changes in neural activity are linked to alterations in blood flow. Dysfunctional SMCs can have significant implications for human health. The activation of SMCs is primarily regulated by the intracellular concentration of calcium ions (Ca2+). A multi-scale model for ion transport in multicellular tissue with varying connectivity has been proposed to investigate SMC activation under different stimuli. The simulation results confirm the critical role of gap junctions in wave propagation and vasoconstriction in the vessel wall. The blockage of gap junctions prevents the spread of the wave. Furthermore, the propagation of membrane potential is the primary cause of wave propagation.
Exosomal microRNA signature from plasma-derived extracellular vesicles in gastric cancer
Authors: Rincón-Riveros Andrés , Villegas Victoria E. , Quintero Motta Nicolle Stefania , López-Kleine Liliana , Rodríguezand Josefa Antonia
Published: April 2023

Background

Gastric cancer is a heterogeneous pathology that represents the fifth most frequent malignancy in the world, with more than 750,000 deaths by 2020. With significant repercussions in public health, this pathology lacks biomarkers for early diagnosis, with endoscopy biopsy being the golden test for its detection. In the exploration of new strategies to control gastric cancer in recent years, liquid biopsy appears as a potential source of biomarkers using non-invasive procedures.

Methods

Here we present the characterization of miRNAs contained in plasma-derived exosomes from patients with gastric cancer. Extracellular vesicles (EVs) were isolated using size-exclusion chromatography (SEC) and their characterization was performed by electron microscopy, protein expression, and nanoparticle analysis techniques. Total RNA from isolated exosomes was obtained for small RNA-seq analysis.

Results

Transcriptomic miRNA data were used to identify differentially expressed miRNAs between patients with benign and malignant gastric diseases, which resulted in a molecular signature of nine miRNAs, that were used in a regression model to classify individuals as either having benign or malignant disease. Further, we compared benign-malignant patients at different stages of gastric cancer, and we detected 15 differentially expressed miRNAs. Among these 15 miRNAs, miR-92a-3p, miR451a, and miR126-3p were identified as winners due to their clinical and regulatory relevance.

Results

Our results offer relevant information of a Colombian case study allowing us to propose three transcriptomic gastric cancer biomarkers in liquid biopsy.

Graphical Abstract

EVs are structures surrounded by a lipid bilayer that facilitate intercellular communication by transporting biomolecules commonly referred to as part of liquid biopsy. In this study, we examine the miRNAs contents of plasma isolated EVs from patients with both benign gastric diseases and gastric cancer to identify potential biomarkers for gastric cancer.
An RNA Damage Response Network Mediates the Lethality of 5-FU in Clinically Relevant Tumor Types
Authors: Chen Jung-Kuei , Merrick Karl A. , Kong Yi Wen , Izrael-Tomasevic Anita , Eng George , Handly Erika D. , Patterson Jesse C. , Cannell Ian G. , Suarez-Lopez Lucia , Hosios Aaron M. , Dinh Anh , Kirkpatrick Donald S. , Yu Kebing , Rose Christopher M. , Hernandez Jonathan M. , Hwangbo Haeun , Palmer Adam C. , Vander Heiden Matthew G. , Yilmaz Ömer H. , Yaffe Michael B.
Published: April 2023

5-fluorouracil (5-FU) is a successful and broadly used anti-cancer therapeutic. A major mechanism of action of 5-FU is thought to be through thymidylate synthase (TYMS) inhibition resulting in dTTP depletion and activation of the DNA damage response. This suggests that 5-FU should synergize with other DNA damaging agents. However, we found that combinations of 5-FU and oxaliplatin or irinotecan failed to display any evidence of synergy in clinical trials, and resulted in sub-additive killing in a panel of colorectal cancer (CRC) cell lines. In seeking to understand this antagonism, we unexpectedly found that an RNA damage response during ribosome biogenesis dominates the drug’s efficacy in tumor types for which 5-FU shows clinical benefit. 5-FU has an inherent bias for RNA incorporation, and blocking this greatly reduced drug-induced lethality, indicating that accumulation of damaged RNA is more deleterious than the lack of new RNA synthesis. Using 5-FU metabolites that specifically incorporate into either RNA or DNA revealed that CRC cell lines and patient-derived colorectal cancer organoids are inherently more sensitive to RNA damage. This difference held true in cell lines from other tissues in which 5-FU has shown clinical utility, whereas cell lines from tumor tissues that lack clinical 5-FU responsiveness typically showed greater sensitivity to the drug’s DNA damage effects. Analysis of changes in the phosphoproteome and ubiquitinome shows RNA damage triggers the selective ubiquitination of multiple ribosomal proteins leading to autophagy-dependent rRNA catabolism and proteasome-dependent degradation of ubiquitinated ribosome proteins. Further, RNA damage response to 5-FU is selectively enhanced by compounds that promote ribosome biogenesis, such as KDM2A inhibitors. These results demonstrate the presence of a strong RNA damage response linked to apoptotic cell death, with clear utility of combinatorially targeting this response in cancer therapy.
Pooled effector library screening in protoplasts rapidly identifies novelAvrgenes
Authors: Arndell Taj , Chen Jian , Sperschneider Jana , Upadhyaya Narayana M , Blundell Cheryl , Niesner Nathalie , Wang Aihua , Swain Steve , Luo Ming , Ayliffe Michael A , Figueroa Melania , Vanhercke Thomas , Dodds Peter N
Published: April 2023

Crop breeding for durable disease resistance is challenging due to the rapid evolution of pathogen virulence. While progress in resistance (R) gene cloning and stacking has accelerated in recent years1-3, the identification of corresponding avirulence (Avr) genes in many pathogens is hampered by the lack of high-throughput screening options. To address this technology gap, we developed a platform for pooled library screening in plant protoplasts for rapid identification of interactingR/Avrpairs. We validated this platform by isolating known and novelAvrgenes from wheat stem rust (Puccinia graminisf. sp.tritici) by screening a designed library of putative effectors against individualRgenes. RapidAvrgene identification provides molecular tools to understand and track pathogen virulence evolution by genotype surveillance and optimiseRgene deployment and stacking strategies. This screening platform is broadly applicable to many crop pathogens, whilst also adaptable for screening genes involved in other protoplast-selectable traits.
Conformational dynamics of the μ-opioid receptor determine ligand intrinsic efficacy
Authors: Zhao Jiawei , Elgeti Matthias , O’Brien Evan S. , Sár Cecília P. , Daibani Amal EI , Heng Jie , Sun Xiaoou , Che Tao , Hubbell Wayne L. , Kobilka Brian K. , Chen Chunlai
Published: April 2023

The μ-opioid receptor (μOR) is an important target for pain management and the molecular understanding of drug action will facilitate the development of better therapeutics. Here we show, using double electron-electron resonance (DEER) and single-molecule fluorescence resonance energy transfer (smFRET), how ligand-specific conformational changes of the μOR translate into a broad range of intrinsic efficacies at the transducer level. We identify several cytoplasmic receptor conformations interconverting on different timescales, including a pre-activated receptor conformation which is capable of G protein binding, and a fully activated conformation which dramatically lowers GDP affinity within the ternary complex. Interaction of β-arrestin-1 with the μOR core binding site appears less specific and occurs with much lower affinity than binding of G protein Gi.

One-Sentence Summary

Ligand-dependent conformational dynamics of the μ-opioid receptor determine downstream signaling efficacy.
Hungarian Grey cattle grazing outperforms mowing during wet meadow restoration following plantation forest clear-cut
Authors: Szitár Katalin , Kabai Melinda , Zimmermann Zita , Szabó Gábor , Reis Bruna Paolinelli , Somay László
Published: April 2023

Land-use change and ecological invasion are two main drivers of biodiversity loss, and the restoration of semi-natural wet grasslands is needed to tackle invasive species and re-establish grassland biodiversity on former forest plantations. This study tested the effectiveness of two widely used management techniques (grazing by traditional Hungarian Grey cattle and mowing once a year in August) as a restoration method of wet meadows in a former forest plantation invaded by goldenrod species in Central Hungary. We compared the vegetation composition of grazed, mowed, and reference areas with semi-natural wet meadow vegetation based on plant biomass, species richness and cover of species groups of species origin, life span, growth form, and social behaviour types of Borhidi determining the grazing value and the nature conservation value of the grasslands. We found that grazing by Hungarian Grey cattle resulted in a vegetation that was more similar to the reference wet meadows than mowing once a year in late summer. Grazing was superior to mowing in terms of goldenrod control, total species richness and cover, as well as the abundance of natives, perennials, herbs, and legumes. However, in the grazed area, we detected more disturbance-tolerant and annual species than in the mowed area. Despite the improved vegetation condition in the grazed area, we identified substantial disparities between the grazed and reference areas after three years of grazing. Based on our results, we advise using continuous extensive grazing to restore and maintain semi-natural wet meadows.
The Soybean Expression Atlas v2: a comprehensive database of over 5000 RNA-seq samples
Authors: Almeida-Silva Fabricio , Pedrosa-Silva Francisnei , Venancio Thiago M.
Published: April 2023

Soybean is a crucial crop worldwide, used as a source of food, feed, and industrial products due to its high protein and oil content. Previously, the rapid accumulation of soybean RNA-seq data in public databases and the computational challenges of processing raw RNA-seq data motivated us to develop the Soybean Expression Atlas, a gene expression database of over a thousand RNA-seq samples. Over the past few years, our database has allowed researchers to explore the expression profiles of important gene families, discover genes associated with agronomic traits, and understand the transcriptional dynamic of cellular processes. Here, we present the Soybean Expression Atlas v2, an updated version of our database with a 4-fold increase in the number of samples, featuring transcript- and gene-level transcript abundance matrices for 5481 publicly available RNA-seq samples. New features in our database include the availability of transcript-level abundance estimates and equivalence classes to explore differential transcript usage, abundance estimates in bias-corrected counts to increase the accuracy of differential gene expression analyses, a new web interface with improved data visualization and user experience, and a reproducible and scalable pipeline available as an R package. The Soybean Expression Atlas v2 is available athttps://soyatlas.venanciogroup.uenf.br/, and it will accelerate soybean research, empowering researchers with high-quality and easily accessible gene expression data.
Magnetic resonance biomarkers for timely diagnostic of radiation dose-rate effects
Authors: Zagrean-Tuza C. , Suditu M. , Popescu R. C. , Bacalum M. , Negut D. , Vasilca S. , Hanganu A. , Fidel I. , Serafin D. , Tesileanu O. , Chiricuta I.C. , Sadet A. , Voda M.A. , Vasos P.R.
Published: April 2023

Diagnostic of radiation effects can be obtained within hours from delivery relying on spectroscopic detection of cell metabolite concentrations. Clinical and pre-clinical studies show that radiation delivery with elevated dose-rates can achieve tumor suppression while minimizing toxicity to surrounding areas. Diagnostic biomarkers detected on short timescales are needed to orient high dose-rate radiation delivery. We have designed an1H magnetic resonance approach to observe metabolite concentrations, in particular Choline, Creatine, and Lactate, in order to detect radiation dose and dose-rate effects within hours from radiation delivery. The results of our metabolic profiling method in glioblastoma cells are consistent with observations from clinical studies guided by magnetic resonance spectroscopy for radiotherapy of head tumors. At 5 Gy/min we have observed increases in lactate concentrations and decreases in [Cho]/[Cr] ratios at increasing radiation doses. An increase of the radiation dose-rate to 35 Gy/min is correlated with an increase of [Cho]/[Cr] consistent with a reduction in radiation-induced oxidative effects at high dose-rates. The observed biomarkers can be translated for radiation pulse sequences optimization.

One Sentence Summary

Magnetic resonance biomarkers to monitor biological effectiveness within hours after radiation delivery can be optimized for glioblastoma cells and are of potential use for the design of radiotherapy with high dose-rates.