bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel soybean malectin-like receptor kinase-encoding gene, GmMLRK1, provides resistance to soybean mosaic virus
Authors: Che Zhijun , Zhang Shuyu , Pu Yixiang , Yang Yuming , Liu Hailun , Yang Hui , Wang Li , Zhang Yuhang , Liu Baohui , Zhang Hengyou , Wang Hui , Cheng Hao , Yu Deyue
Published: February 2023

Soybean mosaic virus (SMV) severely damages soybean [Glycine max (L.) Merr.] yield and seed quality. Moreover, the underlying genetic determinants of resistance to SMV remain largely unknown. Here, we performed a genome-wide association study (GWAS) of SMV resistance in a panel of 219 diverse soybean accessions across four environments and identified a new resistance-related gene, GmMLRK1, at the major resistance locus Rsv4 on chromosome 2. GmMLRK1 encodes a malectin-like receptor kinase (RK) that was induced earlier and to a greater degree in leaves of the SMV-resistant cultivar Kefeng No. 1 than in those of the susceptible cultivar Nannong 1138-2 after inoculation. We demonstrated that soybean plants overexpressing GmMLRK1 show broad-spectrum resistance to both strains SC7 and SC3 on the basis of reduced viral accumulation, increased reactive oxygen species production, and local cell death associated with the hypersensitive response. In contrast, GmMLRK1 knockout mutants were more susceptible to both pathotypes. Haplotype analysis revealed the presence of five haplotypes (H1–H5) within the soybean population, and only H1 provided SMV resistance, which was independent of its tightly linked SMV resistance gene RNase-H at the same locus. These results report a novel gene that adds new understanding of SMV resistance and can be used for breeding resistant soybean accessions.
Tetracycline resistance of Escherichia coli isolated from water, human stool, and fish gills from the Lake Sevan basin
Authors: Pepoyan A Z , Manvelyan A M , Balayan M H , Harutyunyan N A , Tsaturyan V V , Batikyan H , Bren A B , Chistyakov V , Weeks R , Chikindas M L
Published: February 2023

The ecological state of Lake Sevan, the largest drinking water reservoir for the South Caucasus, formed under the influence of climatic and social changes. This study assesses the bacteriological quality of water in the rivers of the Lake Sevan basin and tetracycline-resistant bacteria isolated from fish and people living near the rivers of the Lake Sevan basin in Armenia in autumn 2019 and spring 2020.

No differences have been shown for the tetracycline resistance of the investigated E. coli isolated from the human gut and the Masrik, Argichi, and Gavaraget Rivers. Horizontal gel electrophoresis revealed the same plasmid bands in most of the investigated E. coli with the same tetracycline resistance from the different sources of the Argichi River (obtained from people/fish/water sources where the fish were caught). The results also showed that most of the waters carried Edwardsiella spp., Erwinia spp., Morganella spp., and Proteus spp. in addition to E. coli; the coliform index did not exceed the standard level of 5 × 104 CFU mL-1 there.

These findings highlight the importance of multidisciplinary studies of bacteria from “interacting” ecosystems, which might serve as a basis for the suggestion of microbial antibiotic resistance as another indicator of water pollution.
Qualitative uncertainty and dynamics of argumentation through dynamic logic
Authors: Yuste-Ginel Antonio , Herzig Andreas
Published: February 2023

Dynamics and uncertainty are essential features of real-life argumentation, and many recent studies have focused on integrating both aspects into Dung’s well-known abstract argumentation frameworks (AFs). This paper proposes a combination of the two lines of research through a well-behaved logical tool: dynamic logic of propositional assignments (DL-PA). Our results show that the main reasoning tasks of virtually all existing formalisms qualitatively representing uncertainty about AFs are encodable in DL-PA. Moreover, the same tool is also useful for capturing dynamic structures, such as control AFs, as well as for developing more refined forms of argumentative communication under uncertainty.
The climate and compositional variation of the highly eccentric planet HD 80606 b – the rise and fall of carbon monoxide and elemental sulfur
Authors: Tsai Shang-Min , Steinrueck Maria , Parmentier Vivien , Lewis Nikole , Pierrehumbert Raymond
Published: February 2023

The gas giant HD 80606 b has a highly eccentric orbit (e ∼ 0.93). The variation due to the rapid shift of stellar irradiation provides a unique opportunity to probe the physical and chemical timescales and to study the interplay between climate dynamics and atmospheric chemistry. In this work, we present integrated models to study the atmospheric responses and the underlying physical and chemical mechanisms of HD 80606 b. We first run 3D general circulation models (GCMs) to establish the atmospheric thermal and dynamical structures for different atmospheric metallicities and internal heat. Based on the GCM output, we then adopted a 1D time-dependent photochemical model to investigate the compositional variation along the eccentric orbit. The transition of the circulation patterns of HD 80606 b matched the dynamics regimes in previous works. Our photochemical models show that efficient vertical mixing leads to deep quench levels of the major carbon and nitrogen species and the quenching behaviour does not change throughout the eccentric orbit. Instead, photolysis is the main driver of the time-dependent chemistry. While CH4 dominates over CO through most of the orbits, a transient state of [CO]/[CH4] > 1 after periastron is confirmed for all metallicity and internal heat cases. The upcoming JWST Cycle 1 GO program will be able to track this real-time CH4–CO conversion and infer the chemical timescale. Furthermore, sulfur species initiated by sudden heating and photochemical forcing exhibit both short-term and long-term cycles, opening an interesting avenue for detecting sulfur on exoplanets.
Orbital and radiative properties of wandering intermediate-mass black holes in the ASTRID simulation
Authors: Weller Emma Jane , Pacucci Fabio , Ni Yueying , Chen Nianyi , Di Matteo Tiziana , Siwek Magdalena , Hernquist Lars
Published: February 2023

Intermediate-Mass Black Holes (IMBHs) of $10^3-10^6\, {\rm M_\odot }$ are commonly found at the centre of dwarf galaxies. Simulations and observations convincingly show that a sizeable population of IMBHs could wander off-centre in galaxies. We use the cosmological simulation ASTRID to study the orbital and radiative properties of wandering IMBHs in massive galaxies at z ∼ 3. We find that this population of black holes has large orbital inclinations (60° ± 22°) with respect to the principal plane of the host. The eccentricity of their orbits is also significant (0.6 ± 0.2) and decreases with time. Wandering IMBHs undergo spikes of accretion activity around the pericentre of their orbits, with rates 10−3 − 10−5 times the Eddington rate and a median accretion duty cycle of $\sim 12{{\ \rm per\ cent}}$. Their typical spectral energy distribution peaks in the infrared at $\sim 11 \, \mu \rm m$ rest-frame. Assuming a standard value of $10{{\ \rm per\ cent}}$ for the matter-to-energy radiative efficiency, IMBHs reach 2 − 10 keV X-ray luminosities $\gt 10^{37} \, \mathrm{erg\, s^{-1}}$ for $\sim 10{{\ \rm per\ cent}}$ of the time. This luminosity corresponds to fluxes $\gt 10^{-15} \, \mathrm{erg \, s^{-1} \, cm^{-2}}$ within 10 Mpc. They could be challenging to detect because of competing emissions from X-ray binaries and the interstellar medium. X-ray luminosities $\gt 10^{41} \, \mathrm{erg \, s^{-1}}$, in the hyper-luminous X-ray sources (HLXs) regime, are reached by $\sim 7{{\ \rm per\ cent}}$ of the IMBHs. These findings suggest that HLXs are a small subset of the wandering IMBH population, which is characterized by luminosities 103 − 104 times fainter. Dedicated surveys are needed to assess the demographics of this missing population of black holes.
MusE GAs FLOw and Wind (MEGAFLOW) IX. The impact of gas flows on the relations between the mass, star formation rate, and metallicity of galaxies
Authors: Langan Ivanna , Zabl Johannes , Bouché Nicolas F , Ginolfi Michele , Popping Gergö , Schroetter Ilane , Wendt Martin , Schaye Joop , Boogaard Leindert , Freundlich Jonathan , Richard Johan , Matthee Jorryt , Mercier Wilfried , Contini Thierry , Guo Yucheng , Cherrey Maxime
Published: February 2023

We study the link between gas flow events and key galaxy scaling relations: the relations between star formation rate (SFR) and stellar mass (the main sequence, MS); gas metallicity and stellar mass (the mass–metallicity relation, MZR); and gas metallicity, stellar mass, and SFR (the fundamental metallicity relation, FMR). Using all star-forming galaxies (SFGs) in the 22 MUSE fields of the MusE GAs FLOw and Wind (MEGAFLOW) survey, we derive the MS, MZR, and FMR scaling relations for 385 SFGs with $M_\star = 10^{8} - 10^{11.5}\, {\rm M}_\odot$ at redshifts 0.35 < z < 0.85. Using the MUSE data and complementary X-Shooter spectra at 0.85 < z < 1.4, we determine the locations of 21 SFGs associated with inflowing or outflowing circumgalactic gas (i.e. with strong Mg ii absorption in background quasar spectra) relative to these scaling relations. Compared to a control sample of galaxies without gas flows (i.e. without Mg ii absorption within 70 kpc of the quasar), SFGs with inflow events (i.e. Mg ii absorption along the major axis) are preferentially located above the MS, while SFGs with outflow events (i.e. Mg ii absorption along the minor axis) are preferentially more metal rich. Our observations support the scenario in which gas accretion increases the SFR while diluting the metal content and where circumgalactic outflows are found in more metal-rich galaxies.
Electron heating mechanisms at quasi-perpendicular shocks – revisited with magnetospheric multiscale measurements
Authors: Stasiewicz Krzysztof , Eliasson Bengt
Published: February 2023

We demonstrate that measurements obtained from NASA’s magnetospheric multiscale (MMS) mission support quasi-adiabatic electron heating in quasi-perpendicular shocks with temperature Te⊥ ∝ B1 + α, where B is the magnetic field strength and α represents departure from adiabaticity. Adiabatic heating (α = 0) results from the conservation of magnetic moment on spatially increasing magnetic field inside the shock ramp. Negative α < 0 is observed in most situations, where perpendicular energy gain from adiabatic heating is redistributed by interactions with waves to the parallel direction leading to a lower isotropic temperature increase. Positive α is observed when the stochastic heating of electrons is activated by the E × B wave acceleration mechanism by electrostatic waves leading to a higher temperature increase. By using test-particle simulations in a realistic shock model we have elucidated the process of stochastic wave acceleration. We have also shown the equivalence of adiabatic heating and acceleration by gradient B drift at shocks with low Mach numbers and demonstrated that the cross-shock potential does not contribute to the electron heating. Signatures of quasi-adiabatic heating and/or stochastic heating of electrons are observed in all shocks analysed with measurements by the MMS.
Does a radio jet drive the massive multiphase outflow in the ultra-luminous infrared galaxy IRAS 10565 + 2448?
Authors: Su Renzhi , Mahony Elizabeth K , Gu Minfeng , Sadler Elaine M , Curran S J , Allison James R , Yoon Hyein , Aditya J N H S , Chandola Yogesh , Chen Yongjun , Moss Vanessa A , Wu Zhongzu , Shao Xi , Liu Xiang , Glowacki Marcin , Whiting Matthew T , Weng Simon
Published: February 2023

We present new upgraded Giant Metrewave Radio Telescope H i 21-cm observations of the ultra-luminous infrared galaxy IRAS 10565 + 2448, previously reported to show blueshifted, broad, and shallow H i absorption indicating an outflow. Our higher spatial resolution observations have localized this blueshifted outflow, which is ∼ 1.36 kpc southwest of the radio centre and has a blueshifted velocity of $\sim 148\, \rm km\, s^{-1}$ and a full width at half maximum of $\sim 581\, \rm km\, s^{-1}$. The spatial extent and kinematic properties of the H i outflow are consistent with the previously detected cold molecular outflows in IRAS 10565 + 2448, suggesting that they likely have the same driving mechanism and are tracing the same outflow. By combining the multiphase gas observations, we estimate a total outflowing mass rate of at least $140\, \rm M_\odot \, yr^{-1}$ and a total energy loss rate of at least $8.9\times 10^{42}\, \rm erg\, s^{-1}$, where the contribution from the ionized outflow is negligible, emphasizing the importance of including both cold neutral and molecular gas when quantifying the impact of outflows. We present evidence of the presence of a radio jet and argue that this may play a role in driving the observed outflows. The modest radio luminosity $L_{\rm 1.4GHz}\, \sim 1.3\times 10^{23}\, {\rm W\, Hz^{-1}}$ of the jet in IRAS 10565 + 2448 implies that the jet contribution to driving outflows should not be ignored in low radio luminosity active galactic nuclei.
Probing gas kinematics towards the high-mass protostellar object G358.46−0.39
Authors: Ugwu C J , Chibueze J O , Morgan J , Csengeri T , Chukwude A E , van der Walt D J , Alhassan J A
Published: February 2023

We investigated the nature of protostellar objects in G358.46−0.39 and their gas kinematics using ALMA data, with the aim of understanding the ongoing star formation activities in the region. The dust continuum map reveals multiple cores (MM1a, MM1b, MM1c, and MM2) dominated by MM1a, with no detectable free–free emission. We calculated the masses and the column densities of the various objects (MM1a, MM1b, MM1c, and MM2). A total of 33, 10, 10, and 9 molecular transitions are detected towards MM1a, MM1b, MM1c, and MM2, respectively. The differences in the number of molecular lines detected towards each of the cores support different excitation conditions at different positions. We derived the kinetic temperature ranges of MM1a, MM1b, MM1c, and MM2 to be ∼96–118, 96–114, 72–74, and 80–84 K, respectively. A highly collimated bipolar outflow traced by 12CO emission is observed to be associated with MM1a, with knots along the outflow lobes, which could be an indication of episodic ejection. The C17O emission is observed to be likely tracing a slowly rotating envelope of gas around MM1a. The velocity field map of CH3OH (22, 1 − 31, 2) emission suggests the presence of a rotating structure, possibly a disc. The physical and kinematic properties of MM1a are strong indication of a massive young stellar object, with ongoing outflow activity and accretion in its early stage of formation.
the three hundredproject: a machine learning method to infer clusters of galaxy mass radial profiles from mock Sunyaev–Zel’dovich maps
Authors: Ferragamo A , de Andres D , Sbriglio A , Cui W , De Petris M , Yepes G , Dupuis R , Jarraya M , Lahouli I , De Luca F , Gianfagna G , Rasia E
Published: February 2023

We develop a machine learning algorithm to infer the three-dimensional cumulative radial profiles of total and gas masses in galaxy clusters from thermal Sunyaev–Zel’dovich effect maps. We generate around 73 000 mock images along various lines of sight using 2522 simulated clusters from the three hundred project at redshift z < 0.12 and train a model that combines an auto-encoder and a random forest. Without making any prior assumptions about the hydrostatic equilibrium of the clusters, the model is capable of reconstructing the total mass profile as well as the gas mass profile, which is responsible for the Sunyaev–Zel’dovich effect. We show that the recovered profiles are unbiased with a scatter of about 10 per cent, slightly increasing towards the core and the outskirts of the cluster. We selected clusters in the mass range of $10^{13.5} \le M_{200} /({{\, h^{-1}\,{\rm {{\rm M}_{\odot }}}}}) \le 10^{15.5}$, spanning different dynamical states, from relaxed to disturbed haloes. We verify that both the accuracy and precision of this method show a slight dependence on the dynamical state, but not on the cluster mass. To further verify the consistency of our model, we fit the inferred total mass profiles with a Navarro–Frenk–White model and contrast the concentration values with those of the true profiles. We note that the inferred profiles are unbiased for higher concentration values, reproducing a trustworthy mass–concentration relation. The comparison with a widely used mass estimation technique, such as hydrostatic equilibrium, demonstrates that our method recovers the total mass that is not biased by non-thermal motions of the gas.
Implications of post-kick jets in core-collapse supernovae
Authors: Soker Noam
Published: February 2023

I examine the assumption that the jets that shape the axisymmetrical morphological features of core-collapse supernova (CCSN) remnants are post-kick jets, i.e. the neutron star (NS) launches these jets after the explosion and after it acquired its natal kick velocity. I find that this assumption implies that the pre-collapse cores of CCSN progenitors have sufficient angular momentum fluctuations to support jittering jets that explode the star. From the finding that the shaping-jets neither tend to be aligned with the kick velocity nor to be perpendicular to it I argue that the assumption that the shaping-jets are post-kick jets has the following implications. (1) The NS accretes mass at a radius of $r_{\rm acc} \approx 5000 {~\rm km}$ from the centre of the explosion at $\approx 10 {~\rm s}$ after explosion. (2) The required angular momentum fluctuations of the accreted gas to explain the medium values of jets-kick angles are also sufficient to support an intermittent pre-kick accretion disc, just before and during the explosion. Such an intermittent accretion disc is likely to launch jets that explode the star in the frame of the jittering jets explosion mechanism. This suggests that most likely the shaping-jets are the last jets in the jittering jets explosion mechanism rather than post-kick jets. (3) The jittering jets explosion mechanism expects that black holes have small natal kick velocities.
Clinical disease activity is a major determinant of plasma D-dimer elevation in outpatients with rheumatoid arthritis: A hospital-based cross-sectional study
Authors: Mori Shunsuke , Soejima Hirofumi , Hokamaki Jun , Tsujita Kenichi
Published: February 2023

Objectives

To identify factors associated with plasma D-dimer levels in outpatients with rheumatoid arthritis (RA).

Methods

We consecutively recruited 460 RA patients who visited our hospital for routine follow-ups between June and October 2021. Plasma D-dimer, RA-related characteristics, comorbidities, and cardiovascular and venous thromboembolism (VTE) risk factors were examined at enrolment. Patients with elevated D-dimer levels underwent whole-leg venous ultrasonography to diagnose deep vein thrombosis (DVT).

Results

Participants had no DVT signs or symptoms. Among them, 252 (54.8%) were positive for plasma D-dimer (≥0.5 μg/ml) and 40 (8.7%) had high D-dimer levels (≥3 μg/ml). The mean was 1.07 μg/ml. After adjustments, age [odds ratio (OR) 1.88 per additional 10 years, P = .003], high and moderate clinical disease activity index (OR 8.79, P < .001), and the presence of comorbidities or cardiovascular/VTE risk factors (OR 2.94, P = .017) were identified as the factors independently associated with high D-dimer levels. Among patients with D-dimer levels ≥3 μg/ml, 10 (25%) had DVT in their lower limbs, and D-dimer levels were significantly higher in patients with DVT compared with those without it (mean 6.0  vs. 4.1 μg/ml, P < .001).

Conclusions

Clinical disease activity is a major contributor to plasma D-dimer elevation in RA outpatients.
Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures
Authors: Akcan Toray S , Vilov Sergey , Heinig Matthias
Published: February 2023

Promoter-proximal Polymerase II (Pol II) pausing is a key rate-limiting step for gene expression. DNA and RNA-binding trans-acting factors regulating the extent of pausing have been identified. However, we lack a quantitative model of how interactions of these factors determine pausing, therefore the relative importance of implicated factors is unknown. Moreover, previously unknown regulators might exist. Here we address this gap with a machine learning model that accurately predicts the extent of promoter-proximal Pol II pausing from large-scale genome and transcriptome binding maps and gene annotation and sequence composition features. We demonstrate high accuracy and generalizability of the model by validation on an independent cell line which reveals the model's cell line agnostic character. Model interpretation in light of prior knowledge about molecular functions of regulatory factors confirms the interconnection of pausing with other RNA processing steps. Harnessing underlying feature contributions, we assess the relative importance of each factor, quantify their predictive effects and systematically identify previously unknown regulators of pausing. We additionally identify 16 previously unknown 7SK ncRNA interacting RNA-binding proteins predictive of pausing. Our work provides a framework to further our understanding of the regulation of the critical early steps in transcriptional elongation.
A clade of RHH proteins ubiquitous in Sulfolobales and their viruses regulates cell cycle progression
Authors: Li Xuyang , Lozano-Madueño Cristina , Martínez-Alvarez Laura , Peng Xu
Published: February 2023

Cell cycle regulation is crucial for all living organisms and is often targeted by viruses to facilitate their own propagation, yet cell cycle progression control is largely underexplored in archaea. In this work, we reveal a cell cycle regulator (aCcr1) carrying a ribbon-helix-helix (RHH) domain and ubiquitous in the Thermoproteota of the order Sulfolobales and their viruses. Overexpression of several aCcr1 members including gp21 of rudivirus SIRV2 and its host homolog SiL_0190 of Saccharolobus islandicus LAL14/1 results in impairment of cell division, evidenced by growth retardation, cell enlargement and an increase in cellular DNA content. Additionally, both gp21 and SiL_0190 can bind to the motif AGTATTA conserved in the promoter of several genes involved in cell division, DNA replication and cellular metabolism thereby repressing or inducing their transcription. Our results suggest that aCcr1 silences cell division and drives progression to the S-phase in Sulfolobales, a function exploited by viruses to facilitate viral propagation.
SMAD3 promotes expression and activity of the androgen receptor in prostate cancer
Authors: Jeon Hee-Young , Pornour Majid , Ryu Hyunju , Khadka Sudeep , Xu Rui , Jang Jihyun , Li Deqiang , Chen Hegang , Hussain Arif , Fazli Ladan , Gleave Martin , Dong Xuesen , Huang Furong , Wang Qianben , Barbieri Christopher , Qi Jianfei
Published: February 2023

Overexpression of androgen receptor (AR) is the primary cause of castration-resistant prostate cancer, although mechanisms upregulating AR transcription in this context are not well understood. Our RNA-seq studies revealed that SMAD3 knockdown decreased levels of AR and AR target genes, whereas SMAD4 or SMAD2 knockdown had little or no effect. ChIP-seq analysis showed that SMAD3 knockdown decreased global binding of AR to chromatin. Mechanistically, we show that SMAD3 binds to intron 3 of the AR gene to promote AR expression. Targeting these binding sites by CRISPRi reduced transcript levels of AR and AR targets. In addition, ∼50% of AR and SMAD3 ChIP-seq peaks overlapped, and SMAD3 may also cooperate with or co-activate AR for AR target expression. Functionally, AR re-expression in SMAD3-knockdown cells partially rescued AR target expression and cell growth defects. The SMAD3 peak in AR intron 3 overlapped with H3K27ac ChIP-seq and ATAC-seq peaks in datasets of prostate cancer. AR and SMAD3 mRNAs were upregulated in datasets of metastatic prostate cancer and CRPC compared with primary prostate cancer. A SMAD3 PROTAC inhibitor reduced levels of AR, AR-V7 and AR targets in prostate cancer cells. This study suggests that SMAD3 could be targeted to inhibit AR in prostate cancer.
Early-onset grade 2-3 diffuse gliomas and schwannomas increase the risk of central nervous system tumors among the patients’ relatives
Authors: Alanen Eljas , Heikkinen Sanna , Nurminen Riikka , Nykter Matti , Haapasalo Hannu , Hirvonen Elli , Pitkäniemi Janne , Rautajoki Kirsi J
Published: February 2023

Background

Central nervous system (CNS) tumors are a heterogeneous group of tumors that include several aggressive malignancies with a high mortality rate. This study aimed to evaluate the familial relative risk of CNS tumors in family members of early-onset index cases (probands) in and between diffuse glioma, non-diffuse glioma, meningioma, and other CNS tumors.

Methods

We retrieved tumor data from the Finnish cancer registry and familial relationships data from the population information system. We ascertained 5408 probands diagnosed with primary CNS tumors (age ≤40 years) between 1970 and 2012 in Finland. We report the standardized incidence ratios as a measure of familial aggregation using Poisson regression.

Results

The risk of early-onset diffuse glioma increased among siblings of probands with the same tumor [SIR 3.85, 95% confidence interval (CI): 1.66–7.59], with association mainly returning to grade 2–3 diffuse gliomas. Early-onset other CNS tumors were associated with an increased risk of other CNS tumors, early-onset meningioma, and late-onset diffuse glioma in 1st-degree relatives. The elevated risk of other CNS tumors was largely caused by schwannomas (SIR 59.44, 95% CI: 27.18–112.84 for 1st-degree relatives) and associated with neurofibromatosis. No tumor syndrome was associated with an increased risk of diffuse gliomas.

Conclusions

The early onset of grade 2–3 diffuse gliomas is associated with an increased risk of similar tumor entities. Early-onset schwannomas dramatically increase CNS tumor risk with a broader tumor-type profile. In future studies, it would be important to identify the underlying shared hereditary factors that contribute to the development of familial diffuse gliomas.
Symbiont diversity in the eukaryotic microbiomes of marine crustacean zooplankton
Authors: Savage Rose-Lynne , Maud Jacqueline L , Kellogg Colleen T E , Hunt Brian P V , Tai Vera
Published: February 2023

Protists (eukaryotic microorganisms) commonly form symbiotic associations with crustacean zooplankton, but their diversity, prevalence and ecological roles are underestimated due to the limited scope of previous investigations. Using metabarcoding of the V4 region of the 18S rRNA gene, we characterized the eukaryotic microbiomes of the dominant crustacean zooplankton, specifically copepods, euphausiids, amphipods and ostracods, from the Strait of Georgia, Canada. Sequence reads from the alveolates dominated all zooplankton examined, which mostly comprised ciliates and dinoflagellates of known symbiont lineages. These lineages included not only those of parasitoids but also those of uncharacterized species. Apostome ciliate reads were the most abundant in all hosts except for cyclopoid copepods, which were dominated by the parasitic Syndiniales. Most symbiont lineages showed some degree of host preference, particularly Pseudocolliniidae ciliate parasites with ostracods, but were often detected in all hosts indicating broad host specificity. Reads from free-living protists, including diatoms and surprisingly hydrozoans, were inferred to be part of their diet. Hydrozoans may have been ingested from free organic matter, such as detritus or marine snow, suggesting a likely underestimated pathway of carbon cycling. This investigation contributes to resolving the interactions between zooplankton and protists and the potential ecological significance of symbioses on zooplankton productivity.
Limited effects of macro-nutrient ratios on thiamin content and transfer in phytoplankton and copepods
Authors: Fridolfsson Emil , Majaneva Sanna , Hylander Samuel
Published: February 2023

Vitamin B1 (thiamin) is primarily produced by bacteria, phytoplankton and fungi in aquatic food webs and transferred to higher trophic levels by ingestion. However, much remains unknown regarding the dynamics this water-soluble, essential micronutrient; e.g. how it relates to macronutrients (carbon, nitrogen and phosphorous). Nutrient limitation has been found to be related to periods of thiamin deficiency as well as in models. Hence, thiamin transfer to copepods from three phytoplankton species from different taxa was investigated, along with the effect of various nutrient regimes on thiamin content. Nutrient levels did not affect thiamin content of phytoplankton nor the transfer to copepods. Instead, phytoplankton displayed species-specific thiamin and macronutrient contents and whilst a higher thiamin content in the prey lead to higher levels in copepods, the transfer was lower for Skeletonema compared to Dunaliella and Rhodomonas. In all, thiamin transfer to copepods is not only dependent on thiamin content of the prey, but also the edibility and/or digestibility is of importance. Thiamin is essential for all organisms, and this study offers insights into the limited effect of macronutrients on the dynamics and transfer of thiamin in the aquatic food webs.
Shifting social-ecological fire regimes explain increasing structure loss from Western wildfires
Authors: Higuera Philip E , Cook Maxwell C , Balch Jennifer K , Stavros E Natasha , Mahood Adam L , St. Denis Lise A
Published: February 2023

Structure loss is an acute, costly impact of the wildfire crisis in the western conterminous United States (“West”), motivating the need to understand recent trends and causes. We document a 246% rise in West-wide structure loss from wildfires between 1999–2009 and 2010–2020, driven strongly by events in 2017, 2018, and 2020. Increased structure loss was not due to increased area burned alone. Wildfires became significantly more destructive, with a 160% higher structure-loss rate (loss/kha burned) over the past decade. Structure loss was driven primarily by wildfires from unplanned human-related ignitions (e.g. backyard burning, power lines, etc.), which accounted for 76% of all structure loss and resulted in 10 times more structures destroyed per unit area burned compared with lightning-ignited fires. Annual structure loss was well explained by area burned from human-related ignitions, while decadal structure loss was explained by state-level structure abundance in flammable vegetation. Both predictors increased over recent decades and likely interacted with increased fuel aridity to drive structure-loss trends. While states are diverse in patterns and trends, nearly all experienced more burning from human-related ignitions and/or higher structure-loss rates, particularly California, Washington, and Oregon. Our findings highlight how fire regimes—characteristics of fire over space and time—are fundamentally social-ecological phenomena. By resolving the diversity of Western fire regimes, our work informs regionally appropriate mitigation and adaptation strategies. With millions of structures with high fire risk, reducing human-related ignitions and rethinking how we build are critical for preventing future wildfire disasters.
Upper Extremity Exercise Capacity and Activities of Daily Living in Individuals with Bronchiectasis Versus Healthy Controls
Authors: Cakmak Aslihan , Kocaaga Elif , Sonbahar-Ulu Hazal , Inal-Ince Deniz , Vardar-Yagli Naciye , Calik-Kutukcu Ebru , Saglam Melda , Coplu Lutfi
Published: February 2023

Objective

The purpose of this study was to compare the upper extremity exercise capacity and activities of daily living (ADLs) in individuals with bronchiectasis and controls.

Methods

Twenty-four individuals with bronchiectasis and 24 healthy controls were assessed for upper extremity exercise capacity (6-minute pegboard and ring test [6PBRT]) and ADLs (Glittre ADL test). Energy expenditure was measured using a wearable metabolic monitor during the Glittre ADL test.

Results

The mean 6PBRT score of individuals with bronchiectasis was significantly lower than the mean score of controls (196.50 [SD = 51.75] versus 243.00 [SD = 29.76] number of rings). The Glittre ADL test duration was significantly higher in individuals with bronchiectasis compared with controls (3.54 [SD = 1.53] versus 2.36 [SD = 0.18] min), despite similar energy expenditure during the Glittre ADL test between the groups (17.67 [SD = 5.28] kcal in individuals with bronchiectasis versus 18.13 [SD = 5.71] kcal in controls). The 6PBRT score and the Glittre ADL test duration were negatively correlated in individuals with bronchiectasis (r = −0.694).

Conclusions

The individuals with bronchiectasis had reduced upper extremity exercise capacity compared with healthy controls. Energy expenditure during ADLs was similar between individuals with bronchiectasis and healthy controls, despite lower ADL performance in individuals with bronchiectasis. The upper extremity exercise capacity and ADLs are related in individuals with bronchiectasis. Given the relationship between upper extremity exercise capacity and ADLs in bronchiectasis, inclusion of upper extremity exercise training to pulmonary rehabilitation programs should be considered.

Impact

Considering the impairment of upper extremity exercise capacity and ADLs in individuals with bronchiectasis highlights the necessity to tailor preventive strategies and preclude further unfavorable effects.

Lay Summary

Bronchiectasis may cause deterioration in upper extremity exercise capacity and ADLs. The assessment of upper exercise capacity and ADLs by physical therapists in individuals with bronchiectasis may be useful for designing comprehensive rehabilitation programs and thus the management of bronchiectasis.
Long-term safety and efficacy of sarilumab with or without background csDMARDs in rheumatoid arthritis
Authors: Burmester Gerd R , Strand Vibeke , Kivitz Alan J , Hu Chih-Chi , Wang Sheldon , van Hoogstraten Hubert , Klier Gabriella L , Fleischmann Roy
Published: February 2023

Objective

To evaluate the long-term safety and efficacy of sarilumab with/without conventional synthetic (cs)DMARDs in RA.

Methods

The analyses evaluated two open-label extensions (OLEs): EXTEND and MONARCH OLE, which included patients from six randomized trials. Patients received sarilumab 200 mg once every 2 weeks (q2w) for at least 264 weeks up to 516 weeks (EXTEND: Sarilumab Monotherapy and Sarilumab + csDMARD groups) or for 276 weeks (MONARCH OLE: Continuation and Switch groups). Primary endpoints included safety, immunogenicity and changes in laboratory parameters. Secondary endpoints included clinical signs and symptoms along with health-related quality-of-life (HRQOL) questionnaires.

Results

The Sarilumab Monotherapy (n = 111), Continuation (n = 165) and Switch (n = 155) groups received sarilumab monotherapy, while the Sarilumab + csDMARD group (n = 1910) received sarilumab in combination with csDMARDs. Incidence of one or more treatment-emergent adverse events was 126 (Sarilumab Monotherapy group), 169 (Sarilumab + csDMARD group), 159 (Continuation group) and 159 (Switch group) events/100 patient-years. Neutropenia was the most common adverse event. Neutropenia was not associated with an increased incidence of infections. Most neutropenia cases normalized on-treatment. Adverse events of special interests, such as malignancies, major adverse cardiovascular events, venous thromboembolism and gastrointestinal perforations, were rare. Immunogenicity was low and not associated with hypersensitivity reactions or discontinuations due to lack or loss of efficacy. Improvements in clinical signs and symptoms and HRQOL, observed during the initial blinded trials, were maintained throughout the OLE assessment period.

Conclusions

Long-term sarilumab treatment with/without csDMARDs in patients with RA revealed no new safety findings. Efficacy and HRQOL were maintained or further increased over the open-label assessment period.

Trial registration

EXTEND, ClinicalTrials.gov, https://www.clinicaltrials.gov/ct2/show/NCT01146652, NCT01146652; MONARCH OLE, ClinicalTrials.gov, https://clinicaltrials.gov/ct2/show/NCT02332590, NCT02332590
Serum Metabolic Profile in Schizophrenia Patients With Antipsychotic-Induced Constipation and Its relationship With Gut Microbiome
Authors: Amdanee Nousayhah , Shao Miaomiao , Hu Xiuxiu , Fang Xinyu , Zhou Chao , Chen Jiu , Ridwan Chattun Mohammad , Wen Lu , Pan Xinming , Zhang Xiangrong , Xu Yue
Published: February 2023

Background and Hypothesis

Antipsychotics (APs), the cornerstone of schizophrenia treatment, confer a relatively high risk of constipation. However, the mechanisms underpinning AP-induced constipation are poorly understood. Thus, we hypothesized that (1) schizophrenia patients with AP-induced constipation have distinct metabolic patterns; (2) there is more than one mechanism at play in producing this adverse drug effect; and (3) AP-associated changes in the gut microbiome are related to the altered metabolic profiles.

Study Design

Eighty-eight schizophrenia patients, including 44 with constipation (C) and 44 matched patients without constipation (NC), were enrolled in this study. Constipation was diagnosed by Rome IV criteria for constipation and colonic transit time using radiopaque markers (ROMs) while severity was evaluated with the Bristol Stool Form Scale (BSS) and Constipation Assessment Scale (CAS). Fasting blood samples were drawn from all participants and were subjected to non-targeted liquid chromatography-mass spectrometry (LC-MS) metabolomic analysis.

Study Results

Eleven metabolites were significantly altered in AP-induced constipation which primarily disturbed sphingolipid metabolism, choline metabolism, and sphingolipid signaling pathway (P value < .05, FDR < 0.05). In the C group, changes in the gut bacteria showed a certain degree of correlation with 2 of the significantly altered serum metabolites and were associated with alterations in choline metabolism.

Conclusions

Our findings indicated that there were disturbances in distinct metabolic pathways that were associated with AP-induced constipation. In addition, this study presents evidence of a link between alterations in the gut microbiome and host metabolism which provides additional mechanistic insights on AP-induced constipation.
Prophylactic Administration of Mesenchymal Stromal Cells Does Not Prevent Arrested Lung Development in Extremely Premature-Born Non-Human Primates
Authors: Möbius Marius A , Seidner Steven R , McCurnin Donald C , Menschner Leonhard , Fürböter-Behnert Isabel , Schönfeld Julia , Marzahn Jenny , Freund Daniel , Münch Nadine , Hering Sandra , Mustafa Shamimunisa B , Anzueto Diana G , Winter Lauryn A , Blanco Cynthia L , Hanes Martha A , Rüdiger Mario , Thébaud Bernard
Published: February 2023

Premature birth is a leading cause of childhood morbidity and mortality and often followed by an arrest of postnatal lung development called bronchopulmonary dysplasia. Therapies using exogenous mesenchymal stromal cells (MSC) have proven highly efficacious in term-born rodent models of this disease, but effects of MSC in actual premature-born lungs are largely unknown. Here, we investigated thirteen non-human primates (baboons; Papio spp.) that were born at the limit of viability and given a single, intravenous dose of ten million human umbilical cord tissue-derived MSC per kilogram or placebo immediately after birth. Following two weeks of human-equivalent neonatal intensive care including mechanical ventilation, lung function testing and echocardiographic studies, lung tissues were analyzed using unbiased stereology. We noted that therapy with MSC was feasible, safe and without signs of engraftment when administered as controlled infusion over 15 minutes, but linked to adverse events when given faster. Administration of cells was associated with improved cardiovascular stability, but neither benefited lung structure, nor lung function after two weeks of extrauterine life. We concluded that a single, intravenous administration of MSC had no short- to mid-term lung-protective effects in extremely premature-born baboons, sharply contrasting data from term-born rodent models of arrested postnatal lung development and urging for investigations on the mechanisms of cell-based therapies for diseases of prematurity in actual premature organisms.
Tree-ring isotopes from the Swiss Alps reveal non-climatic fingerprints of cyclic insect population outbreaks over the past 700 years
Authors: Vitali Valentina , Peters Richard L , Lehmann Marco M , Leuenberger Markus , Treydte Kerstin , Büntgen Ulf , Schuler Philipp , Saurer Matthias
Published: February 2023

Recent experiments have underlined the potential of δ2H in tree-ring cellulose as a physiological indicator of shifts in autotrophic versus heterotrophic processes (i.e., the use of fresh versus stored non-structural carbohydrates). However, the impact of these processes has not yet been quantified under natural conditions. Defoliator outbreaks disrupt tree functioning and carbon assimilation, stimulating remobilization, therefore providing a unique opportunity to improve our understanding of changes in δ2H. By exploring a 700-year tree-ring isotope chronology from Switzerland, we assessed the impact of 79 larch budmoth (LBM, Zeiraphera griseana [Hübner]) outbreaks on the growth of its host tree species, Larix decidua [Mill]. The LBM outbreaks significantly altered the tree-ring isotopic signature, creating a 2H-enrichment and an 18O- and 13C-depletion. Changes in tree physiological functioning in outbreak years are shown by the decoupling of δ2H and δ18O (O–H relationship), in contrast to the positive correlation in non-outbreak years. Across the centuries, the O–H relationship in outbreak years was not significantly affected by temperature, indicating that non-climatic physiological processes dominate over climate in determining δ2H. We conclude that the combination of these isotopic parameters can serve as a metric for assessing changes in physiological mechanisms over time.
Limited cross-species virus transmission in a spatially restricted coral reef fish community
Authors: Costa Vincenzo A , Bellwood David R , Mifsud Jonathon C O , Van Brussel Kate , Geoghegan Jemma L , Holmes Edward C , Harvey Erin
Published: February 2023

The Great Barrier Reef (GBR)—the largest coral reef ecosystem in the world—supports over 1,200 fish species with some of the highest population densities and diversities observed in vertebrates, offering a high potential for virus transmission among species. As such, the GBR represents an exceptional natural ecosystem to determine the impact of host community diversity on virus evolution and emergence. In recent decades, the GBR has also experienced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet. Despite the global importance of the GBR, our understanding of virus diversity and connectivity in tropical reef fishes remains poor. Here, we employed metatranscriptomic sequencing to reveal the viromes of sixty-one reef fish species. This identified transcripts representing 132 putative viral sequences, 38 of which exhibited strong phylogenetic relationships with known vertebrate-associated viral genera, including a novel Santee-Cooper ranavirus (Iridoviridae). We found little evidence for virus transmission between fish species living within a very restricted geographical space—a 100-m2 coral reef ecosystem—suggesting that there might be important host barriers to successful cross-species transmission despite regular exposure. We also identified differences in virome composition among reef fish families, such that cryptobenthic reef fishes—characterized by small body sizes and short life spans—exhibited greater virome richness compared to large reef fishes. This study suggests that there are important barriers to cross-species virus transmission and that successful emergence in a reef fish community likely requires active host adaptation, even among closely related host species.
Enhancing Racial Justice and Equity Through Simulation
Authors: Abram Marissa D. , Mancini Karen
Published: February 2023

Diversity, equity, inclusion, and antiracism (DEI-A) are critical to providing adequate health care to all populations. High-fidelity simulations and role-play scenarios allow students to experience caring for clients from diverse backgrounds. This article discusses the project development and implementation of a DEI-A simulation day placed in a community health clinical course.
Digital Storytelling: Sharing Palliative Care Experiences as an Innovative Educational Approach
Authors: Glassman Emily , Lewis Laura Foran
Published: February 2023

When students are exposed to digital stories about a particular nursing field, they feel more prepared to practice in that field. The purpose of this innovative teaching project was to introduce undergraduate nursing students to palliative care nursing through digital storytelling. Digital interviews with experienced nurses from five specialties were compiled and shared with students. Student responses indicated a positive impact on their professional identity and greater awareness about palliative care. Students benefited from hearing about “real” experiences and exploring diverse specialties and reported that this activity helped decrease their fear, find beauty in death, and value nursing presence.
Assessing Professional Competencies Among Undergraduate Nurses
Authors: Suliman Mohammad , Aljezawi Maen , Tawalbeh Loai , Ta'an Wafa'a , Abdalrhim Asem , AlBashtawy Mohammed , Alkhawaldeh Abdullah
Published: February 2023

AIM

The study aimed to identify nursing students’ professional competencies and examine which factors of the clinical learning environment affect these competencies.

BACKGROUND

Professional competencies are vital for the quality and safety of nursing practice. The learning environment is important for the development of professional competencies.

METHOD

Data were collected from 178 nursing students using the Clinical Learning Environment and Supervision Scale and the Nursing Professional Competencies Scale-Short Form.

RESULTS

The highest competency was achieved in value-based nursing care; the lowest competency was achieved in development, leadership, and organization of nursing. Factors such as positive pedagogical atmosphere, nursing care on the ward, and good supervisory relationship affected learning and, in turn, improved professional competencies.

CONCLUSION

The results establish a link between the clinical environment and reported professional competencies, leading to a call for more focused coverage of these factors in the academic curricula.
Social determinants of health and asthma
Authors: Espaillat Andre E. , Hernandez Michelle L. , Burbank Allison J.
Published: February 2023

Purpose of review

Social determinants of health play a major role in healthcare utilization and outcomes in patients with asthma. Continuing to understand how these complex and interwoven relationships interact to impact patient care will be crucial to creating innovative programmes that address these disparities.

Recent findings

The current literature continues to support the association of substandard housing, urban and rural neighbourhoods, and race/ethnicity with poor asthma outcomes. Targeted interventions with community health workers (CHWs), telemedicine and local environmental rectifications can help improve outcomes.

The link between social determinants and poor asthma outcomes continues to be supported by recent literature. These factors are both nonmodifiable and consequences of institutionalized racist policies that require innovative ideas, technologic equity and funding for groups most at risk for poorer outcomes.