bluuebunny/crossref_metadata_2025 huggingface dataset:
Longitudinal association between disability and suicide mortality in Republic of Korea
Authors: Lee Hwa-Young , Shin Dong Wook , Han Kyung-Do , Kawachi Ichiro
Published: December 2024

Background

The Republic of Korea has reported the highest suicide rate globally since 2018. Previous studies have highlighted disability as a significant risk factor for suicide. However, comprehensive examination on the association between suicide mortality and severities and types of disabilities, and on how these associations vary according to sociodemographic characteristics, health behaviours and comorbidity profiles has never been performed.

Methods

We performed a retrospective cohort study of a nationally representative sample of 3 591 398 individuals subject to the health check-up provided by the Korean National Health Insurance in 2009, including individuals with (n = 126 508) and without (n = 3 734 890) disabilities, and followed-up until December 2021

Results

Overall, the presence of disability was associated with an increased risk of suicide mortality [hazard ratio (HR), 1.38; 95% confidence interval (CI), 1.30–1.47] compared to the absence of disability. This risk was more pronounced in individuals with Grade 1–3 disabilities (HR, 1.68; 95% CI, 1.52–1.85) than those with Grade 4–6 disabilities (HR, 1.28; 95% CI, 1.20–1.47). Among various types of disabilities, individuals with a disability associated with a mental disorder had the highest HR (HR, 4.49; 95% CI, 3.38–5.97), followed by those with visual impairment (HR, 1.47; 95% CI, 1.26–1.73), brain damage (HR, 1.45; 95% CI, 1.18–1.79), hearing impairment (HR, 1.35; 95% CI, 1.15–1.58) and extremity disability (HR, 1.30; 95% CI, 1.21–1.40). Stratified analyses revealed that the suicide risk associated with disabilities was more pronounced in individuals with specific sociodemographic characteristics and health behaviours.

Conclusion

Our findings highlight the need to prioritize policy efforts to address suicide mortality among people with disabilities, considering the distinct risks associated with disability types and severity.
Two waves of photosymbiosis acquisition in extant planktonic foraminifera explained by ecological incumbency
Authors: Takagi Haruka , Nakamura Yasuhide , Schmidt Christiane , Kucera Michal , Saito Hiroaki , Moriya Kazuyoshi
Published: December 2024

Photosymbiosis, a mode of mixotrophy by algal endosymbiosis, provides key advantages to pelagic life in oligotrophic oceans. Despite its ecological importance, mechanisms underlying its emergence and association with the evolutionary success of photosymbiotic lineages remain unclear. We used planktonic foraminifera, a group of pelagic test-forming protists with an excellent fossil record, to reveal the history of symbiont acquisition among their three main extant clades. We used single-cell 18S rRNA gene amplicon sequencing to reveal symbiont identity and mapped the symbiosis on a phylogeny time-calibrated by fossil data. We show that the highly specific symbiotic interaction with dinoflagellates emerged in the wake of a major extinction of symbiont-bearing taxa at the end of the Eocene. In contrast, less specific and low-light-adapted symbioses with pelagophytes emerged 20 million years later, in multiple independent lineages in the Late Neogene, at a time when the vertical structure of pelagic ecosystems was transformed by global cooling. We infer that in foraminifera, photosymbiosis can evolve easily and that its establishment leads to diversification and ecological dominance to such an extent, that the proliferation of new symbioses is prevented by the incumbent lineages.
A rice rhizosphere plant growth-promoting Streptomyces corchorusii isolate antagonizes Magnaporthe oryzae and elicits defense responses in rice
Authors: Njoroge Hellen Wambui , Hu Jiangfei , Yu Yijie , Yuan Zhixiang , Lin Yuqing , Han Xixi , Liu Zhuang , Muia Anastasia Wairimu , Liu Hongxia
Published: December 2024

Aims

Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases of rice (Oryza sativa L.). The aim of this study was to investigate the biocontrol potential of rice rhizosphere actinomycetes against M. oryzae Guy 11, and elucidate the antagonistic mechanisms.

Methods and results

An isolate characterized as a Streptomyces corchorusii strain (Sc75) using the 16S rRNA gene exhibited superior antifungal activity. Sc75 had an inhibitory effect of 69.25% ± 0.15% against M. oryzae and broad antifungal activity on other fungal plant pathogens in the dual culture assay. Its cell-free culture filtrate inhibited fungal growth and reduced mycelial mass. Also, the ethyl acetate crude extract completely inhibited conidia germination and appressoria formation on the hydrophobic coverslips and detached leaf at a concentration of 20 mg/ml. Its volatile organic compounds (VOCs) suppressed fungal growth by 98.42%. GC–MS analysis of the VOCs identified butanoic acid, 2-methyl-, methyl ester; di-tert-butyl peroxide; furan, 2-pentyl-; and undecanoic acid, 10-methyl-, methyl ester as the main components. In the greenhouse experiment, the disease severity was reduced and growth promotion was evident. Molecular investigation revealed that Sc75 upregulated defense-related genes involved in the synthesis of jasmonic acid, salicylic acid signaling pathway, and led to callose deposition and ROS production in the leaves. Finally, Sc75 produced hydrolytic enzymes, siderophore, indole acetic acid, gibberellic acid, phosphate solubilization, and 1-aminocyclopropane-1-carboxylate deaminase.

Conclusions

The rice rhizosphere soil harbors actinomycetes that can be explored as biocontrol agents against fungal pathogens such as M. oryzae. The isolate Sc75 had superior antifungal activity against M. oryzae and other selected plant pathogenic fungi. It showed remarkable antagonistic activity through direct antibiosis, production of VOCs, antifungal metabolites in the culture filtrates and crude extracts, and produced enzymes. In addition, the isolate promoted plant growth, reduced rice blast disease index in the greenhouse experiment, and elicited defense-related responses. Sc75 is a promising candidate for future exploration as a biofungicide and a biofertilizer.
Using large language models to detect outcomes in qualitative studies of adolescent depression
Authors: Xin Alison W , Nielson Dylan M , Krause Karolin Rose , Fiorini Guilherme , Midgley Nick , Pereira Francisco , Lossio-Ventura Juan Antonio
Published: December 2024

Objective

We aim to use large language models (LLMs) to detect mentions of nuanced psychotherapeutic outcomes and impacts than previously considered in transcripts of interviews with adolescent depression. Our clinical authors previously created a novel coding framework containing fine-grained therapy outcomes beyond the binary classification (eg, depression vs control) based on qualitative analysis embedded within a clinical study of depression. Moreover, we seek to demonstrate that embeddings from LLMs are informative enough to accurately label these experiences.

Materials and Methods

Data were drawn from interviews, where text segments were annotated with different outcome labels. Five different open-source LLMs were evaluated to classify outcomes from the coding framework. Classification experiments were carried out in the original interview transcripts. Furthermore, we repeated those experiments for versions of the data produced by breaking those segments into conversation turns, or keeping non-interviewer utterances (monologues).

Results

We used classification models to predict 31 outcomes and 8 derived labels, for 3 different text segmentations. Area under the ROC curve scores ranged between 0.6 and 0.9 for the original segmentation and 0.7 and 1.0 for the monologues and turns.

Discussion

LLM-based classification models could identify outcomes important to adolescents, such as friendships or academic and vocational functioning, in text transcripts of patient interviews. By using clinical data, we also aim to better generalize to clinical settings compared to studies based on public social media data.

Conclusion

Our results demonstrate that fine-grained therapy outcome coding in psychotherapeutic text is feasible, and can be used to support the quantification of important outcomes for downstream uses.
Investigation on the preferences for data quality assessment indicators of electronic health records: user-oriented perspective
Authors: Yang Liu , Ren Mudan , Sun Shuifa , Lu Ji , Wu Yirong
Published: December 2024

Objectives

This study aims to investigate whether different types of electronic health record (EHR) users have distinct preferences for data quality assessment indicators (DQAI) and explore how these preferences can guide the enhancement of EHR systems and the optimization of related policies.

Materials and Methods

High-frequency indicators were identified by a systematic literature review to construct a DQAI system, which was assessed by a user-oriented investigation involving doctors, nurses, hospital supervisors, and clinical researchers. The entropy weight method and fuzzy comprehensive evaluation model were employed for the system comprehensive evaluation. Exploratory factor analysis was used to construct dimensions, and visualization analysis was utilized to explore preferences at both the indicator and dimension levels.

Results

Sixteen indicators were identified to construct the DQAI system and grouped into 2 dimensions: structural and relational. The DQAI system achieved a comprehensive evaluation score of 90.445, corresponding to a “very important” membership level (62.5%). Doctors and nurses exhibited a higher score mean (4.43-4.66 out of 5) than supervisors (3.73-4.55 out of 5). Researchers emphasized credibility, with a score mean of 4.79 out of 5.

Discussion

The findings reveal that different types of EHR users exhibit distinct preferences for the DQAI at both indicator and dimension levels. Doctors and nurses thought that all indicators were important, clinical researchers emphasized credibility, and supervisors focused mainly on accuracy. Indicators in the relational dimension were generally more valued than structural ones. Doctors and nurses prioritized indicators of relational dimension, while researchers and supervisors leaned towards indicators of structural dimension. These insights suggest that tailored approaches in EHR system development and policy-making could enhance EHR data quality.

Conclusion

This study underscores the importance of user-centered approaches in optimizing EHR systems, highlighting diverse user preferences at both indicator and dimension levels.
Unraveling melorheostosis: insights into clinical features, diagnosis, and treatment
Authors: Bhattacharyya Timothy
Published: December 2024

Melorheostosis is a rare bone disease characterized by abundant bone formation with a characteristic radiographic appearance that resembles “dripping candle wax.” Recent data have shown that the majority of cases are due to somatic activating mutations in bone. Melorheostosis has several clinical and radiographic presentations, which are now known to be caused by different somatic mutations such as MAP2K1, SMAD3, KRAS, and LEMD3. This review provides a comprehensive look at the clinical features, diagnostic approaches, and current treatment options for melorheostosis, alongside future research directions aimed at improving patient outcomes.
Development of a DDP-Based Trajectory Generation Method Considering the Manipulability Measure for 6-DOF Collaborative Robots
Authors: Lee Jaesoon , Cho Baek-Kyu
Published: December 2024

This paper presents a trajectory generation method for 6-DOF collaborative robots using the Differential Dynamic Programming algorithm, integrating the Manipulability Measure to effectively avoid singularities. Traditional trajectory generation methods often neglect the robot’s dynamics, leading to non-optimized trajectories and potential singularity issues. Our approach integrates Manipulability Measure into the Differential Dynamic Programming algorithm, ensuring consideration of the robot’s dynamics while effectively avoiding singularities. The proposed algorithm is applied to the 6-Degrees of freedom collaborative robot RB1-500e and validated on the actual robot. The results demonstrate that the proposed method significantly improves trajectory generation and singularity avoidance compared to traditional methods. This study offers a robust solution that enhances both efficiency and safety in dynamic trajectory planning for collaborative robots.
Early progressive disease within 2 years in isocitrate dehydrogenase (IDH)–mutant astrocytoma may indicate radiation necrosis
Authors: Ozeki Yukie , Honda-Kitahara Mai , Yanagisawa Shunsuke , Takahashi Masamichi , Ohno Makoto , Miyakita Yasuji , Kikuchi Miu , Nakano Tomoyuki , Hosoya Tomohiro , Sugino Hirokazu , Satomi Kaishi , Yoshida Akihiko , Igaki Hiroshi , Kubo Yuko , Ichimura Koichi , Suzuki Hiromichi , Masutomi Kenkichi , Kondo Akihide , Narita Yoshitaka
Published: December 2024

Background

Isocitrate dehydrogenase–mutant astrocytoma without cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) homozygous deletion typically follows a slow clinical course. However, some cases show early progression on magnetic resonance imaging, and these characteristics remain under-reported. This study aimed to elucidate the characteristics of isocitrate dehydrogenase–mutant astrocytoma showing early progression on magnetic resonance imaging.

Methods

This retrospective study included 52 cases of primary astrocytoma, isocitrate dehydrogenase–mutant, Central Nervous System (CNS) 5 World Health Organization grade 2–3 according to the World Health Organization 2021 classification. Patients underwent surgery followed by radiation therapy and/or chemotherapy at our institution from 2006 to 2019. Progression-free survival and overall survival were analyzed.

Results

There were 24 and 28 grade 2 and grade 3 astrocytomas, respectively. The median patient age was 38 years. Forty-three patients underwent radiotherapy. Progression was diagnosed by magnetic resonance imaging in 22 patients with initial radiotherapy. Thirteen of the 22 patients underwent surgery, and seven of the 13 patients received surgery within 24 months of the initial radiotherapy. Histopathologically, radiation necrosis was confirmed in four of these seven patients (57.1%). The true progression-free survival rate, excluding radiation necrosis, at 2 years after surgery was 91.3% for grade 2 astrocytoma and 88.5% for grade 3 astrocytoma. The 5-year overall survival rate was 85.7% for grade 2 tumours and 76.4% for grade 3 tumours.

Conclusions

Radiation necrosis should be considered in cases showing early progression of isocitrate dehydrogenase–mutant astrocytoma, and a second surgery should be performed to confirm true recurrence or radiation necrosis. Astrocytomas with telomerase reverse-transcriptase promoter mutations may relapse relatively early and should be followed up with caution.
Influence of a nearby hemisphere on the immersed on-wall collision dynamics of a sphere
Authors: Wu H , Yang F-L
Published: December 2024

Systematic experiments were conducted to elucidate how the dynamics of a fully immersed spherical pendulum in a normal approach to a wall may change with the presence of a third object–a hemisphere added to the wall at different vertical distances from the collision point. The studied collision regime ranges from non-bouncing to bouncing by changing the pendulum’s size, density, release angle, and liquid viscosity. In the non-bouncing regime, we analyzed the approach motion and found that the hemisphere decelerates the pendulum approach when it enters the area within one diameter of the pendulum sphere. The deceleration is stronger with decreasing particle Reynolds number. In the cases with rebounds, we measured the wet coefficient of restitution and correlated it to the impact Stokes number. A critical Stokes number was identified to signal the rebound transition, whose value is slightly augmented by the adjacent hemisphere when this third boundary is within one diameter. Most importantly, the previously reported relation between the wet coefficient of restitution and Stokes number remains feasible as long as the decelerated impact velocity of the pendulum is taken into account.
Capsaicin: pharmacological applications and prospects for drug designing
Authors: Gupta Anshita , Joshi Renjil , Dewangan Lokkanya , Shah Kamal , Soni Deependra , Patil Umesh K , Chauhan Nagendra Singh
Published: December 2024

Objectives

A primary objective of this review is to summarize the evidence-based pharmacological applications of capsaicin, particularly its use to manage pain and treat various health conditions. A second goal of the review is to research how recent technological advances are improving the bioavailability and therapeutic index of capsaicin, as well as the development of novel capsaicin-mimetics that are able to enhance therapeutic responses in various human diseases.

Methods

In the review, numerous human clinical trials and preclinical studies are examined to determine how effective, safe, and optimal dosages of capsaicin can be used in pain management and therapeutic applications. Furthermore, it discusses capsaicin’s mechanisms of action, specifically its interactions with the transient receptor potential vanilloid 1 (TRPV1) channel. As a result of this review, the potential of nanotechnology systems for bypassing the limits of capsaicin’s pungency is discussed. The review takes into account individual factors such as pain tolerance and skin sensitivity.

Key findings

For topical applications, capsaicin is typically used in concentrations ranging from 0.025% to 0.1%, with higher concentrations being used under medical supervision for neuropathic pain. The formulation can come in the form of creams, gels, or patches, which provide sustained release over the course of time. A condition such as arthritis or neuropathy can be relieved with capsaicin as it depletes substance P from nerves. Neuropathy and osteoarthritis as well as musculoskeletal disorders have been treated successfully with this herbal medicine. A major mechanism through which capsaicin relieves pain is through activating TRPV1 channels, which induce calcium influx and neurotransmitter release. Additionally, it affects the transcription of genes related to pain modulation and inflammation, particularly when disease conditions or stress are present. There have been recent developments in technology to reduce capsaicin’s pungency and improve its bioavailability, including nanotechnology.

Conclusions

It is proven that capsaicin is effective in pain management as well as a variety of therapeutic conditions because of its ability to deplete substance P and desensitize nerve endings. Although capsaicin is highly pungent and associated with discomfort, advancements in delivery technologies and the development of capsaicin-mimetics promise improved therapeutic outcomes. There is a great deal of complexity in the pharmacological action of capsaicin due to its interaction with TRPV1 channels and its ability to affect gene transcription. There is a need for further research and development in order to optimize capsaicin’s clinical applications and to enhance its therapeutic index in a variety of human diseases.
Perineal hernia repair with a combined abdominoperineal approach with biologic mesh placement and peritoneal flap reconstruction
Authors: Massé Gabrielle , Al Khaldi M , Schwenter F , Coeugniet E , Sebajang H
Published: December 2024

Perineal hernias occur rarely following abdominoperineal resections. No standardized surgical approach exists for treating PH. We herein present the case of a large, symptomatic PH that was repaired with a combined abdominal and perineal approach, with peritoneal flap reconstruction of the pelvic floor and placement of a biological mesh. The patient has not recurred after 3 years of follow-up. In conclusion, despite the lack of a standardized approach for tackling perineal hernias, a combined one with peritoneal flap reconstruction can be successfully used.
Collisional excitation of c-MgC2 by Helium
Authors: M’hamdi M , Bop C T , Lique F , Ben Houria A , Hammami K
Published: December 2024

The cyclic form of magnesium dicarbide molecule (c-MgC$_2$) has been detected in the carbon-rich circumstellar envelope of IRC+10216 and is considered as a valuable tracer for characterizing the physical conditions of the surrounding gas. In order to make the most of c-MgC$_2$ observations and accurately derive the physical conditions of the media where c-MgC$_2$ is detected, radiative transfer modelling, including collisional and radiative (de-)excitations, have to be performed. Here, we study the excitation of c-MgC$_{2}$ induced by collisions with He (as a proxy for H$_2$). A new 3D potential energy surface (PES) is constructed using highly correlated ab initio methods. This PES reveals a minimum with a well depth of 20.66 cm$^{-1}$ below the c-MgC$_2$-He dissociation limit. Using this PES, we compute excitation cross sections for transitions between the low-lying rotational energy levels of c-MgC$_2$ using the time-independent quantum mechanical close-coupling formalism. These cross sections are then thermally averaged over a Boltzmann energy distribution in order to derive excitation rate coefficients at low temperatures ($T \le 30$ K). To evaluate the impact of these new rate coefficients on the interpretation of c-MgC$_2$ observational spectra, we perform radiative transfer calculations. We find that a very high gas density ($n \gt 10^6$ cm$^{-3}$) is needed in order for the collisional excitation to compete with the radiative de-excitation. We also find that the excitation temperatures of the observed lines predicted by our model differ by a factor two from the value derived from the observations in IRC+10216 circumstellar envelope, indicating that the excitation of c-MgC$_{2}$ may also be driven by a strong radiative pumping in such media. Therefore, a more sophisticated non-LTE modelling, that takes into account the collisional and radiative excitations as well as the radiative pumping, is required to accurately interpret the observational spectra of c-MgC$_2$.
Precision of meteor trajectory and orbital measurements by the MIOS
Authors: Li Yi , Li Guozhu , Hu Lianhuan , Zhao Xiukuan , Sun Wenjie , Xie Haiyong , Dai Guofeng , Liu Jianfei , Ning Baiqi
Published: December 2024

Measurement errors of meteors can substantially affect the accuracy of meteoroid trajectory and orbit determinations, potentially leading to spurious meteoroid orbits. Here, we evaluate the measurement errors associated with the meteor and ionospheric irregularity observation system (MIOS) developed at low-latitude Ledong and Sanya, China, aimed at observing various meteors and their associated plasma density irregularity phenomena, and investigate how these errors affect the determination of meteor trajectories and orbits. The measurement error of meteor position is estimated to be $\sim$2 pixels, corresponding to 0.04$^\circ$, which is sufficient to detect true radiant dispersion and structural characteristics in younger meteor showers. By simulating meteoroids from the Draconid, Geminid, and Perseid meteor showers with the $\sim$2 pixels measurement error and the Monte Carlo trajectory method, the precision of corresponding meteoroid trajectories is derived. The radiant accuracy is 1.09$^\circ$, with right ascension and declination accuracies of 0.78$^\circ$ and 0.77$^\circ$, respectively. The velocity accuracy is 0.64 km/s. The comparison of estimated and true radiant uncertainties shows that the estimated errors of the MIOS are generally consistent with the true meteor trajectory errors. Finally, we estimate the orbital measurement errors, which include an eccentricity of 0.05, a perihelion distance of 0.0086 au, an inclination of 1.4$^\circ$, and an argument of the perihelion of 1.86$^\circ$. Based on observations of eight representative meteor showers during 2019–2023, the accuracy of the MIOS in detecting meteor trajectories and orbits is further validated.
DUVET: sub-kiloparsec resolved star formation driven outflows in a sample of local starbursting disc galaxies
Authors: Reichardt Chu Bronwyn , Fisher Deanne B , Chisholm John , Berg Danielle , Bolatto Alberto , Cameron Alex J , Fielding Drummond B , Herrera-Camus Rodrigo , Kacprzak Glenn G , Li Miao , McLeod Anna F , McPherson Daniel K , Nielsen Nikole M , Rickards Vaught Ryan J , Ridolfo Sophia G , Sandstrom Karin
Published: December 2024

We measure resolved (kiloparsec-scale) outflow properties in a sample of 10 starburst galaxies from the Deep near-UV observations of Entrained gas in Turbulent (DUVET) galaxies sample, using Keck/KCWI observations of H $\beta$ and [O iii] $\lambda$5007. We measure $\sim 460$ lines of sight that contain outflows, and use these to study scaling relationships of outflow velocity ($v_{\rm out}$), mass-loading factor ($\eta$; mass outflow rate per star formation rate) and mass flux ($\dot{\Sigma }_{\rm out}$; mass outflow rate per area) with co-located star formation rate surface density ($\Sigma _{\rm SFR}$) and stellar mass surface density ($\Sigma _{\ast }$). We find strong, positive correlations of $\dot{\Sigma }_{\rm out} \propto \Sigma _{\rm SFR}^{1.2}$ and $\dot{\Sigma }_{\rm out} \propto \Sigma _{\ast }^{1.5}$. We also find shallow correlations between $v_{\rm out}$ and both $\Sigma _{\rm SFR}$ and $\Sigma _{\ast }$. Our resolved observations do not suggest a threshold in outflows with $\Sigma _{\rm SFR}$, but rather we find that the local specific star formation rate ($\Sigma _{\rm SFR}/\Sigma _\ast$) is a better predictor of where outflows are detected. We find that outflows are very common above $\Sigma _{\rm SFR}/\Sigma _\ast \gtrsim 0.1$ Gyr$^{-1}$ and rare below this value. We argue that our results are consistent with a picture in which outflows are driven by supernovae, and require more significant injected energy in higher mass surface density environments to overcome local gravity. The correlations we present here provide a statistically robust, direct comparison for simulations and higher redshift results from JWST.
Deep imaging of three accelerating stars using SHARK-NIR and LMIRCam at LBT
Authors: Mesa D , Gratton R , D’Orazi V , Carolo E , Vassallo D , Farinato J , Marafatto L , Wagner K , Hom J , Ertel S , Henning Th , Desgrange C , Barbato D , Bergomi M , Cerpelloni P , Desidera S , Filippo S Di , Doelman D , Machado T S Gomes , Greggio D , Grenz P , Kenworthy M , Laudisio F , Lazzoni C , Leisenring J , Lorenzetto A , Santhakumari K K R , Ricci D , Snik F , Umbriaco G , Pallauta M C Vega , Viotto V
Published: December 2024

The combination of detection techniques enhances our ability to identify companions orbiting nearby stars. We employed high-contrast imaging to constrain mass and separation of possible companions responsible for the significant proper motion anomalies of the nearby stars HIP 11696, HIP 47110, and HIP 36277. These targets were observed using the LBT’s high-contrast camera, SHARK-NIR, in H band using a Gaussian coronagraph, and with the LMIRCam instrument in the L’ band and using a vAPP coronagraph. Both observations were conducted simultaneously. Additionally, constraints at short separations from the host star are derived analysing the renormalized unit weight error values from the Gaia catalogue. We find that the companion responsible for the anomaly signal of HIP 11696 is likely positioned at a distance from 2.5 to 28 astronomical units from its host. Its mass is estimated to be between 4 and 16 Jupiter masses, with the greater mass possible only at the upper end of the separation range. Similar limits were obtained for HIP 47110 where the companion should reside between 3 and 30 au with a mass between 3 and 10 MJup. For HIP 36277, we identified a faint stellar companion at large separation, though it might be substellar depending on the assumed age for the star. Considering the older age, this object accounts for the absolute value of the PMa vector but not for its direction. Additionally, we found a substellar candidate companion at a closer separation that could explain the PMa signal, considering a younger age for the system.
Reconciling S8: insights from interacting dark sectors
Authors: Shah Rahul , Mukherjee Purba , Pal Supratik
Published: December 2024

We do a careful investigation of the prospects of dark energy (DE) interacting with cold dark matter in alleviating the $S_8$ clustering tension. To this end, we consider various well-known parametrizations of the DE equation of state (EoS) and consider perturbations in both the dark sectors, along with an interaction term. Moreover, we perform a separate study for the phantom and non-phantom regimes. Using cosmic microwave background (CMB), baryon acoustic oscillations, and Type Ia supernovae data sets, constraints on the model parameters for each case have been obtained and a generic reduction in the $H_0 \!\!-\!\! \sigma _{8,0}$ correlation has been observed, both for constant and dynamical DE EoS. This reduction, coupled with a significant negative correlation between the interaction term and $\sigma _{8,0}$, contributes to easing the clustering tension by lowering $\sigma _{8,0}$ to somewhere in between the early CMB and late-time clustering measurements for the phantom regime, for almost all the models under consideration. Additionally, this is achieved without exacerbating the Hubble tension. In this regard, the interacting Chevallier–Polarski–Linder and Jassal–Bagla–Padmanabhan models perform the best in relaxing the $S_8$ tension to $<\!\! 1\sigma$. However, for the non-phantom regime the $\sigma _{8,0}$ tension tends to have worsened, which reassures the merits of phantom DE from latest data. We further investigate the role of redshift space distortion data sets and find an overall reduction in tension, with a $\sigma _{8,0}$ value relatively closer to the CMB value. We finally check whether further extensions of this scenario, such as the inclusion of the sound speed of DE and warm dark matter interacting with DE, can have some effects.
Neutrino-driven core-collapse supernova yields in Galactic chemical evolution
Authors: Jost Finia P , Molero Marta , Navó Gerard , Arcones Almudena , Obergaulinger Martin , Matteucci Francesca
Published: December 2024

We provide yields from 189 neutrino-driven core-collapse supernova (CCSN) simulations covering zero-age main sequence masses between 11 and $75\ \mathrm{M}_\odot$ and three different metallicities. Our CCSN simulations have two main advantages compared to previous methods used for applications in Galactic chemical evolution (GCE). First, the mass cut between remnant and ejecta evolves naturally. Secondly, the neutrino luminosities and thus the electron fraction are not modified. Both are key to obtain an accurate nucleosynthesis. We follow the composition with an in situ nuclear reaction network including the 16 most abundant isotopes and use the yields as input in a GCE model of the Milky Way. We adopt a GCE that takes into account infall of gas as well as nucleosynthesis from a large variety of stellar sources. The GCE model is calibrated to reproduce the main features of the solar vicinity. For the CCSN models, we use different calibrations and propagate the uncertainty. We find a big impact of the CCSN yields on our GCE predictions. We compare the abundance ratios of C, O, Ne, Mg, Si, S, Ar, Ca, Ti, and Cr with respect to Fe to an observational data set as homogeneous as possible. From this, we conclude that at least half of the massive stars have to explode to match the observed abundance ratios. If the explosions are too energetic, the high amount of iron will suppress the abundance ratios. With this, we demonstrate how GCE models can be used to constrain the evolution and death of massive stars.
The reliability of gas-phase metallicities immediately adjacent to non-star-forming spaxels in MaNGA
Authors: Scudder Jillian M , Khelil Aidan , Ordower Jonah Z
Published: December 2024

In this work, we use gas phase metallicities calculated from the Sloan Digital Sky Survey (SDSS) Mapping Nearby Galaxies at Apache Point (MaNGA) Data Release 17 (DR17) to assess the extent of potential biases in spaxels which are spatially adjacent to spaxels identified as non-star forming (non-SF) on a BPT diagram. We identify a sample of $\sim 21\,000$ such spaxels with calculable metallicities from the full metallicity catalogue ($\sim$1.57 million), representing a small fraction ($\sim 1.3$ per cent) of the full metallicity sample. $\sim$23 per cent of all galaxies with at least one spaxel with a calculable metallicity also contain at least one spaxel with a calculated metallicity adjacent to a non-SF spaxel, with a typical galaxy hosting 9 non-SF-adjacent spaxels. From our suite of 6 different metallicity calibrations, we find that only the metallicity calibrations based entirely on the [N ii]$_{6584}$/H $\alpha$ ratio are affected, showing systematic offsets to higher metallicities by up to $\sim$0.04 dex if they are located adjacent to a non-SF flagged spaxel, relative to a radially matched control sample. The inclusion of additional diagnostic diagrams (based on [O i]$_{6300}$ and/or [S ii]$_{6717+6731}$) is insufficient to remove the observed offset in the [N ii]$_{6584}$/H $\alpha$ based calibrations. Using a stricter diagnostic line on the BPT diagram removes $\sim$94 per cent of identified bordering spaxels with metallicities for all metallicity calibrations, and removes the residual offset to higher metallicity values seen in [N ii]$_{6584}$/H $\alpha$ calibrations. If science cases demand an exceptionally clean metallicity sample, we recommend either a stricter BPT cut, and/or a non-[N ii]$_{6584}$/H $\alpha$ based metallicity calibration.
Properties of the lower segment of M31’s North West stream
Authors: Preston Janet , Erkal Denis , Collins Michelle L M , Ibata Rodrigo , Rich R Michael
Published: December 2024

We present a kinematic and spectroscopic analysis of 40 red giant branch stars, in 9 fields, exquisitely delineating the lower segment of the North West stream (NW-K2), which extends for $\sim$80 kpc from the centre of the Andromeda galaxy. We measure the stream’s systemic velocity as −439.3$^{+4.1}_{-3.8}$ km s$^{-1}$ with a velocity dispersion =16.4$^{+5.6}_{-3.8}$ km s$^{-1}$ that is in keeping with its progenitor being a dwarf galaxy. We find no detectable velocity gradient along the stream. We determine $-1.3\pm0.1$$\le$$\langle[\mathrm{ Fe/H}]_{\rm spec}\rangle$$\le$$-1.2\pm0.8$ but find no metallicity gradient along the stream. We are able to plausibly associate NW-K2 with the globular clusters PAndAS-04, PAndAS-09, PAndAS-10, PAndAS-11, and PAndAS-12 but not with PAndAS-13 or PAndAS-15, which we find to be superimposed on the stream but not kinematically associated with it.
Saltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group
Authors: Prediger Carolina , Ferreira Erina A , Zorzato Samara Videira , Hua-Van Aurélie , Klasson Lisa , Miller Wolfgang J , Yassin Amir , Madi-Ravazzi Lilian
Published: December 2024

Phylogenomics reveals reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power or it is a true evolutionary pattern remains a field of study. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species whose relationships have long been problematic. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria. We extended the ABBA-BABA test of asymmetry in phylogenetic discordance to cases where no “true” species tree could be inferred, and applied our new test (called 2A2B) to whole genome data and to individual loci. We used four strategies, two based on our new assemblies using either conserved genes or ≥50 kb-long syntenic blocks with conserved collinearity across Neotropical Sophophora, and two consisted of windows from pseudo-reference genomes aligned to either an ingroup or outgroup species. Evidence for reticulation varied among the strategies, being lowest in the synteny-based approach, where it did not exceed ∼7% of the blocks in the most conflicting species quartets. High incidences of reticulation were restricted to three nodes on the tree that coincided with major paleogeographical events in South America. Our results identify possible technical biases in quantifying reticulate evolution and indicate that episodic rapid radiations have played a major role in the evolution of a largely understudied Neotropical clade.
RNA binding by Periphilin plays an essential role in initiating silencing by the HUSH complex
Authors: Bloor Stuart , Wit Niek , Lehner Paul J
Published: December 2024

The human silencing hub (HUSH) complex is a transcription-dependent, epigenetic repressor complex that provides a genome-wide immunosurveillance system for the recognition and silencing of newly-integrated retroelements. The core HUSH complex of TASOR, MPP8 and Periphilin, represses these retroelements through SETDB1-mediated H3K9me3 deposition and MORC2-dependent chromatin compaction. HUSH-dependent silencing is RNA-mediated, yet no HUSH component contains a recognised RNA-binding domain. Here we used an unbiased approach to identify which HUSH component was able to bind RNA and determine whether RNA-binding was essential for HUSH function. We identify Periphilin as the major RNA-binding component of the HUSH complex and show that Periphilin's N-terminal domain is essential for both RNA binding and HUSH function. Periphilin binding to RNA was independent of its interaction with TASOR or MPP8, as its N-terminal domain was sufficient for RNA targeting. The artificial tethering of Periphilin to a HUSH-insensitive, nascent transcript, enabled the HUSH-dependent silencing of the transcript. This tethering of Periphilin allowed the RNA-binding region of Periphilin to be removed such that only its C-terminal domain was required for oligomerisation and interaction with TASOR. We therefore show that Periphilin is the predominant RNA-binding protein of the HUSH complex and this RNA-binding is essential for HUSH activity.
Translation of circular RNAs
Authors: Margvelani Giorgi , Maquera Karol Andrea Arizaca , Welden Justin Ralph , Rodgers David W , Stamm Stefan
Published: December 2024

Circular RNAs (circRNAs) are covalently closed RNAs that are present in all eukaryotes tested. Recent RNA sequencing (RNA-seq) analyses indicate that although generally less abundant than messenger RNAs (mRNAs), over 1.8 million circRNA isoforms exist in humans, much more than the number of currently known mRNA isoforms. Most circRNAs are generated through backsplicing that depends on pre-mRNA structures, which are influenced by intronic elements, for example, primate-specific Alu elements, leading to species-specific circRNAs. CircRNAs are mostly cytosolic, stable and some were shown to influence cells by sequestering miRNAs and RNA-binding proteins. We review the increasing evidence that circRNAs are translated into proteins using several cap-independent translational mechanisms, that include internal ribosomal entry sites, N6-methyladenosine RNA modification, adenosine to inosine RNA editing and interaction with the eIF4A3 component of the exon junction complex. CircRNAs are translated under conditions that favor cap-independent translation, notably in cancer and generate proteins that are shorter than mRNA-encoded proteins, which can acquire new functions relevant in diseases.
Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering
Authors: Vujaklija Ivan , Biđin Siniša , Volarić Marin , Bakić Sara , Li Zhe , Foo Roger , Liu Jianjun , Šikić Mile
Published: December 2024

To date, over 40 epigenetic and 300 epitranscriptomic modifications have been identified. However, current short-read sequencing-based experimental methods can detect <10% of these modifications. Integrating long-read sequencing technologies with advanced computational approaches, including statistical analysis and machine learning, offers a promising new frontier to address this challenge. While supervised machine learning methods have achieved some success, their usefulness is restricted to a limited number of well-characterized modifications. Here, we introduce Modena, an innovative unsupervised learning approach utilizing long-read nanopore sequencing capable of detecting a broad range of modifications. Modena outperformed other methods in five out of six benchmark datasets, in some cases by a wide margin, while being equally competitive with the second best method on one dataset. Uniquely, Modena also demonstrates consistent accuracy on a DNA dataset, distinguishing it from other approaches. A key feature of Modena is its use of ‘dynamic thresholding’, an approach based on 1D score-clustering. This methodology differs substantially from the traditional statistics-based ‘hard-thresholds.’ We show that this approach is not limited to Modena but has broader applicability. Specifically, when combined with two existing algorithms, ‘dynamic thresholding’ significantly enhances their performance, resulting in up to a threefold improvement in F1-scores.
Motif distribution in genomes gives insights into gene clustering and co-regulation
Authors: Chakraborty Atreyi , Chopde Sumant , Madhusudhan Mallur Srivatsan
Published: December 2024

We read the genome as proteins in the cell would – by studying the distributions of 5–6 base motifs of DNA in the whole genome or smaller stretches such as parts of, or whole chromosomes. This led us to some interesting findings about motif clustering and chromosome organization. It is quite clear that the motif distribution in genomes is not random at the length scales we examined: 1 kb to entire chromosomes. The observed-to-expected (OE) ratios of motif distributions show strong correlations in pairs of chromosomes that are susceptible to translocations. With the aid of examples, we suggest that similarity in motif distributions in promoter regions of genes could imply co-regulation. A simple extension of this idea empowers us with the ability to construct gene regulatory networks. Further, we could make inferences about the spatial proximity of genomic fragments using these motif distributions. Spatially proximal regions, as deduced by Hi-C or pcHi-C, were ∼3.5 times more likely to have their motif distributions correlated than non-proximal regions. These correlations had strong contributions from the CTCF protein recognizing motifs which are known markers of topologically associated domains. In general, correlating genomic regions by motif distribution comparisons alone is rife with functional information.
Isoleucine-to-valine substitutions support cellular physiology during isoleucine deprivation
Authors: Kok Gautam , Schene Imre F , Ilcken Eveline F , Alcaraz Paula Sobrevals , Mendes Marisa I , Smith Desiree E C , Salomons Gajja , Shehata Sawsan , Jans Judith J M , Maroofian Reza , Hoek Tim A , van Es Robert M , Rehmann Holger , Nieuwenhuis Edward E S , Vos Harmjan R , Fuchs Sabine A
Published: December 2024

Aminoacyl-tRNA synthetases (ARSs) couple tRNAs with their corresponding amino acids. While ARSs can bind structurally similar amino acids, extreme specificity is ensured by subsequent editing activity. Yet, we found that upon isoleucine (I) restriction, healthy fibroblasts consistently incorporated valine (V) into proteins at isoleucine codons, resulting from misacylation of tRNAIle with valine by wildtype IARS1. Using a dual-fluorescent reporter of translation, we found that valine supplementation could fully compensate for isoleucine depletion and restore translation to normal levels in healthy, but not IARS1 deficient cells. Similarly, the antiproliferative effects of isoleucine deprivation could be fully restored by valine supplementation in healthy, but not IARS1 deficient cells. This indicates I > V substitutions help prevent translational termination and maintain cellular function in human primary cells during isoleucine deprivation. We suggest that this is an example of a more general mechanism in mammalian cells to preserve translational speed at the cost of translational fidelity in response to (local) amino acid deficiencies.
High throughput variant libraries and machine learning yield design rules for retron gene editors
Authors: Crawford Kate D , Khan Asim G , Lopez Santiago C , Goodarzi Hani , Shipman Seth L
Published: December 2024

The bacterial retron reverse transcriptase system has served as an intracellular factory for single-stranded DNA in many biotechnological applications. In these technologies, a natural retron non-coding RNA (ncRNA) is modified to encode a template for the production of custom DNA sequences by reverse transcription. The efficiency of reverse transcription is a major limiting step for retron technologies, but we lack systematic knowledge of how to improve or maintain reverse transcription efficiency while changing the retron sequence for custom DNA production. Here, we test thousands of different modifications to the Retron-Eco1 ncRNA and measure DNA production in pooled variant library experiments, identifying regions of the ncRNA that are tolerant and intolerant to modification. We apply this new information to a specific application: the use of the retron to produce a precise genome editing donor in combination with a CRISPR-Cas9 RNA-guided nuclease (an editron). We use high-throughput libraries in Saccharomyces cerevisiae to additionally define design rules for editrons. We extend our new knowledge of retron DNA production and editron design rules to human genome editing to achieve the highest efficiency Retron-Eco1 editrons to date.
New developments for the Quest for Orthologs benchmark service
Authors: Altenhoff Adrian , Nevers Yannis , Tran Vinh , Jyothi Dushyanth , Martin Maria , Cosentino Salvatore , Majidian Sina , Marcet-Houben Marina , Fuentes-Palacios Diego , Persson Emma , Walsh Thomas , Lecompte Odile , Gabaldón Toni , Kelly Steven , Hu Yanhui , Iwasaki Wataru , Capella-Gutierrez Salvador , Dessimoz Christophe , Thomas Paul D , Ebersberger Ingo , Sonnhammer Erik
Published: December 2024

The Quest for Orthologs (QfO) orthology benchmark service (https://orthology.benchmarkservice.org) hosts a wide range of standardized benchmarks for orthology inference evaluation. It is supported and maintained by the QfO consortium, and is used to gather ortholog predictions and to examine strengths and weaknesses of newly developed and existing orthology inference methods. The web server allows different inference methods to be compared in a standardized way using the same proteome data. The benchmark results are useful for developing new methods and can help researchers to guide their choice of orthology method for applications in comparative genomics and phylogenetic analysis. We here present a new release of the Orthology Benchmark Service with a new benchmark based on feature architecture similarity as well as updated reference proteomes. We further provide a meta-analysis of the public predictions from 18 different orthology assignment methods to reveal how they relate in terms of ortholog predictions and benchmark performance. These results can guide users of orthologs to the best suited method for their purpose.