bluuebunny/crossref_metadata_2025 huggingface dataset:
Sociodemographic inequities in the burden of carcinogenic industrial air emissions in the United States
Authors: Madrigal Jessica M , Flory Abigail , Fisher Jared A , Sharp Elizabeth , Graubard Barry I , Ward Mary H , Jones Rena R
Published: January 2024

Background

Industrial facilities are not located uniformly across communities in the United States, but how the burden of exposure to carcinogenic air emissions may vary across population characteristics is unclear. We evaluated differences in carcinogenic industrial pollution among major sociodemographic groups in the United States and Puerto Rico.

Methods

We evaluated cross-sectional associations of population characteristics including race and ethnicity, educational attainment, and poverty at the census tract level with point-source industrial emissions of 21 known human carcinogens using regulatory data from the US Environmental Protection Agency. Odds ratios and 95% confidence intervals comparing the highest emissions (tertile or quintile) to the referent group (zero emissions [ie, nonexposed]) for all sociodemographic characteristics were estimated using multinomial, population density–adjusted logistic regression models.

Results

In 2018, approximately 7.4 million people lived in census tracts with nearly 12 million pounds of carcinogenic air releases. The odds of tracts having the greatest burden of benzene, 1,3-butadiene, ethylene oxide, formaldehyde, trichloroethylene, and nickel emissions compared with nonexposed were 10%-20% higher for African American populations, whereas White populations were up to 18% less likely to live in tracts with the highest emissions. Among Hispanic and Latino populations, odds were 16%-21% higher for benzene, 1,3-butadiene, and ethylene oxide. Populations experiencing poverty or with less than high school education were associated with up to 51% higher burden, irrespective of race and ethnicity.

Conclusions

Carcinogenic industrial emissions disproportionately impact African American and Hispanic and Latino populations and people with limited education or experiencing poverty thus representing a source of pollution that may contribute to observed cancer disparities.
Meta-theorizing framing in communication research (1992–2022): toward academic silos or professionalized specialization?
Authors: Walter Dror , Ophir Yotam
Published: January 2024

Framing, a prominent communication theory, is often lamented as a fractured paradigm, leading some to offer radical changes to its conceptualization, operationalization, and application. Using a meta-theoretical and computational approach, we analyze three decades of framing research to examine academic silos, specializations, the canon’s formation, gender inequalities, authors’ origins, countries studied, and methods used in framing research. Instead of silos, our analysis of 5,291 papers and over 170,000 citations identified specializations formed around a core of canonic texts. While framing research has become more diverse over the years, males affiliated with U.S. institutions still predominately author canonical works. Results reject the isolated-silos hypothesis in favor of a view of framing as a bridging networked paradigm, coalescing around core assumptions, definitions, and approaches. These findings contrast with the common fractured-paradigm narrative and challenge calls for radical solutions.
Sexual counseling for female sexual interest/arousal disorders: a randomized controlled trial based on the “good enough sex” model
Authors: Farahi Zahra , HashemZadeh Mozhgan , Farnam Farnaz
Published: January 2024

Background

Female sexual interest/arousal disorder (FSIAD) is the most common female sexual disorder with adverse effects on women’s health and interpersonal relationships.

Aim

This survey evaluated the effects of sexual counseling based on the “good enough sex” (GES) model on the sexual health variables of women with FSIAD.

Methods

A randomized clinical trial with a 1:1 allocation ratio was conducted among 80 women with FSIAD in Iran in 2021. Eligible participants were randomly assigned to group A (women) and group B (couples). Women attended 4 weekly online group sexual counseling sessions based on the GES model, each lasting 120 minutes. In group B, husbands participated in sessions 2 and 3.

Outcomes

Women’s sexual health parameters—including sexual desire, sexual satisfaction, sexual function, sexual distress, sexual communication, frequency of sexual intercourse, and dysfunctional beliefs—were evaluated before and 3 months after counseling. The significance threshold considered P < .007 due to Bonferroni correction.

Results

After the intervention, all sexual parameters except sexual dysfunctional beliefs showed significant improvement (P < .001) in both groups. During the follow-up period, the average scores for all sexual variables were slightly higher in group B vs group A. The between-group difference was significant only for frequency of sexual intercourse (P < .01).

Clinical Implications

This study reaffirms the impact of the GES model as biopsychosocial therapy in managing female sexual problems. Considering men’s reluctance to accompany their wives to sex clinics, counseling for women alone can play a significant role in solving sexual problems, especially in the case of FSIAD. Online sexual consultation offers cost and time savings, provides a secure space for discussing sensitive topics, and facilitates group program coordination. It ensures universal access to counseling, thereby addressing gender incompatibility issues. It is a powerful, interactive, and acceptable alternative to in-person visits, providing convenience and confidentiality for clients seeking sexual health support.

Strengths and Limitations

The following were among the survey strengths: conducting a randomized controlled trial on women with FSIAD by applying an appropriate model and scales, involving spouses, and evaluating online group sexual counseling. However, the results of this study may not be generalizable to women without partners.

Conclusion

The GES model, emphasizing intimacy and sexual dialogue, reduces unrealistic sexual expectations and improves women’s sexual desire and overall health. Our results showed that instead of insisting on the physical presence of husbands in counseling sessions, clinicians should emphasize their emotional support and companionship during the treatment process.
Modelling the seasonal cycle of Uranus’s colour and magnitude, and comparison with Neptune
Authors: Irwin Patrick G J , Dobinson Jack , James Arjuna , Teanby Nicholas A , Simon Amy A , Fletcher Leigh N , Roman Michael T , Orton Glenn S , Wong Michael H , Toledo Daniel , Pérez-Hoyos Santiago , Beck Julie
Published: January 2024

We present a quantitative analysis of the seasonal record of Uranus’s disc-averaged colour and photometric magnitude in Strömgren b and y filters (centred at 467 and 551 nm, respectively), recorded at the Lowell Observatory from 1950 to 2016, and supplemented with HST/WFC3 observations from 2016 to 2022. We find that the seasonal variations of magnitude can be explained by the lower abundance of methane at polar latitudes combined with a time-dependent increase of the reflectivity of the aerosol particles in layer near the methane condensation level at 1 – 2 bar. This increase in reflectivity is consistent with the addition of conservatively scattering particles to this layer, for which the modelled background haze particles are strongly absorbing at both blue and red wavelengths. We suggest that this additional component may come from a higher proportion of methane ice particles. We suggest that the increase in reflectivity of Uranus in both filters between the equinoxes in 1966 and 2007, noted by previous authors, might be related to Uranus’s distance from the Sun and the production rate of dark photochemical haze products. Finally, we find that although the visible colour of Uranus is less blue than Neptune, due to the increased aerosol thickness on Uranus, and this difference is greatest at Uranus’s solstices, it is much less significant than is commonly believed due to a long-standing misperception of Neptune’s ‘true’ colour. We describe how filter-imaging observations, such as those from Voyager-2/ISS and HST/WFC3, should be processed to yield accurate true colour representations.
Synthetic gravitational lens image of the Sagittarius A* black hole with a thin disc model
Authors: Boero Ezequiel F , Moreschi Osvaldo M
Published: January 2024

The images of Sagittarius A* published by the Event Horizon Telescope (ETH) Collaboration in 2022 present features that were associated with an emission ring consistent with what is expected from an accretion disc surrounding the supermassive black hole at the centre of our Galaxy. Here, we generate images of Sgr A* across different configurations of a simple accretion disc model that became successful, in our previous work, in reproducing the main features observed in M87*. Their best image, here reproduced in Fig. 1, suggests a geometric configuration of an inclined disc with three bright regions; which we have considered as our first configuration. Since we were not convinced with the results of this first configuration, we also explore in detail the case of nearly edge-on orientations which are a priori the expected geometry for a relaxed disc, as seen from the plane of the Galaxy. We have produced simulated images using an efficient ray tracing and geodesic deviation methodology that allows to account for deformation, relativistic, and magnification effects. We compare our synthetic images with the EHT images reconstructed with data from April 6 and 7 of 2017. We found that, although the EHT Collaboration seems to discard the image from April 6, our best suggested image resembles the output from the themis pipeline for April 6; which for us gives support for the edge-on configuration.
nirdust: probing hot dust emission around type 2 AGN using K-band spectra
Authors: Gaspar Gaia , Chalela Martín , Cabral Juan , Alacoria José , Mast Damián , Díaz Rubén J
Published: January 2024

Hot dust in the proximity of active galactic nuclei (AGNs) strongly emits in the near-infrared producing a red excess that, in type 2 sources, can be modelled to measure its temperature. In the era of high spatial resolution multiwavelength data, mapping the hot dust around supermassive black holes is important for the efforts to achieve a complete picture of the dust’s role and distribution around these compact objects. In this work, we propose a methodology to detect the hot dust emission in the proximity of type 2 AGNs and measure its temperature using K-band spectra (λc = 2.2 µm). To achieve this, we have developed nirdust, a python package for modelling K-band spectra, estimating the dust temperature, and characterizing the involved uncertainties. We tested synthetic and real spectra in order to check the performance and suitability of the physical model over different types of data. Our tests on synthetic spectra demonstrated that the obtained results are influenced by the signal-to-noise ratio (S/N) of the input spectra. However, we accurately characterized the uncertainties, which remained below ∼150 K for an average S/N per pixel exceeding 20. Applying nirdust to NGC 5128 (Centaurus A), observed with the Gemini South Telescope, we estimated a dust temperature of 662 and 667 K from Flamingos-2 spectra and 697 and 607  K from Gemini Near-Infrared Spectrograph (GNIRS) spectra using two different approaches.
Individual and averaged power density spectra of X-ray bursts from SGR J1935+2154: quasi-periodic oscillation search and slopes
Authors: Xiao Shuo , Li Xiao-Bo , Xue Wang-Chen , Xiong Shao-Lin , Zhang Shuang-Nan , Peng Wen-Xi , Dong Ai-Jun , Tuo You-Li , Cai Ce , Luo Xi-Hong , Yang Jiao-Jiao , Wang Yue , Zheng Chao , Zhang Yan-Qiu , Liu Jia-Cong , Tan Wen-Jun , Wang Chen-Wei , Wang Ping , Li Cheng-Kui , Yi Shu-Xu , Dang Shi-Jun , Shang Lun-Hua , Zhao Ru-shuang , Ma Qing-Bo , Xie Wei , Feng Jian-Chao , Zhang Bin , Zhang Zhen , Ge Ming-Yu , Zheng Shi-Jie , Song Li-Ming , Zhi Qi-Jun
Published: January 2024

The study of quasi-periodic oscillations (QPOs) and power density spectra (PDSs) continuum properties can help shed light on the still elusive emission physics of magnetars and as a window into the interiors of neutron stars using asteroseismology. In this work, we employ a PDS method to search for the QPOs in the hundreds of X-ray bursts from SGR J1935+2154 observed by Insight-HXMT, GECAM, and Fermi/GBM from 2014 July to 2022 January. Although no definitive QPO signal (significance >3 σ) is detected in individual bursts or the averaged periodogram of the bursts grouped by duration, we identify several bursts exhibiting features at ∼40 Hz, attributed to the the proximity intervals between adjacent pulses and consistent with that reported in the X-ray burst associated with FRB 200428. We investigate the PDS continuum properties and find that the distribution of the PDS slope in the simple power-law model peaks at ∼2.5, which is consistent with other magnetars but higher than 5/3 commonly seen in gamma-ray bursts. Besides, the distribution of the break frequency in the broken power-law model peaks at ∼60 Hz. Finally, we report that the power-law index of PDS has an anti-correlation and power-law dependence on the burst duration as well as the minimum variation time-scale.
The dual role of outflows in quenching satellites of low-mass hosts: NGC 3109
Authors: Garling Christopher T , Peter Annika H G , Spekkens Kristine , Sand David J , Hargis Jonathan , Crnojević Denija , Carlin Jeffrey L
Published: January 2024

While dwarf galaxies observed in the field are overwhelmingly star forming, dwarf galaxies in environments as dense or denser than the Milky Way are overwhelmingly quenched. In this paper, we explore quenching in the lower density environment of the Small-Magellanic-Cloud-mass galaxy NGC 3109 (M$_* \sim 10^8 \, \text{M}_\odot$), which hosts two known dwarf satellite galaxies (Antlia and Antlia B), both of which are ${\rm H}\, \rm{\small I}$ deficient compared to similar galaxies in the field and have recently stopped forming stars. Using a new semi-analytic model in concert with the measured star formation histories and gas masses of the two dwarf satellite galaxies, we show that they could not have been quenched solely by direct ram pressure stripping of their interstellar media, as is common in denser environments. Instead, we find that separation of the satellites from pristine gas inflows, coupled with stellar-feedback-driven outflows from the satellites (jointly referred to as the starvation quenching model), can quench the satellites on time-scales consistent with their likely infall times into NGC 3109’s halo. It is currently believed that starvation is caused by ‘weak’ ram pressure that prevents low-density, weakly bound gas from being accreted on to the dwarf satellite, but cannot directly remove the denser interstellar medium. This suggests that star-formation-driven outflows serve two purposes in quenching satellites in low-mass environments: outflows from the host form a low-density circumgalactic medium that cannot directly strip the interstellar media from its satellites, but is sufficient to remove loosely bound gaseous outflows from the dwarf satellites driven by their own star formation.
Liquid-phase epitaxy of neutron star crusts and white dwarf cores
Authors: Baiko D A
Published: January 2024

Near-equilibrium bottom-up crystallization of fully ionized neutron star crusts or white dwarf cores is considered. We argue that this process is similar to liquid-phase epitaxial (i.e. preserving order of previous layers) crystal growth or crystal pulling from melt in Earth laboratories whereby lateral positions of newly crystallizing ions are anchored by already solidified layers. Their vertical positions are set by charge neutrality. Consequently, interplane spacing of a growing crystal either gradually increases, tracing ne decrease, as the crystallization front moves away from the stellar centre, or decreases, tracing decrease of 〈Z〉, when the crystallization front crosses a boundary between layers of different compositions. This results in the formation of stretched Coulomb crystals, in contrast to the standard assumption of cubic crystal formation, which is based on energetics arguments but does not take into account growth kinetics. Overstretched crystals break, which limits the vertical sizes of growing crystallites. We study breaking shear strain and effective shear modulus of stretched matter and discuss possibility of macrocrystallite formation. The latter has interesting astrophysical implications, for instance, appearance of weak crustal layers, whose strength may increase by a few orders of magnitude upon breaking and refreezing at a late-time event. We also analyse interaction of adjacent Coulomb crystals, having different ion compositions, and estimate the strength of such interfaces.
Discovery of radio eclipses from 4FGL J1646.5−4406: a new candidate redback pulsar binary
Authors: Zic Andrew , Wang Ziteng , Lenc Emil , Kaplan David L , Murphy Tara , Ridolfi A , Sengar Rahul , Hurley-Walker Natasha , Dobie Dougal , Leung James K , Pritchard Joshua , Wang Yuanming
Published: January 2024

Large widefield surveys make possible the serendipitous discovery of rare subclasses of pulsars. One such class are ‘spider’-type pulsar binaries, comprised of a pulsar in a compact orbit with a low-mass (sub)stellar companion. In a search for circularly polarized radio sources in Australian Square Kilometre Array Pathfinder (ASKAP) Pilot Survey observations, we discovered highly variable and circularly polarized emission from a radio source within the error region of the γ-ray source 4FGL J1646.5−4406. The variability is consistent with the eclipse of a compact, steep-spectrum source behind ablated material from a companion in an ∼5.3 h binary orbit. Based on the eclipse properties and spatial coincidence with 4FGL J1646.5−4406, we argue that the source is likely a recycled pulsar in a ‘redback’ binary system. Using properties of the eclipses from ASKAP and Murchison Widefield Array observations, we provide broad constraints on the properties of the eclipse medium. We identified a potential optical/infrared counterpart in archival data consistent with a variable low-mass star. Using the Parkes radio telescope ‘Murriyang’ and the Meer Karoo Array Telescope (MeerKAT) , we searched extensively for radio pulsations but yielded no viable detections of pulsed emission. We suggest that the non-detection of pulses is due to scattering in the intra-binary material, but scattering from the interstellar medium can also plausibly explain the pulse non-detections if the interstellar dispersion measure exceeds ∼600 pc cm−3. Orbital constraints derived from optical observations of the counterpart would be highly valuable for future γ-ray pulsation searches, which may confirm the source nature as a pulsar.
The dark matter profile of the Milky Way inferred from its circular velocity curve
Authors: Ou Xiaowei , Eilers Anna-Christina , Necib Lina , Frebel Anna
Published: January 2024

In this paper, we construct the circular velocity curve of the Milky Way out to ∼30 kpc, providing an updated model of the dark matter density profile. We derive precise parallaxes for 120 309 stars with a data-driven model, using APOGEE DR17 spectra combined with GaiaDR3, 2MASS, and WISE photometry. At outer galactic radii up to 30 kpc, we find a significantly faster decline in the circular velocity curve compared to the inner parts. This decline is better fit with a cored Einasto profile with a slope parameter $0.91^{+0.04}_{-0.05}$ than a generalized Navarro–Frenk–White (NFW) profile. The virial mass of the best-fitting dark matter halo profile is only $1.81^{+0.06}_{-0.05}\times 10^{11}$ M⊙, significantly lower than what a generalized NFW profile delivers. We present a study of the potential systematics, affecting mainly large radii. Such a low mass for the Galaxy is driven by the functional forms tested, given that it probes beyond our measurements. It is found to be in tension with mass measurements from globular clusters, dwarf satellites, and streams. Our best-fitting profile also lowers the expected dark matter annihilation signal flux from the galactic centre by more than an order of magnitude, compared to an NFW profile-fit. In future work, we will explore profiles with more flexible functional forms to more fully leverage the circular velocity curve and observationally constrain the properties of the Milky Way’s dark matter halo.
An insight into chromatic behaviour of jitter in pulsars and its modelling: a case study of PSR J0437−4715
Authors: Kulkarni A D , Shannon R M , Reardon D J , Miles M T , Bailes M , Shamohammadi M
Published: January 2024

Pulse-to-pulse profile shape variations introduce correlations in pulsar times of arrival across radio frequency measured at the same observational epoch. This leads to a broad-band noise in excess of radiometer noise, which is termed as pulse jitter noise. The presence of jitter noise limits the achievable timing precision and decreases the sensitivity of pulsar timing data sets to signals of interest such as nanohertz-frequency gravitational waves. Current white noise models used in pulsar timing analyses attempt to account for this, assuming complete correlation of uncertainties through the arrival times collected in a unique observation and no frequency dependence of jitter (which corresponds to a rank-one covariance matrix). However, previous studies show that the brightest millisecond pulsar at decimetre wavelengths, PSR J0437−4715, shows decorrelation and frequency dependence of jitter noise. Here, we present a detailed study of the decorrelation of jitter noise in PSR J0437−4715 and implement a new technique to model it. We show that the rate of decorrelation due to jitter can be expressed as a power law in frequency. We analyse the covariance matrix associated with the jitter noise process and find that a higher rank approximation is essential to account for the decorrelation and to account for frequency dependence of jitter noise. We show that the use of this novel method significantly improves the estimation of other chromatic noise parameters such as dispersion measure variations. However, we find no significant improvement in errors and estimation of other timing model parameters suggesting that current methods are not biased for other parameters, for this pulsar due to this misspecification. We show that pulse energy variations show a similar decorrelation to the jitter noise, indicating a common origin for both observables.
The dust attenuation scaling relation of star-forming galaxies in the eagle simulations
Authors: Qiao Man , Zheng Xian Zhong , Katsianis Antonios , Qin Jianbo , Pan Zhizheng , Liu Wenhao , Tan Qing-Hua , An Fang Xia , Shi Dong Dong , Lyu Zongfei , Zhang Yuheng , Wen Run , Liu Shuang , Yang Chao
Published: January 2024

Dust attenuation in star-forming galaxies (SFGs), as parametrized by the infrared excess (IRX ≡ LIR/LUV), is found to be tightly correlated with star formation rate, metallicity, and galaxy size, following a universal IRX relation up to z = 3. This scaling relation can provide a fundamental constraint for theoretical models to reconcile galaxy star formation, chemical enrichment, and structural evolution across cosmic time. We attempt to reproduce the universal IRX relation over 0.1 ≤ z ≤ 2.5 using the Evolution and Assembly of GaLaxies and their Environments (EAGLE) hydrodynamical simulations and examine sensitive parameters in determining galaxy dust attenuation. Our findings show that while the predicted universal IRX relation from EAGLE approximately aligns with observations at z ≤ 0.5, noticeable disparities arise at different stellar masses and higher redshifts. Specifically, we investigate how modifying various galaxy parameters can affect the predicted universal IRX relation in comparison to the observed data. We demonstrate that the simulated gas-phase metallicity is the critical quantity for the shape of the predicted universal IRX relation. We find that the influence of the infrared luminosity and infrared excess is less important while galaxy size has virtually no significant effect. Overall, the EAGLE simulations are not able to replicate some of the observed characteristics between IRX and galaxy parameters of SFGs, emphasizing the need for further investigation and testing for our current state-of-the-art theoretical models.
Edge-on galaxies in the HST COSMOS field: the evolution of stellar discs up to z ∼ 0.5
Authors: Usachev Pavel A , Reshetnikov Vladimir P , Savchenko Sergey S
Published: January 2024

We present a sample of 950 edge-on spiral galaxies found with the use of an artificial neural network in the Hubble Space Telescope COSMOS field. This is currently the largest sample of distant edge-on galaxies. For all galaxies we analysed the 2D brightness distributions in the F814W filter and measured the radial and vertical exponential scales (h and hz correspondingly) of the brightness distribution. By comparing the characteristics of distant galaxies with those of nearby objects, we conclude that thin stellar discs with h/hz ≥ 10 at z ≈ 0.5 should be rarer than today. Both exponential scales of the stellar disc show evidence of luminosity-dependent evolution: in faint galaxies the h and hz values do not change with z, in bright (and massive) spiral galaxies both scales, on average, grow towards our epoch.
Addition of rapamycin or co-culture with cumulus cells from younger reproductive age women does not improve rescue in vitro oocyte maturation or euploidy rates in older reproductive age women
Authors: Esbert Marga , Tao Xin , Ballesteros Agustín , Yildirim Raziye Melike , Scott Richard T , Seli Emre
Published: January 2024

Both spontaneously conceived pregnancies and those achieved using assisted reproduction decline with advancing maternal age. In this study, we tested if rapamycin and/or cumulus cells (CCs) from young donors could improve oocyte maturation and euploidy rates of germinal vesicle (GV) stage oocytes obtained from older women of reproductive age. A total of 498 GVs from 201 women >38 years (40.6 ± 1.8, mean ± SD) were included. GVs were randomly assigned into five groups for rescue IVM: control (with no CCs and no rapamycin); with autologous CCs; with autologous CCs and rapamycin; with CCs from young women (<35 years); and with CCs from young women and rapamycin. After 24 h of culture, the first polar body (PB) was biopsied in metaphase II oocytes, and the cytogenetic constitution was assessed using next-generation sequencing for both oocytes and PBs. Comparable maturation rates were found (56.2%, 60.0%, 46.5%, 51.7%, and 48.5% for groups 1–5, respectively; P = 0.30). Similarly, comparable euploidy rates were observed in the five groups (41.5%, 37.8%, 47.2%, 43.6%, and 47.8% for Groups 1–5, respectively; P = 0.87). Our findings indicate that rescue IVM is effective for obtaining mature euploid oocytes in older women of reproductive age, and that incubation with rapamycin or CCs obtained from young donors does not improve the maturation or euploidy rate.
The pAblo·pCasso self-curing vector toolset for unconstrained cytidine and adenine base-editing in Gram-negative bacteria
Authors: Kozaeva Ekaterina , Nielsen Zacharias S , Nieto-Domínguez Manuel , Nikel Pablo I
Published: January 2024

A synthetic biology toolkit, exploiting clustered regularly interspaced short palindromic repeats (CRISPR) and modified CRISPR-associated protein (Cas) base-editors, was developed for genome engineering in Gram-negative bacteria. Both a cytidine base-editor (CBE) and an adenine base-editor (ABE) have been optimized for precise single-nucleotide modification of plasmid and genome targets. CBE comprises a cytidine deaminase conjugated to a Cas9 nickase from Streptococcus pyogenes (SpnCas9), resulting in C→T (or G→A) substitutions. Conversely, ABE consists of an adenine deaminase fused to SpnCas9 for A→G (or T→C) editing. Several nucleotide substitutions were achieved using these plasmid-borne base-editing systems and a novel protospacer adjacent motif (PAM)-relaxed SpnCas9 (SpRY) variant. Base-editing was validated in Pseudomonas putida and other Gram-negative bacteria by inserting premature STOP codons into target genes, thereby inactivating both fluorescent proteins and metabolic (antibiotic-resistance) functions. The functional knockouts obtained by engineering STOP codons via CBE were reverted to the wild-type genotype using ABE. Additionally, a series of induction-responsive vectors was developed to facilitate the curing of the base-editing platform in a single cultivation step, simplifying complex strain engineering programs without relying on homologous recombination and yielding plasmid-free, modified bacterial cells.
METTL3 drives telomere targeting of TERRA lncRNA through m6A-dependent R-loop formation: a therapeutic target for ALT-positive neuroblastoma
Authors: Vaid Roshan , Thombare Ketan , Mendez Akram , Burgos-Panadero Rebeca , Djos Anna , Jachimowicz Daniel , Lundberg Kristina Ihrmark , Bartenhagen Christoph , Kumar Navinder , Tümmler Conny , Sihlbom Carina , Fransson Susanne , Johnsen John Inge , Kogner Per , Martinsson Tommy , Fischer Matthias , Mondal Tanmoy
Published: January 2024

Telomerase-negative tumors maintain telomere length by alternative lengthening of telomeres (ALT), but the underlying mechanism behind ALT remains poorly understood. A proportion of aggressive neuroblastoma (NB), particularly relapsed tumors, are positive for ALT (ALT+), suggesting that a better dissection of the ALT mechanism could lead to novel therapeutic opportunities. TERRA, a long non-coding RNA (lncRNA) derived from telomere ends, localizes to telomeres in a R-loop-dependent manner and plays a crucial role in telomere maintenance. Here we present evidence that RNA modification at the N6 position of internal adenosine (m6A) in TERRA by the methyltransferase METTL3 is essential for telomere maintenance in ALT+ cells, and the loss of TERRA m6A/METTL3 results in telomere damage. We observed that m6A modification is abundant in R-loop enriched TERRA, and the m6A-mediated recruitment of hnRNPA2B1 to TERRA is critical for R-loop formation. Our findings suggest that m6A drives telomere targeting of TERRA via R-loops, and this m6A-mediated R-loop formation could be a widespread mechanism employed by other chromatin-interacting lncRNAs. Furthermore, treatment of ALT+ NB cells with a METTL3 inhibitor resulted in compromised telomere targeting of TERRA and accumulation of DNA damage at telomeres, indicating that METTL3 inhibition may represent a therapeutic approach for ALT+ NB.
The roles of DNA methylation on pH dependent i-motif (iM) formation in rice
Authors: Feng Yilong , Ma Xing , Yang Ying , Tao Shentong , Ahmed Asgar , Gong Zhiyun , Cheng Xuejiao , Zhang Wenli
Published: January 2024

I-motifs (iMs) are four-stranded non-B DNA structures containing C-rich DNA sequences. The formation of iMs is sensitive to pH conditions and DNA methylation, although the extent of which is still unknown in both humans and plants. To investigate this, we here conducted iMab antibody-based immunoprecipitation and sequencing (iM-IP-seq) along with bisulfite sequencing using CK (original genomic DNA without methylation-related treatments) and hypermethylated or demethylated DNA at both pH 5.5 and 7.0 in rice, establishing a link between pH, DNA methylation and iM formation on a genome-wide scale. We found that iMs folded at pH 7.0 displayed higher methylation levels than those formed at pH 5.5. DNA demethylation and hypermethylation differently influenced iM formation at pH 7.0 and 5.5. Importantly, CG hypo-DMRs (differentially methylated regions) and CHH (H = A, C and T) hyper-DMRs alone or coordinated with CG/CHG hyper-DMRs may play determinant roles in the regulation of pH dependent iM formation. Thus, our study shows that the nature of DNA sequences alone or combined with their methylation status plays critical roles in determining pH-dependent formation of iMs. It therefore deepens the understanding of the pH and methylation dependent modulation of iM formation, which has important biological implications and practical applications.
Mutational profile of the regenerative process and de novo genome assembly of the planarian Schmidtea polychroa
Authors: Póti Ádám , Szüts Dávid , Vermezovic Jelena
Published: January 2024

Planarians are organisms with a unique capacity to regenerate any part of their body. New tissues are generated in a process that requires many swift cell divisions. How costly is this process to an animal in terms of mutational load remains unknown. Using whole genome sequencing, we defined the mutational profile of the process of regeneration in the planarian species Schmidtea polychroa. We assembled de novo the genome of S. polychroa and analyzed mutations in animals that have undergone regeneration. We observed a threefold increase in the number of mutations and an altered mutational spectrum. High allele frequencies of subclonal mutations in regenerated animals suggested that most of the cells in the regenerated animal were descendants of a small number of stem cells with high expansion potential. We provide, for the first time, the draft genome assembly of S. polychroa, an estimation of the germline mutation rate for a planarian species and the mutational spectrum of the regeneration process of a living organism.
Data-driven mathematical and visualization approaches for removing rare features for Compositional Data Analysis (CoDA)
Authors: Ortiz-Velez Adrian , Kelley Scott T
Published: January 2024

Sparse feature tables, in which many features are present in very few samples, are common in big biological data (e.g. metagenomics). Ignoring issues of zero-laden datasets can result in biased statistical estimates and decreased power in downstream analyses. Zeros are also a particular issue for compositional data analysis using log-ratios since the log of zero is undefined. Researchers typically deal with this issue by removing low frequency features, but the thresholds for removal differ markedly between studies with little or no justification. Here, we present CurvCut, an unsupervised data-driven approach with human confirmation for rare-feature removal. CurvCut implements two distinct approaches for determining natural breaks in the feature distributions: a method based on curvature analysis borrowed from thermodynamics and the Fisher-Jenks statistical method. Our results show that CurvCut rapidly identifies data-specific breaks in these distributions that can be used as cutoff points for low-frequency feature removal that maximizes feature retention. We show that CurvCut works across different biological data types and rapidly generates clear visual results that allow researchers to confirm and apply feature removal cutoffs to individual datasets.
Investigation of the usefulness of liver-specific deconvolution method by establishing a liver benchmark dataset
Authors: Azuma Iori , Mizuno Tadahaya , Morita Katsuhisa , Suzuki Yutaka , Kusuhara Hiroyuki
Published: January 2024

Immune responses in the liver are related to the development and progression of liver failure, and precise prediction of their behavior is important. Deconvolution is a methodology for estimating the immune cell proportions from the transcriptome, and it is mainly applied to blood-derived samples and tumor tissues. However, the influence of tissue-specific modeling on the estimation results has rarely been investigated. Here, we constructed a system to evaluate the performance of the deconvolution method on liver transcriptome data. We prepared seven mouse liver injury models using small-molecule compounds and established a benchmark dataset with corresponding liver bulk RNA-Seq and immune cell proportions. RNA-Seq expression for nine leukocyte subsets and four liver-associated cell types were obtained from the Gene Expression Omnibus to provide a reference. We found that the combination of reference cell sets affects the estimation results of reference-based deconvolution methods and established a liver-specific deconvolution by optimizing the reference cell set for each cell to be estimated. We applied this model to independent datasets and showed that liver-specific modeling is highly extrapolatable. We expect that this approach will enable sophisticated estimation from rich tissue data accumulated in public databases and to obtain information on aggregated immune cell trafficking.
Association between urinary C4d levels and disease progression in IgA nephropathy
Authors: Dong Yaping , Wang Zi , Guo Weiyi , Zhu Li , Zhou Xujie , Shi Sufang , Liu Lijun , Lv Jicheng , Zhang Hong
Published: January 2024

Background

C4d mesangial deposition, a hallmark of lectin pathway activation in immunoglobulin A nephropathy (IgAN), has been shown to be associated with risk of kidney failure. To date, the relationship between urinary C4d and renal outcome remain unelucidated.

Methods

A total of 508 patients with biopsy-proven IgAN were enrolled in this study, whose baseline urine samples at the time of biopsy were collected and the levels of urinary C4d were quantified by enzyme-linked immunosorbent assay. The time-averaged C4d (TA-C4d) and the change in proteinuria were measured in sequential urine samples obtained from IgAN patients. The kidney progression event was defined as a 50% estimated glomerular filtration rate (eGFR) decline or end-stage kidney disease or death.

Results

After a median follow-up of 36 months, 70 (13.8%) of the participants reached the kidney progression event. Higher levels of urinary C4d/Ucr were found to be associated with decreased eGFR, massive proteinuria, lower serum albumin levels, hypertension, and severe Oxford E and T scores. Upon adjusting for traditional risk factors (including demographics, eGFR, proteinuria, hypertension, Oxford pathologic score and immunosuppressive therapy), elevated levels of urinary C4d/Ucr were independently associated with an increased risk of chronic kidney disease progression [adjusted hazard ratio (HR) per standard deviation increment of log-transformed C4d/Ucr: 1.46; 95% CI 1.04–2.06; P = .030]. In reference to the low C4d group, the risk of poor renal outcome increased for the high C4d group (adjusted HR 1.93; 95% CI 1.05–3.54; P = .033). Additionally, a low baseline C4d level was independently associated with a favorable proteinuria response to immunosuppressive therapy at 3 months (adjusted relative risk 2.20; 95% CI 1.04–4.63, P = .038).

Conclusion

The urinary C4d, serving as a non-invasive biomarker, is associated with the progression of IgAN and holds the potential to predict proteinuria response in this disease.
Ternary superhydrides for high-temperature superconductivity at low pressures
Authors: Shan Pengfei , Ma Liang , Cheng Jinguang
Published: January 2024

Focusing on the ternary hydrides, the new hope of Room-Temperature Superconductivity, this perspective delves into the research background, highlights current challenges, and illuminates promising avenues for future studies.
Thermospermine Is an Evolutionarily Ancestral Phytohormone Required for Organ Development and Stress Responses in Marchantia Polymorpha
Authors: Furumoto Takuya , Yamaoka Shohei , Kohchi Takayuki , Motose Hiroyasu , Takahashi Taku
Published: January 2024

Thermospermine suppresses auxin-inducible xylem differentiation, whereas its structural isomer, spermine, is involved in stress responses in angiosperms. The thermospermine synthase, ACAULIS5 (ACL5), is conserved from algae to land plants, but its physiological functions remain elusive in non-vascular plants. Here, we focused on MpACL5, a gene in the liverwort Marchantia polymorpha, that rescued the dwarf phenotype of the acl5 mutant in Arabidopsis. In the Mpacl5 mutants generated by genome editing, severe growth retardation was observed in the vegetative organ, thallus, and the sexual reproductive organ, gametangiophore. The mutant gametangiophores exhibited remarkable morphological defects such as short stalks, fasciation and indeterminate growth. Two gametangiophores fused together, and new gametangiophores were often initiated from the old ones. Furthermore, Mpacl5 showed altered responses to heat and salt stresses. Given the absence of spermine in bryophytes, these results suggest that thermospermine has a dual primordial function in organ development and stress responses in M. polymorpha. The stress response function may have eventually been assigned to spermine during land plant evolution.
Seasonal variation in the population structure and production of the copepod Calanus sinicus in the Yellow Sea
Authors: Kim Garam , Park Wongyu , Lee Yeonjung , Kang Hyung-Ku
Published: January 2024

We estimated the total production of Calanus sinicus over four seasons by measuring somatic and egg production rates in the Yellow Sea. In the process of measuring somatic production, the length–weight relationship and growth rates of C. sinicus in this region were also derived. The population abundance and biomass of C. sinicus were especially high in spring. All copepodite stages had similar proportions in spring, whereas the late stages and adults were most common in summer. The mean total production of the C. sinicus population was 107.6–259.7 μg C m−3 day−1, ranging from higher values in spring to lower values in summer. The annual total production of C. sinicus in the Yellow Sea was 64.3 mg C m−3 year−1 (4032 mg C m−2 year−1). The production of C. sinicus was positively correlated with chlorophyll a concentration, rather than water temperature or salinity. This study is the first to quantify the secondary production of C. sinicus in the Yellow Sea. These findings will broaden our understanding of the ecology of C. sinicus and its contribution to the Yellow Sea food web.
GLK transcription factors accompany ELONGATED HYPOCOTYL5 to orchestrate light-induced seedling development in Arabidopsis
Authors: Zhang Ting , Zhang Rui , Zeng Xi-Yu , Lee Sanghwa , Ye Lu-Huan , Tian Shi-Long , Zhang Yi-Jing , Busch Wolfgang , Zhou Wen-Bin , Zhu Xin-Guang , Wang Peng
Published: January 2024

Light-induced de-etiolation is an important aspect of seedling photomorphogenesis. GOLDEN2 LIKE (GLK) transcriptional regulators are involved in chloroplast development, but to what extent they participate in photomorphogenesis is not clear. Here, we show that ELONGATED HYPOCOTYL5 (HY5) binds to GLK promoters to activate their expression, and also interacts with GLK proteins in Arabidopsis (Arabidopsis thaliana). The chlorophyll content in the de-etiolating Arabidopsis seedlings of the hy5 glk2 double mutants was lower than that in the hy5 single mutant. GLKs inhibited hypocotyl elongation, and the phenotype could superimpose on the hy5 phenotype. Correspondingly, GLK2 regulated the expression of photosynthesis and cell elongation genes partially independent of HY5. Before exposure to light, DE-ETIOLATED 1 (DET1) affected accumulation of GLK proteins. The enhanced etioplast development and photosystem gene expression observed in the det1 mutant were attenuated in the det1 glk2 double mutant. Our study reveals that GLKs act downstream of HY5, or additive to HY5, and are likely quantitatively adjusted by DET1, to orchestrate multiple developmental traits during the light-induced skotomorphogenesis-to-photomorphogenesis transition in Arabidopsis.
Differences in Pain Experience Among Different Racial and Ethnic Groups
Authors: Lane Elizabeth , Barnes Chris , Fritz Julie M
Published: January 2024

Objective

The objective of this study was to examine the role of pain catastrophizing and pain self-efficacy as possible mediators of race-based differences in pain intensity and to evaluate the possible moderating role of race on the relationship between pain catastrophizing and pain self-efficacy with pain outcomes among persons with chronic spinal pain receiving physical therapy.

Methods

This study was a secondary analysis of a cluster-randomized trial. Participants were persons with chronic spinal pain in outpatient physical therapy clinics who consented to complete assessments at baseline and after 2 weeks and 12 weeks. Assessments included pain intensity, physical function, pain catastrophizing, and self-efficacy. Baseline comparisons between Black and non-Hispanic White participants were made. Mediation analyses used a regression-based framework to examine whether baseline pain catastrophizing and self-efficacy mediated the association between race and pain intensity. Moderation analyses used multiple linear regression to evaluate the role of race in the relationship of baseline pain catastrophizing and self-efficacy with 12-week pain intensity outcomes.

Results

A total of 274 participants were included (51 [18.6%] Black and 223 [81.4%] non-Hispanic White; mean age = 51.6 years [standard deviation = 14.9]; 180 [65.7%] female). At baseline, Black participants had higher pain intensity scores (mean difference = 0.80; 95% CI =1.5 to 0.12). Both pain catastrophizing and self-efficacy mediated the relationship between race and baseline pain intensity. Race moderated the relationships between baseline pain catastrophizing and self-efficacy and 12-week pain intensity scores.

Conclusion

Pain catastrophizing and self-efficacy had differential impacts on pain intensity based on race for both cross-sectional and longitudinal analyses among persons receiving physical therapy for chronic spinal pain.

Impact

Improved understanding of the differences in pain experience based on factors such as race, ethnicity, cultural background, and experience with the health care system may help reduce disparities in pain management.
Risk of non-thyroidal autoimmune diseases in patients with Graves’ disease: a nationwide retrospective cohort study
Authors: Sohn Seo Young , Ahn Jiyeon , Lee Min Kyung , Lee Jae Hyuk , Kwon Ji-Won , Kweon Ji-Min , Lee Ju-Yeun
Published: January 2024

Objective

Graves’ disease (GD) is a major autoimmune thyroid disorder and is associated with non-thyroidal autoimmune disease (NTAD). We aimed to investigate the risk of NTAD in patients with GD compared with age- and sex-matched controls and to evaluate whether the risk differs between individuals with or without Graves’ ophthalmopathy (GO).

Methods

This was a retrospective cohort study using data from the Korean National Health Claims database. We included 77 401 patients with GD (2310 with GO) and 77 401 age- and sex-matched controls. Risk of NTAD were compared between the entire cohort and within the GD cohort.

Results

During a mean follow-up period of 9 years, NTAD developed in 12 341 (16.1%) patients in the GD cohort. Risk for SLE [adjusted hazard ratio (aHR) 1.15, 95% CI 1.02–1.29], vitiligo (aHR 1.24, 95% CI 1.10–1.40) and alopecia areata (aHR 1.11, 95% CI 1.04–1.20) were higher in the GD cohort than in the control cohort. In the GD cohort, risk for SLE (aHR 1.60, 95% CI 1.11–2.33), SS (aHR 1.89, 95% CI 1.30–2.74) and AS (aHR 1.53, 95% CI 1.08–2.17) were higher in the GO group than in the non-GO group.

Conclusion

This study demonstrated an increased risk of SLE, vitiligo and alopecia areata in patients with GD. In the GD cohort, patients with GO had an increased risk of SLE, SS and AS. These findings suggest the importance of implementing a strategy for early detection of NTAD based on the presence of GO.