bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT
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

ABSTRACT
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

ABSTRACT
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

ABSTRACT
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

Abstract
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 &gt;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 (&lt;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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

ABSTRACT

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.
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

Abstract
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

Abstract
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.