bluuebunny/crossref_metadata_2025_split huggingface dataset:
Broad-band study of gamma-ray blazars at redshifts z = 2.0–2.5
Authors: Sahakyan N , Harutyunyan G , Gasparyan S , Israyelyan D 
Published: February 2024

ABSTRACT
High redshift blazars are among the most powerful non-explosive sources in the Universe and play a crucial role in understanding the evolution of relativistic jets. To understand these bright objects, we performed a detailed investigation of the multiwavelength properties of 79 γ-ray blazars with redshifts ranging from z = 2.0 to 2.5, using data from Fermi LAT, Swift XRT/UVOT, and NuSTAR observations. In the γ-ray band, the spectral analysis revealed a wide range of flux and photon indices, from 5.32 × 10−10 to 3.40 × 10−7 photon cm−2 s−1 and from 1.66 to 3.15, respectively, highlighting the diverse nature of these sources. The detailed temporal analysis showed that flaring activities were observed in 31 sources. Sources such as 4C+71.07, PKS 1329-049, and 4C + 01.02, demonstrated significant increase in the γ-ray luminosity and flux variations, reaching peak luminosity exceeding 1050 erg s−1. The temporal analysis extended to X-ray and optical/ultraviolet (UV) bands, showed clear flux changes in some sources in different observations. The time-averaged properties of high redshift blazars were derived through modeling the spectral energy distributions with a one-zone leptonic scenario, assuming the emission region is within the broad-line region (BLR) and the X-ray and γ-ray emissions are due to inverse Compton scattering of synchrotron and BLR-reflected photons. This modeling allowed us to constrain the emitting particle distribution, estimate the magnetic field inside the jet, and evaluate the jet luminosity, which is discussed in comparison with the disc luminosity derived from fitting the excess in the UV band.
AstroSat and NICER timing view of the Z−type neutron star X-ray binary GX 340 + 0
Authors: Pahari Mayukh , Suman Shree , Bhargava Yash , Weston Alexander , Zhang Liang , Bhattacharyya Sudip , Misra Ranjeev , McHardy Ian 
Published: February 2024

ABSTRACT
The timing properties of the Z-type low-mass X-ray binaries provide insights into the emission components involved in producing the unique Z-shaped track in the hardness–intensity diagrams of these sources. In this work, we investigate the AstroSat and NICER observations of the GX 340 + 0 covering the complete ‘Z’-track from the horizontal branch (HB) to the extended flaring branch (EFB). For the first time, we present the Z-track as seen in soft X-rays using the AstroSat/Soft X-ray Telescope and NICER (the soft colour is defined as a ratio of 3–6 to 0.5–3 keV). The shape of the track is distinctly different in soft X-rays, strongly suggesting the presence of additional components active in soft X-rays. The detailed timing analysis revealed significant quasi-periodic oscillation throughout the HB and the normal branch (NB) using large area X-ray proportional counter and the first NICER detection of 33.1 ± 1.1 Hz HB oscillation (HBO) in 3–6 keV. The oscillations at the HB/NB vertex are observed to have higher frequencies (41–52 Hz) than the HBOs (16–31 Hz) and NB oscillations (6.2–8 Hz) but significantly lower rms (∼1.6 per cent). The HBO is also limited to the energy range 3–20 keV, indicating an association of HBO origin with the non-thermal component. It is also supported by earlier studies that found the strongest X-ray polarization during HB.
The MASSIVE survey – XIX. Molecular gas measurements of the supermassive black hole masses in the elliptical galaxies NGC 1684 and NGC 0997
Authors: Dominiak Pandora , Bureau Martin , Davis Timothy A , Ma Chung-Pei , Greene Jenny E , Gu Meng 
Published: February 2024

ABSTRACT
Supermassive black hole (SMBH) masses can be measured by observing their dynamical effects on tracers, such as molecular gas. We present high angular resolution Atacama Large Millimeter/submillimeter Array observations of the 12CO(2–1) line emission of the early-type galaxies (ETGs) NGC 1684 and NGC 0997, obtained as part of the MASSIVE survey, a volume-limited integral-field spectroscopic study of the most massive local ETGs. NGC 1684 has a regularly rotating central molecular gas disc, with a spatial extent of ≈6 arcsec (≈1.8 kpc) in radius and a central hole slightly larger than the expected SMBH sphere of influence. We forward model the data cube in a Bayesian framework with the Kinematic Molecular Simulation (KinMS) code and infer a SMBH mass of $1.40^{+0.44}_{-0.39}\times 10^9$ M⊙ (3σ confidence interval) and an F110W-filter stellar mass-to-light ratio of (2.50 ± 0.05) M⊙/L⊙, F110W. NGC 0997 has a regularly rotating central molecular gas disc, with a spatial extent of ≈5 arcsec (≈2.2 kpc) in radius and a partially filled central hole much larger than the expected SMBH sphere of influence, thus preventing a robust SMBH mass determination. With the same modelling method, we nevertheless constrain the SMBH mass to be in the range 4.0 × 107–1.8 × 109 M⊙ and the F160W-filter stellar mass-to-light ratio to be (1.52 ± 0.11) M⊙/L⊙, F160W. Both SMBH masses are consistent with the SMBH mass–stellar velocity dispersion (MBH–σe) relation, suggesting that the overmassive SMBHs present in other very massive ETGs are fairly uncommon.
The Three Hundred: Msub–Vcirc relation
Authors: Srivastava Atulit , Cui Weiguang , Meneghetti Massimo , Dave Romeel , Knebe Alexander , Ragagnin Antonio , Giocoli Carlo , Calura Francesco , Despali Giulia , Moscardini Lauro , Yepes Gustavo 
Published: February 2024

ABSTRACT
In this study, we investigate a recent finding based on strong lensing observations, which suggests that the sub-haloes observed in clusters exhibit greater compactness compared to those predicted by ΛCDM simulations. To address this discrepancy, we compare the cumulative sub-halo mass function and the Msub–Vcirc relation between observed clusters and 324 simulated clusters from $\rm \small {The\,Three\,\,Hundred}$ project, focusing on the hydrodynamic resimulations using $\rm \small {Gadget-X}$ and $\rm \small {Gizmo-Simba}$ baryonic models. The cumulative sub-halo mass function of $\rm \small {Gizmo-Simba}$ simulated clusters aligns with observations, while $\rm \small {Gadget-X}$ simulations exhibit discrepancies in the lower sub-halo mass range, possibly due to its strong supernova feedback. Both $\rm \small {Gadget-X}$ and $\rm \small {Gizmo-Simba}$ simulations demonstrate a redshift evolution of the sub-halo mass function and the Vcirc function, with slightly fewer sub-haloes observed at lower redshifts. Neither the $\rm \small {Gadget-X}$ nor $\rm \small {Gizmo-Simba}$ (albeit a little closer) simulated clusters’ predictions for the Msub–Vcirc relation align with the observational result. Further investigations on the correlation between sub-halo/halo properties and the discrepancy in the Msub–Vcirc relation reveal that the sub-halo’s half mass radius and galaxy stellar age, the baryon fraction, and sub-halo distance from the cluster’s centre, as well as the halo relaxation state, play important roles on reproducing this relation. Nonetheless, challenges persist in accurately reproducing the observed Msub–Vcirc relationship within our current hydrodynamic cluster simulation that adheres to the standard ΛCDM cosmology. These challenges may stem from shortcomings in our baryon modelling, numerical intricacies within the simulation, or even potential limitations of the ΛCDM framework.
A jingmenvirus RNA-dependent RNA polymerase structurally resembles the flavivirus counterpart but with different features at the initiation phase
Authors: Wang Xinyu , Jing Xuping , Shi Junming , Liu Qiaojie , Shen Shu , Cheung Peter Pak-Hang , Wu Jiqin , Deng Fei , Gong Peng 
Published: February 2024

Abstract
Jingmenviruses are a category of emerging segmented viruses that have garnered global attention in recent years, and are close relatives of the flaviviruses in the Flaviviridae family. One of their genome segments encodes NSP1 homologous to flavivirus NS5. NSP1 comprises both the methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRP) modules playing essential roles in viral genome replication and capping. Here we solved a 1.8-Å resolution crystal structure of the NSP1 RdRP module from Jingmen tick virus (JMTV), the type species of jingmenviruses. The structure highly resembles flavivirus NS5 RdRP despite a sequence identity less than 30%. NSP1 RdRP enzymatic properties were dissected in a comparative setting with several representative Flaviviridae RdRPs included. Our data indicate that JMTV NSP1 produces characteristic 3-mer abortive products similar to the hepatitis C virus RdRP, and exhibits the highest preference of terminal initiation and shorter-primer usage. Unlike flavivirus NS5, JMTV RdRP may require the MTase for optimal transition from initiation to elongation, as an MTase-less NSP1 construct produced more 4–5-mer intermediate products than the full-length protein. Taken together, this work consolidates the evolutionary relationship between the jingmenvirus group and the Flaviviridae family, providing a basis to the further understanding of their viral replication/transcription process.
Dimeric structures of DNA ATTTC repeats promoted by divalent cations
Authors: Trajkovski Marko , Pastore Annalisa , Plavec Janez 
Published: February 2024

Abstract
Structural studies of repetitive DNA sequences may provide insights why and how certain repeat instabilities in their number and nucleotide sequence are managed or even required for normal cell physiology, while genomic variability associated with repeat expansions may also be disease-causing. The pentanucleotide ATTTC repeats occur in hundreds of genes important for various cellular processes, while their insertion and expansion in noncoding regions are associated with neurodegeneration, particularly with subtypes of spinocerebellar ataxia and familial adult myoclonic epilepsy. We describe a new striking domain-swapped DNA–DNA interaction triggered by the addition of divalent cations, including Mg2+ and Ca2+. The results of NMR characterization of d(ATTTC)3 in solution show that the oligonucleotide folds into a novel 3D architecture with two central C:C+ base pairs sandwiched between a couple of T:T base pairs. This structural element, referred to here as the TCCTzip, is characterized by intercalative hydrogen-bonding, while the nucleobase moieties are poorly stacked. The 5′- and 3′-ends of TCCTzip motif are connected by stem-loop segments characterized by A:T base pairs and stacking interactions. Insights embodied in the non-canonical DNA structure are expected to advance our understanding of why only certain pyrimidine-rich DNA repeats appear to be pathogenic, while others can occur in the human genome without any harmful consequences.
Tet-mediated DNA methylation dynamics affect chromosome organization
Authors: Tian Hao , Luan Pengfei , Liu Yaping , Li Guoqiang 
Published: February 2024

Abstract
DNA Methylation is a significant epigenetic modification that can modulate chromosome states, but its role in orchestrating chromosome organization has not been well elucidated. Here we systematically assessed the effects of DNA Methylation on chromosome organization with a multi-omics strategy to capture DNA Methylation and high-order chromosome interaction simultaneously on mouse embryonic stem cells with DNA methylation dioxygenase Tet triple knock-out (Tet-TKO). Globally, upon Tet-TKO, we observed weakened compartmentalization, corresponding to decreased methylation differences between CpG island (CGI) rich and poor domains. Tet-TKO could also induce hypermethylation for the CTCF binding peaks in TAD boundaries and chromatin loop anchors. Accordingly, CTCF peak generally weakened upon Tet-TKO, which results in weakened TAD structure and depletion of long-range chromatin loops. Genes that lost enhancer–promoter looping upon Tet-TKO showed DNA hypermethylation in their gene bodies, which may compensate for the disruption of gene expression. We also observed distinct effects of Tet1 and Tet2 on chromatin organization and increased DNA methylation correlation on spatially interacted fragments upon Tet inactivation. Our work showed the broad effects of Tet inactivation and DNA methylation dynamics on chromosome organization.
Glomerular hyperfiltration as a therapeutic target for CKD
Authors: Kanbay Mehmet , Copur Sidar , Bakir Cicek N , Covic Adrian , Ortiz Alberto , Tuttle Katherine R 
Published: February 2024

ABSTRACT
The global burden of chronic kidney disease (CKD) is high and increasing. Early diagnosis and intervention are key to improve outcomes. Single-nephron glomerular hyperfiltration is an early pathophysiologic manifestation of CKD that may result in absolute glomerular hyperfiltration, i.e. a high glomerular filtration rate (GFR), or be associated with normal or low GFR because of nephron loss (relative glomerular hyperfiltration). Even though compensatory glomerular hyperfiltration may contribute to maintain kidney function after the loss of kidney mass, the associated increased glomerular capillary pressure and glomerular and podocyte size drive podocyte loss, albuminuria and proximal tubular overload, contributing to CKD progression. In this regard, all kidney protective drugs in clinical use so far, from renin–angiotensin system blockers to mineralocorticoid receptor blockers to sodium–glucose co-transporter 2 inhibitors to tolvaptan, induce an early dip in glomerular filtration that is thought to represent reversal of hyperfiltration. As glomerular hyperfiltration may be present early in the course of kidney disease, its recognition may provide an effective intervention window that may predate current criteria based on high albuminuria or loss of GFR. Nevertheless, there is no diagnostic method with high sensitivity and specificity to identify single-nephron glomerular hyperfiltration, except when it leads to obvious absolute glomerular hyperfiltration, as observed in the early stages of diabetic kidney disease when nephron mass is still preserved. We now review the concept of glomerular hyperfiltration as an indicator of CKD risk, including definitions, challenges in diagnosis and evaluation, underlying pathophysiological mechanisms, potential therapeutic approaches and unanswered questions.
Rice transcriptional repressor OsTIE1 controls anther dehiscence and male sterility by regulating JA biosynthesis
Authors: Fang Yuxing , Guo Dongshu , Wang Yi , Wang Ning , Fang Xianwen , Zhang Yunhui , Li Xiao , Chen Letian , Yu Diqiu , Zhang Baolong , Qin Genji 
Published: February 2024

Abstract
Proper anther dehiscence is essential for successful pollination and reproduction in angiosperms, and jasmonic acid (JA) is crucial for the process. However, the mechanisms underlying the tight regulation of JA biosynthesis during anther development remain largely unknown. Here, we demonstrate that the rice (Oryza sativa L.) ethylene-response factor-associated amphiphilic repression (EAR) motif-containing protein TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTORS (TCP) INTERACTOR CONTAINING EAR MOTIF PROTEIN1 (OsTIE1) tightly regulates JA biosynthesis by repressing TCP transcription factor OsTCP1/PCF5 during anther development. The loss of OsTIE1 function in Ostie1 mutants causes male sterility. The Ostie1 mutants display inviable pollen, early stamen filament elongation, and precocious anther dehiscence. In addition, JA biosynthesis is activated earlier and JA abundance is precociously increased in Ostie1 anthers. OsTIE1 is expressed during anther development, and OsTIE1 is localized in nuclei and has transcriptional repression activity. OsTIE1 directly interacts with OsTCP1, and overexpression of OsTCP1 caused early anther dehiscence resembling that of Ostie1. JA biosynthesis genes including rice LIPOXYGENASE are regulated by the OsTIE1-OsTCP1 complex. Our findings reveal that the OsTIE1-OsTCP1 module plays a critical role in anther development by finely tuning JA biosynthesis and provide a foundation for the generation of male sterile plants for hybrid seed production.
Epigenetic stress memory in gymnosperms
Authors: Fossdal Carl Gunnar , Krokene Paal , Olsen Jorunn Elisabeth , Strimbeck Richard , Viejo Marcos , Yakovlev Igor , Mageroy Melissa H 
Published: February 2024

Abstract
Gymnosperms are long-lived, cone-bearing seed plants that include some of the most ancient extant plant species. These relict land plants have evolved to survive in habitats marked by chronic or episodic stress. Their ability to thrive in these environments is partly due to their phenotypic flexibility, and epigenetic regulation likely plays a crucial part in this plasticity. We review the current knowledge on abiotic and biotic stress memory in gymnosperms and the possible epigenetic mechanisms underlying long-term phenotypic adaptations. We also discuss recent technological improvements and new experimental possibilities that likely will advance our understanding of epigenetic regulation in these ancient and hard-to-study plants.
The Utilization of Preoperative Steroids Safely Decreases the Risk of Postoperative Delirium in Geriatric Patients after Hip Fracture Surgery: A Systematic Review and Meta-Analysis of Randomized Controlled Trials
Authors: Baumann Anthony N. , Talaski Grayson M. , Uhler Mathias A. , Anastasio Albert T. , Walley Kempland C. , Pean Christian A. , Tampi Rajesh R. , Farivar Michel 
Published: February 2024

OBJECTIVES:
Postoperative delirium is an acute neurocognitive complication that can have adverse effects on outcomes of geriatric patients after undergoing hip fracture surgery. The objective of this study was to examine the efficacy of preoperative steroids in preventing postoperative delirium after hip fracture surgery.

METHODS:

Data Sources: A systematic review and meta-analysis was performed using PubMed, SPORTDiscus, CINAHL, MEDLINE, and Web of Science from database inception until September 28th, 2023.

Study Selection:
Inclusion criteria were randomized controlled trials (RCTs) of patients who underwent surgical intervention for hip fracture, were examined for postoperative delirium, and utilized preoperative steroids.

Data Extraction:
Data included the risk of postoperative delirium, postoperative all-cause infection, and postoperative hyperglycemia. Articles were graded via the Cochrane Collaboration’s tool.

Data Synthesis:
Statistical analysis included a random-effects binary model with relative risk (RR), 95% confidence intervals (CI) along with a defined “number needed to treat” threshold (NNT).

RESULTS:
Four RCTs were included from 128 articles initially retrieved. Patients (n=416; average age: 82.2 ± 2.2 years old) underwent surgical intervention for hip fracture after receiving either preoperative steroids (n=209) or control interventions (n=207). There was a statistically significant decrease in the incidence of postoperative delirium among patients who received preoperative steroids (12.9%; 27 cases) as compared to patients who received control interventions (26.7%; 55 cases) after hip fracture surgery (p<0.001; RR: 0.84). The absolute risk difference was 13.8% and the NNT was 7.2 patients. There was no statistically significant difference in the risk of postoperative all-cause infection among patients who received preoperative steroids as compared to patients who received normal saline as placebo after hip fracture surgery (p=0.850; RR: 0.96).

CONCLUSIONS:
The utilization of preoperative steroids appears to decrease the risk of postoperative delirium after hip fracture surgery in elderly adults. Furthermore, this decreased risk of postoperative delirium was not associated with a significant increase in postoperative infection, indicating possible safety of preoperative steroid administration.

LEVEL OF EVIDENCE:
Level I. See Instructions for Authors for a complete description of levels of evidence.
Application of a Web-based Tool for Quantitative Bias Analysis: The Example of Misclassification Due to Self-reported Body Mass Index
Authors: Banack Hailey R. , Smith Samantha N. , Bodnar Lisa M. 
Published: February 2024

Background:We describe the use of Apisensr, a web-based application that can be used to implement quantitative bias analysis for misclassification, selection bias, and unmeasured confounding. We apply Apisensr using an example of exposure misclassification bias due to use of self-reported body mass index (BMI) to define obesity status in an analysis of the relationship between obesity and diabetes.Methods:We used publicly available data from the National Health and Nutrition Examination Survey. The analysis consisted of: (1) estimating bias parameter values (sensitivity, specificity, negative predictive value, and positive predictive value) for self-reported obesity by sex, age, and race–ethnicity compared to obesity defined by measured BMI, and (2) using Apisensr to adjust for exposure misclassification.Results:The discrepancy between self-reported and measured obesity varied by demographic group (sensitivity range: 75%–89%; specificity range: 91%–99%). Using Apisensr for quantitative bias analysis, there was a clear pattern in the results: the relationship between obesity and diabetes was underestimated using self-report in all age, sex, and race–ethnicity categories compared to measured obesity. For example, in non-Hispanic White men aged 40–59 years, prevalence odds ratios for diabetes were 3.06 (95% confidence inerval = 1.78, 5.30) using self-reported BMI and 4.11 (95% confidence interval = 2.56, 6.75) after bias analysis adjusting for misclassification.Conclusion:Apisensr is an easy-to-use, web-based Shiny app designed to facilitate quantitative bias analysis. Our results also provide estimates of bias parameter values that can be used by other researchers interested in examining obesity defined by self-reported BMI.
Glomus Tumors: A Systematic Review of the Sub-Saharan Africa Experience
Authors: Nthumba Peter M. , Oundoh Leahcaren Naguria 
Published: February 2024

Background:
Glomus tumors are rare benign tumors that were first described in 1812 by Wood. They arise from normal glomus apparatus, usually located in the reticular dermis of the body. Although glomus tumors are universal in occurrence, the sub-Saharan Africa experience has not been well documented.

Methods:
The authors performed a systematic literature review of eligible studies between 1960 and August 2023, using the terms “glomus,” “tumor,” “glomangioma,” “glomangiomyoma,” and “Africa.” We also performed a search of the AIC Kijabe Hospital pathology department database of about 140,000 records, covering 30 years, for the terms “glomus tumor,” “glomangioma” and “glomangiomyoma.”

Results:
The systematic literature search and institutional database search produced a total of 74 patients who had glomus tumors. These patients had a lag of between 3 months and 20 years from symptom development to definitive treatment.

Conclusions:
There are very few reports of glomus tumors from sub-Saharan Africa in the current literature: the authors’ histopathology database of 140,000 specimens had 46 glomus tumors (0.03%), and only 28 additional patients were found in literature from sub-Saharan Africa. The low numbers of African patients may indicate racial differences in the occurrence of glomus tumors, although this may also be due to failure of clinicians to recognize glomus tumors. The prolonged lag period between symptom development and definitive treatment for glomus tumors indicates the need for diligence in the diagnosis and treatment of a simple problem that is otherwise the cause of incapacitating pain and misery.