bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for intrinsic DNA dynamics and deformability in damage sensing by the Rad4/XPC nucleotide excision repair complex
Authors: Baral Saroj , Chakraborty Sagnik , Steinbach Peter J , Paul Debamita , Min Jung-Hyun , Ansari Anjum 
Published: January 2025

Abstract
Altered DNA dynamics at lesion sites are implicated in how DNA repair proteins sense damage within genomic DNA. Using laser temperature-jump (T-jump) spectroscopy combined with cytosine-analog Förster Resonance Energy Transfer (FRET) probes that sense local DNA conformations, we measured the intrinsic dynamics of DNA containing 3 base-pair mismatches recognized in vitro by Rad4 (yeast ortholog of XPC). Rad4/XPC recognizes diverse lesions from environmental mutagens and initiates nucleotide excision repair. T-jump measurements, together with a novel and rigorous comparison with equilibrium FRET, uncovered conformational dynamics spanning multiple timescales and revealed key differences between Rad4-specific and non-specific DNA. AT-rich non-specific sites (matched or mismatched) exhibited dynamics primarily within the T-jump observation window, albeit with some amplitude in ‘missing’ fast (&lt;20 μs) kinetics. These fast-kinetics amplitudes were dramatically larger for specific sites (CCC/CCC and TTT/TTT), which also exhibited ‘missing’ slow (&gt;50 ms) kinetics at elevated temperatures, unseen in non-specific sites. We posit that the rapid (μs–ms) intrinsic DNA fluctuations help stall a diffusing protein at AT-rich/damaged sites and that the &gt;50-ms kinetics in specific DNA reflect a propensity to adopt unwound/bent conformations resembling Rad4-bound DNA structures. These studies provide compelling evidence for sequence/structure-dependent intrinsic DNA dynamics and deformability that likely govern damage sensing by Rad4.
The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae
Authors: Fournes Florian , Campos Manuel , Cury Jean , Schiavon Caroline , Pagès Carine , Touchon Marie , Rocha Eduardo P C , Rousseau Philippe , Cornet François 
Published: January 2025

Abstract
Bacterial genomes contain a plethora of secondary replicons of divergent size. Circular replicons must carry a system for resolving dimeric forms, resulting from recombination between sister copies. These systems use site-specific recombinases. Among these, the XerCD recombinase resolves dimers of chromosomes and certain plasmids, using different modes of regulation. We have analyzed the dimer resolution functions in enterobacterial secondary replicons and show that, in addition to the main chromosomes, XerCD is preferentially used by small plasmids and by the largest secondary replicons, megaplasmids and secondary chromosomes. Indeed, all replicons longer than 250 kb host an active XerCD recombination site. These sites, in contrast to those of small plasmids, use the same control as chromosomes, coupled to cell division by the FtsK protein. We conclude that a chromosome-like mode of dimer resolution is mandatory for the faithful inheritance of large plasmids and chromids, its acquisition being a prerequisite for the genesis of secondary chromosomes from plasmids.
A cross-species inducible system for enhanced protein expression and multiplexed metabolic pathway fine-tuning in bacteria
Authors: Li Yang , Wu Yaokang , Xu Xianhao , Liu Yanfeng , Li Jianghua , Du Guocheng , Lv Xueqin , Li Yangyang , Liu Long 
Published: January 2025

Abstract
Inducible systems are crucial to metabolic engineering and synthetic biology, enabling organisms that function as biosensors and produce valuable compounds. However, almost all inducible systems are strain-specific, limiting comparative analyses and applications across strains rapidly. This study designed and presented a robust workflow for developing the cross-species inducible system. By applying this approach, two reconstructed inducible systems (a 2,4-diacetylphloroglucinol-inducible system PphlF3R1 and an anhydrotetracycline-inducible system Ptet2R2*) were successfully developed and demonstrated to function in three model microorganisms, including Escherichia coli, Bacillus subtilis and Corynebacterium glutamicum. To enhance their practicality, both inducible systems were subsequently placed on the plasmid and genome for detailed characterization to determine the optimal expression conditions. Furthermore, the more efficient inducible system Ptet2R2* was employed to express various reporter proteins and gene clusters in these three strains. Moreover, the aTc-inducible system Ptet2R2*, combined with T7 RNA polymerase and dCas12a, was utilized to develop a single-input genetic circuit that enables the simultaneous activation and repression of gene expression. Overall, the cross-species inducible system serves as a stringent, controllable and effective tool for protein expression and metabolic pathway control in different bacteria.
A mobile genetic element-derived primase-polymerase harbors multiple activities implicated in DNA replication and repair
Authors: Fu Pan , Wang Yuwei , Liu Yanqiu , Han Zhenhao , Peng Zhangzhong , Liu Linfeng , Han Wenyuan 
Published: January 2025

Abstract
Primase-polymerases (PrimPols) play divergent functions from DNA replication to DNA repair in all three life domains. In archaea and bacteria, numerous and diverse PPs are encoded by mobile genetic elements (MGEs) and act as the replicases for their MGEs. However, their varying activities and functions are not fully understood. In this study, we characterized a group of PrimPols that are genetically associated with prokaryotic argonaute proteins (pAgos). The pAgo-associated PrimPol (AgaPP) is likely derived from a MGE. AgaPP has polymerase and primase activities and physically interacts with a helicase encoded by its downstream gene, suggesting that they constitute a functional replication module. Further, AgaPP performs translesion DNA synthesis, terminal transfer and microhomology-mediated end joining (MMEJ), showing striking similarity to human DNA repair polymerase θ. AgaPP can promote the MMEJ repair of Cas9-induced double-stranded DNA breaks and increase cell survival post DNA damage in Escherichia coli. In addition, the MMEJ activity of AgaPP can be repurposed to assist DNA assembly in vitro. Together, the findings reveal dual role of AgaPP in both DNA replication and repair.
Dent disease: clinical practice recommendations
Authors: Bökenkamp Arend , Ariceta Gema , Böckenhauer Detlef , Devuyst Olivier , Emma Francesco , van Bennekom David , Levtchenko Elena , Sayer John , Servais Aude , Vargas Rosa , Zaniew Marcin , Prikhodina Larisa 
Published: January 2025

ABSTRACT
Dent disease is a rare X-linked tubulopathy that is characterized by low-molecular-weight proteinuria associated with hypercalciuria, which may lead to nephrolithiasis, nephrocalcinosis, and kidney failure between the third and fifth decades of life in 30%–80% of affected males. The disease is most often associated with various manifestations of proximal tubular dysfunction. Affected individuals may present nephrotic-range proteinuria which may be misinterpreted and cause diagnostic delay. Due to its rarity, there is limited evidence to guide diagnosis and management. These clinical practice recommendations summarize the current knowledge on Dent disease and provide guidance for diagnosis and management. The recommendations are based on a systematic search of the literature and were endorsed by a Delphi procedure among stakeholders in the field as well as the respective ERA and ESPN working groups.
Disease stage-specific role of the mitochondrial pyruvate carrier suppresses differentiation in temozolomide and radiation-treated glioblastoma
Authors: Martell Emma , Kuzmychova Helgi , Senthil Harshal , Chawla Ujala , Kaul Esha , Grewal Akaljot , Banerji Versha , Anderson Christopher M , Venugopal Chitra , Miller Donald , Werbowetski-Ogilvie Tamra E , Singh Sheila K , Sharif Tanveer 
Published: January 2025

Abstract

Background
The mitochondrial pyruvate carrier (MPC), a central metabolic conduit linking glycolysis and mitochondrial metabolism, is instrumental in energy production. However, the role of the MPC in cancer is controversial. In particular, the importance of the MPC in glioblastoma (GBM) disease progression following standard temozolomide (TMZ) and radiation therapy (RT) remains unexplored.

Methods
Leveraging in vitro and in vivo patient-derived models of TMZ-RT treatment in GBM, we characterize the temporal dynamics of MPC abundance and downstream metabolic consequences using state-of-the-art molecular, metabolic, and functional assays.

Results
Our findings unveil a disease stage-specific role for the MPC, where in posttreatment GBM, but not therapy-naïve tumors, the MPC acts as a central metabolic regulator that suppresses differentiation. Temporal profiling reveals a dynamic metabolic rewiring where a steady increase in MPC abundance favors a shift towards enhanced mitochondrial metabolic activity across patient GBM samples. Intriguingly, while overall mitochondrial metabolism is increased, acetyl-CoA production is reduced in posttreatment GBM cells, hindering histone acetylation and silencing neural differentiation genes in an MPC-dependent manner. Finally, the therapeutic translations of these findings are highlighted by the successful pre-clinical patient-derived orthotopic xenograft trials utilizing a blood-brain-barrier permeable MPC inhibitor, MSDC-0160, which augments standard TMZ-RT therapy to mitigate disease relapse and prolong animal survival.

Conclusion
Our findings demonstrate the critical role of the MPC in mediating GBM aggressiveness and molecular evolution following standard TMZ-RT treatment, illuminating a therapeutically-relevant metabolic vulnerability to potentially improve survival outcomes for GBM patients.
Prevalence of and factors associated with formula feeding among mothers with infants 0–6 months of age in Ethiopia: a systematic review and meta-analysis
Authors: Gebreegziabher Zenebe Abebe , Semagn Birhan Ewunu , Walle Agmasie Damtew , Tilahun Werkneh Melkie , Belay Mahider Awoke , Wondie Wubet Tazeb , Gedefaw Gezahagn Demsu , Dejene Tadesse Mamo , Mohammed Fitsum Zekarias 
Published: January 2025

Abstract

Context
Inconsistent results have been reported regarding the prevalence of and factors associated with formula feeding in Ethiopia.

Objective
This study aimed to determine the pooled prevalence of and factors associated with formula feeding among mothers with infants 0–6 months of age in Ethiopia.

Data Sources
A comprehensive systematic search was conducted across 3 databases (PubMed, EMBASE, and ScienceDirect) and the Google Scholar search engine to identify relevant studies published up to April 2, 2024.

Data Extraction
After assessing the quality of each study using the Joanna Briggs Institute Critical Appraisal Checklist for Prevalence Studies, data were independently extracted by 2 authors using pre-designed forms in an Excel spreadsheet. Any disagreements were resolved through discussion and consultation with additional authors.

Data Analysis
Statistical heterogeneity across studies was assessed using the I2 statistic. A random-effects meta-analysis was used to pool the proportions, due to high heterogeneity, while a fixed-effect meta-analysis was used to pool associated factors with low heterogeneity. A sensitivity analysis was performed to assess the potential impact of outlier studies on the overall estimates. Five studies, with a combined sample size of 2344 participants, were included. The pooled prevalence of formula feeding was 34.0% (95% CI: 23.0%, 44.0%). Factors significantly associated with formula feeding included cesarean delivery (POR [pooled odds ratio] = 4.72, 95% CI: 3.32, 6.71) compared with vaginal delivery, a positive attitude toward formula feeding (POR = 2.26, 95% CI: 1.45, 3.53) compared with a negative attitude, initiation of breastfeeding more than 1 hour after delivery (POR = 2.27, 95% CI: 1.25, 4.13) compared with initiation within 1 hour, and receiving information about formula feeding from friends or family (POR = 2.47, 95% CI: 1.46, 4.20) compared with receiving information from health-care professionals.

Conclusion
The prevalence of formula feeding in Ethiopia is significant. Cesarean delivery, a positive attitude toward formula feeding, late initiation of breastfeeding, and receiving formula feeding-related information from friends and family were positively associated with formula feeding. Given these findings, the authors recommend that public health interventions in Ethiopia target these key determinants to decrease the high prevalence of formula feeding practices observed in the country. Strategies addressing factors such as promoting vaginal delivery, improving attitudes toward breastfeeding, encouraging early breastfeeding initiation, and limiting the influence of social networks on formula-feeding decisions may be beneficial.
Hepatitis C Virus Seroprevalence, Incidence, and Screening Patterns in Ontario Preexposure Prophylaxis Users
Authors: McGarrity Matthew W , Lisk Ryan , MacPherson Paul , Knox David , Woodward Kevin S , Reinhart Jeff , MacLeod John , Bogoch Isaac I , Clatworthy Deanna , Biondi Mia J , Sullivan Sean T , Li Alan T W , Burchell Ann N , Tan Darrell H S 
Published: January 2025

Abstract

Background
Hepatitis C virus (HCV) has emerged as a sexually transmitted infection in gay, bisexual, and other men who have sex with men (GBM). We estimated the seroprevalence and incidence of HCV infection and examined patterns of HCV testing among GBM using human immunodeficiency virus preexposure prophylaxis (PrEP) in Ontario, Canada.

Methods
We analyzed data from the Ontario PrEP Cohort Study (ON-PrEP), a prospective cohort of PrEP users from 10 Ontario clinics. Participants completed an online questionnaire and study staff collected clinical information into a study database biannually for 2 years. We estimated the baseline seroprevalence and incidence of HCV infection and examined patterns of HCV testing during follow-up. We further explored differences in sociodemographic/clinical variables between those with and without prevalent/incident HCV infection through bivariate analysis.

Results
Among 557 eligible PrEP users, 382 (68.6%) underwent baseline HCV antibody testing, of whom 5 tested HCV seropositive, giving a seroprevalence of 1.3% (95% confidence interval [CI], .43%–3.03%). Only 245 (43.9%) participants underwent HCV antibody testing after baseline, and median time to participants’ first follow-up test was 245 days. During follow-up, 2 participants tested newly HCV seropositive, giving an incidence of 0.47/100 person-years (95% CI, .06–1.69) over 428.9 years of follow-up. Participants with prevalent/incident HCV infection during the study appeared more likely to report giving money, drugs, gifts, or services for sex in the 3 months preceding enrollment compared to those who never tested HCV seropositive (P = .02).

Conclusions
HCV seroprevalence and incidence were low but not negligible among Ontario PrEP users. HCV antibody and RNA testing were suboptimal.
Cycling Dof Factor 3 mediates light-dependent ascorbate biosynthesis by activating GDP-l-galactose phosphorylase in Rosa roxburghii fruit
Authors: Huang Qianmin , Yan Yali , Zhang Xue , Cao Xuejiao , Ludlow Richard , Lu Min , An Huaming 
Published: January 2025

Abstract
Light plays an important role in determining the l-ascorbate (AsA) pool size in plants, primarily through the transcriptional regulation of AsA metabolism-related genes. However, the specific mechanism of transcriptional induction responsible for light-dependent AsA biosynthesis remains unclear. In this study, we used a promoter sequence containing light-responsive motifs from GDP-L-galactose phosphorylase 2 (RrGGP2), a key gene involved in AsA overproduction in Rosa roxburghii fruits, to identify participating transcription factors. Among these factors, Cycling Dof Factor 3 (RrCDF3) was highly responsive to variations in light intensity, quality, and photoperiod, leading to alterations in RrGGP2 expression. Further yeast one-hybrid and dual-luciferase assays confirmed that RrCDF3 acts as a transcriptional activator of RrGGP2 by binding specifically to its promoter. Modulating the expression of RrCDF3 in fruits through transient overexpression and silencing resulted in significant changes in RrGGP2 expression and AsA synthesis. Additionally, the stable overexpression of RrCDF3 in R. roxburghii calli and Solanum lycopersicum plants resulted in a significant increase in AsA content. Notably, the well-known photo-signal transcription factor ELONGATED HYPOCOTYL5 (RrHY5) directly interacted with the RrCDF3 promoter, enhancing its transcription. These findings reveal a special mechanism involving the RrHY5-RrCDF3-RrGGP2 module that mediates light-induced AsA biosynthesis in R. roxburghii fruit.
Chromatin accessibility mediated by CHROMATIN REMODELING 11 promotes chilling tolerance in rice
Authors: Li Jing , Liu He , Qian Hanying , Lu Shan , Wu Yufeng , Hua Jian , Zou Baohong 
Published: January 2025

Abstract
Chromatin remodeling plays a crucial role in controlling gene transcription by modifying chromatin structure. However, the involvement of chromatin remodeling in plant stress responses, especially cold tolerance, through chromatin accessibility remains largely unexplored. Here, we report that rice (Oryza sativa L.) CHROMATIN REMODELING 11 (OsCHR11) positively regulates chilling tolerance by enhancing chromatin accessibility and facilitating changes in gene expression. Loss-of-function mutants of OsCHR11 exhibited increased susceptibility to chilling stress compared to wild-type rice plants. Transcriptome analysis revealed that the chr11 mutant displays diminished transcriptomic responses to chilling. Additionally, assay for transposase-accessible chromatin indicated that chilling treatment increases chromatin accessibility in the promoter regions, and this process depended on OsCHR11 function. Chromatin immunoprecipitation sequencing showed that OsCHR11 is physically associated with the promoters of cold-responsive genes. Integrated multiomics analysis further demonstrated a correlation between OsCHR11 enrichment and chromatin accessibility, as well as a correlation between chromatin accessibility and gene expression. Furthermore, OsCHR11 is required for the full expression of key cold-response genes, including those involved in trehalose biosynthesis. The exogenous application of trehalose partially rescued the chilling-susceptible phenotype of the chr11 mutant, suggesting that trehalose biosynthesis contributes to the chilling tolerance promoted by OsCHR11. Collectively, these findings indicate that OsCHR11 enhances cold tolerance in plants, likely by increasing chromatin accessibility and elevating the expression levels of cold-response genes in response to chilling.
Steering the future: expert knowledge and stakeholder voices in autonomous vehicle policy reports
Authors: Hicks Diana , Kingsley Gordon , Isett Kimberley R 
Published: January 2025

Abstract
The anticipated arrival of autonomous vehicles has created considerable uncertainty for US states because they govern roads. In response, states activated their policy advisory systems. While policy advising at the national level has been studied, less is known about the sub-national level. Similarly, more is known about the use of scientific knowledge by policymakers than about the full range of knowledge deployed in policy advising. This study analyzes reports written for states to help them make sense of an emerging technology in preparation for governance. Committees, university researchers, staff at Department of Transportation, and legislative staff produced different types of reports, for example, more and less academic, focused more or less on topics associated with governance or engineering. Our analysis reveals that state policy advisory systems used two types of processes—convening and expert—and employed three types of expertise—academic, practical, and political—to help prepare to govern this emerging technology. The study provides insight into how states mobilized expertise to address uncertainty around an emerging technology, showing how different actors balanced the need for credible technical knowledge with legitimate stakeholder engagement.
Charged Pion Condensation and Color Superconductivity Phenomena in Chirally Asymmetric Dense Quark Matter
Authors: Khunjua T G , Klimenko K G , Zhokhov R N 
Published: January 2025

Abstract
In this paper, the question of the influence of color superconductivity on the formation of a phase with condensation of charged pions in dense, chirally asymmetric quark matter is studied. We consider it within the framework of the massless Nambu–Jona-Lasinio (NJL) model with a diquark interaction channel at zero temperature, but in the presence of baryon $\mu _B$, isospin $\mu _I$, chiral $\mu _{5}$, and chiral isospin $\mu _{I5}$ chemical potentials. It has been shown in the mean-field approximation that in the presence of chiral imbalance, when $\mu _{5}\ne 0$ and/or $\mu _{I5}\ne 0$, the color superconductivity phenomenon does not hinder the generation of charged pion condensation in dense quark matter even at the largest baryon densities attainable in heavy-ion collision experiments and in cores of neutron stars and their mergers, highlighting the resilience of this phase in dense quark matter. This makes the phase structure of dense quark matter even more rich, multifaceted, and interesting, and shows that pion condensation in dense quark matter is a viable phenomenon to be explored, e.g. in intermediate-energy heavy-ion collision experiments.
Impact of Finite Volume on Kaon, Antikaon, and ϕ Meson Masses and Decay Widths in Asymmetric Strange Hadronic Matter
Authors: Ahmad Zeeshan , Chahal Nisha , Kumar Arvind , Dutt Suneel 
Published: January 2025

Abstract
In the present work, we investigate the impact of finite volume on the in-medium properties of kaons ($K^+$, $K^0$), antikaons ($K^-$, $\bar{K^0}$), and $\phi$ mesons in the isospin asymmetric strange hadronic medium at finite density and temperature. We use the chiral SU(3) hadronic mean-field model, which accounts for the interactions between baryons through the exchange of scalar ($\sigma , \zeta , \delta$) and vector ($\omega$, $\rho$, $\phi$) fields. To investigate the effects of finite volume, we apply the multiple reflection expansion technique for calculations of the density of states. At high baryon density, an increase of the isospsin asymmetry of the medium from zero to a finite value is found to impact the nonstrange scalar field $\sigma$ more than the strange scalar field $\zeta$, whereas the opposite is the case as a function of the strangeness fraction of the medium. For example, in an infinite nuclear medium at $\rho _B = 4\rho _0$, for an increase of isospin asymmetry from zero to ${\sim}0.3$, the magnitudes of the scalar fields $\sigma$ and $\zeta$ increase by ${\sim}3.0$% and ${\sim}0.1$%, respectively. On the other hand, for a symmetric medium, an increase of $f_s$ from 0 to 0.5 leads to an increase in the magnitude of $\sigma$ by ${\sim}0.4$% and a decrease in $\zeta$ by ${\sim}16$%. We use the medium-modified masses of kaons and antikaons calculated using the chiral SU(3) model to obtain the masses and decay widths of $\phi$ mesons in the finite volume hadronic medium. To obtain the masses and decay widths of $\phi$ mesons, an effective Lagrangian approach with $\phi$K$\bar{K}$ interactions at the one-loop level is used in the present work. We obtain the effective masses and decay widths in the finite volume matter for a spherical geometry of a medium with Neumann and Dirichlet boundary conditions as well as for a cubic geometry. At baryon density 4$\rho _0$, the Dirichlet boundary conditions with spherical geometry of the medium leads to changes of ${\sim}4$%, ${\sim}3$%, and ${\sim}0.6$% in the effective masses of the K, $\bar{K}$, and $\phi$ mesons, as the system size decreases from $R = \infty$ to 2 fm in a symmetric nuclear medium.