bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular basis for thiocarboxylation and release of Urm1 by its E1-activating enzyme Uba4
Authors: Sokołowski Mikołaj , Kwasna Dominika , Ravichandran Keerthiraju E , Eggers Cristian , Krutyhołowa Rościsław , Kaczmarczyk Magdalena , Skupien-Rabian Bozena , Jaciuk Marcin , Walczak Marta , Dahate Priyanka , Pabis Marta , Jemioła-Rzemińska Małgorzata , Jankowska Urszula , Leidel Sebastian A , Glatt Sebastian 
Published: December 2024

Abstract
Ubiquitin-related modifier 1 (Urm1) is a highly conserved member of the ubiquitin-like (UBL) family of proteins. Urm1 is a key component of the eukaryotic transfer RNA (tRNA) thiolation cascade, responsible for introducing sulfur at wobble uridine (U34) in several eukaryotic tRNAs. Urm1 must be thiocarboxylated (Urm1-SH) by its E1 activating enzyme UBL protein activator 4 (Uba4). Uba4 first adenylates and then thiocarboxylates the C-terminus of Urm1 using its adenyl-transferase (AD) and rhodanese (RHD) domains. However, the detailed mechanisms of Uba4, the interplay between the two domains, and the release of Urm1 remain elusive. Here, we report a cryo-EM-based structural model of the Uba4/Urm1 complex that reveals the position of its RHD domains after Urm1 binding, and by analyzing the in vitro and in vivo consequence of mutations at the interface, we show its importance for the thiocarboxylation of Urm1. Our results confirm that the formation of the Uba4-Urm1 thioester and thiocarboxylation of Urm1’s C-terminus depend on conserved cysteine residues of Uba4 and that the complex avoids unwanted side-reactions of the adenylate by forming a thioester intermediate. We show how the Urm1-SH product can be released and how Urm1 interacts with upstream (Tum1) and downstream (Ncs6) components of the pathway. Our work provides a detailed mechanistic description of the reaction steps that are needed to produce Urm1-SH, which is required to thiolate tRNAs and persulfidate proteins.
Adaptive immunity of type VI CRISPR-Cas systems associated with reverse transcriptase–Cas1 fusion proteins
Authors: Molina-Sánchez María Dolores , Martínez-Abarca Francisco , Millán Vicenta , Mestre Mario Rodríguez , Stehantsev Pavlo , Stetsenko Artem , Guskov Albert , Toro Nicolás 
Published: December 2024

Abstract
Cas13-containing type VI CRISPR-Cas systems specifically target RNA; however, the mechanism of spacer acquisition remains unclear. We have previously reported the association of reverse transcriptase–Cas1 (RT–Cas1) fusion proteins with certain types of VI-A systems. Here, we show that RT–Cas1 fusion proteins are also recruited by type VI-B systems in bacteria from gut microbiomes, constituting a VI-B1 variant system that includes a CorA-encoding locus in addition to the CRISPR array and the RT–Cas1/Cas2 adaptation module. We found that type VI RT-CRISPR systems were functional for spacer acquisition, CRISPR array processing and interference activity, demonstrating that adaptive immunity mediated by these systems can function independently of other in trans systems. We provide evidence that the RT associated with these systems enables spacer acquisition from RNA molecules. We also found that CorA encoded by type VI-B1 RT-associated systems can transport divalent metal ions and downregulate Cas13b-mediated RNA interference. These findings highlight the importance of RTs in RNA-targeting CRISPR-Cas systems, potentially enabling the integration of RNA-derived spacers into CRISPR arrays as a mechanism against RNA-based invaders in specific environments.
RPA and Rad27 limit templated and inverted insertions at DNA breaks
Authors: Yu Yang , Wang Xin , Fox Jordan , Li Qian , Yu Yang , Hastings P J , Chen Kaifu , Ira Grzegorz 
Published: December 2024

Abstract
Formation of templated insertions at DNA double-strand breaks (DSBs) is very common in cancer cells. The mechanisms and enzymes regulating these events are largely unknown. Here, we investigated templated insertions in yeast at DSBs using amplicon sequencing across a repaired locus. We document very short (most ∼5–34 bp), templated inverted duplications at DSBs. They are generated through a foldback mechanism that utilizes microhomologies adjacent to the DSB. Enzymatic requirements suggest a hybrid mechanism wherein one end requires Polδ-mediated synthesis while the other end is captured by nonhomologous end joining (NHEJ) or by alternative end joining (Alt-EJ). This process is exacerbated in mutants with low levels or mutated RPA (rtt105Δ; rfa1-t33) or extensive resection deficiency (sgs1Δ exo1Δ). Templated insertions from various distant genomic locations also increase in RPA mutants as well as in rad27Δ and originate from fragile regions of the genome. Among complex insertions, common events are insertions of two sequences, originating from the same locus and with inverted orientation. We propose that these inversions are also formed by microhomology-mediated template switching. Together, we propose that a shortage of RPA, typical in cancer cells, may be a factor that stimulates the formation of templated insertions.
Repeated fasting events sensitize enhancers, transcription factor activity and gene expression to support augmented ketogenesis
Authors: Korenfeld Noga , Charni-Natan Meital , Bruse Justine , Goldberg Dana , Marciano-Anaki Dorin , Rotaro Dan , Gorbonos Tali , Radushkevitz-Frishman Talia , Polizzi Arnaud , Nasereddin Abed , Gover Ofer , Bar-Shimon Meirav , Fougerat Anne , Guillou Hervé , Goldstein Ido 
Published: December 2024

Abstract
Mammals withstand frequent and prolonged fasting periods due to hepatic production of glucose and ketone bodies. Because the fasting response is transcriptionally regulated, we asked whether enhancer dynamics impose a transcriptional program during recurrent fasting and whether this generates effects distinct from a single fasting bout. We found that mice undergoing alternate-day fasting (ADF) respond profoundly differently to a following fasting bout compared to mice first experiencing fasting. Hundreds of genes enabling ketogenesis are ‘sensitized’ (i.e. induced more strongly by fasting following ADF). Liver enhancers regulating these genes are also sensitized and harbor increased binding of PPARα, the main ketogenic transcription factor. ADF leads to augmented ketogenesis compared to a single fasting bout in wild-type, but not hepatocyte-specific PPARα-deficient mice. Thus, we found that past fasting events are ‘remembered’ in hepatocytes, sensitizing their enhancers to the next fasting bout and augment ketogenesis. Our findings shed light on transcriptional regulation mediating adaptation to repeated signals.
Spatial regulation of NSUN2-mediated tRNA m5C installation in cognitive function
Authors: Gonskikh Yulia , Tirrito Christian , Bommisetti Praneeth , Mendoza-Figueroa Maria Saraí , Stoute Julian , Kim Joshua , Wang Qin , Song Yuanquan , Liu Kathy Fange 
Published: December 2024

Abstract
Enzyme-mediated modifications of tRNA, such as 5-methylcytosine (m5C) installed by nuclear-enriched NOP2/Sun RNA methyltransferase 2 (NSUN2), play a critical role in neuronal development and function. However, our understanding of these modifications' spatial installation and biological functions remains incomplete. In this study, we demonstrate that a nucleoplasm-localized G679R NSUN2 mutant, linked to intellectual disability, diminishes NSUN2-mediated tRNA m5C in human cell lines and Drosophila. Our findings indicate that inability of G679R-NSUN2 to install m5C is primarily attributed to its reduced binding to tRNA rather than its nucleoplasmic localization. Conversely, an NSUN2 variant lacking an internal intrinsically disordered region (ΔIDR-NSUN2) can install ∼80% m5C within the nucleoplasm. Furthermore, we show that tRNA m5C levels are positively correlated to cognitive performance in Drosophila, where expressing G679R-NSUN2 leads to the most severe social behavioral deficits while expressing ΔIDR-NSUN2 results in less pronounced deficits. This work illuminates the molecular mechanism underlying G679R disease mutation in cognitive function and offers valuable insights into the significance of the cellular localization of m5C installation on tRNA for neuronal function.
When repetita no-longer iuvant: somatic instability of the CAG triplet in Huntington’s disease
Authors: Cattaneo Elena , Scalzo Davide , Zobel Martina , Iennaco Raffaele , Maffezzini Camilla , Besusso Dario , Maestri Simone 
Published: December 2024

Abstract
Trinucleotide repeats in DNA exhibit a dual nature due to their inherent instability. While their rapid expansion can diversify gene expression during evolution, exceeding a certain threshold can lead to diseases such as Huntington’s disease (HD), a neurodegenerative condition, triggered by &gt;36 C–A–G repeats in exon 1 of the Huntingtin gene. Notably, the discovery of somatic instability (SI) of the tract allows these mutations, inherited from an affected parent, to further expand throughout the patient’s lifetime, resulting in a mosaic brain with specific neurons exhibiting variable and often extreme CAG lengths, ultimately leading to their death. Genome-wide association studies have identified genetic variants—both cis and trans, including mismatch repair modifiers—that modulate SI, as shown in blood cells, and influence HD’s age of onset. This review will explore the evidence for SI in HD and its role in disease pathogenesis, as well as the therapeutic implications of these findings. We conclude by emphasizing the urgent need for reliable methods to quantify SI for diagnostic and prognostic purposes.
Fast intraoperative detection of primary central nervous system lymphoma and differentiation from common central nervous system tumors using stimulated Raman histology and deep learning
Authors: Reinecke David , Maarouf Nader , Smith Andrew , Alber Daniel , Markert John , Goff Nicolas K , Hollon Todd C , Chowdury Asadur , Jiang Cheng , Hou Xinhai , Meissner Anna-Katharina , Fürtjes Gina , Ruge Maximilian I , Ruess Daniel , Stehle Thomas , Al-Shughri Abdulkader , Körner Lisa I , Widhalm Georg , Roetzer-Pejrimovsky Thomas , Golfinos John G , Snuderl Matija , Neuschmelting Volker , Orringer Daniel A 
Published: December 2024

Abstract

Background
Accurate intraoperative diagnosis is crucial for differentiating between primary central nervous system (CNS) lymphoma (PCNSL) and other CNS entities, guiding surgical decision-making, but represents significant challenges due to overlapping histomorphological features, time constraints, and differing treatment strategies. We combined stimulated Raman histology (SRH) with deep learning to address this challenge.

Methods
We imaged unprocessed, label-free tissue samples intraoperatively using a portable Raman scattering microscope, generating virtual H&E-like images within &lt;3 min. We developed a deep learning pipeline called RapidLymphoma based on a self-supervised learning strategy to (1) detect PCNSL, (2) differentiate from other CNS entities, and (3) test the diagnostic performance in a prospective international multicenter cohort and 2 additional independent test cohorts. We trained on 54 000 SRH patch images sourced from surgical resections and stereotactic-guided biopsies, including various CNS neoplastic/nonneoplastic lesions. Training and test data were collected from 4 tertiary international medical centers. The final histopathological diagnosis served as ground truth.

Results
In the prospective test cohort of PCNSL and non-PCNSL entities (n = 160), RapidLymphoma achieved an overall balanced accuracy of 97.81% ± 0.91, non-inferior to frozen section analysis in detecting PCNSL (100% vs. 77.77%). The additional test cohorts (n = 420, n = 59) reached balanced accuracy rates of 95.44% ± 0.74 and 95.57% ± 2.47 in differentiating IDH-wildtype diffuse gliomas and various brain metastasis from PCNSL. Visual heatmaps revealed RapidLymphoma’s capabilities to detect class-specific histomorphological key features.

Conclusions
RapidLymphoma proves reliable and valid for intraoperative PCNSL detection and differentiation from other CNS entities. It provides visual feedback within 3 min, enabling fast clinical decision-making and subsequent treatment strategy planning.
Level I and II deficits—A clinical survey on international practice of awake craniotomy and definitions of postoperative “major” and “minor” deficits
Authors: Vooijs Manuela , Robertson Faith C , Blitz Sarah E , Jungk Christine , Krieg Sandro M , Schucht Philippe , De Vleeschouwer Steven , Vincent Arnaud J P E , Berger Mitchel S , Nahed Brian V , Broekman Marike L D , Gerritsen Jasper K W 
Published: December 2024

Abstract

Background
Awake craniotomy (AC) is a technique that balances maximum resection and minimal postoperative deficits in patients with intracranial tumors. To aid in the comparability of functional outcomes after awake surgery, this study investigated its international practice and aimed to define categories of postoperative deficits.

Methods
A survey was distributed via neurosurgical networks in Europe (European Association of Neurosurgical Societies, EANS), the Netherlands (Nederlandse Vereniging voor Neurochirurgie, NVVN), Belgium (Belgian Society of Neurosurgery, BSN), and the United States (Congress of Neurological Surgeons, CNS) between April 2022 and April 2023. Questions involved decision-making, including patient selection, anxiety assessment, and termination of resection. Interpretation of “major” and “minor” deficits, respectively labeled “level I” and “level II,” was assessed.

Results
Three hundred and ninety-five neurosurgeons from 46 countries completed the survey. Significant heterogeneity was found in the domains of indications, anxiety assessment, seizure management, and termination of resection. Moreover, the interpretation of “major” deficits mainly included language and motor impairments. Analysis across deficit categories showed significant overlap in the domains of executive function, social cognition, and vision. Secondly, “minor” deficits and “minor cognitive” deficits showed vast overlap.

Conclusions
This survey demonstrates high variability between neurosurgeons in AC practice across multiple domains, inviting international efforts to reach a consensus regarding the standardization and grading of postoperative deficits. The proposed categories of “level I” and “level II” deficits may aid in this standardization. It allows for systematic assessment of the benefit of surgery in neuro-oncology patients and allows for comparison of surgical outcomes between institutions and surgeons. This may help to optimize international guidelines for surgical neuro-oncology, including AC.
Stalking the stalk: Isolated pituitary stalk thickening and predictive factors for proliferative disease
Authors: Bennett Julie , Nobre Liana , Bouffet Eric , Abla Oussama , Maguire Bryan , Amirabadi Afsaneh , Hawkins Cynthia , Wasserman Jonathan D , Ertl-Wagner Birgit , Bartels Ute 
Published: December 2024

Abstract

Background
Few studies have evaluated predictive factors of isolated pituitary stalk thickening (iPST) in children.

Methods
In this retrospective study, radiology, endocrinology, and neuro-oncology databases were interrogated to identify patients with iPST between January 2000 and June 2019. A blinded, longitudinal assessment of MRIs was performed using quantitative, semi-quantitative, and qualitative metrics. Neuroimaging parameters were correlated to clinical parameters.

Results
Forty-seven patients were identified, with 40 meeting the inclusion criteria. Median age at baseline MRI was 9.6 years (range 0.9–17.5) with median follow-up of 5.2 years (range 0.3–18.6). Twenty-five (63%) were female. Thirty-four (85%) had pituitary dysfunction, including 31 with central diabetes insipidus (cDI). cDI was not predictive of proliferative disease (PfD): 69% of those with presumed primary hypophysitis (PPH) versus 93% with PfD (P = .1). Fourteen (35%) patients were diagnosed with PfD (germinoma = 8, Langerhans cell histiocytosis = 5, lymphoma = 1) at median of 1.3 years (range 0.3–4.0) after initial MRI. Progressive thickening of the stalk over time was associated with PfD (86% vs 4% in PPH, P &lt; .0001), as was thickening of the entire stalk (56% in PfD vs 27% in PPH, P &lt; .0001) with different imaging trends over time observed in PfD versus PPH. A “sack of marbles” appearance with heterogeneous enhancement on post-contrast imaging was associated with germinoma.

Conclusions
In this cohort, 35% of children with iPST were diagnosed with PfD. The association of cDI and PfD was not statistically significant. Progressive thickening of the entire stalk was predictive of PfD and a “sack of marbles” pattern was found to be highly suggestive of germinoma.
The evolution of chemical ordering and property in Fe1+xSe2 upon intercalation ratios
Authors: Zhao Zijing , Han Xiaocang , Zhu Shengcai , Fang Zhi , Han Ziyi , Liang Zhongyu , Li Bailing , Zhang Biao , Li Wei , Luo Zhaochu , Peng Licong , Zhao Xiaoxu , Li Xiangguo , Zhou Jiadong , Gao Song , Wang Chengxin , Kläui Mathias , Hou Yanglong 
Published: December 2024

ABSTRACT
Intercalation has been considered as an effective method to explore innovative two-dimensional (2D) materials and modify their properties. However, the relationship between intercalation concentration, structure, and property remains a largely uncharted territory, and the controllable synthesis of desired intercalated phases faces challenges. Here, a general intercalated rule for the effect of self-intercalation ratio on atomic arrangements is revealed. Then, the controllable synthesis of a series of Fe-intercalated 2D materials is realized. Scanning transmission electron microscopy illustrates that their intercalation structures undergo disordered/ordered/half-ordered/ordered transformation, which confirms the intercalated rule and proposes a new structure termed half-ordered intercalation. Notably, their magnetic and electrical properties can be significantly modulated by intercalation. Orderly intercalated nanoflakes possess room-temperature magnetism with composition-regulated magnetic domains. Moreover, Fe1.5Se2 and Fe1.6Se2 are scarce half-metallic materials showing different magneto-resistance behaviors. This work would guide the design and synthesis of new intercalated materials, and deepen the understanding of the relationship between structure and properties.
CHRNA5-A3-B4, CYP2A6, and DBH Genetic Associations With Smoking Cessation Throughout Adulthood Within Two Longitudinal Studies of Women
Authors: Jones Stephanie K , Alberg Anthony J , Wallace Kristin , Froeliger Brett , Carpenter Matthew J , Wolf Bethany J 
Published: December 2024

Abstract

Introduction
Genetic studies of smoking cessation have been limited by short-term follow-up or cross-sectional design. Within seven genes (CHRNA3, CHRNA5, CHRNB2, CHRNB4, DRD2, DBH, and CYP2A6) influencing biological mechanisms relevant to smoking, this study aimed to identify single nucleotide polymorphisms (SNPs) associated with smoking cessation throughout up to 38 years of follow-up.

Aims and Methods
Participants were from two all-female cohort studies, Nurses’ Health Study (NHS) (n = 10 017) and NHS-2 (n = 2793). For 132 SNPs providing coverage of these genes, genotype associations with the probability of quitting smoking over time were evaluated using generalized estimating equations models. For SNPs reaching nominal statistical significance (p &lt; .05) within NHS, NHS-2 was used as the replication cohort to control for multiple testing (false discovery rate [FDR] &lt; 0.05). SNP genotype by smoking intensity (lifetime light vs. non-light smoking) interactions were also evaluated.

Results
Five SNPs identified in NHS were replicated in NHS-2 with FDR &lt; 0.05. Women with the minor alleles of CHRNA5 SNPs rs637137 (odd ratio [OR] = 1.21) and rs503464 (OR = 1.24) had increased odds of cessation. Women with the minor alleles of CYP2A6 SNPs rs56113850 (OR = 0.81) and rs56267346 (OR = 0.82) and DBH SNP rs6479643 (OR = 0.78) had lower odds of cessation throughout adulthood. An interaction with smoking intensity was indicated for three SNPs, CHRNB4 rs4887074, CHRNA3 SNP rs77438700, and CHRNA5 SNP rs76474922.

Conclusion
Genetic associations with smoking cessation over decades of follow-up were observed and may guide targeted approaches for smokers most at risk for long-term relapse.

Implications
This study identified single nucleotide polymorphisms within CHRNA5-A3-B4, CYP2A6, and DBH that were associated with smoking cessation in women over decades of follow-up. This study is the first to examine these genetic associations over years of follow-up. Some associations were novel while others replicated previous findings from short-term studies for the first time. Potential differences in some associations between light and non-light smokers were also observed. Genetic factors associated with long-term smoking behavior may help inform interventions modeled on long-term chronic disease management approaches; specifically, targeted maintenance interventions to sustain abstinence could be implemented among high-risk smokers.
A Stop-Smoking Strategy After Cervical Cancer Screening: Results of a Cluster-Randomized Controlled Trial in Dutch General Practice
Authors: Mansour Marthe B L , Crone Mathilde R , van Weert Henk C , Chavannes Niels H , van Asselt Kristel M 
Published: December 2024

Abstract

Introduction
This study aimed to assess whether brief stop-smoking advice given to women who smoke and visit their general practice for cervical cancer screening improves smoking cessation outcomes.

Aims and Methods
This two-arm cluster-randomized controlled trial was conducted in 75 Dutch general practices. Participants in the intervention group received brief stop-smoking advice based on the Ask-Advise-Connect method, delivered by a practice assistant. Patient-reported outcomes were measured at 6 months: undertaking a serious quit attempt of at least 24 hours during follow-up (primary outcome), 7-day point prevalence abstinence at 6 months, reduction in number of cigarettes smoked, increase in motivation to quit smoking, exposure to advice or support, and other psychological and behavioral measurements.

Results
There was no significant difference in undertaking a serious quit attempt between the intervention (39.8% of n = 266) and control group (36.0% of n = 214), odds ratio 1.18 (95% confidence intervals: 0.80–1.72, p = .41). Neither did the point prevalence abstinence significantly differ between groups: 21.1% versus 16.3%, odds ratio 1.38 (95% confidence interval: 0.83–2.29, p = .21). Although nonsignificant, the direction of effects for the aforementioned outcomes was in favor of the intervention group. The reduction in the number of cigarettes smoked and increase in motivation to quit did not differ between groups. The uptake of cessation counseling was higher in the intervention (14.7%) than in the control group (2.8%).

Conclusions
A brief stop-smoking strategy after the smear test for cervical screening might encourage women who smoke to attempt quitting and seek cessation counseling, but a significant effect could not be demonstrated in this trial.

Implications
The results of this cluster-randomized trial suggest that brief advice to stop-smoking delivered by a practice assistant after routine cervical screening in general practice might encourage women who smoke to attempt quitting, but a significant effect could not be proven. Also, women who receive advice show a higher uptake of professional cessation counseling compared to their controls. Providing brief advice after the cervical smear might therefore be a useful opportunistic approach to stimulate cessation in women who smoke.