bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular basis of an atypical dsDNA 5mC/6mA bifunctional dioxygenase CcTet from Coprinopsis cinerea in catalyzing dsDNA 5mC demethylation
Authors: Zhang Lin , Mu Yajuan , Li Tingting , Hu Jingyan , Lin Houwen , Zhang Liang 
Published: February 2024

Abstract
The eukaryotic epigenetic modifications 5-methyldeoxycytosine (5mC) and N6-methyldeoxyadenine (6mA) have indispensable regulatory roles in gene expression and embryonic development. We recently identified an atypical bifunctional dioxygenase CcTet from Coprinopsis cinerea that works on both 5mC and 6mA demethylation. The nonconserved residues Gly331 and Asp337 of CcTet facilitate 6mA accommodation, while D337F unexpectedly abolishes 5mC oxidation activity without interfering 6mA demethylation, indicating a prominent distinct but unclear 5mC oxidation mechanism to the conventional Tet enzymes. Here, we assessed the molecular mechanism of CcTet in catalyzing 5mC oxidation by representing the crystal structure of CcTet–5mC-dsDNA complex. We identified the distinct mechanism by which CcTet recognizes 5mC-dsDNA compared to 6mA-dsDNA substrate. Moreover, Asp337 was found to have a central role in compensating for the loss of a critical 5mC-stablizing H-bond observed in conventional Tet enzymes, and stabilizes 5mC and subsequent intermediates through an H-bond with the N4 atom of the substrates. These findings improve our understanding of Tet enzyme functions in the dsDNA 5mC and 6mA demethylation pathways, and provide useful information for future discovery of small molecular probes targeting Tet enzymes in DNA active demethylation processes.
Differential expression of paralog RNA binding proteins establishes a dynamic splicing program required for normal cerebral cortex development
Authors: Cesari Eleonora , Farini Donatella , Medici Vanessa , Ehrmann Ingrid , Guerra Marika , Testa Erika , Naro Chiara , Geloso Maria Concetta , Pagliarini Vittoria , La Barbera Livia , D’Amelio Marcello , Orsini Tiziana , Vecchioli Stefano Farioli , Tamagnone Luca , Fort Philippe , Viscomi Maria Teresa , Elliott David J , Sette Claudio 
Published: February 2024

Abstract
Sam68 and SLM2 are paralog RNA binding proteins (RBPs) expressed in the cerebral cortex and display similar splicing activities. However, their relative functions during cortical development are unknown. We found that these RBPs exhibit an opposite expression pattern during development. Sam68 expression declines postnatally while SLM2 increases after birth, and this developmental pattern is reinforced by hierarchical control of Sam68 expression by SLM2. Analysis of Sam68:Slm2 double knockout (Sam68:Slm2dko) mice revealed hundreds of exons that respond to joint depletion of these proteins. Moreover, parallel analysis of single and double knockout cortices indicated that exons regulated mainly by SLM2 are characterized by a dynamic splicing pattern during development, whereas Sam68-dependent exons are spliced at relatively constant rates. Dynamic splicing of SLM2-sensitive exons is completely suppressed in the Sam68:Slm2dko developing cortex. Sam68:Slm2dko mice die perinatally with defects in neurogenesis and in neuronal differentiation, and develop a hydrocephalus, consistent with splicing alterations in genes related to these biological processes. Thus, our study reveals that developmental control of separate Sam68 and Slm2 paralog genes encoding homologous RBPs enables the orchestration of a dynamic splicing program needed for brain development and viability, while ensuring a robust redundant mechanism that supports proper cortical development.
Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma
Authors: Fitzsimmons Christina M , Mandler Mariana D , Lunger Judith C , Chan Dalen , Maligireddy Siddhardha S , Schmiechen Alexandra C , Gamage Supuni Thalalla , Link Courtney , Jenkins Lisa M , Chan King , Andresson Thorkell , Crooks Daniel R , Meier Jordan L , Linehan W Marston , Batista Pedro J 
Published: February 2024

Abstract
Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of an aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxoglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1α, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively affects the levels of N6-methyladenosine (m6A), while the levels of 5-formylcytosine (f5C) in mitochondrial tRNA are unaffected. This supports the hypothesis of a differential impact of fumarate accumulation on distinct RNA demethylases. The observation that metabolites modulate specific subsets of RNA-modifying enzymes offers new insights into the intersection between metabolism and the epitranscriptome.
ChEC-seq2: an improved chromatin endogenous cleavage sequencing method and bioinformatic analysis pipeline for mapping in vivo protein–DNA interactions
Authors: VanBelzen Jake , Duan Chengzhe , Brickner Donna Garvey , Brickner Jason H 
Published: February 2024

Abstract
Defining the in vivo DNA binding specificity of transcription factors (TFs) has relied nearly exclusively on chromatin immunoprecipitation (ChIP). While ChIP reveals TF binding patterns, its resolution is low. Higher resolution methods employing nucleases such as ChIP-exo, chromatin endogenous cleavage (ChEC-seq) and CUT&RUN resolve both TF occupancy and binding site protection. ChEC-seq, in which an endogenous TF is fused to micrococcal nuclease, requires neither fixation nor antibodies. However, the specificity of DNA cleavage during ChEC has been suggested to be lower than the specificity of the peaks identified by ChIP or ChIP-exo, perhaps reflecting non-specific binding of transcription factors to DNA. We have simplified the ChEC-seq protocol to minimize nuclease digestion while increasing the yield of cleaved DNA. ChEC-seq2 cleavage patterns were highly reproducible between replicates and with published ChEC-seq data. Combined with DoubleChEC, a new bioinformatic pipeline that removes non-specific cleavage sites, ChEC-seq2 identified high-confidence cleavage sites for three different yeast TFs that are strongly enriched for their known binding sites and adjacent to known target genes.
Access to appropriate interpretation is essential for the health of children
Authors: Hui Charles 
Published: February 2024

Abstract
With 20% of Canadians reporting a mother tongue other than English or French, it is not uncommon for health professionals and patients to be proficient in different languages. When a physician and patient cannot properly communicate, there is potential for misunderstanding, which can lead to poor clinical outcomes and hospital readmission. Professional interpretation services are associated with improved communication, health care use, clinical outcomes, and satisfaction with care. Using untrained or ad hoc interpreters—including family members—has been shown to increase errors of omission, substitution, editorialization, and addition. Children and youth are not sufficiently developmentally mature to act as interpreters in health care. Using children and youth as interpreters in health care settings places them in an inappropriate and potentially difficult situation that may have lasting negative effects on both their own mental health and their relationships with other family members.
Variation in leaf dark respiration among C3 and C4 grasses is associated with use of different substrates
Authors: Fan Yuzhen , Tcherkez Guillaume , Scafaro Andrew P , Taylor Nicolas L , Furbank Robert T , von Caemmerer Susanne , Atkin Owen K 
Published: February 2024

Abstract
Measurements of respiratory properties have often been made at a single time point either during daytime using dark-adapted leaves or during nighttime. The influence of the day–night cycle on respiratory metabolism has received less attention but is crucial to understand photosynthesis and photorespiration. Here, we examined how CO2- and O2-based rates of leaf dark respiration (Rdark) differed between midday (after 30-min dark adaptation) and midnight in 8 C3 and C4 grasses. We used these data to calculate the respiratory quotient (RQ; ratio of CO2 release to O2 uptake), and assessed relationships between Rdark and leaf metabolome. Rdark was higher at midday than midnight, especially in C4 species. The day–night difference in Rdark was more evident when expressed on a CO2 than O2 basis, with the RQ being higher at midday than midnight in all species, except in rice (Oryza sativa). Metabolomic analyses showed little correlation of Rdark or RQ with leaf carbohydrates (sucrose, glucose, fructose, or starch) but strong multivariate relationships with other metabolites. The results suggest that rates of Rdark and differences in RQ were determined by several concurrent CO2-producing and O2-consuming metabolic pathways, not only the tricarboxylic acid cycle (organic acids utilization) but also the pentose phosphate pathway, galactose metabolism, and secondary metabolism. As such, Rdark was time-, type- (C3/C4) and species-dependent, due to the use of different substrates.
Serum protein profiling reveals distinct patient clusters in giant cell arteritis
Authors: Zingg Flavia , Ryser Fabio S , Gloor Andrea D , Polysopoulos Christos , Villiger Peter M , Maurer Britta , Christ Lisa 
Published: February 2024

Abstract

Objectives
We investigated the potential of serum proteins for distinguishing clinical and molecular subtypes in patients with GCA.

Methods
Proximity extension assays were used to analyse 1463 proteins in serum samples from patients with new-onset GCA (n = 16) and patients who have achieved remission (n = 13). Unsupervised and supervised cluster analyses were performed.

Results
Unsupervised cluster analysis identified three distinct clusters based on the protein signature. Compared with cluster 2, patients of cluster 1 had fewer PMR symptoms, increased levels of macrophage migration inhibitory factor (MIF) and pronounced NF-κB, STAT5 and IL-1 signalling. The changes in serum proteins upon remission differed between cluster 1 and 2.
Patients with cranial GCA were characterized by altered endothelial and Th17 signalling, whereas patients not responding to treatment within the GUSTO-trial showed increased Th1 and diminished B cell signalling. Patients with anterior ischaemic optic neuropathy displayed higher levels of CHI3L1 (YKL40) and MMP12, and reduced levels of TIMP3.

Conclusion
Protein profiling identified patient clusters in GCA with distinct proteomic features and therefore likely different pathophysiology. These unique proteomic footprints might lead to more targeted treatments in future.
Preliminary nomogram model for predicting irreversible organ damage of patients with systemic sclerosis
Authors: Huo Xiaocong , Huang Xinxiang , Yang Yanting , Wei Chengcheng , Meng Danli , Huang Rongjun , Lin Jinying 
Published: February 2024

Abstract

Objective
To investigate predictive factors for irreversible organ damage in systemic sclerosis (SSc) and establish a nomogram model.

Methods
This retrospective study included patients with SSc who were treated at our hospital between March 2013 and March 2023. Irreversible organ damage included heart failure, respiratory failure, renal failure, and gangrene of the hands and feet. Cox and LASSO regression analyses were performed to determine the predictive factors. Based on the results, a nomogram model was developed. The model was evaluated using the C-indices, calibration plots and DCA.

Results
A total of 361 patients with systemic sclerosis were randomly divided into the development (n = 181) and validation (n = 180) groups. Multivariate Cox regression analysis showed that age ≥65 years, weight loss, digital ulcers, mRSS ≥16, elevated creatinine, elevated myoglobin, elevated C-reactive protein, renal involvement and cardiac involvement were independent risk factors. Based on the LASSO analysis, a nomogram model of irreversible organ damage was established. The C-indices of the development group at 24, 60 and 96 m were 96.7, 84.5 and 85.7, whereas those of the validation group at 24, 60 and 96 m were 86.6, 79.1 and 78.5, respectively. The results of the DCA showed that the nomogram can be used as a valuable tool to predict irreversible organ damage in patients with SSc.

Conclusion
We included commonly used clinical indicators. According to the nomogram, the probability of irreversible organ damage can be calculated and high-risk patients can be identified.
Public Child Care Provision: Unraveling the Consequences of Implementation Variations for Women's Time Allocation
Authors: Mata Catherine 
Published: February 2024

Abstract
From analysis of the effects of a national childcare policy on women's time allocation in Costa Rica, it is found that childcare services are associated with increased female labor force participation, greater educational enrollment, and reduced unpaid care work. However, a comparison of two implementing agencies indicates that the overall effects vary by agency. One agency's services yield positive outcomes, such as increased labor force participation, reduced unpaid care work, and increased educational attendance; the other agency's results are less favorable, particularly for part-time childcare users. These findings highlight the challenges governments face when scaling up interventions, as different implementing agencies may modify program criteria, serve distinct populations, and offer varying services. While policies can be effective on a smaller scale, impacts may differ when they are scaled up. Understanding these variations can help governments adapt policies and reallocate resources to achieve their intended goals.
Mitochondrial sodium/calcium exchanger (NCLX) regulates basal and starvation‐induced autophagy through calcium signaling
Authors: Ramos Vitor M. , Serna Julian D. C. , Vilas‐Boas Eloisa A. , Cabral‐Costa João Victor , Cunha Fernanda M. , Kataura Tetsushi , Korolchuk Viktor I. , Kowaltowski Alicia J. 
Published: February 2024

AbstractMitochondria shape intracellular Ca2+ signaling through the concerted activity of Ca2+ uptake via mitochondrial calcium uniporters and efflux by Na+/Ca2+ exchangers (NCLX). Here, we describe a novel relationship among NCLX, intracellular Ca2+, and autophagic activity. Conditions that stimulate autophagy in vivo and in vitro, such as caloric restriction and nutrient deprivation, upregulate NCLX expression in hepatic tissue and cells. Conversely, knockdown of NCLX impairs basal and starvation‐induced autophagy. Similarly, acute inhibition of NCLX activity by CGP 37157 affects bulk and endoplasmic reticulum autophagy (ER‐phagy) without significant impacts on mitophagy. Mechanistically, CGP 37157 inhibited the formation of FIP200 puncta and downstream autophagosome biogenesis. Inhibition of NCLX caused decreased cytosolic Ca2+ levels, and intracellular Ca2+ chelation similarly suppressed autophagy. Furthermore, chelation did not exhibit an additive effect on NCLX inhibition of autophagy, demonstrating that mitochondrial Ca2+ efflux regulates autophagy through the modulation of Ca2+ signaling. Collectively, our results show that the mitochondrial Ca2+ extrusion pathway through NCLX is an important regulatory node linking nutrient restriction and autophagy regulation.
Survival in Patients With Spinal Metastatic Disease Treated Nonoperatively With Radiotherapy
Authors: Fenn Brian P. , Karhade Aditya V. , Groot Olivier Q. , Collins Austin K. , Balboni Tracy A. , Oh Kevin S. , Ferrone Marco L. , Schwab Joseph H. 
Published: February 2024

Summary of Background Data:
The SORG-ML algorithms for survival in spinal metastatic disease were developed in patients who underwent surgery and were externally validated for patients managed operatively.

Objective:
To externally validate the SORG-ML algorithms for survival in spinal metastatic disease in patients managed nonoperatively with radiation.

Study Design:
Retrospective cohort.

Methods:
The performance of the SORG-ML algorithms was assessed by discrimination [receiver operating curves and area under the receiver operating curve (AUC)], calibration (calibration plots), decision curve analysis, and overall performance (Brier score). The primary outcomes were 90-day and 1-year mortality.

Results:
Overall, 2074 adult patients underwent radiation for spinal metastatic disease and 29% (n=521) and 59% (n=917) had 90-day and 1-year mortality, respectively. On complete case analysis (n=415), the AUC was 0.76 (95% CI: 0.71–0.80) and 0.78 (95% CI: 0.73–0.83) for 90-day and 1-year mortality with fair calibration and positive net benefit confirmed by the decision curve analysis. With multiple imputation (n=2074), the AUC was 0.85 (95% CI: 0.83–0.87) and 0.87 (95% CI: 0.85–0.89) for 90-day and 1-year mortality with fair calibration and positive net benefit confirmed by the decision curve analysis.

Conclusion:
The SORG-ML algorithms for survival in spinal metastatic disease generalize well to patients managed nonoperatively with radiation.
Does Intrawound Vancomycin Decrease Postoperative Surgical Site Infection in Spine Surgery
Authors: Pinter Zachariah , Honig Rachel , Sebastian Arjun , Nassr Ahmad , Freedman Brett , Yaszemski Michael , Huddleston Paul , Berbari Elie , Currier Bradford 
Published: February 2024

Study Design:
Retrospective Case-Control series.

Objective:
The objective of this study is to define the overall postoperative rate of surgical site infection (SSI) in patients undergoing spine surgery and examine the effects of intrawound Vancomycin on postoperative infection rates.

Summary of Background Data:
Surgical site infections (SSI) account for 22% of all health care-associated infections. The use of intrawound Vancomycin in an attempt to reduce the incidence of postoperative SSI has not been sufficiently evaluated in the existing literature.

Methods:
All spine surgeries (n=19,081) from our institution were reviewed from 2003 to 2013. All cases of verified SSI were identified from the database. Cases were then matched to controls in a 1:1 fashion based on age, gender, and date of surgery (+/−30 d). Patient demographics, comorbidities, estimated blood loss, duration of surgery, intrawound administration of Vancomycin, and smoking status were evaluated.

Results:
At total of 316 cases of SSI after spine surgery were identified, representing an infection rate of 1.7%. The mean follow-up for cases and controls was 31.5 and 41.6 months, respectively. OR for intrawound Vancomycin was 0.44 (95% CI 0.23–0.88, P=0.019). OR for BMI greater than 30 was 1.63 (95% CI 1.04–2.56, P=0.03).

Conclusions:
In this large cohort of spine surgery patients, administration of intrawound Vancomycin was associated with a significant reduction in postoperative surgical site infections. Further studies are needed to determine appropriate dosing and application as well as long-term safety in spine surgery.
One Tube Does Not Fit All: Parent Experiences and Decision-Making for Choosing a Nasogastric Tube or Gastrostomy for Their Child During Allogeneic Bone Marrow Transplant
Authors: Evans James , Lanigan Julie , Green Dan , O’Connor Graeme , Gibson Faith 
Published: February 2024

Background:
Children undergoing bone marrow transplant (BMT) are at risk of developing malnutrition. A feeding tube becomes a requirement for most children to meet their nutritional and medication requirements. Two tubes are typically used: nasogastric tube (NGT) or gastrostomy. At the UK center where this study took place, parents are offered a choice between these tubes.

Objective:
This qualitative data collection in a mixed methods study explored why parents choose either tube and their experiences of using it.

Methods:
Parents participated in 2 semistructured interviews. First, on admission to explore why they chose either tube. Second, 1–2 months postdischarge to explore their experience of using the tube. Interviews took place over 18 months. Transcripts were thematically analyzed.

Results:
Sixteen parents whose child had an NGT, 17 a gastrostomy, were interviewed. Choice was experienced across a continuum of difficulty and freedom. Many parents deferred to the expertise of professionals; others felt they were the experts in their child. Influential factors in decision-making included expected duration of need, the child’s age and activity, cosmetic differences, balancing gastrostomy surgery against NGT dislodgement, lay advice, healthcare professionals’ recommendations and prior tube feeding experiences.

Conclusions:
Parents valued choice appreciating 1 feeding tube might not suit every child.

Implications for Practice:
Choice of a gastrostomy or NGT should be offered to children prior to BMT.

What is Foundational:
Parents navigate a complex decision-making process when choosing a feeding tube for their child. Healthcare professionals can facilitate informed decision-making through collaborative discussions, inclusion of peer support, and provision of balanced information.
Multiple Chronic Conditions and the Receipt of Cancer Survivorship Care Plans
Authors: Oyinbo Atinuke G. , Castaneda-Avila Maira A. , Tisminetzky Mayra S. , Faro Jamie M. , Epstein Mara M. , Lapane Kate L. 
Published: February 2024

Background:
Most cancer survivors have multiple chronic conditions (MCC) that make it challenging to navigate disease management processes post cancer treatment.

Objective:
To examine associations between having MCC and receiving a survivorship care plan (SCP), which has potential benefits for improved follow-up care, among cancer survivors.

Methods:
Behavioral Risk Factor Surveillance System respondents with a self-reported history of cancer not actively receiving cancer treatment were included (N = 5449). SCP receipt was defined as being provided a written summary of cancer treatments received and instructions for follow-up care upon treatment completion. MCC was categorized as 0, 1, 2, or ≥3 based on a sum of 10 chronic conditions. Multivariable-adjusted logistic models were used to assess the association between MCC and SCP receipt.

Results:
Most cancer survivors were age 65 or older (59%) and female (58%). Sixty percent reported receiving an SCP and 50% had at least 2 chronic conditions. Compared to those with no chronic conditions, cancer survivors with 2 and 3 or more conditions were less likely to have received an SCP.

Conclusions:
Professional organizations recommend that cancer survivors receive SCPs; however, having MCC was inversely associated with SCP provision.

Implications for Practice:
The high necessity for SCPs among cancer survivors with MCC and the potential barriers associated with their delivery should be recognized by healthcare professionals.

What is Foundational:
This work highlights unmet survivorship care needs in cancer survivors with MCC. The findings emphasize the need to promote greater access to SCPs in healthcare settings that cater to cancer survivors with comorbid conditions.