bluuebunny/crossref_metadata_2025_split huggingface dataset:
MethParquet: an R package for rapid and efficient DNA methylation association analysis adopting Apache Parquet
Authors: Wang Ziqing , Cassidy Michael , Wallace Danielle A , Sofer Tamar 
Published: June 2024

Abstract

Summary
Genome-wide DNA methylation (DNAm) profiling is indispensable for unveiling how DNAm regulates biological pathways and individual phenotypes. However, managing and analyzing extensive DNAm data generated from large cohort studies present computational obstacles. Apache Parquet is a data file format that allows for efficient data storage, retrieval, and manipulation, alleviating computational hurdles associated with conventional row-based formats. We here introduce MethParquet, the first R package leveraging the columnar Parquet format for efficient DNAm data analysis. It can be used for data extraction, methylation risk score calculation, epigenome-wide association analyses, and other standard post-quality control tasks. The package flexibly implements diverse regression models. Via a public methylation dataset, we show the efficiency of this package in reducing running time and RAM usage in large-scale EWAS.

Availability and implementation
The MethParquet R package is publicly available on the GitHub repository https://github.com/ZWangTen/MethParquet. It includes a vignette and a toy dataset derived from a public resource.
DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes
Authors: Tiberi Simone , Meili Joël , Cai Peiying , Soneson Charlotte , He Dongze , Sarkar Hirak , Avalos-Pacheco Alejandra , Patro Rob , Robinson Mark D 
Published: June 2024

Summary
Although transcriptomics data is typically used to analyze mature spliced mRNA, recent attention has focused on jointly investigating spliced and unspliced (or precursor-) mRNA, which can be used to study gene regulation and changes in gene expression production. Nonetheless, most methods for spliced/unspliced inference (such as RNA velocity tools) focus on individual samples, and rarely allow comparisons between groups of samples (e.g. healthy vs. diseased). Furthermore, this kind of inference is challenging, because spliced and unspliced mRNA abundance is characterized by a high degree of quantification uncertainty, due to the prevalence of multi-mapping reads, ie reads compatible with multiple transcripts (or genes), and/or with both their spliced and unspliced versions. Here, we present DifferentialRegulation, a Bayesian hierarchical method to discover changes between experimental conditions with respect to the relative abundance of unspliced mRNA (over the total mRNA). We model the quantification uncertainty via a latent variable approach, where reads are allocated to their gene/transcript of origin, and to the respective splice version. We designed several benchmarks where our approach shows good performance, in terms of sensitivity and error control, vs. state-of-the-art competitors. Importantly, our tool is flexible, and works with both bulk and single-cell RNA-sequencing data. DifferentialRegulation is distributed as a Bioconductor R package.
Default mode network electrophysiological dynamics and causal role in creative thinking
Authors: Bartoli Eleonora , Devara Ethan , Dang Huy Q , Rabinovich Rikki , Mathura Raissa K , Anand Adrish , Pascuzzi Bailey R , Adkinson Joshua , Kenett Yoed N , Bijanki Kelly R , Sheth Sameer A , Shofty Ben 
Published: June 2024

Abstract
The default mode network (DMN) is a widely distributed, intrinsic brain network thought to play a crucial role in internally directed cognition. The present study employs stereo-EEG in 13 human patients, obtaining high resolution neural recordings across multiple canonical DMN regions during two processes that have been associated with creative thinking: spontaneous and divergent thought. We probe these two DMN-associated higher cognitive functions through mind wandering and alternate uses tasks, respectively. Our results reveal DMN recruitment during both tasks, as well as a task-specific dissociation in spatiotemporal response dynamics.
When compared to the fronto-parietal network, DMN activity was characterized by a stronger increase in gamma band power (30–70 Hz) coupled with lower theta band power (4–8 Hz). The difference in activity between the two networks was especially strong during the mind wandering task. Within the DMN, we found that the tasks showed different dynamics, with the alternate uses task engaging the DMN more during the initial stage of the task, and mind wandering in the later stage. Gamma power changes were mainly driven by lateral DMN sites, while theta power displayed task-specific effects. During alternate uses task, theta changes did not show spatial differences within the DMN, while mind wandering was associated to an early lateral and late dorsomedial DMN engagement. Furthermore, causal manipulations of DMN regions using direct cortical stimulation preferentially decreased the originality of responses in the alternative uses task, without affecting fluency or mind wandering.
Our results suggest that DMN activity is flexibly modulated as a function of specific cognitive processes and supports its causal role in divergent thinking. These findings shed light on the neural constructs supporting different forms of cognition and provide causal evidence for the role of DMN in the generation of original connections among concepts.
Neurovascular coupling dysfunction associated with cognitive impairment in presbycusis
Authors: Xing Chunhua , Feng Jianhua , Yao Jun , Xu Xiao-Min , Wu Yuanqing , Yin Xindao , Salvi Richard , Chen Yu-Chen , Fang Xiangming 
Published: June 2024

AbstractThe neuropathological mechanism underlying presbycusis remains unclear. This study aimed to illustrate the mechanism of neurovascular coupling associated with cognitive impairment in patients with presbycusis. We assessed the coupling of cerebral blood perfusion with spontaneous neuronal activity by calculating the correlation coefficients between cerebral blood flow and blood oxygen level-dependent-derived quantitative maps (amplitude of low-frequency fluctuation, fractional amplitude of low-frequency fluctuation, regional homogeneity, degree centrality). Four neurovascular coupling metrics (cerebral blood flow-amplitude of low-frequency fluctuation, cerebral blood flow-fractional amplitude of low-frequency fluctuation, cerebral blood flow-regional homogeneity and cerebral blood flow-degree centrality) were compared at the global and regional levels between the presbycusis group and the healthy control group, and the intrinsic association between the altered neurovascular coupling metrics and the neuropsychological scale was further analysed in the presbycusis group. At the global level, neurovascular coupling was significantly lower in the presbycusis group than in the control group and partially related to cognitive level. At the regional level, neurovascular biomarkers were significantly elevated in three brain regions and significantly decreased in one brain region, all of which involved the Papez circuit. Regional neurovascular coupling provides more information than global neurovascular coupling, and neurovascular coupling dysfunction within the Papez circuit has been shown to reveal the causes of poor cognitive and emotional responses in age-related hearing loss patients.
Uncovering the power of neurofeedback: a meta-analysis of its effectiveness in treating major depressive disorders
Authors: Xia Zheng , Yang Peng-Yuan , Chen Si-Lu , Zhou Han-Yu , Yan Chao 
Published: June 2024

Abstract
Neurofeedback, a non-invasive intervention, has been increasingly used as a potential treatment for major depressive disorders. However, the effectiveness of neurofeedback in alleviating depressive symptoms remains uncertain. To address this gap, we conducted a comprehensive meta-analysis to evaluate the efficacy of neurofeedback as a treatment for major depressive disorders. We conducted a comprehensive meta-analysis of 22 studies investigating the effects of neurofeedback interventions on depression symptoms, neurophysiological outcomes, and neuropsychological function. Our analysis included the calculation of Hedges’ g effect sizes and explored various moderators like intervention settings, study designs, and demographics. Our findings revealed that neurofeedback intervention had a significant impact on depression symptoms (Hedges’ g = −0.600) and neurophysiological outcomes (Hedges’ g = −0.726). We also observed a moderate effect size for neurofeedback intervention on neuropsychological function (Hedges’ g = −0.418). As expected, we observed that longer intervention length was associated with better outcomes for depressive symptoms (β = −4.36, P &lt; 0.001) and neuropsychological function (β = −2.89, P = 0.003). Surprisingly, we found that shorter neurofeedback sessions were associated with improvements in neurophysiological outcomes (β = 3.34, P &lt; 0.001). Our meta-analysis provides compelling evidence that neurofeedback holds promising potential as a non-pharmacological intervention option for effectively improving depressive symptoms, neurophysiological outcomes, and neuropsychological function in individuals with major depressive disorders.
Compound heterozygous variants of ANKFY1 in a child with infantile-onset proteinuria and movement disorder
Authors: Zhang Luyan , Cheng Xueqin , Wang Chunli , Zhou Wei , Zheng Bixia , Zhang Aihua 
Published: June 2024

ABSTRACT
The ANKFY1 gene encodes a protein that belongs to double zinc finger proteins involved in endocytosis. Only one family with steroid-resistant nephrotic syndrome has been reported carrying a homozygous variant in ANKFY1 so far. Here we describe the second case where a 13-year-old boy presented with infantile-onset proteinuria and movement disorder. Whole-exome sequencing showed compound heterozygous variants (NM_001330063.2: c.2753C&gt;G; p.Ser918Ter, and c.3287–11_3287–10del) in ANKFY1. In vitro functional study revealed the two variants led to reduced protein expression level of ANKFY1. This is the first case of co-existence of renal and nervous system phenotypes in a child with variants in ANKFY1, suggesting that bi-allelic variants in ANKFY1 might be associated with a new neuro-renal syndrome.
Acute kidney injury after non-cardiac major surgery: has it reduced?
Authors: Cho Jeong Min , Kwon Soie , Yang Sunah , Park Jina , Jeong Subin , Park Sehoon , Ryu Jiwon , Kim Sejoong , Lee Jeonghwan , Lee Jung Pyo , Yoon Hyung-Jin , Kim Dong Ki , Joo Kwon Wook , Kim Yon Su , Kim Kwangsoo , Park Minsu , Lee Hajeong 
Published: June 2024

ABSTRACT

Background
It remains unclear whether the incidence of post-operative acute kidney injury (PO-AKI) has been reduced despite the recent emphasis on its early recognition and prevention in clinical practice. We aimed to investigate the trend in the incidence of PO-AKI and to identify the associated factors affecting its changes.

Methods
We gathered clinical data from patients who underwent non-cardiac major surgeries at three referral hospitals from 2005 to 2020. PO-AKI was defined as KDIGO AKI criteria within 7 days after surgery. Severe PO-AKI (S-PO-AKI) was defined as stage 2 or 3 AKI. The temporal change of PO-AKI was evaluated by joinpoint regression analysis and multivariable logistic regression based on a 3-year interval.

Results
Among 138 235 patients, 8156 (5.9%) PO-AKI and 1127 (0.8%) S-PO-AKI occurred, respectively. The patients enrolled in recent years were older and more were women. They had more comorbidities and a higher PO-AKI risk compared with those included in past years. As time passed, the PO-AKI incidence decreased from 8.6% in 2005–07 to 5.1% in 2017–20, whereas S-PO-AKI incidence did not change (0.8% to 0.9%). In joinpoint analysis, PO-AKI incidence tended to decrease with annual percentage change (APC) of –4.2% per year [95% confidence interval (CI) –5.5% to –2.8%, P-value &lt;.001), although S-PO-AKI did not (APC 0.9%, 95% CI –1.1 to 2.9%, P-value = .347). Similarly, the overall PO-AKI incidence decreased but S-PO-AKI did not, even after adjusting covariables.

Conclusion
The incidence of PO-AKI has decreased recently despite the increase in known risk factors; however, the incidence of S-PO-AKI has not decreased in recent years.

Trial registration information
ClinicalTrials.gov Identifier: NCT05986474. Name of registry: Development of Synthetic Medical Data Generation Technology to Predict Postoperative Complications. URL: https://classic.clinicaltrials.gov/ct2/show/NCT05986474. Date of registration: 14 August 2023. Date of enrollment of the first participant to the trial: 27 September 2022, retrospectively registered.
Atrial septal defect becoming clinically evident after cardiac surgery for annuloaortic ectasia: a case report
Authors: Meguro Kentaro , Koitabashi Toshimi , Fujita Teppei , Ako Junya 
Published: June 2024

Abstract

Background
Right ventricular volume overload is the key finding in a patient with previously undiagnosed atrial septal defect (ASD).

Case summary
A 68-year-old female was referred to our hospital due to progressive pulmonary artery dilatation observed on her chest X-ray. Echocardiography revealed a secundum ASD with right ventricular dilatation. She had undergone aortic root replacement and aortic valve replacement for annuloaortic ectasia and aortic insufficiency 12 years prior to the diagnosis. She was also diagnosed with Marfan syndrome, which was supported by family histories. Computed tomography did not show a secundum ASD before the surgery. We finally closed the secundum ASD with catheter closure device.

Discussion
Ascending aneurysm might mask the presence of secundum ASD. Monitoring the change in pulmonary artery dilatation overtime is useful for the diagnosing secundum ASD.
Ventricular septal defect complicating acute myocardial infarction: diagnosis and management. A Clinical Consensus Statement of the Association for Acute CardioVascular Care (ACVC) of the ESC, the European Association of Percutaneous Cardiovascular Interventions (EAPCI) of the ESC and the ESC Working Group on Cardiovascular Surgery
Authors: Schlotter Florian , Huber Kurt , Hassager Christian , Halvorsen Sigrun , Vranckx Pascal , Pöss Janine , Krychtiuk Konstantin , Lorusso Roberto , Bonaros Nikolaos , Calvert Patrick A , Montorfano Matteo , Thiele Holger 
Published: June 2024

Abstract
Ventricular septal defects are a rare complication after acute myocardial infarction with a mortality close to 100% if left untreated. However, even surgical or interventional closure is associated with a very high mortality and currently no randomized controlled trials are available addressing the optimal treatment strategy of this disease. This state-of-the-art review and clinical consensus statement will outline the diagnosis, hemodynamic consequences and treatment strategies of ventricular septal defects complicating acute myocardial infarction with a focus on current available evidence and a focus on major research questions to fill the gap in evidence.
Digest: Are female miniature geckos larger than males?
Authors: Tarimo Eliza 
Published: June 2024

Abstract
What shapes the differences in body size between males and females in miniature species? One potential key factor is reproduction, which could constrain body size evolution because females of miniature species need to remain large enough to lay viable eggs. Glynne and Adams (2024) tested this hypothesis in two gecko families, the Sphaerodactylidae and Phyllodactylidae. Their findings support this hypothesis, indicating that female-biased size differences in miniature species are shaped by selection for reproductive success.
Clinical audit of quality of care among patients with viral hepatitis in primary care in a low endemic region
Authors: Koc Özgür M , Vaes Bert , Robaeys Geert , Catalan Cristian F , Aertgeerts Bert , Nevens Frederik 
Published: June 2024

Abstract

Background
The current hepatitis B (HBV) and hepatitis C virus (HCV) screening practices may fail to detect many infected patients who could benefit from new therapeutic agents to limit progression to cirrhosis and hepatocellular carcinoma.

Objectives
This study assessed the test positivity rate and cascade of care of viral hepatitis patients in primary care in a low endemic region as well as the testing policy of abnormal alanine aminotransferase (ALT) level.

Methods
This is a retrospective clinical audit among primary health care practices in Flanders, Belgium, assessing patients with an active medical file between 2019 and 2021.

Results
A total of 84/89 (94.4%) primary health care practices participated representing 621,573 patients of which 1069 patients (0.17%) were registered as having viral hepatitis, not further specified. Detailed information was available from 38 practices representing 243,723/621,573 (39.2%) patients of which 169 (0.07%) were HBsAg positive and 99 (0.04%) anti-HCV positive. A total of 96/134(71.6%) chronic HBV-infected and 31/77(40.3%) chronic HCV-infected patients were referred to a hepatologist. A total of 30,573/621,573(4.9%) patients had an abnormal ALT level, and by at random selection, more detailed information was obtained on 211 patients. Information on high-risk groups was missing in up to 60%. In patients with abnormal ALT level, HBsAg and anti-HCV testing were conducted in 37/211(17.5%) and 25/211(11.8%), respectively.

Conclusion
In a low endemic region, the testing rate and cascade of care of HBV and HCV-infected patients can be improved in primary care, especially in high-risk groups and patients with abnormal ALT levels.
Response of aerobic anoxygenic phototrophic bacteria to limitation and availability of organic carbon
Authors: Piwosz Kasia , Villena-Alemany Cristian , Całkiewicz Joanna , Mujakić Izabela , Náhlík Vít , Dean Jason , Koblížek Michal 
Published: June 2024

Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, enhancing their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light (near-infrared light, λ &gt; 800 nm) conditions to elucidate how they profit from photoheterotrophy. We found that AAP bacteria induce photoheterotrophic metabolism under carbon limitation, but they overcompete heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. Interestingly, recalcitrant (lignin) or low-energy (acetate) carbon sources inhibited the growth of AAP bacteria, especially in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria in pelagic environments.
The Nitroplast and Its Relatives Support a Universal Model of Features Predicting Gene Retention in Endosymbiont and Organelle Genomes
Authors: Johnston Iain G 
Published: June 2024

Abstract
Endosymbiotic relationships have shaped eukaryotic life. As endosymbionts coevolve with their host, toward full integration as organelles, their genomes tend to shrink, with genes being completely lost or transferred to the host nucleus. Modern endosymbionts and organelles show diverse patterns of gene retention, and why some genes and not others are retained in these genomes is not fully understood. Recent bioinformatic study has explored hypothesized influences on these evolutionary processes, finding that hydrophobicity and amino acid chemistry predict patterns of gene retention, both in organelles across eukaryotes and in less mature endosymbiotic relationships. The exciting ongoing elucidation of endosymbiotic relationships affords an independent set of instances to test this theory. Here, we compare the properties of retained genes in the nitroplast, recently reported to be an integrated organelle, two related cyanobacterial endosymbionts that form “spheroid bodies” in their host cells, and a range of other endosymbionts, with free-living relatives of each. We find that in each case, the symbiont's genome encodes proteins with higher hydrophobicity and lower amino pKa than their free-living relative, supporting the data-derived model predicting the retention propensity of genes across endosymbiont and organelle genomes.
Understanding Longevity: SIN-3 and DAF-16 Revealed as Independent Players in Lifespan Regulation
Authors: Konwar Chandrika , Maini Jayant , Saluja Daman 
Published: June 2024

Abstract
Aging is the process of gradual physio-biochemical deterioration. Although aging is inevitable, healthy aging is the key to individual and communal well-being. Therefore, it is essential to understand the regulation of aging. SIN-3/Sin-3 is a unique regulatory protein that regulates aging without DNA-binding activity. It functions by establishing multiple protein interactions. To understand the functional mechanism of this transcriptional regulator, the Caenorhabditis elegans protein interactome was assessed for SIN-3 interactions. DAF-16/FOXO emerged as one of the leading contenders for SIN-3-mediated regulation of aging. This study looks at the concerted role of SIN-3 and DAF-16 proteins in lifespan regulation. Phenotypic profiling for the mutants of these genes shows the functional accord between these 2 proteins with similar functions in stress response and vital biological processes. However, there were no significant physical interactions when checked for protein–protein interaction between SIN-3 and DAF-16 proteins. C. elegans genomics and transcriptomics data also indicated the possibilities of concerted gene regulation. This genetic regulation is more likely related to SIN-3 dominance on DAF-16 function. Overall, SIN-3 and DAF-16 proteins have strong functional interactions that ensure healthy aging. The influence of SIN-3 on DAF-16-mediated stress response is one of their convergence points in longevity regulation.
Characterizing Features of Creative Writing in Older Adults
Authors: Orwig William , Schacter Daniel L 
Published: June 2024

Abstract

Objectives
How does creative expression change across the life span? Although creativity is generally preserved well into adulthood, certain cognitive functions, such as episodic detail and ideational fluency, have been shown to decline with age. The present study employs computational linguistic analyses to investigate the salient features of creative writing in older adults.

Methods
We collected short stories from a sample of 50 older adults (age 65≤) which were subsequently rated for creativity by an independent set of participants. Mixed-effects linear regression models were used to describe semantic diversity and perceptual details as predictors of creativity. Semantic diversity reflects the extent to which a narrative connects divergent ideas and is closely associated with creativity. Perceptual details, characterized by sensorial descriptions, have been previously associated with creative writing and may serve to transport readers to alternative times and places. Additionally, we compare these measures to a previously collected sample of stories from younger adults.

Results
Results indicate that the presence of perceptual details and semantic diversity were significant positive predictors of creativity (p &lt; .05). Moreover, we find that stories written by older adults contain fewer perceptual details compared with stories written by younger adults.

Discussion
These results advance our understanding of age-related changes in creativity and highlight the potential role of episodic simulation in writing creative short stories.