bluuebunny/crossref_metadata_2025_split huggingface dataset:
The C-terminal 4CXXC-type zinc finger domain of CDCA7 recognizes hemimethylated DNA and modulates activities of chromatin remodeling enzyme HELLS
Authors: Shinkai Akeo , Hashimoto Hideharu , Shimura Chikako , Fujimoto Hiroaki , Fukuda Kei , Horikoshi Naoki , Okano Masaki , Niwa Hitoshi , Debler Erik W , Kurumizaka Hitoshi , Shinkai Yoichi 
Published: August 2024

Abstract
The chromatin-remodeling enzyme helicase lymphoid-specific (HELLS) interacts with cell division cycle-associated 7 (CDCA7) on nucleosomes and is involved in the regulation of DNA methylation in higher organisms. Mutations in these genes cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, which also results in DNA hypomethylation of satellite repeat regions. We investigated the functional domains of human CDCA7 in HELLS using several mutant CDCA7 proteins. The central region is critical for binding to HELLS, activation of ATPase, and nucleosome sliding activities of HELLS-CDCA7. The N-terminal region tends to inhibit ATPase activity. The C-terminal 4CXXC-type zinc finger domain contributes to CpG and hemimethylated CpG DNA preference for DNA-dependent HELLS-CDCA7 ATPase activity. Furthermore, CDCA7 showed a binding preference to DNA containing hemimethylated CpG, and replication-dependent pericentromeric heterochromatin foci formation of CDCA7 with HELLS was observed in mouse embryonic stem cells; however, all these phenotypes were lost in the case of an ICF syndrome mutant of CDCA7 mutated in the zinc finger domain. Thus, CDCA7 most likely plays a role in the recruitment of HELLS, activates its chromatin remodeling function, and efficiently induces DNA methylation, especially at hemimethylated replication sites.
Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein–protein interactions
Authors: Chen Ziyuan , Seman Melissa , Fyodorova Yekaterina , Farhat Ali , Ames Amanda , Levashkevich Alexander , Biswas Saikat , Huang Fengting , Freddolino Lydia , Biteen Julie S , Ragunathan Kaushik 
Published: August 2024

Abstract
Visualizing and measuring molecular-scale interactions in living cells represents a major challenge, but recent advances in single-molecule super-resolution microscopy are bringing us closer to achieving this goal. Single-molecule super-resolution microscopy enables high-resolution and sensitive imaging of the positions and movement of molecules in living cells. HP1 proteins are important regulators of gene expression because they selectively bind and recognize H3K9 methylated (H3K9me) histones to form heterochromatin-associated protein complexes that silence gene expression, but several important mechanistic details of this process remain unexplored. Here, we extended live-cell single-molecule tracking studies in fission yeast to determine how HP1 proteins interact with their binding partners in the nucleus. We measured how genetic perturbations that affect H3K9me alter the diffusive properties of HP1 proteins and their binding partners, and we inferred their most likely interaction sites. Our results demonstrate that H3K9 methylation spatially restricts HP1 proteins and their interactors, thereby promoting ternary complex formation on chromatin while simultaneously suppressing off-chromatin binding. As opposed to being an inert platform to direct HP1 binding, our studies propose a novel function for H3K9me in promoting ternary complex formation by enhancing the specificity and stimulating the assembly of HP1–protein complexes in living cells.
Segmentation of pre- and posttreatment diffuse glioma tissue subregions including resection cavities
Authors: Baig Saif , Vidic Igor , Mastorakos George M , Smith Robert X , White Nathan , Bash Suzie , Dale Anders M , McDonald Carrie R , Beaumont Thomas , Seibert Tyler M , Hattangadi-Gluth Jona , Kesari Santosh , Farid Nikdokht , Rudie Jeffrey D 
Published: August 2024

Abstract

Background
Evaluating longitudinal changes in gliomas is a time-intensive process with significant interrater variability. Automated segmentation could reduce interrater variability and increase workflow efficiency for assessment of treatment response. We sought to evaluate whether neural networks would be comparable to expert assessment of pre- and posttreatment diffuse gliomas tissue subregions including resection cavities.

Methods
A retrospective cohort of 647 MRIs of patients with diffuse gliomas (average 55.1 years; 29%/36%/34% female/male/unknown; 396 pretreatment and 251 posttreatment, median 237 days post-surgery) from 7 publicly available repositories in The Cancer Imaging Archive were split into training (536) and test/generalization (111) samples. T1, T1-post-contrast, T2, and FLAIR images were used as inputs into a 3D nnU-Net to predict 3 tumor subregions and resection cavities. We evaluated the performance of networks trained on pretreatment training cases (Pre-Rx network), posttreatment training cases (Post-Rx network), and both pre- and posttreatment cases (Combined networks).

Results
Segmentation performance was as good as or better than interrater reliability with median dice scores for main tumor subregions ranging from 0.82 to 0.94 and strong correlations between manually segmented and predicted total lesion volumes (0.94 &lt; R2 values &lt; 0.98). The Combined network performed similarly to the Pre-Rx network on pretreatment cases and the Post-Rx network on posttreatment cases with fewer false positive resection cavities (7% vs 59%).

Conclusions
Neural networks that accurately segment pre- and posttreatment diffuse gliomas have the potential to improve response assessment in clinical trials and reduce provider burden and errors in measurement.
The Role of the Gut, Urine, and Vaginal Microbiomes in the Pathogenesis of Urinary Tract Infection in Women and Consideration of Microbiome Therapeutics
Authors: Naji Amal , Siskin Drew , Woodworth Michael H , Lee John R , Kraft Colleen S , Mehta Nirja 
Published: August 2024

Abstract
The gut, urine, and vaginal microbiomes play significant roles in the pathogenesis of recurrent urinary tract infections (rUTIs). Analysis of these microbiota has shown distinct associations with urinary tract infections. Encouraging data indicate that rUTIs may be responsive to microbiome treatments such as fecal microbiota transplantation, expanding potential treatments beyond antibiotics, hydration, and behavioral interventions. If successful, these nonantibiotic therapies have the potential to increase time between rUTI episodes and reduce the prevalence of multidrug-resistant organisms. In this review, we discuss the role of the 3 microbiomes in the pathogenesis of rUTI and utilization of live biotherapeutic products as therapy for rUTI.
A Draft Genome Resource for a Cacao Thread Blight Disease–Causing Strain of Paramarasmius palmivorus
Authors: Baruah Indrani K. , Amoako-Attah Ishmael , Bukari Yahaya , Meinhardt Lyndel W. , Bailey Bryan A. , Cohen Stephen P. 
Published: August 2024

Thread blight disease (TBD) is an emerging foliar disease on cacao ( Theobroma cacao), the source of chocolate. Multiple species of pathogenic fungi in the Marasmiinae suborder of Agaricales are responsible for causing TBD in cacao. A recent phylogenetic study showed that Marasmius palmivorus, the second most frequently isolated TBD-causing fungus in Ghana, was phylogenetically distinct from the Marasmiaceae genera Marasmius and Moniliophthora, leading to the naming of a new genus, Paramarasmius. The genus currently contains two species, the type species P. palmivorus and P. mesosporus. This report describes our release of a draft nuclear genome assembly and annotation of P. palmivorus strain GH-12 derived from long- and short-read sequencing. This high-quality draft is the first released genome for P. palmivorus and provides insight into the pathogenicity and evolution of an emerging pathogen. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Barbed Sutures Compared With Conventional Sutures During Laparoscopic Myomectomy
Authors: Kathopoulis Nikolaos , Prodromidou Anastasia , Douligeris Athanasios , Diakosavvas Michail , Zacharakis Dimitrios , Kypriotis Konstantinos , Chatzipapas Ioannis , Grigoriadis Themos , Protopapas Athanasios 
Published: August 2024

OBJECTIVE:
To accumulate the currently available literature on the safety and efficacy of the use of knotless barbed sutures for the reconstruction of the uterine wall during laparoscopic myomectomy based on comparison with traditional suture studies.

DATA SOURCES:
We searched PubMed/Medline, Scopus, ClinicalTrials.gov, and Google Scholar up to February 29, 2024.

METHODS OF STUDY SELECTION:
Following PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines and PICO criteria, we included all English-language, full-text articles that evaluated the perioperative outcomes of patients who had laparoscopic myomectomy and repair of the uterine wall defect with either barbed or traditional (extracorporeal or intracorporeal sutures).

TABULATION, INTEGRATION, AND RESULTS:
The application of barbed sutures resulted in significantly reduced operative time (2,111 patients, mean difference −12.04 minutes, 95% CI, −16.94 to −7.14, P<.001). This was also reflected when suturing time was separately analyzed (437 patients, mean difference −6.04 minutes, 95% CI, −7.43 to −4.65, P<.001) The mean difference in hemoglobin levels before and after surgery was significantly lower in the barbed suture group (1,277 patients, mean difference −0.40 g/dL, 95% CI, −0.72 to −0.09, P<.01) This was also observed in case of estimated blood loss, which was found to be lower in the barbed suture group (1,823 patients, mean difference −47.22 mL, 95% CI, −78.54 to −15.90, P=.003). Finally, the barbed suture group presented lower transfusion rates (1,217 patients, odds ratio 0.43, 95% CI, 0.19–1.00, P=.05). Concerning visual analog scale (VAS) score as evaluated by the surgeons for surgical difficulty, the control group proved to be more technically challenging compared with the barbed sutures group (184 patients, mean difference −1.66 95% CI, −2.37 to −0.94, P<.001). The VAS score for pain at 24 hours postoperatively, postoperative complication rates, and length of hospital stay were similar for both groups. Regarding reproductive outcomes, there was no difference in pregnancy, live birth, and birth complication rates.

CONCLUSION:
The use of barbed sutures during laparoscopic myomectomy presents many clinical benefits for the patient and the surgeon in terms of shorter operative and suturing time, less estimated blood loss, and ease of use. This pioneer technology may contribute to the expansion of laparoscopy on more complex myomectomies.

SYSTEMATIC REVIEW REGISTRATION:
PROSPERO, CRD42023477304.
Prenatal Care Clinician Preferences Among Patients With Spanish-Preferred Language
Authors: Butler Haylie M. , Bazan Maria , Rivera Luis , Salinas Kevin E. , Hacker Michele R. , DeLevie-Orey Sophia , Siegel Molly R. , Larson Elysia , Molina Rose L. 
Published: August 2024

OBJECTIVE:
To measure what patients with Spanish language preference and limited English proficiency value most when selecting a prenatal care clinician.

METHODS:
A discrete choice experiment was administered at two large academic medical centers in Boston, Massachusetts. Participants were identified by electronic medical record, had preferred Spanish language and self-identified limited English proficiency, and either were pregnant with a completed fetal anatomy scan or had given birth within the past 12 months at the time of the study. The discrete choice experiment consisted of eight attributes to consider when selecting a prenatal care clinician: clinician Spanish proficiency, type of interpreter used, interpersonal dynamics (ie, making patients feel seen, heard, and cared for), cultural concordance, continuity of care, shared decision making, distance from home, and wait times for appointments. Descriptive statistics of demographic variables were calculated. Hierarchical Bayesian models were used to analyze discrete choice experiment data.

RESULTS:
The attributes that were most important to 166 participants when choosing their prenatal care clinician were interpersonal dynamics within the patient–clinician dyad and clinician Spanish language proficiency (average importance 21.4/100 and 20.8/100, respectively). Of lowest importance were wait time to receive an appointment and continuity of care (average importance 5.1 and 6.1, respectively). Although participants highly preferred that their clinician be “fluent or near fluent in Spanish,” the second most preferred option was having a clinician with only basic Spanish proficiency rather than a more advanced level of Spanish proficiency with some misunderstandings.

CONCLUSION:
Our study demonstrates the importance of positive clinician–patient interpersonal dynamics and language-concordant care for patients with Spanish language preference in prenatal care. Promoting equitable patient-centered care for patients with limited English proficiency requires responding to preferences regarding clinician language proficiency and demonstrating attentiveness, empathy, and concern for prenatal care experiences.
Covert Consciousness in the ICU
Authors: Edlow Brian L. , Menon David K. 
Published: August 2024

OBJECTIVES:
For critically ill patients with acute severe brain injuries, consciousness may reemerge before behavioral responsiveness. The phenomenon of covert consciousness (i.e., cognitive motor dissociation) may be detected by advanced neurotechnologies such as task-based functional MRI (fMRI) and electroencephalography (EEG) in patients who appear unresponsive on the bedside behavioral examination. In this narrative review, we summarize the state-of-the-science in ICU detection of covert consciousness. Further, we consider the prognostic and therapeutic implications of diagnosing covert consciousness in the ICU, as well as its potential to inform discussions about continuation of life-sustaining therapy for patients with severe brain injuries.

DATA SOURCES:
We reviewed salient medical literature regarding covert consciousness.

STUDY SELECTION:
We included clinical studies investigating the diagnostic performance characteristics and prognostic utility of advanced neurotechnologies such as task-based fMRI and EEG. We focus on clinical guidelines, professional society scientific statements, and neuroethical analyses pertaining to the implementation of advanced neurotechnologies in the ICU to detect covert consciousness.

DATA EXTRACTION AND DATA SYNTHESIS:
We extracted study results, guideline recommendations, and society scientific statement recommendations regarding the diagnostic, prognostic, and therapeutic relevance of covert consciousness to the clinical care of ICU patients with severe brain injuries.

CONCLUSIONS:
Emerging evidence indicates that covert consciousness is present in approximately 15–20% of ICU patients who appear unresponsive on behavioral examination. Covert consciousness may be detected in patients with traumatic and nontraumatic brain injuries, including patients whose behavioral examination suggests a comatose state. The presence of covert consciousness in the ICU may predict the pace and extent of long-term functional recovery. Professional society guidelines now recommend assessment of covert consciousness using task-based fMRI and EEG. However, the clinical criteria for patient selection for such investigations are uncertain and global access to advanced neurotechnologies is limited.
A Novel Approach to Incision Marking in Abdominoplasty Using 3D Printing Technology: A Description of Technique
Authors: Mortada Hatan , Alnaim Muna F. , Alhazmi Bushra , Alfawzan Mohammed , Alshomer Feras 
Published: August 2024

Summary:
Abdominoplasty is one of the most common plastic surgery procedures used to improve the appearance and contour of the abdominal region. Despite advances in surgical techniques, achieving optimal aesthetic results with minimal scarring remains a challenge. In this study, we describe a feasible approach to incision marking in abdominoplasty using a three-dimensional-printed incision marking tool. This technique with open source nature has the potential to revolutionize the field of plastic surgery and enhance patient satisfaction. Further studies are needed to confirm our findings and explore the potential applications of three-dimensional printing technology in other aesthetic procedures.
CD8+ T-cell deficiency protects mice from abdominal aortic aneurysm formation in response to calcium chloride2
Authors: Lin Zhuo , Zhao Mantong , Zhang Xian , Piao Jinshun , Zheng Xintong , Shu Shangzhi , Zhao Longguo , Zhang Meiping , Shi Guo-Ping , Lei Yanna , Cui Rihua , Yue Xueling , Cheng Xian Wu 
Published: August 2024

Objective:
Abdominal aortic aneurysm (AAA) is an aneurysm-like dilated and highly fatal cardiovascular disease. CD8+ T cells have been shown to be critical for vascular pathological processes, but the contribution of these lymphocytes to vascular diseases remains elusive.

Methods and results:
Eight-week-old male wildtype (CD8+/+) and Cd8a knockout (CD8−/−) mice were used in a calcium chloride2 (CaCl2)-induced experimental AAA model. At 6 weeks after surgery, CD8+ T-cell deletion prevented the formation of AAA, accompanied by reductions of the levels of inflammatory (interferon-γ [IFN-γ], interleukin-1β, monocyte chemoattractant protein-1, intracellular adhesion molecule-1, vascular cell adhesion molecule-1, NOD-like receptor protein 3, caspase-1), oxidative stress [NADPH oxidase and gp91phox], and proteolysis (cathepsin S, cathepsin K, matrix metalloproteinase-2 [MMP-2] and MMP-9) proteins and/or genes in plasma and/or AAA tissues. Immunoreactivities of MMP-2 and MMP-9 were observed in macrophages. An injection of IFN-γ and adoptive transfer of CD8+ T cells of IFN-γ+/+ mice diminished CD8−/−-mediated vasculoprotective actions in the AAA mice. In vitro, IFN-γ enhanced MMP-2 and MMP-9 gelatinolytic activities in macrophage and/or vascular smooth muscle cells.

Conclusion:
The vasculoprotective effects of CD8+ T-cell deletion in a mouse CaCl2-induced AAA model were likely attributable to, at least in part, the attenuation of IFN-γ-dependent inflammation action, oxidative stress production, and proteolysis, suggesting a novel therapeutic target for AAA formation by regulating CD8+ T-cell-derived IFN-γ secretion.
Extreme monovision with EDOF intraocular lenses
Authors: Lentz P. Connor , Stockard Alyssa , Wagner Isabella V. , Ten Hulzen Richard D. 
Published: August 2024

Introduction:
The successful outcome of maintaining natural extreme monovision in a patient through the implantation of extended depth-of-focus (EDOF) intraocular lenses (IOLs) in both eyes is reported.

Patient and Clinical Findings:
A 75-year-old woman with a history of extreme monovision (−3.50 diopters [D] spheroequivalent left eye) presented to the clinic for cataract evaluation. At presentation, bilateral blurry vision (both distance and near) was observed with or without spectacles. The patient noted that previous attempts at restoring binocularity with spectacles correction had been unsuccessful, and she maintained a strong desire to maintain her natural extreme monovision.

Diagnosis, Intervention, and Outcomes:
The patient underwent EDOF IOL implantation (both eyes) with full monovision refractive targets of plano (right eye) and −1.50 D (left eye). Postoperatively, the patient expressed dissatisfaction about her limited near vision (left eye). 7 months later, she underwent an EDOF IOL exchange (left eye) with a new refractive target of −3.25 D. The patient perceived her extreme monovision correction to be a success.

Conclusions:
This case highlights that although EDOF IOLs are not specifically designed for monovision correction, they may still provide satisfactory results for certain patients.
Newborn congenital cytomegalovirus screening and hearing outcomes: a systematic review of current literature
Authors: Pollick Sarah A. , Mansour Yusra , Pesch Megan H. 
Published: August 2024

Purpose of review
The purpose of this review is to summarize the very recent literature surrounding hearing outcomes of children with congenital cytomegalovirus (cCMV) detected through systematic screening programs.

Recent findings
There are several different approaches to cCMV screening including forms of targeted vs. universal screening of newborns as well as maternally-derived prenatal testing. However, many studies fail to document hearing-related outcomes both in the newborn period and further into childhood when late-onset sensorineural hearing loss (SNHL) can occur. This systematic review included studies of neonates screened for cCMV reporting hearing outcomes for at least one point in time. Hearing targeted screening appeared the most widely reported for detection of unilateral and bilateral SNHL in those with cCMV. A few studies examined these clinical findings in relation to antiviral treatment.

Summary
Congenital CMV is an important and common cause of childhood hearing loss. Newborn screening programs may expand opportunities for early diagnosis and treatment of the infection and its sequelae.
Salivary pepsin testing for laryngopharyngeal reflux: will it change our management?
Authors: Li Jinrang , Allen Jacqueline 
Published: August 2024

Purpose of review
This review focus on the clinical value of salivary and laryngopharyngeal tissue pepsin measurement in the diagnosis and treatment of laryngopharyngeal reflux (LPR).

Recent findings
A growing body of research suggests that salivary pepsin detection provides a noninvasive method for the identifying LPR occurrence. Pepsin detection testing is still variable, and an optimal method that balances utility with accuracy has not been agreed. Timing and number of test samples recommended also remains controversial, however literature indicates that increasing the number of tests over a day increases pepsin detection rate. It remains unclear whether detection of pepsin alone can be used to confirm LPR diagnosis. Pepsin positivity is correlated with improved response to proton pump inhibitor (PPI) therapy, and therefore may play a role in guiding therapeutic choices. Detection of pepsin in laryngeal tissue has the same clinical value as detection in saliva and requires further investigation to determine utility.

Summary
As a noninvasive method for the diagnosis of LPR, the detection of salivary pepsin in the oropharynx shows potential clinical value, however the exact method of detection and diagnostic values are unclear. Salivary or tissue-based pepsin detection may be helpful in predicting therapeutic effects of PPI and providing personalized treatment options. The detection threshold of salivary pepsin may be different in different countries and regions. Timing and number of samples needed for detection is still controversial.