bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging rhegmatogenous retinal lesions and peripheral vitreo-retinal interface with wide-field optical coherence tomography
Authors: Govetto Andrea , Sebag J , Lucchini Sara , Ballabio Chiara , Matteucci Martina , Ranno Stefano , Carini Elisa , Virgili Gianni , Bacherini Daniela , Radice Paolo 
Published: October 2023

ABSTRACT

Purpose:
Analyze the peripheral vitreo-retinal interface with widefield optical coherence tomography (WF-OCT).

Methods:
Retrospective chart analysis and WF-OCT in 120 consecutive cases of rhegmatogenous pathology.

Results:
There were 166 lesions in 120 eyes, including 106 horseshoe tears, 22 operculated (OH), 30 non-operculated (NOH) holes, 6 giant tears, and 2 peripheral lamellar defects followed for 6.1±1.2 months. Posterior vitreous detachment was present in all eyes (101/101, 100%) with tears and OHs, but only in 5/19 eyes (26.3%) with NOHs (p<0.001). Axial vitreous traction was evident at the anterior edge of horseshoe tears (106/106, 100%), but not the posterior border (18/106, 17%, p<0.001). OHs located posterior to the vitreous base were free from vitreous traction, displaying a morphology similar to macular hole. NOHs were farther anterior with signs of tangential traction in 23/30 (76.7%) cases. Peripheral vitreoschisis was more often associated with NOHs (25/30, 83.3%), than horseshoe tears (17/106, 16%; p<0.001). Horseshoe tears and NOHs were more often associated with retinal detachment (58/106 (54.7%) and 15/30 (50%), respectively) than OHs (5/22, 22.7%), p=0.023.

Conclusions:
Peripheral vitreo-retinal interactions are similar to vitreo-maculopathies, with axial and vitreoschisis-related tangential traction playing different roles in different rhegmatogenous pathologies. Peripheral OCT improves understanding of pathophysiology and risks of retinal detachment.
Comparing Outcomes of 45 Xen Implantation Ab Interno With Closed Conjunctiva to Ab Externo With Open Conjunctiva Approaches
Authors: El Helwe Hani , Ingram Zoë , Neeson Cameron E. , Falah Henisk , Trzcinski Jonathan , Lin Jonathan B. , Solá-Del Valle David A. 
Published: October 2023

Précis:
Ab externo with open conjunctiva placement may lead to improved gelatin stent (XEN Gel Stent; Allergan) success rate compared with ab interno with closed conjunctiva because it conferred more favorable intraocular pressure (IOP) and medication burden reduction based on our complete and qualified success criteria.

Purpose:
To compare outcomes of a gelatin stent (XEN 45 Gel Stent; Allergan) placed either ab interno with closed conjunctiva (AIC) or ab externo with open conjunctiva (AEO) with or without cataract surgery in patients with glaucoma.

Design:
Retrospective, nonrandomized comparative study of 85 eyes from 85 glaucoma patients who received XEN 45 Gel Stent placed either AIC (N=32) or AEO (N=53) with or without cataract surgery between July 2018 and January 2022 at Massachusetts Eye and Ear. Patients were included if they were 18 years of age or above and had at least 30 days of follow-up without any disqualifying event.

Results:
Baseline demographics were similar between both groups, except for the glaucoma type. Both AIC and AEO procedures resulted in significant patterns of IOP and medication reduction from baseline up to 1 year. At postoperative year (POY)1, mean IOP was reduced to 11.34±4 mmHg on 1.29±1.34 medications after AEO and 13.70±3.32 mmHg on 2±1.81 medications after AIC. The average IOP reduction was significantly greater in the AEO group at all postoperative time points beyond postoperative week 2. There were significant differences in the survival curves of AEO and AIC groups under both the complete success criteria and the qualified success criteria. Under the complete success criteria, the cumulative probability of survival at POY1 was 28.5% in the AEO group and 3.8% in the AIC group. Under the qualified success criteria, the cumulative probability of survival at POY1 was 60.3% in the AEO group and 21.9% in the AIC group.

Conclusions:
In our study, we demonstrate that both placements reduce IOP and medication from baseline, with AEO placement having more favorable success rates compared with AIC placement.
Association of abdominal aortic calcification and lower back pain in patients with degenerative spondylolisthesis
Authors: Schönnagel Lukas , Muellner Maximilian , Suwalski Phillip , Guven Ali E. , Camino-Willhuber Gaston , Tani Soji , Caffard Thomas , Zhu Jiaqi , Haffer Henryk , Arzani Artine , Chiapparelli Erika , Amoroso Krizia , Shue Jennifer , Duculan Roland , Sama Andrew A. , Cammisa Frank P. , Girardi Federico P. , Mancuso Carol A. , Hughes Alexander P. 
Published: October 2023

Abstract
Abdominal aortic calcification (AAC) is hypothesized to lead to ischemic pain of the lower back. This retrospective study aims to identify the relationship between AAC and lower back pain (LBP) in patients with degenerative lumbar spondylolisthesis. Lower back pain was assessed preoperatively and 2 years after surgery using the numeric analogue scale. Abdominal aortic calcification was assessed according to the Kauppila classification and was grouped into no, moderate, and severe. A multivariable regression, adjusted for age, sex, body mass index, hypertension, and smoking status, was used to assess the association between AAC and preoperative/postoperative LBP as well as change in LBP after surgery. A total of 262 patients were included in the final analysis. The multivariable logistic regression demonstrated an increased odds ratio (OR) for preoperative LBP ≥ 4 numeric analogue scale (OR = 9.49, 95% confidence interval [CI]: 2.71-40.59, P < 0.001) and postoperative LBP ≥ 4 (OR = 1.72, 95% CI: 0.92-3.21, P = 0.008) in patients with severe AAC compared with patients with no AAC. Both moderate and severe AAC were associated with reduced improvement in LBP after surgery (moderate AAC: OR = 0.44, 95% CI: 0.22-0.85, P = 0.016; severe AAC: OR = 0.41, 95% CI: 0.2-0.82, P = 0.012). This study demonstrates an independent association between AAC and LBP and reduced improvement after surgery. Evaluation of AAC could play a role in patient education and might be considered part of the differential diagnosis for LBP, although further prospective studies are needed.
Use of Human-Centered Design Methodology to Develop a Digital Toolkit to Optimize Heart Failure Guideline-Directed Medical Therapy
Authors: Spaulding Erin M. , Isakadze Nino , Molello Nancy , Khoury Shireen R. , Gao Yumin , Young Lisa , Antonsdottir Inga M. , Azizi Zahra , Dorsch Michael P. , Golbus Jessica R. , Ciminelli Ana , Brant Luisa C. C. , Himmelfarb Cheryl R. , Coresh Josef , Marvel Francoise A. , Longenecker Chris T. , Commodore-Mensah Yvonne , Gilotra Nisha A. , Sandhu Alexander , Nallamothu Brahmajee , Martin Seth S. 
Published: October 2023

Background
Guideline-directed medical therapies (GDMTs) improve quality of life and health outcomes for patients with heart failure (HF). However, GDMT utilization is suboptimal among patients with HF.

Objective
The aims of this study were to engage key stakeholders in semistructured, virtual human-centered design sessions to identify challenges in GDMT optimization posthospitalization and inform the development of a digital toolkit aimed at optimizing HF GDMTs.

Methods
For the human-centered design sessions, we recruited (a) clinicians who care for patients with HF across 3 hospital systems, (b) patients with HF with reduced ejection fraction (ejection fraction ≤ 40%) discharged from the hospital within 30 days of enrollment, and (c) caregivers. All participants were 18 years or older, English speaking, with Internet access.

Results
A total of 10 clinicians (median age, 37 years [interquartile range, 35–41], 12 years [interquartile range, 10–14] of experience caring for patients with HF, 80% women, 50% White, 50% nurse practitioners) and three patients and one caregiver (median age 57 years [IQR: 53–60], 75% men, 50% Black, 75% married) were included. Five themes emerged from the clinician sessions on challenges to GDMT optimization (eg, barriers to patient buy-in). Six themes on challenges (eg, managing medications), 4 themes on motivators (eg, regaining independence), and 3 themes on facilitators (eg, social support) to HF management arose from the patient and caregiver sessions.

Conclusions
The clinician, patient, and caregiver insights identified through human-centered design will inform a digital toolkit aimed at optimizing HF GDMTs, including a patient-facing smartphone application and clinician dashboard. This digital toolkit will be evaluated in a multicenter, clinical trial.
Cytokine Profiling of Cyst Fluid and Tumor-Associated Macrophages in Cystic Vestibular Schwannoma
Authors: Nisenbaum Eric , Wiefels Matthew , Telischi Julia , Marasigan Mikhail , Kanumuri Vivek , Pena Stefanie , Thielhelm Torin , Bracho Olena , Bhatia Rita , Scaglione Tricia , Telischi Fred , Fernandez-Valle Cristina , Liu Xue-Zhong , Luther Evan , Morcos Jacques , Ivan Michael , Dinh Christine T. 
Published: October 2023

Background
The vestibular schwannoma (VS) secretome can initiate monocyte recruitment and macrophage polarization to M1 (proinflammatory) and/or M2 (protumorigenic) phenotypes, which in turn secrete additional cytokines that contribute to the tumor microenvironment. Profiling cyst fluid and cerebrospinal fluid (CSF) in cystic VS provides a unique opportunity to understand mechanisms that may contribute to tumor progression and cyst formation.

Hypothesis
Cystic VSs secrete high levels of cytokines into cyst fluid and express abundant M1 and M2 macrophages.

Methods
Tumor, CSF, and cyst fluid were prospectively collected from 10 cystic VS patients. Eighty cytokines were measured in fluid samples using cytokine arrays and compared with normal CSF from normal donors. Immunofluorescence was performed for CD80+ M1 and CD163+ M2 macrophage markers. Demographic, audiometric, and radiographic information was obtained through retrospective chart review.

Results
Cyst fluid expressed more osteopontin and monocyte chemotactic protein-1 (MCP-1; p < 0.0001), when compared with normal CSF. Cyst fluid also expressed more protein (p = 0.0020), particularly MCP-1 (p < 0.0001), than paired CSF from the same subjects. MCP-1 expression in cyst fluid correlated with CD80+ staining in VS tissue (r = 0.8852; p = 0.0015) but not CD163+ staining.

Conclusion
Cyst fluid from cystic VS harbored high levels of osteopontin and MCP-1, which are cytokines important in monocyte recruitment and macrophage polarization. MCP-1 may have a significant role in molding the tumor microenvironment, by polarizing monocytes to CD80+ M1 macrophages in cystic VS. Further investigations into the role of cytokines and macrophages in VS may lead to new avenues for therapeutic intervention.
Temporal Trends in Early Pediatric Cochlear Implantations in California from 2018 to 2020
Authors: Fujiwara Rance J. T. , Wong Emily C. , Ishiyama Gail , Ishiyama Akira 
Published: October 2023

Objective
To characterize the demographics of children receiving cochlear implantations, identify factors associated with delayed implantations, and trend these factors over time.

Design
Retrospective cross-sectional study.

Setting
Healthcare Cost and Utilization Project California State Ambulatory Surgery Database for calendar years 2018–2020.

Patients
Children 5 years or younger undergoing cochlear implantation.

Interventions
Cochlear implantation.

Main Outcomes Measures
The population-controlled number of cochlear implantations was calculated and stratified by race and insurance. Early implantation was defined as implantation at age 2 years or younger. A mixed-effects logistic regression model was generated to identify factors associated with early implantation and how that association changed from 2018 to 2020.

Results
The final cohort included 467 children. The number of implantations increased from 141 to 175 implants from 2018 to 2020 (24.1% increase); 229 (49.0%) children were implanted at 2 years or younger. Medicaid insurance was associated with decreased odds of early implantation (odds ratio, 0.18 [95% confidence interval, 0.15–0.23], p < 0.001); this association with Medicaid insurance was significant when stratified across all racial groups. The percentage of children with Medicaid who were implanted at 2 years or younger increased from 20.9 to 62.0% from 2018 to 2020.

Conclusions and Relevance
Among children in California, socioeconomic factors, in particular public insurance, are correlated with age of cochlear implantation. These disparities improved significantly from 2018 to 2020. Further investigation into changes and initiatives in California during this time frame may aid in directing national efforts to improve pediatric cochlear implantation access.
Historical Review of Acute Pancreatitis Research Over the Last 80 Years
Authors: Han Chao , Dong Zhi-Qi , Li Zhao-Shen , Hu Liang-Hao 
Published: October 2023

Objectives
Research on acute pancreatitis (AP) has been ongoing for a long time. It is necessary to summarize and investigate the history of AP research.

Methods
Publications related to AP research were retrieved from PubMed. Medical Subject Headings (MeSH) terms, countries, journals, and publication dates were analyzed. Co-occurrence analysis was conducted to illustrate the holistic trend in AP research. A dynamic bar graph, heat maps, and line charts were created to illustrate change trends of MeSH terms.

Results
In total, 28,222 publications with 8558 MeSH terms were retrieved from 1941 to 2020. Among these, 16,575 publications with 7228 MeSH terms were from 2001 to 2020. The top 10 MeSH terms showed a considerable change from 1941 to 1970 but remained stable since the 1970s. Four clusters obtained from the co-occurrence analysis were “experiments on animals,” “diagnosis and treatment,” “prognosis and expectation,” and “protein and enzyme.” From 1941 to 2020, 33 MeSH terms with increasing trends (MH-I) and 15 MeSH terms with decreasing trends (MH-D) were selected to create a heat map (every decade). Meanwhile, 16 MH-I and 41 MH-D were selected to create the heat map from 2001 to 2020 (every 2 years).

Conclusion
Over the past 80 years, the pathogenesis, treatment, risk management, and experimental model were the main research highlights. Optimal supportive management, minimally invasive treatment, and prediction of prognosis are subjects of interest for clinical practitioners; signal transduction to identify a target for precise treatment is the focus of experimental research in AP.
Measurement of Abdominal Aortic Aneurysm Strain Using MR Deformable Image Registration
Authors: Dong Huiming , Leach Joseph R. , Kao Evan , Zhou Ang , Chitiboi Teodora , Zhu Chengcheng , Ballweber Megan , Jiang Fei , Lee Yoo Jin , Iannuzzi James , Gasper Warren , Saloner David , Hope Michael D. , Mitsouras Dimitrios 
Published: October 2023

Background
Management of asymptomatic abdominal aortic aneurysm (AAA) based on maximum aneurysm diameter and growth rate fails to preempt many ruptures. Assessment of aortic wall biomechanical properties may improve assessment of progression and rupture risk. This study aimed to assess the accuracy of AAA wall strain measured by cine magnetic resonance imaging (MRI) deformable image registration (MR strain) and investigate its relationship with recent AAA progression.

Methods
The MR strain accuracy was evaluated in silico against ground truth strain in 54 synthetic MRIs generated from a finite element model simulation of an AAA patient's abdomen for different aortic pulse pressures, tissue motions, signal intensity variations, and image noise. Evaluation included bias with 95% confidence interval (CI) and correlation analysis. Association of MR strain with AAA growth rate was assessed in 25 consecutive patients with >6 months of prior surveillance, for whom cine balanced steady-state free-precession imaging was acquired at the level of the AAA as well as the proximal, normal-caliber aorta. Univariate and multivariate regressions were used to associate growth rate with clinical variables, maximum AAA diameter (Dmax), and peak circumferential MR strain through the cardiac cycle. The MR strain interoperator variability was assessed using bias with 95% CI, intraclass correlation coefficient, and coefficient of variation.

Results
In silico experiments revealed an MR strain bias of 0.48% ± 0.42% and a slope of correlation to ground truth strain of 0.963. In vivo, AAA MR strain (1.2% ± 0.6%) was highly reproducible (bias ± 95% CI, 0.03% ± 0.31%; intraclass correlation coefficient, 97.8%; coefficient of variation, 7.14%) and was lower than in the nonaneurysmal aorta (2.4% ± 1.7%). Dmax (β = 0.087) and MR strain (β= −1.563) were both associated with AAA growth rate. The MR strain remained an independent factor associated with growth rate (β= −0.904) after controlling for Dmax.

Conclusions
Deformable image registration analysis can accurately measure the circumferential strain of the AAA wall from standard cine MRI and may offer patient-specific insight regarding AAA progression.
Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story
Authors: Spöri Yann , Flot Jean-François 
Published: October 2023

1AbstractHaxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript and Python. Although Haxe is becoming more and more used for a variety of purposes, including games, it has not yet attracted much attention from bioinformaticians. This is surprising, as Haxe allows generating different versions of the same program (e.g. a graphical user interface version in JavaScript running in a web browser for beginners and a command-line version in C++ or Python for increased performance) while maintaining a single code, a feature that should be of interest for many bioinformatic applications. To demonstrate the usefulness of Haxe in bioinformatics, we present here the case story of the program SeqPHASE, written originally in Perl (with a CGI version running on a server) and published in 2010. As Perl+CGI is not desirable anymore for security purposes, we decided to rewrite the SeqPHASE program in Haxe and to host it at Github Pages (https://eeg-ebe.github.io/SeqPHASE), thereby alleviating the need to configure and maintain a dedicated server. Using SeqPHASE as an example, we discuss the advantages and disadvantages of Haxe’s source code conversion functionality when it comes to implementing bioinformatic software.
Grain versus AIN: Common rodent diets differentially affect breeding and metabolic health outcomes in adult C57BL/6j mice
Authors: Schipper Lidewij , Tims Sebastian , Timmer Eva , Lohr Julia , Rakhshandehroo Maryam , Harvey Louise 
Published: October 2023

AbstractSemi-synthetic and grain-based diets are common rodent diets for biomedical research. Both diet types are considered nutritionally adequate to support breeding, growth, and long life, yet there are fundamental differences between them that may affect metabolic processes. We have characterized the effects of diet type on breeding outcomes, metabolic phenotype, and microbiota profile in adult mice. Healthy 8-week-old female and male C57BL/6J mice were fed a semi-synthetic or a grain-based diet for 12 weeks and changes in body weight and body composition were monitored. Breeding outcomes were determined. Body fat accumulation of female mice was lower on the semi-synthetic diet than on the grain-based diet. Pregnancy rate and newborn pup survival appeared to be lower in mice exposed to semi-synthetic diet compared to grain-based diet. Both female and male mice showed a profound change in fecal microbiota alpha and beta diversity depending on diet type. Our study shows that type of rodent diet may affect breeding outcomes whilst influencing metabolism and health of female laboratory mice. These factors have the potential to influence other experimental outcomes and the results suggest that semi-synthetic and grain-based diets are not interchangeable in research using rodent models. Careful consideration and increased understanding of the consequences of diet choice would lead to improvements in experimental design and reproducibility of study results.
Exercise Training and Cold Exposure Trigger Distinct Molecular Adaptations to Inguinal White Adipose Tissue
Authors: Vamvini Maria , Nigro Pasquale , Caputo Tiziana , Stanford Kristin I. , Hirshman Michael F. , Middelbeek Roeland J.W. , Goodyear Laurie J. 
Published: October 2023

ABSTRACTExercise training and cold exposure both improve systemic metabolism, but the mechanisms are not well-established. We tested the hypothesis that adaptations to inguinal white adipose tissue (iWAT) are critical for these beneficial effects by determining the impact of exercise-trained and cold-exposed iWAT on systemic glucose metabolism and the iWAT proteome and secretome. Transplanting trained iWAT into sedentary mice improved glucose tolerance, while cold-exposed iWAT transplantation showed no such benefit. Compared to training, cold led to more pronounced alterations in the iWAT proteome and secretome, downregulating >2,000 proteins but also boosting iWAT’s thermogenic capacity. In contrast, only training increased extracellular space and vesicle transport proteins, and only training upregulated proteins that correlate with favorable fasting glucose, suggesting fundamental changes in trained iWAT that mediate tissue-to-tissue communication. This study defines the unique exercise training- and cold exposure-induced iWAT proteomes, revealing distinct mechanisms for the beneficial effects of these interventions on metabolic health.GRAPHICAL ABSTRACT
Chromosome size-dependent polar ejection force impairs mammalian mitotic error correction
Authors: Chong Megan K. , Rosas-Salvans Miquel , Tran Vanna , Dumont Sophie 
Published: October 2023

AbstractAccurate chromosome segregation requires sister kinetochores to biorient, attaching to opposite spindle poles. To this end, the mammalian kinetochore destabilizes incorrect attachments and stabilizes correct ones, but how it discriminates between these is not yet clear. Here, we test the model that kinetochore tension is the stabilizing cue and ask how chromosome size impacts that model. We live image PtK2 cells, with just 14 chromosomes, widely ranging in size, and find that long chromosomes align at the metaphase plate later than short chromosomes. Enriching for errors and imaging error correction live, we show that long chromosomes exhibit a specific delay in correcting attachments. Using chromokinesin overexpression and laser ablation to perturb polar ejection forces, we find that chromosome size and force on arms determine alignment order. Thus, we propose a model where increased force on long chromosomes can falsely stabilize incorrect attachments, delaying their biorientation. As such, long chromosomes may require compensatory mechanisms for correcting errors to avoid chromosomal instability.