bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examination of residency program websites for the use of gendered language and imagery
Authors: Read Catherine E. , Tracz Jovanna A. , Mhaimeed Nour , Mainville Rylie N. , Elzie Carrie A. 
Published: September 2023

Abstract
Background
Significant disparity in gender distribution exists among medical specialties. Residency program websites are a main source of preliminary program information for candidates, and website content may influence a prospective applicant’s sense of belongingness within a particular program. Given the importance of the residency program website as a recruiting tool, this study sought to examine and compare the presence of gendered language and imagery on residency program websites across various specialties.

Methods
A list of words considered masculine or feminine was used to evaluate residency program websites of the two most male-dominated specialties (orthopedic and thoracic surgery), female-dominated specialties (pediatrics and obstetrics and gynecology), and gender-balanced specialties (dermatology and family medicine) in the United States in 2022. Forty-five residency programs were randomly selected from each specialty across different regions of the US, with the exception of thoracic surgery of which there are only 33 programs. Masculine and feminine words were evaluated using a parsing and scraping program. Representation of female and male-presenting team members in photos on program websites was also evaluated.

Results
Masculine wording occurred more frequently in male-dominated specialties compared to gender-balanced (p = 0.0030), but not female-dominated specialties (p = 0.2199). Feminine language was used more frequently in female-dominated compared to male dominated fields (p = 0.0022), but not gender balanced (p = 0.0909). The ratio of masculine-to-feminine words used was significantly higher in male-dominated specialties compared to both gender-balanced (p < 0.0001) and female-dominated specialties. (p < 0.0001). There was an average of 1, 7, and 10 female-presenting residency team members pictured on each male-dominated, gender balanced, and female-dominated specialty RPW respectively, with significantly more female-presenting team members pictured in the photographs on female-dominated specialty websites when compared to male-dominated and gender-balanced specialty websites (p < 0.0001, p = 0.014).

Conclusions
The use of gendered language and female representation in photographs varies significantly across specialties and is directly correlated with gender representation within the specialty. Given that students’ perceptions of specialty programs may be affected by the use of language and photos on residency program websites, programs should carefully consider the language and pictures depicted on their program websites.
CNN-Res: deep learning framework for segmentation of acute ischemic stroke lesions on multimodal MRI images
Authors: Gheibi Yousef , Shirini Kimia , Razavi Seyed Naser , Farhoudi Mehdi , Samad-Soltani Taha 
Published: September 2023

Abstract
Background
Accurate segmentation of stroke lesions on MRI images is very important for neurologists in the planning of post-stroke care. Segmentation helps clinicians to better diagnose and evaluation of any treatment risks. However, manual segmentation of brain lesions relies on the experience of neurologists and is also a very tedious and time-consuming process. So, in this study, we proposed a novel deep convolutional neural network (CNN-Res) that automatically performs the segmentation of ischemic stroke lesions from multimodal MRIs.

Methods
CNN-Res used a U-shaped structure, so the network has encryption and decryption paths. The residual units are embedded in the encoder path. In this model, to reduce gradient descent, the residual units were used, and to extract more complex information in images, multimodal MRI data were applied. In the link between the encryption and decryption subnets, the bottleneck strategy was used, which reduced the number of parameters and training time compared to similar research.

Results
CNN-Res was evaluated on two distinct datasets. First, it was examined on a dataset collected from the Neuroscience Center of Tabriz University of Medical Sciences, where the average Dice coefficient was equal to 85.43%. Then, to compare the efficiency and performance of the model with other similar works, CNN-Res was evaluated on the popular SPES 2015 competition dataset where the average Dice coefficient was 79.23%.

Conclusion
This study presented a new and accurate method for the segmentation of MRI medical images using a deep convolutional neural network called CNN-Res, which directly predicts segment maps from raw input pixels.
Prevalence and predictors of asymptomatic malaria infection in Boricha District, Sidama Region, Ethiopia: implications for elimination strategies
Authors: Dabaro Desalegn , Birhanu Zewdie , Adissu Wondimagegn , Yilma Daniel , Yewhalaw Delenasaw 
Published: September 2023

Abstract
Background
Malaria remains a major public health threat in Ethiopia despite the tremendous progress made towards the 2030 elimination targets. The silent transmission of asymptomatic infection is one of the factors that enhance the persistence of the disease as a public health issue and impedes efforts to eliminate malaria. Thus, this study aimed at investigating the prevalence and risk factors of asymptomatic malaria infection in Boricha district, Sidama region of Ethiopia.

Methods
A community-based cross-sectional study was conducted in eight selected kebeles (smallest administrative unit) in Boricha district. Representative households were chosen using a multi-stage sampling technique. A total of 573 participants were included in the study. Malaria diagnosis was performed using rapid diagnostic test (RDT) and microscopy. A structured questionnaire was administered to collect socio-demographic information. Epi data 3.1 was employed for data entry, and SPSS version 25 was used for analysis.

Results
Of the 573 asymptomatic participants tested, 6.1% were found to be positive by RDT and 4.0% by microscopy. Participants aged under 5 years (AOR = 1.57, 95% CI 0.46–5.39) and 5–14 years old (AOR = 2.42, 95% CI 1.08–5.40), Insecticide-treated net utilization (AOR = 8.41; 95% CI 1.09–65.08), travel history (AOR = 6.85, 95% CI 2.32–20.26) and living in a house with windows (AOR = 2.11, 95% CI 1.02–4.36) were significantly associated with the asymptomatic malaria infection.

Conclusion
The findings of this study revealed that prevalence of asymptomatic malaria infection was higher in the study area. As a result, rigorous implementation of existing interventions, such as vector control and anti-malaria drugs, is strongly recommended. In addition, devising new ones that are suited to the contextual situations is highly suggested.
Capturing emergency dispatch address points as geocoding candidates to quantify delimited confidence in residential geolocation
Authors: Klaus Christian A. , Henry Kevin A. , Il’yasova Dora 
Published: September 2023

Abstract
Background
In response to citizens’ concerns about elevated cancer incidence in their locales, US CDC proposed publishing cancer incidence at sub-county scales. At these scales, confidence in patients’ residential geolocation becomes a key constraint of geospatial analysis. To support monitoring cancer incidence in sub-county areas, we presented summary metrics to numerically delimit confidence in residential geolocation.

Results
We defined a concept of Residential Address Discriminant Power (RADP) as theoretically perfect within all residential addresses and its practical application, i.e., using Emergency Dispatch (ED) Address Point Candidates of Equivalent Likelihood (CEL) to quantify Residential Geolocation Discriminant Power (RGDP) to approximate RADP. Leveraging different productivity of probabilistic, deterministic, and interactive geocoding record linkage, we simultaneously detected CEL for 5,807 cancer cases reported to North Carolina Central Cancer Registry (NC CCR)- in January 2022. Batch-match probabilistic and deterministic algorithms matched 86.0% cases to their unique ED address point candidates or a CEL, 4.4% to parcel site address, and 1.4% to street centerline. Interactively geocoded cases were 8.2%. To demonstrate differences in residential geolocation confidence between enumeration areas, we calculated sRGDP for cancer cases by county and assessed the existing uncertainty within the ED data, i.e., identified duplicate addresses (as CEL) for each ED address point in the 2014 version of the NC ED data and calculated ED_sRGDP by county. Both summary RGDP (sRGDP) (0.62–1.00) and ED_sRGDP (0.36–1.00) varied across counties and were lower in rural counties (p < 0.05); sRGDP correlated with ED_sRGDP (r = 0.42, p < 0.001). The discussion covered multiple conceptual and economic issues attendant to quantifying confidence in residential geolocation and presented a set of organizing principles for future work.

Conclusions
Our methodology produces simple metrics – sRGDP – to capture confidence in residential geolocation via leveraging ED address points as CEL. Two facts demonstrate the usefulness of sRGDP as area-based summary metrics: sRGDP variability between counties and the overall lower quality of residential geolocation in rural vs. urban counties. Low sRGDP for the cancer cases within the area of interest helps manage expectations for the uncertainty in cancer incidence data. By supplementing cancer incidence data with sRGDP and ED_sRGDP, CCRs can demonstrate transparency in geocoding success, which may help win citizen trust.
Ceramides are decreased after liraglutide treatment in people with type 2 diabetes: a post hoc analysis of two randomized clinical trials
Authors: Wretlind Asger , Curovic Viktor Rotbain , de Zawadzki Andressa , Suvitaival Tommi , Xu Jin , Zobel Emilie Hein , von Scholten Bernt Johan , Ripa Rasmus Sejersten , Kjaer Andreas , Hansen Tine Willum , Vilsbøll Tina , Vestergaard Henrik , Rossing Peter , Legido-Quigley Cristina 
Published: September 2023

Abstract
Background
Specific ceramides have been identified as risk markers for cardiovascular disease (CVD) years before onset of disease. Treatment with the glucagon-like peptide-1 receptor agonist (GLP-1RA) liraglutide has been shown to induce beneficial changes in the lipid profile and reduce the risk of CVD. Reducing lipotoxic lipids with an antidiabetic drug therapy could be a path towards precision medicine approaches for the treatment of complications to diabetes. In this post-hoc study, an investigation was carried out on the effect of liraglutide on CVD-risk associated ceramides in two randomized clinical trials including participants with type 2 diabetes (T2D).

Methods
This study analyzed plasma samples from two independent randomized placebo-controlled clinical trials. The first trial, Antiproteinuric Effects of Liraglutide Treatment (LirAlbu12) followed a crossover design where 27 participants were treated for 12 weeks with either liraglutide (1.8 mg/d) or placebo, followed by a four-week washout period, and then another 12 weeks of the other treatment. The second clinical trial, Effect of Liraglutide on Vascular Inflammation in Type-2 Diabetes (LiraFlame26), lasted for 26 weeks and followed a parallel design, where 102 participants were randomized 1:1 to either liraglutide or placebo. Heresix prespecified plasma ceramides were measured using liquid chromatography mass spectrometry and assessed their changes using linear mixed models. Possible confounders were assessed with mediation analyses.

Results
In the LiraFlame26 trial, 26-week treatment with liraglutide resulted in a significant reduction of two ceramides associated with CVD risk, C16 Cer and C24:1 Cer (p < 0.05) compared to placebo. None of the remaining ceramides showed statistically significant changes in response to liraglutide treatment compared to placebo. Significant changes in ceramides were not found after 12-weeks of liraglutide treatment in the LirAlbu12 trial. Mediation analyses showed that weight loss did not affect ceramide reduction.

Conclusions
It was demonstrated that treatment with liraglutide resulted in a reduction in C16 Cer and C24:1 Cer after 26 weeks of treatment. These findings suggest the GLP-1RA can be used to modulate ceramides in addition to its other properties.

Trial registration
Clinicaltrial.gov identifier: NCT02545738 and NCT03449654.
18F-FDG-PET/CT-based machine learning model evaluates indeterminate adrenal nodules in patients with extra-adrenal malignancies
Authors: Cao Lixiu , Zhang Dejiang , Yang Haoxuan , Xu Wengui , Liu Yongliang 
Published: September 2023

Abstract
Background
To assess the value of an 18F-FDG-positron emission tomography/computed tomography (PET/CT)-based machine learning model for distinguishing between adrenal benign nodules (ABNs) and adrenal metastases (AMs) in patients with indeterminate adrenal nodules and extra-adrenal malignancies.

Methods
A total of 303 patients who underwent 18F-FDG-PET/CT with indeterminate adrenal nodules and extra-adrenal malignancies from March 2015 to June 2021 were included in this retrospective study (training dataset (n = 182): AMs (n = 97), ABNs (n = 85); testing dataset (n = 121): AMs (n = 68), ABNs (n = 55)). The clinical and PET/CT imaging features of the two groups were analyzed. The predictive model and simplified scoring system for distinguishing between AMs and ABNs were built based on clinical and PET/CT risk factors using multivariable logistic regression in the training cohort. The performances of the predictive model and simplified scoring system in both the training and testing cohorts were evaluated by the areas under the receiver operating characteristic curves (AUCs) and calibration curves. The comparison of AUCs was evaluated by the DeLong test.

Results
The predictive model included four risk factors: sex, the ratio of the maximum standardized uptake value (SUVmax) of adrenal lesions to the mean liver standardized uptake value, the value on unenhanced CT (CTU), and the clinical stage of extra-adrenal malignancies. The model achieved an AUC of 0.936 with a specificity, sensitivity and accuracy of 0.918, 0.835, and 0.874 in the training dataset, respectively, while it yielded an AUC of 0.931 with a specificity, sensitivity, and accuracy of 1.00, 0.735, and 0.851 in the testing dataset, respectively. The simplified scoring system had comparable diagnostic value to the predictive model in both the training (AUC 0.938, sensitivity: 0.825, specificity 0.953, accuracy 0.885; P = 0.5733) and testing (AUC 0.931, sensitivity 0.735, specificity 1.000, accuracy 0.851; P = 1.00) datasets.

Conclusions
Our study showed the potential ability of a machine learning model and a simplified scoring system based on clinical and 18F-FDG-PET/CT imaging features to predict AMs in patients with indeterminate adrenal nodules and extra-adrenal malignancies. The simplified scoring system is simple, convenient, and easy to popularize.
Spotlights on ubiquitin-specific protease 12 (USP12) in diseases: from multifaceted roles to pathophysiological mechanisms
Authors: Niu Kaiyi , Shi Yanlong , Lv Qingpeng , Wang Yizhu , Chen Jiping , Zhang Wenning , Feng Kung , Zhang Yewei 
Published: September 2023

AbstractUbiquitination is one of the most significant post-translational modifications that regulate almost all physiological processes like cell proliferation, autophagy, apoptosis, and cell cycle progression. Contrary to ubiquitination, deubiquitination removes ubiquitin from targeted protein to maintain its stability and thus regulate cellular homeostasis. Ubiquitin-Specific Protease 12 (USP12) belongs to the biggest family of deubiquitinases named ubiquitin-specific proteases and has been reported to be correlated with various pathophysiological processes. In this review, we initially introduce the structure and biological functions of USP12 briefly and summarize multiple substrates of USP12 as well as the underlying mechanisms. Moreover, we discuss the influence of USP12 on tumorigenesis, tumor immune microenvironment (TME), disease, and related signaling pathways. This study also provides updated information on the roles and functions of USP12 in different types of cancers and other diseases, including prostate cancer, breast cancer, lung cancer, liver cancer, cardiac hypertrophy, multiple myeloma, and Huntington's disease. Generally, this review sums up the research advances of USP12 and discusses its potential clinical application value which deserves more exploration in the future.
Semiautomated pipeline for quantitative analysis of heart histopathology
Authors: Droste Patrick , Wong Dickson W. L. , Hohl Mathias , von Stillfried Saskia , Klinkhammer Barbara M. , Boor Peter 
Published: September 2023

Abstract
Background
Heart diseases are among the leading causes of death worldwide, many of which lead to pathological cardiomyocyte hypertrophy and capillary rarefaction in both patients and animal models, the quantification of which is both technically challenging and highly time-consuming. Here we developed a semiautomated pipeline for quantification of the size of cardiomyocytes and capillary density in cardiac histology, termed HeartJ, by generating macros in ImageJ, a broadly used, open-source, Java-based software.

Methods
We have used modified Gomori silver staining, which is easy to perform and digitize in high throughput, or Fluorescein-labeled lectin staining. The latter can be easily combined with other stainings, allowing additional quantitative analysis on the same section, e.g., the size of cardiomyocyte nuclei, capillary density, or single-cardiomyocyte protein expression. We validated the pipeline in a mouse model of cardiac hypertrophy induced by transverse aortic constriction, and in autopsy samples of patients with and without aortic stenosis.

Results
In both animals and humans, HeartJ-based histology quantification revealed significant hypertrophy of cardiomyocytes reflecting other parameters of hypertrophy and rarefaction of microvasculature and enabling the analysis of protein expression in individual cardiomyocytes. The analysis also revealed that murine and human cardiomyocytes had similar diameters in health and extent of hypertrophy in disease confirming the translatability of our murine cardiac hypertrophy model. HeartJ enables a rapid analysis that would not be feasible by manual methods. The pipeline has little hardware requirements and is freely available.

Conclusions
In summary, our analysis pipeline can facilitate effective and objective quantitative histological analyses in preclinical and clinical heart samples.
Treat-to-target strategies for the management of familial Mediterranean Fever in children
Authors: Ehlers Lisa , Rolfes Elisabeth , Lieber Mareike , Müller Dominik , Lainka Elke , Gohar Faekah , Klaus Günter , Girschick Hermann , Hörstermann Jana , Kümmerle-Deschner Jasmin , Brunner Jürgen , Palm-Beden Katharina , Tenbrock Klaus , von Wrangel Lusine , Faßhauer Maria , Blank Norbert , Trauzeddel Ralf , von Stuckrad Anne Sae Lim , Higgins Sonja , Welzel Tatjana , Lutz Thomas , Hentgen Véronique , Foell Dirk , Wittkowski Helmut , Kallinich Tilmann 
Published: September 2023

Abstract
Background
The objective of this initiative was to develop a treat-to-target (T2T) approach for the management of patients with Familial Mediterranean Fever (FMF), including the definition of a complex treatment target, and establish strategies that improve patient care and long-term outcome.

Methods
An initial set of statements as well as a flow chart visualising the proposed concept was developed. To adapt the preliminary statements to the current state of knowledge, a systematic literature search was performed and the modified statements were subject to a Delphi approach. To ensure the applicability of the statements in daily practice, an online survey was conducted among paediatric rheumatologists in Germany. In addition, data from the national AID-NET registry were analysed with respect to therapeutic response.

Results
This T2T initiative yielded a total of 26 statements guiding FMF management with respect to diagnosis, treatment targets, treatment strategies and monitoring. The online survey identified cut-off values for inflammatory markers indicating treatment intensification and appropriate measures in case of colchicine intolerance or non-adherence. The analysis of data derived from the national AID-NET showed that colchicine therapy was successfully terminated in 61% of patients (27 out of 44) with heterozygous MEFV mutations. Multidimensional treatment targets incorporating objective and subjective reported outcome measures were developed. These provide the basis for stratifying patients into the following treatment paths: continue colchicine, persisting attacks / inflammation, colchicine intolerance, persisting arthritis, colchicine reduction and adjustment/reduction of biologics.

Conclusions
The proposed consensus treatment plan for the management of FMF incorporates multidimensional targets allowing transparent treatment decisions, which will promote personalised disease management and increase adherence to therapy.
Extended interval dosing of ocrelizumab modifies the repopulation of B cells without altering the clinical efficacy in multiple sclerosis
Authors: Rodriguez-Mogeda Carla , van Lierop Zoë Y. G. J. , van der Pol Susanne M. A. , Coenen Loet , Hogenboom Laura , Kamermans Alwin , Rodriguez Ernesto , van Horssen Jack , van Kempen Zoé L. E. , Uitdehaag Bernard M. J. , Teunissen Charlotte E. , Witte Maarten E. , Killestein Joep , de Vries Helga E. 
Published: September 2023

AbstractBackgroundRecent studies suggest that extended interval dosing of ocrelizumab, an anti-B cell therapy, does not affect its clinical effectiveness in most patients with multiple sclerosis (MS). However, it remains to be established whether certain B cell subsets are differentially repopulated after different dosing intervals and whether these subsets relate to clinical efficacy.MethodsWe performed high-dimensional single-cell characterization of the peripheral immune landscape of patients with MS after standard (SID; n = 43) or extended interval dosing (EID; n = 37) of ocrelizumab and in non-ocrelizumab-treated (control group, CG; n = 28) patients with MS, using mass cytometry by time of flight (CyTOF).ResultsThe first B cells that repopulate after both ocrelizumab dosing schemes were immature, transitional and regulatory CD1d+CD5+B cells. In addition, we observed a higher percentage of transitional, naïve and regulatory B cells after EID in comparison with SID, but not of memory B cells or plasmablasts. The majority of repopulated B cell subsets showed an increased migratory phenotype, characterized by higher expression of CD49d, CD11a, CD54 and CD162. Interestingly, after EID, repopulated B cells expressed increased CD20 levels compared to B cells in CG and after SID, which was associated with a delayed repopulation of B cells after a subsequent ocrelizumab infusion. Finally, the number of/changes in B cell subsets after both dosing schemes did not correlate with any relapses nor progression of the disease.ConclusionsTaken together, our data highlight that extending the dosing interval of ocrelizumab does not lead to increased repopulation of effector B cells. We show that the increase of CD20 expression on B cell subsets in EID might lead to longer depletion or less repopulation of B cells after the next infusion of ocrelizumab. Lastly, even though extending the ocrelizumab interval dosing alters B cell repopulation, it does not affect the clinical efficacy of ocrelizumab in our cohort of patients with MS.