bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using deep learning–derived image features in radiologic time series to make personalised predictions: proof of concept in colonic transit data
Authors: Kelly Brendan S. , Mathur Prateek , Plesniar Jan , Lawlor Aonghus , Killeen Ronan P. 
Published: June 2023

Abstract
Objectives
Siamese neural networks (SNN) were used to classify the presence of radiopaque beads as part of a colonic transit time study (CTS). The SNN output was then used as a feature in a time series model to predict progression through a CTS.

Methods
This retrospective study included all patients undergoing a CTS in a single institution from 2010 to 2020. Data were partitioned in an 80/20 Train/Test split. Deep learning models based on a SNN architecture were trained and tested to classify images according to the presence, absence, and number of radiopaque beads and to output the Euclidean distance between the feature representations of the input images. Time series models were used to predict the total duration of the study.

Results
In total, 568 images of 229 patients (143, 62% female, mean age 57) patients were included. For the classification of the presence of beads, the best performing model (Siamese DenseNET trained with a contrastive loss with unfrozen weights) achieved an accuracy, precision, and recall of 0.988, 0.986, and 1. A Gaussian process regressor (GPR) trained on the outputs of the SNN outperformed both GPR using only the number of beads and basic statistical exponential curve fitting with MAE of 0.9 days compared to 2.3 and 6.3 days (p < 0.05) respectively.

Conclusions
SNNs perform well at the identification of radiopaque beads in CTS. For time series prediction our methods were superior at identifying progression through the time series compared to statistical models, enabling more accurate personalised predictions.

Clinical relevance statement
Our radiologic time series model has potential clinical application in use cases where change assessment is critical (e.g. nodule surveillance, cancer treatment response, and screening programmes) by quantifying change and using it to make more personalised predictions.

Key Points
• Time series methods have improved but application to radiology lags behind computer vision. Colonic transit studies are a simple radiologic time series measuring function through serial radiographs.
• We successfully employed a Siamese neural network (SNN) to compare between radiographs at different points in time and then used the output of SNN as a feature in a Gaussian process regression model to predict progression through the time series.
• This novel use of features derived from a neural network on medical imaging data to predict progression has potential clinical application in more complex use cases where change assessment is critical such as in oncologic imaging, monitoring for treatment response, and screening programmes.
From methylation to myelination: epigenomic and transcriptomic profiling of chronic inactive demyelinated multiple sclerosis lesions
Authors: Tiane Assia , Schepers Melissa , Reijnders Rick A. , van Veggel Lieve , Chenine Sarah , Rombaut Ben , Dempster Emma , Verfaillie Catherine , Wasner Kobi , Grünewald Anne , Prickaerts Jos , Pishva Ehsan , Hellings Niels , van den Hove Daniel , Vanmierlo Tim 
Published: June 2023

AbstractIn the progressive phase of multiple sclerosis (MS), the hampered differentiation capacity of oligodendrocyte precursor cells (OPCs) eventually results in remyelination failure. We have previously shown that DNA methylation of Id2/Id4 is highly involved in OPC differentiation and remyelination. In this study, we took an unbiased approach by determining genome-wide DNA methylation patterns within chronically demyelinated MS lesions and investigated how certain epigenetic signatures relate to OPC differentiation capacity. We compared genome-wide DNA methylation and transcriptional profiles between chronically demyelinated MS lesions and matched normal-appearing white matter (NAWM), making use of post-mortem brain tissue (n = 9/group). DNA methylation differences that inversely correlated with mRNA expression of their corresponding genes were validated for their cell-type specificity in laser-captured OPCs using pyrosequencing. The CRISPR–dCas9-DNMT3a/TET1 system was used to epigenetically edit human-iPSC-derived oligodendrocytes to assess the effect on cellular differentiation. Our data show hypermethylation of CpGs within genes that cluster in gene ontologies related to myelination and axon ensheathment. Cell type-specific validation indicates a region-dependent hypermethylation of MBP, encoding for myelin basic protein, in OPCs obtained from white matter lesions compared to NAWM-derived OPCs. By altering the DNA methylation state of specific CpGs within the promotor region of MBP, using epigenetic editing, we show that cellular differentiation and myelination can be bidirectionally manipulated using the CRISPR–dCas9-DNMT3a/TET1 system in vitro. Our data indicate that OPCs within chronically demyelinated MS lesions acquire an inhibitory phenotype, which translates into hypermethylation of crucial myelination-related genes. Altering the epigenetic status of MBP can restore the differentiation capacity of OPCs and possibly boost (re)myelination.
Greater rate of return to play and re-injury following all-inside meniscal repair compared to the inside-out technique: a systematic review
Authors: Migliorini Filippo , Asparago Giovanni , Oliva Francesco , Bell Andreas , Hildebrand Frank , Maffulli Nicola 
Published: June 2023

Abstract
Introduction
Inside-out and all-inside arthroscopic meniscal repairs are widely performed. However, it remains unclear which method promotes greater clinical outcomes. This study compared inside-out versus all-inside arthroscopic meniscal repair in terms of patient-reported outcome measures (PROMs), failures, return to play, and symptoms.

Methods
This systematic review was conducted in accordance with the PRISMA guidelines. Two authors independently performed the literature search by accessing the following databases: PubMed, Google Scholar, and Scopus in February 2023. All clinical studies which investigated the outcomes of all-inside and/or inside-out meniscal repair were considered.

Results
Data from 39 studies (1848 patients) were retrieved. The mean follow-up was 36.8 (9 to 120) months. The mean age of the patients was 25.8 ± 7.9 years. 28% (521 of 1848 patients) were women. No difference was found in PROMs: Tegner Activity Scale (P = 0.4), Lysholm score (P = 0.2), and International Knee Document Committee score (P = 0.4) among patients undergoing meniscal repair with all inside or inside-out techniques. All-inside repairs showed a greater rate of re-injury (P = 0.009) but also a greater rate of return to play at the pre-injury level (P = 0.0001). No difference was found in failures (P = 0.7), chronic pain (P = 0.05), reoperation (P = 0.1) between the two techniques. No difference was found in the rate of return to play (P = 0.5) and to daily activities (P = 0.1) between the two techniques.

Conclusion
Arthroscopic all-inside meniscal repair may be of special interest in patients with a particular interest in a fast return to sport, while, for less demanding patients, the inside-out suture technique may be recommended. High-quality comparative trials are required to validate these results in a clinical setting.

Level of Evidence
Level III, systematic review.
ChatGPT’s quiz skills in different otolaryngology subspecialties: an analysis of 2576 single-choice and multiple-choice board certification preparation questions
Authors: Hoch Cosima C. , Wollenberg Barbara , Lüers Jan-Christoffer , Knoedler Samuel , Knoedler Leonard , Frank Konstantin , Cotofana Sebastian , Alfertshofer Michael 
Published: June 2023

Abstract
Purpose
With the increasing adoption of artificial intelligence (AI) in various domains, including healthcare, there is growing acceptance and interest in consulting AI models to provide medical information and advice. This study aimed to evaluate the accuracy of ChatGPT’s responses to practice quiz questions designed for otolaryngology board certification and decipher potential performance disparities across different otolaryngology subspecialties.

Methods
A dataset covering 15 otolaryngology subspecialties was collected from an online learning platform funded by the German Society of Oto-Rhino-Laryngology, Head and Neck Surgery, designed for board certification examination preparation. These questions were entered into ChatGPT, with its responses being analyzed for accuracy and variance in performance.

Results
The dataset included 2576 questions (479 multiple-choice and 2097 single-choice), of which 57% (n = 1475) were answered correctly by ChatGPT. An in-depth analysis of question style revealed that single-choice questions were associated with a significantly higher rate (p < 0.001) of correct responses (n = 1313; 63%) compared to multiple-choice questions (n = 162; 34%). Stratified by question categories, ChatGPT yielded the highest rate of correct responses (n = 151; 72%) in the field of allergology, whereas 7 out of 10 questions (n = 65; 71%) on legal otolaryngology aspects were answered incorrectly.

Conclusion
The study reveals ChatGPT’s potential as a supplementary tool for otolaryngology board certification preparation. However, its propensity for errors in certain otolaryngology areas calls for further refinement. Future research should address these limitations to improve ChatGPT’s educational use. An approach, with expert collaboration, is recommended for the reliable and accurate integration of such AI models.
Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology
Authors: Zupanič Pajnič Irena , Leskovar Tamara , Črešnar Matija 
Published: June 2023

Abstract
Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old. When processing the petrous bones, precautions were taken to prevent contamination with modern DNA. The MillMix tissue homogenizer was used for grinding, 0.5 g of bone powder was decalcified, and DNA was purified in Biorobot EZ1. The PowerQuant System was used for quantification and a customized version of the HIrisPlex panel for massive parallel sequencing (MPS) analysis. Library preparation and templating were performed on the HID Ion Chef Instrument and sequencing on the Ion GeneStudio S5 System. Up to 21 ng DNA/g of powder was obtained from ancient petrous bones. Clean negative controls and no matches with elimination database profiles confirmed no contamination issue. Brown eyes and dark brown or black hair were predicted for the adult skeleton and blue eyes and brown or dark brown hair for the subadult skeleton. The MPS analysis results obtained proved that it is possible to predict hair and eye color not only for an adult from the Early Middle Ages, but also for a subadult skeleton dating to this period.
Proteomic profiling of sudden cardiac death with acquired cardiac hypertrophy
Authors: Kakimoto Yu , Ueda Atsushi , Ito Masatoshi , Tanaka Masayuki , Kubota Tomoko , Isozaki Shotaro , Osawa Motoki 
Published: June 2023

Abstract

Background
Cardiac hypertrophy, which develops in middle-aged and older individuals as a consequence of hypertension and obesity, is an established risk factor for sudden cardiac death (SCD). However, it is sometimes difficult to differentiate SCD with acquired cardiac hypertrophy (SCH) from compensated cardiac hypertrophy (CCH), at autopsy. We aimed to elucidate the proteomic alteration in SCH, which can be a guideline for future postmortem diagnosis.

Methods
Cardiac tissues were sampled at autopsy. SCH group consisted of ischemic heart failure, hypertensive heart failure, and aortic stenosis. CCH group included cases of non-cardiac death with cardiac hypertrophy. The control group comprised cases of non-cardiac death without cardiac hypertrophy. All patients were aged > 40 years, and hypertrophic cardiomyopathy was not included in this study. We performed histological examination and shotgun proteomic analysis, followed by quantitative polymerase chain reaction analysis.

Results
Significant obesity and myocardial hypertrophy, and mild myocardial fibrosis were comparable in SCH and CCH cases compared to control cases. The proteomic profile of SCH cases was distinguishable from those of CCH and control cases, and many sarcomere proteins were increased in SCH cases. Especially, the protein and mRNA levels of MYH7 and MYL3 were significantly increased in SCH cases.

Conclusion
This is the first report of cardiac proteomic analysis in SCH and CCH cases. The stepwise upregulation of sarcomere proteins may increase the risk for SCD in acquired cardiac hypertrophy before cardiac fibrosis progresses significantly. These findings can possibly aid in the postmortem diagnosis of SCH in middle-aged and older individuals.
Evaluating mismatch repair deficiency in colorectal cancer biopsy specimens
Authors: Grillo F. , Paudice M. , Gambella A. , Bozzano S. , Sciallero S. , Puccini A. , Lastraioli S. , Dono M. , Parente P. , Vanoli A. , Angerilli V. , Fassan M. , Mastracci L. 
Published: June 2023

AbstractMismatch repair (MMR) testing on all new cases of colorectal cancer (CRC) has customarily been preferably performed on surgical specimens, as more tissue is available; however, new clinical trials for the use of immune checkpoint inhibitors in the neoadjuvant setting require MMR testing on biopsy samples. This study aims at identifying advantages, disadvantages and any potential pitfalls in MMR evaluation on biopsy tissue and how to cope with them. The study is prospective-retrospective, recruiting 141 biopsies (86 proficient (p)MMR and 55 deficient (d)MMR) and 97 paired surgical specimens (48 pMMR; 49 dMMR). In biopsy specimens, a high number of indeterminate stains was observed, in particular for MLH1 (31 cases, 56.4%). The main reasons were a punctate nuclear expression of MLH1, relatively weak MLH1 nuclear expression compared to internal controls, or both (making MLH1 loss difficult to interpret), which was solved by reducing primary incubation times for MLH1. A mean of  ≥﻿ 5 biopsies had adequate immunostains, compared to ≤ 3 biopsies in inadequate cases. Conversely, surgical specimens rarely suffered from indeterminate reactions, while weaker staining intensity (p < 0.007) for MLH1 and PMS2 and increased patchiness grade (p < 0.0001) were seen. Central artefacts were almost exclusive to surgical specimens. MMR status classification was possible in 92/97 matched biopsy/resection specimen cases, and all of these were concordant (47 pMMR and 45 dMMR). Evaluation of MMR status on CRC biopsy samples is feasible, if pitfalls in interpretation are known, making laboratory-specific appropriate staining protocols fundamental for high-quality diagnoses.
The role of acrolein for E-cigarette vapour condensate mediated activation of NADPH oxidase in cultured endothelial cells and macrophages
Authors: Kuntic Ivana , Kuntic Marin , Oelze Matthias , Stamm Paul , Karpi Angelica , Kleinert Hartmut , Hahad Omar , Münzel Thomas , Daiber Andreas 
Published: June 2023

AbstractElectronic cigarettes (E-cigarettes) have recently become a popular alternative to traditional tobacco cigarettes. Despite being marketed as a healthier alternative, increasing evidence shows that E-cigarette vapour could cause adverse health effects. It has been postulated that degradation products of E-cigarette liquid, mainly reactive aldehydes, are responsible for those effects. Previously, we have demonstrated that E-cigarette vapour exposure causes oxidative stress, inflammation, apoptosis, endothelial dysfunction and hypertension by activating NADPH oxidase in a mouse model. To better understand oxidative stress mechanisms, we have exposed cultured endothelial cells and macrophages to condensed E-cigarette vapour (E-cigarette condensate) and acrolein. In both endothelial cells (EA.hy 926) and macrophages (RAW 264.7), we have observed that E-cigarette condensate incubation causes cell death. Since recent studies have shown that among toxic aldehydes found in E-cigarette vapour, acrolein plays a prominent role, we have incubated the same cell lines with increasing concentrations of acrolein. Upon incubation with acrolein, a translocation of Rac1 to the plasma membrane has been observed, accompanied by an increase in oxidative stress. Whereas reactive oxygen species (ROS) formation by acrolein in cultured endothelial cells was mainly intracellular, the release of ROS in cultured macrophages was both intra- and extracellular. Our data also demonstrate that acrolein activates the nuclear factor erythroid 2-related factor 2 (Nrf2) antioxidant pathway and, in general, could mediate E-cigarette vapour-induced oxidative stress and cell death. More mechanistic insight is needed to clarify the toxicity associated with E-cigarette consumption and the possible adverse effects on human health.
Home-visiting programs based on the Brazelton approach: a scoping review
Authors: Tazza Cecilia , Ioverno Salvatore , Pallini Susanna 
Published: June 2023

AbstractThis review maps and summarizes the quantitative studies on the main outcomes associated with home visiting (HV) programs using Brazelton methods aimed at supporting expectant and new parents. One hundred thirty-seven records were identified, and 19 records were selected. The design of our study was based on the methodological framework for conducting scoping reviews. Quality was assessed through the Jadad scale. Studies were coded for participant characteristics (number, mean age, and risk status), methodology (recruitment, home visit frequency, age of the child, Brazelton method, and research design), and intervention outcomes (on infants, parents, and home visitors). The studies mostly focused on the impact of Brazelton HV programs on infant development, the mother’s psychological well-being, mother-infant interaction, and home visitor satisfaction. Experimental and quasi-experimental studies consistently have shown that parents receiving the intervention have greater knowledge of their children. Results are less conclusive regarding the intervention’s impact on other domains of child development, mothers’ psychological well-being, and mothers’ sensitivity to the relationship with the child. Overall, the results suggest that the improvements associated with the intervention are mainly influenced by the risk status of families. Further research is needed to better understand the benefits of HV based on the Brazelton approach and the target population that may benefit most from this intervention.Conclusion: Although the impact of the Brazelton home visiting intervention is not yet fully understood, there is promising evidence of its positive effects on child development, maternal well-being, and parental knowledge. Further research with consistent methodologies and larger sample sizes is needed to strengthen our understanding. However, existing findings in the literature underscore the importance of preventive interventions such as the Brazelton program in improving family well-being, with potential long-term benefits.

What is Known:

• Home visiting programs based on the Brazelton approach aim to increase parents’ knowledge and sensitivity to their children.

• There is no clear picture in the literature of the effectiveness of these programs.

What is New:

• Existing studies consistently show the effectiveness of these programs to improve parents’ knowledge of their children.

• Findings on the impact of these programs on child development, mothers' psychological well-being and sensitivity to their child are inconclusive and may be influenced by the risk status.
Der Zentrumbereichskern Wilmersdorfer Straße in Berlin-Charlottenburg in Zeiten multipler Krisen – gestärkt durch Nutzungsmischung, Kiezcharakter und Kuration?
Authors: Suwala Lech , Pfeil Nina , Lange Max , Pfeiffer Linus , Albers Hans-Hermann 
Published: June 2023

ZusammenfassungDie Coronapandemie hat zwischenzeitlich für einen durchschnittlichen Rückgang der Passantenfrequenzen von bis zu 40 % in den Hauptgeschäftsstraßen der deutschen Großstädte gesorgt. In Kombination mit den Schreckgespenstern Onlinehandel, der zunehmenden Einzelhandels- und Filialdichte und neuerdings der Inflation kommen besondere Herausforderungen auf innerstädtische Geschäftsstraßen und ihre Erdgeschosseinheiten zu. Dieser Beitrag setzt sich mit dem Zentrumbereichskern Wilmersdorfer Straße in Berlin-Charlottenburg auseinander und hat das Ziel, zu zeigen, dass Nutzungsmischung, Kiezcharakter und Kuration im Verbund innerstädtischen Geschäftsstraßen und ihren Erdgeschosseinheiten gerade in Krisenzeiten helfen können. Dies geschieht basierend auf einem sozio- und regionalökonomischen Profil der Geschäftsstraße, das sich aus lokalen sekundärstatistischen Daten, einer Kartierung der Liegenschaften und 13 Expertengesprächen mit mannigfaltigen Stakeholdern speist. Es kann gezeigt werden, dass ein breit gefächerter Nutzungs- und Funktionsmix jenseits von Handelsaktivitäten mit einer integrierten Nahversorgungsfunktion, gepaart mit Kiezcharakter und einer Kuration, die offen für neuartige institutionelle Verbünde mit der Zivilgesellschaft ist, innerstädtische Geschäftsstraßen sehr widerstandsfähig machen kann. Dies gilt insbesondere dann, wenn die Geschäftsstraße zusätzlich in einen Kiez eingebettet ist, auf einen räumlich verwurzelten Kundenstamm trifft und eben auf dessen lokaleren Lebensradien (z. B. als gesellschaftlicher Treffpunkt) Bezug nimmt.
Automating the Calibration of Flat-Jointed Bonded Particle Model Microproperties for the Rewan Sandstone Case Study
Authors: Tsang Matthew , Clark Ian , Karlovšek Jurij 
Published: June 2023

AbstractThe flat joint contact model (FJM) provides significant improvements over its predecessors, the parallel bond and contact bond models, for bonded particle modelling of rocks due to its unique microstructure that allows for the reproduction of the macroscopic compressive–tensile strength ratio, σc/|σt|; internal friction angle, ϕ; and the Hoek–Brown constant, mi. However, the microproperty calibration process is tedious and time-consuming to perform manually due to the various microproperty interdependencies that exist in the FJM. Previous attempts at automating the bonded particle model microproperty calibration process have typically utilised advanced statistical methods, such as artificial neural networks, but they have not yet been widely applied to the FJM over a representative range of confining stresses for calculation of ϕ and mi. In this study, a new method is proposed for automating the FJM microproperty calibration process based on a numerical root-finding algorithm and specific calibration sequencing. The new method is applied to a Rewan Sandstone case study with similar natural porosity to a 2D bonded particle model packed to a low initial mean stress. The resulting FJM microproperties are shown to reproduce both the target macroscopic laboratory properties and a realistic damage evolution, including a normalised crack initiation stress of 0.46 and a normalised crack damage stress of 0.83 coinciding with a reversal of the axial stress–volumetric strain curve in an unconfined compression test simulation. It is also demonstrated that the absolute change in the instantaneous lateral–axial strain ratio (Poisson’s ratio in the linear-elastic phase) provides a reasonable proxy to the acoustic emissions which may be measured in the laboratory.