bluuebunny/crossref_metadata_2025_split huggingface dataset:
NnU-Net versus mesh growing algorithm as a tool for the robust and timely segmentation of neurosurgical 3D images in contrast-enhanced T1 MRI scans
Authors: de Boer Mathijs , Kos Tessa M. , Fick Tim , van Doormaal Jesse A. M. , Colombo Elisa , Kuijf Hugo J. , Robe Pierre A. J. T. , Regli Luca P. , Bartels Lambertus W. , van Doormaal Tristan P. C. 
Published: February 2024

Abstract

Purpose
This study evaluates the nnU-Net for segmenting brain, skin, tumors, and ventricles in contrast-enhanced T1 (T1CE) images, benchmarking it against an established mesh growing algorithm (MGA).

Methods
We used 67 retrospectively collected annotated single-center T1CE brain scans for training models for brain, skin, tumor, and ventricle segmentation. An additional 32 scans from two centers were used test performance compared to that of the MGA. The performance was measured using the Dice-Sørensen coefficient (DSC), intersection over union (IoU), 95th percentile Hausdorff distance (HD95), and average symmetric surface distance (ASSD) metrics, with time to segment also compared.

Results
The nnU-Net models significantly outperformed the MGA (p < 0.0125) with a median brain segmentation DSC of 0.971 [95CI: 0.945–0.979], skin: 0.997 [95CI: 0.984–0.999], tumor: 0.926 [95CI: 0.508–0.968], and ventricles: 0.910 [95CI: 0.812–0.968]. Compared to the MGA’s median DSC for brain: 0.936 [95CI: 0.890, 0.958], skin: 0.991 [95CI: 0.964, 0.996], tumor: 0.723 [95CI: 0.000–0.926], and ventricles: 0.856 [95CI: 0.216–0.916]. NnU-Net performance between centers did not significantly differ except for the skin segmentations Additionally, the nnU-Net models were faster (mean: 1139 s [95CI: 685.0–1616]) than the MGA (mean: 2851 s [95CI: 1482–6246]).

Conclusions
The nnU-Net is a fast, reliable tool for creating automatic deep learning-based segmentation pipelines, reducing the need for extensive manual tuning and iteration. The models are able to achieve this performance despite a modestly sized training set. The ability to create high-quality segmentations in a short timespan can prove invaluable in neurosurgical settings.
Unleashing the potential of metaphors: a categorization system for exploring return to work after maternity
Authors: Rapisarda Sebastiano , Santoro Valentina , Dal Corso Laura 
Published: February 2024

Abstract
Purpose
Return to work after maternity leave represents a radical change in women’s lives. This paper aims to present a new metaphor categorization system based on two studies, which could assist working mothers in expressing the nuances of their experience when returning to work after maternity leave.

Methods
We carried out the analysis of the metaphors according to the method for thematic analysis, through a multistep, iterative coding process. To ensure the researchers encode the data similarly, inter-coder reliability was achieved through the judges’ agreement method. The level of agreement between the two judges was measured by Cohen’s kappa.

Results
In Study 1, we established a system comprising ten metaphor categories (namely, Natural event and/or element, Challenge and destination, Movement and/or action, Fresh start, Fight, Game and hobby, Animal, Alternate reality, Means of transport, Hostile place). In Study 2, we recognized the same metaphor categories observed in Study 1, except “Means of transport”, even with data sourced from a distinct participant group, an indicator of credibility in terms of inter-coder reliability.

Conclusion
Findings highlight the usefulness of this new metaphor categorization system (named Meta4Moms@Work—Metaphors system for Moms back to Work) to facilitate a more straightforward elicitation of the meanings employed by working mothers to depict their return to work after maternity leave. Leveraging these insights, researchers/practitioners can develop and execute primary and secondary interventions aimed to enhance working mothers’ work-life balance, well-being, and mental health.
Feasibility study of wearable capillary refill time measurement device
Authors: Shinozaki Masayoshi , Saito Daiki , Nakada Taka-aki , Nomura Yukihiro , Nakaguchi Toshiya 
Published: February 2024

AbstractCapillary refill time (CRT) is an internationally accepted indicator of peripheral circulation. The CRT is measured by applying compression to the fingernail for a few seconds, releasing it, and observing the process of refilling of blood at the fingertip. The international guidelines for the management of sepsis and septic shock 2021 contains an additional new recommendation for CRT measurement to determine the peripheral circulation statuses of adult patients with septic shock. However, the current CRT measurement method lacks objectivity. Previous studies have reported the development of measurement devices and video analysis systems, which involve complex measurement environment construction and assume only in-hospital measurements. In addition, since medical workers are limited in the number of carrying medical devices, devices that can be used to obtain multiple biometric indicators in a single measurement are needed. Hence, a prototype wearable CRT measurement device was developed in this study, and its feasibility was evaluated by comparing the agreement, intra-class correlation coefficient, and coefficient of variation with those of a CRT measurement device developed in the past. The results indicated that mean CRTs between measurement methods were agreement, with moderate or better intra-rater reliability and no difference in coefficient of variation. Therefore, the results indicate the feasibility of the proposed wearable CRT device.
Bioturbation by Benthic Stingrays Alters the Biogeomorphology of Tidal Flats
Authors: Nauta Janne , Leurs Guido , Nieuwenhuis Brian O. , Mathijssen Donné R. A. H. , Olff Han , Bouma Tjeerd J. , van der Wal Daphne , Hijner Nadia , Regalla Aissa , Pontes Samuel Ledo , Govers Laura L. 
Published: February 2024

AbstractFishing-down-marine-food-webs has resulted in alarming declines of various species worldwide. Benthic rays are one examples of such overexploited species. On tidal flats, these rays are highly abundant and play an ecologically important role. They use tidal flats as refuge, feeding and resting grounds, during which they bury into the sediment, which results in sediment bioturbation. Changes in bioturbation intensity, following ray removal, may affect the biogeomorphology of tidal flats with possible cascading effects on the macrozoobenthic community. However, it is poorly understood how these indirect effects could influence ecosystem function. We therefore studied the geomorphic impact of benthic rays (specifically the pearl whipray/stingray Fontitrygon margaritella) on the tropical tidal flats of the Bijagós Archipelago, Guinea-Bissau, on a landscape scale. We investigated 1) bioturbation rates by rays using drone and ground surveys, 2) the spatial distribution of ray pits on multiple tidal flats, 3) the impact of rays on sediment properties and macrozoobenthos by experimental exclusion (15 months). Benthic rays bioturbated 3.7 ± 0.35% of the tidal flat’s sediment surface per day over one single 24-h period, which equals a complete top-sediment-surface turnover every 27 days. The spatial distribution of ray pits was affected by tidal flat geomorphology since pits decayed faster at areas exposed to strong hydrodynamic forces. Predator exclusion altered sediment properties, leading to changes in sedimentation (− 17%) and erosion (− 43%) rates. In addition, macrozoobenthic species composition changed, marked by an increase in Capitellidae worms and a greater biomass of Malacostraca over time. These changes indicated substantial effects of ray bioturbation on the biotic and geomorphic landscape of tidal flats. Overall, we conclude that changing abundances of benthic rays can have clear landscape-wide geomorphological effects on intertidal ecosystems. These indirect consequences of fisheries should be incorporated in integrative management plans to preserve tidal flats and connected ecosystems.
miR-34c-5p inhibited fibroblast proliferation, differentiation and epithelial-mesenchymal transition in benign airway stenosis via MDMX/p53 pathway
Authors: Wei Jinmei , Chen Yan , Feng Tingmei , Wei Yuihui , Yang Caizhen , Zhang Changwen , Li Wentao , Liu Guangnan 
Published: February 2024

AbstractBenign airway stenosis (BAS) means airway stenosis or obstruction that results from a variety of non-malignant factors, including tuberculosis, trauma, benign tumors, etc. In consideration of the currently limited research on microRNAs in BAS, this study aimed to explore the role and mechanism of miR-34c-5p in BAS. The expression of miR-34c-5p in BAS granulation tissues showed a significant down-regulation compared with the normal control group. Moreover, miR-34c-5p mimics suppressed the proliferation and differentiation of human bronchial fibroblasts (HBFs) and the epithelial-mesenchymal transition (EMT) of human bronchial epithelial cells (HBE). Conversely, miR-34c-5p inhibitors aggravated those effects. A dual-luciferase reporter assay confirmed that miR-34c-5p can target MDMX rather than Notch1. The over-expression of MDMX can reverse the inhibiting effect of miR-34c-5p on HBFs proliferation, differentiation and EMT. Furthermore, the expressions of tumor protein (p53) and PTEN were down-regulated following the over-expression of MDMX. In addition, the expressions of PI3K and AKT showed an up-regulation. In conclusion, miR-34c-5p was down-regulated in BAS and may inhibit fibroblast proliferation differentiation and EMT in BAS via the MDMX/p53 signaling axis. These findings expand the understanding of the role of miR-34c-5p and will help develop new treatment strategies for BAS.
Understanding the Mechanisms and Implications of the First Flush in Mine Pools: Insights from Field Studies in Europe’s Deepest Metal Mine and Analogue Modelling
Authors: Mugova Elke , Molaba Leshego , Wolkersdorfer Christian 
Published: February 2024

AbstractThe chemical composition of mine water discharged from flooded underground mines typically improves over time. This phenomenon is called first flush and can be described by a characteristic curve. Shortly after the mine water begins to discharge, water constituent concentrations rise and then fall in an almost exponential curve, improving water quality over time. In this study, the change in mine water quality was investigated throughout the mine water body. This mine water body commonly consists of different water bodies with individual densities, resulting in mine water stratification. Anthropogenic disturbance of the mine water body can disrupt this stratification and also the positive effect of the first flush. To better understand and predict the first flush, the first flush was simulated experimentally using an analogue model of a flooded underground mine, the Agricola Model Mine. The results were compared with field studies to help understanding and predicting the change in mine water quality. Overall, the results suggest that the first flush occurs throughout the mine water body, making it similar to a chemical reactor. This better understanding of the process can lead to more effective mine water management and design of mine water treatment facilities.
Graphical Abstract
Effect of direct oral anticoagulants on bleeding during and after cataract surgery
Authors: Maytal Anat , Naidorf Rosenblatt Hadar , Rotem Reut , Segev Fani 
Published: February 2024

Abstract
Purpose
To assess the risk for intraoperative and postoperative ocular bleeding associated with direct oral anticoagulant treatment in patients undergoing phacoemulsification surgery.

Methods
Consecutive patients had phacoemulsification and intraocular lens implantation while taking uninterrupted direct oral anticoagulants (dabigatran, rivaroxaban, or apixaban). Gender and age-matched patients without antithrombotic therapy were used as the control group. Patients were examined one week postoperatively. Intraoperative and postoperative hemorrhagic and non-hemorrhagic complications were assessed.

Results
Forty patients (56 eyes) on direct oral anticoagulants and 120 patients (172 eyes) without anticoagulation, at a mean age of 77 years, had phacoemulsification. There was no significant difference between the groups in the rate of intraoperative and postoperative bleeding. One eye (1.8%) in the treatment group and 3 eyes (1.7%) in the control group had hyphema (p = 0.72). No patient had thromboembolic event during or after surgery.

Conclusions
Cataract surgery was safely performed while continuing direct oral anticoagulation.
Validation of a methylation-based signature for subventricular zone involvement in glioblastoma
Authors: Ehret Felix , Zühlke Oliver , Schweizer Leonille , Kahn Johannes , Csapo-Schmidt Christoph , Roohani Siyer , Zips Daniel , Capper David , Adeberg Sebastian , Abdollahi Amir , Knoll Maximilian , Kaul David 
Published: February 2024

Abstract
Purpose
Glioblastomas (GBM) with subventricular zone (SVZ) contact have previously been associated with a specific epigenetic fingerprint. We aim to validate a reported bulk methylation signature to determine SVZ contact.

Methods
Methylation array analysis was performed on IDHwt GBM patients treated at our institution. The v11b4 classifier was used to ensure the inclusion of only receptor tyrosine kinase (RTK) I, II, and mesenchymal (MES) subtypes. Methylation-based assignment (SVZM ±) was performed using hierarchical cluster analysis. Magnetic resonance imaging (MRI) (T1ce) was independently reviewed for SVZ contact by three experienced readers.

Results
Sixty-five of 70 samples were classified as RTK I, II, and MES. Full T1ce MRI-based rater consensus was observed in 54 cases, which were retained for further analysis. Epigenetic SVZM classification and SVZ were strongly associated (OR: 15.0, p = 0.003). Thirteen of fourteen differential CpGs were located in the previously described differentially methylated LRBA/MAB21L2 locus. SVZ + tumors were linked to shorter OS (hazard ratio (HR): 3.80, p = 0.02) than SVZM + at earlier time points (time-dependency of SVZM, p < 0.05). Considering the SVZ consensus as the ground truth, SVZM classification yields a sensitivity of 96.6%, specificity of 36.0%, positive predictive value (PPV) of 63.6%, and negative predictive value (NPV) of 90.0%.

Conclusion
Herein, we validated the specific epigenetic signature in GBM in the vicinity of the SVZ and highlighted the importance of methylation of a part of the LRBA/MAB21L2 gene locus. Whether SVZM can replace MRI-based SVZ assignment as a prognostic and diagnostic tool will require prospective studies of large, homogeneous cohorts.
Spectra and Anisotropy of Solar Energetic Protons During GLE #65 on 28 October, 2003 and GLE #66 on 29 October, 2003
Authors: Mishev Alexander L. , Koldobskiy Sergey A. , Larsen Nicholas , Usoskin Ilya G. 
Published: February 2024

AbstractSolar Cycle 23 was the most active in ground-level enhancements (GLEs) with 16 events registered by the global neutron monitor network. In this paper, we study a very active period in October–November, 2003, which revealed an intense solar activity burst that led to several eruptive processes and produced a sequence of three GLEs. By applying state-of-the-art modelling to records from the global neutron monitor network as well as space-borne data, we derived the spectral and anisotropy characteristics of accelerated solar protons during the GLE #65 event on 28 October, 2003 and GLE #66 on 29 October, 2003. The spectra and the pitch angle distributions are obtained with a 5-min time resolution, providing their dynamical evolution throughout the event. The spectra are parameterised with a modified power-law rigidity spectrum, whilst the angular distribution with a Gaussian. The constraints and uncertainties of the derived characteristics are evaluated by corresponding modelling.
Regulation of nerve-evoked contractions of the murine vas deferens
Authors: Wong Pei Yee , Fong Zhihui , Hollywood Mark A. , Thornbury Keith D. , Sergeant Gerard P. 
Published: February 2024

AbstractStimulation of sympathetic nerves in the vas deferens yields biphasic contractions consisting of a rapid transient component resulting from activation of P2X1 receptors by ATP and a secondary sustained component mediated by activation of α1-adrenoceptors by noradrenaline. Noradrenaline can also potentiate the ATP-dependent contractions of the vas deferens, but the mechanisms underlying this effect are unclear. The purpose of the present study was to investigate the mechanisms underlying potentiation of transient contractions of the vas deferens induced by activation of α1-adrenoceptors. Contractions of the mouse vas deferens were induced by electric field stimulation (EFS). Delivery of brief (1s duration) pulses (4 Hz) yielded transient contractions that were inhibited tetrodotoxin (100 nM) and guanethidine (10 µM). α,β-meATP (10 µM), a P2X1R desensitising agent, reduced the amplitude of these responses by 65% and prazosin (100 nM), an α1-adrenoceptor antagonist, decreased mean contraction amplitude by 69%. Stimulation of α1-adrenoceptors with phenylephrine (3 µM) enhanced EFS and ATP-induced contractions and these effects were mimicked by the phorbol ester PDBu (1 µM), which activates PKC. The PKC inhibitor GF109203X (1 µM) prevented the stimulatory effects of PDBu on ATP-induced contractions of the vas deferens but only reduced the stimulatory effects of phenylephrine by 40%. PDBu increased the amplitude of ATP-induced currents recorded from freshly isolated vas deferens myocytes and HEK-293 cells expressing human P2X1Rs by 93%. This study indicates that: (1) potentiation of ATP-evoked contractions of the mouse vas deferens by α1-adrenoceptor activation were not fully blocked by the PKC inhibitor GF109203X and (2) that the stimulatory effect of PKC on ATP-induced contractions of the vas deferens is associated with enhanced P2X1R currents in vas deferens myocytes.
Current Trends and Challenges of Microbiome Research in Bladder Cancer
Authors: Isali Ilaha , Helstrom Emma K. , Uzzo Nicole , Lakshmanan Ankita , Nandwana Devika , Valentine Henkel , Sindhani Mohit , Abbosh Philip , Bukavina Laura 
Published: February 2024

Abstract
Purpose of the Review
Microbiome research has provided valuable insights into the associations between microbial communities and bladder cancer. However, this field faces significant challenges that hinder the interpretation, generalization, and translation of findings into clinical practice. This review aims to elucidate these challenges and highlight the importance of addressing them for the advancement of microbiome research in bladder cancer.

Recent Findings
Recent findings underscore the complexities involved in microbiome research, particularly in the context of bladder cancer. Challenges include low microbial biomass in urine samples, potential contamination issues during collection and processing, variability in sequencing methods and primer selection, and the difficulty of establishing causality between microbiota and bladder cancer. Studies have shown the impact of sample storage conditions and DNA isolation kits on microbiome analysis, emphasizing the need for standardization. Additionally, variations in urine collection methods can introduce contamination and affect results. The choice of 16S rRNA gene amplicon sequencing or shotgun metagenomic sequencing introduces technical challenges, including primer selection and sequencing read length. Establishing causality between the microbiota and bladder cancer requires experimental methods like fecal microbiota transplantation and human microbiota-associated murine models, which face their own set of challenges. Translating microbiome research into therapeutic applications is hindered by methodological variability, incomplete understanding of bioactive molecules, imperfect animal models, and the inherent heterogeneity of microbiome communities among individuals.

Summary
Microbiome research in bladder cancer presents significant challenges stemming from technical and conceptual complexities. Addressing these challenges through standardization, improved experimental models, and advanced analytical approaches is essential for advancing our understanding of the microbiome’s role in bladder cancer and its potential clinical applications. Achieving this goal can lead to improved patient outcomes and novel therapeutic strategies in the future.
Concomitant double-fusion of PLEKHA7-ALK and INPP5D-ALK reveals favorable alectinib sensitivity in lung adenocarcinoma: a case report and literature review
Authors: Li Pei , Ju Xiao , Yang Guangjian 
Published: February 2024

AbstractAnaplastic lymphoma kinase (ALK) gene fusion is a classic driver mutation in non-small cell lung cancer (NSCLC); however, ALK double-fusion variants in NSCLC have rarely been reported. In this study, we reported a case with extremely uncommon ALK double-fusion variants. A 32-year-old female diagnosed with lung adenocarcinoma, who had developed multiple intrapulmonary and brain metastases, experienced worsening of her condition despite undergoing prior chemotherapy. Subsequent testing using next-generation sequencing (NGS) detected the presence of PLEKHA7-ALK and INPP5D-ALK double-fusion. The prescription of alectinib revealed potent efficacy and resulted in an increase in the survival rate. This case presented two uncommon and concomitant ALK fusion partners in NSCLC; more importantly, the INPP5D-ALK subtype has not been reported, therefore this study broadens the spectrum of ALK double-fusion variants and provides insight into the use of ALK inhibitors for the treatment of NSCLC in patients with double ALK fusions.
Transition from pediatric to adult care in patients with Turner syndrome in Italy: a consensus statement by the TRAMITI project
Authors: Aversa T. , De Sanctis L. , Faienza M. F. , Gambineri A. , Balducci A. , D’Aprile R. , Di Somma C. , Giavoli C. , Grossi A. , Meriggiola M. C. , Profka E. , Salerno M. , Stagi S. , Scarano E. , Zatelli M. C. , Wasniewska M. 
Published: February 2024

Abstract
Purpose
Transition from pediatric to adult care is associated with significant challenges in patients with Turner syndrome (TS). The objective of the TRansition Age Management In Turner syndrome in Italy (TRAMITI) project was to improve the care provided to patients with TS by harnessing the knowledge and expertise of various Italian centers through a Delphi-like consensus process.

Methods
A panel of 15 physicians and 1 psychologist discussed 4 key domains: transition and referral, sexual and bone health and oncological risks, social and psychological aspects and systemic and metabolic disorders.

Results
A total of 41 consensus statements were drafted. The transition from pediatric to adult care is a critical period for patients with TS, necessitating tailored approaches and early disclosure of the diagnosis to promote self-reliance and healthcare autonomy. Fertility preservation and bone health strategies are recommended to mitigate long-term complications, and psychiatric evaluations are recommended to address the increased prevalence of anxiety and depression. The consensus also addresses the heightened risk of metabolic, cardiovascular and autoimmune disorders in patients with TS; regular screenings and interventions are advised to manage these conditions effectively. In addition, cardiac abnormalities, including aortic dissections, require regular monitoring and early surgical intervention if certain criteria are met.

Conclusions
The TRAMITI consensus statement provides valuable insights and evidence-based recommendations to guide healthcare practitioners in delivering comprehensive and patient-centered care for patients with TS. By addressing the complex medical and psychosocial aspects of the condition, this consensus aims to enhance TS management and improve the overall well-being and long-term outcomes of these individuals.