bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proton and carbon ion beam treatment with active raster scanning method in 147 patients with skull base chordoma at the Heidelberg Ion Beam Therapy Center—a single-center experience
Authors: Mattke Matthias , Ohlinger Matteo , Bougatf Nina , Harrabi Semi , Wolf Robert , Seidensaal Katharina , Welzel Thomas , Röder Falk , Gerum Sabine , Ellerbrock Malte , Jäkel Oliver , Haberer Thomas , Herfarth Klaus , Uhl Matthias , Debus Jürgen 
Published: September 2022

Abstract
Background
This study aimed to compare the results of irradiation with protons versus irradiation with carbon ions in a raster scan technique in patients with skull base chordomas and to identify risk factors that may compromise treatment results.

Methods
A total of 147 patients (85 men, 62 women) were irradiated with carbon ions (111 patients) or protons (36 patients) with a median dose of 66 Gy (RBE (Relative biological effectiveness); carbon ions) in 4 weeks or 74 Gy (RBE; protons) in 7 weeks at the Heidelberg Ion Beam Therapy Center (HIT) in Heidelberg, Germany. The median follow-up time was 49.3 months. All patients had gross residual disease at the beginning of RT. Compression of the brainstem was present in 38%, contact without compression in 18%, and no contact but less than 3 mm distance in 16%. Local control and overall survival were evaluated using the Kaplan–Meier Method based on scheduled treatment (protons vs. carbon ions) and compared via the log rank test. Subgroup analyses were performed to identify possible prognostic factors.

Results
During the follow-up, 41 patients (27.9%) developed a local recurrence. The median follow-up time was 49.3 months (95% CI: 40.8–53.8; reverse Kaplan–Meier median follow-up time 56.3 months, 95% CI: 51.9–60.7). No significant differences between protons and carbon ions were observed regarding LC, OS, or overall toxicity. The 1‑year, 3‑year, and 5‑year LC rates were 97%, 80%, and 61% (protons) and 96%, 80%, and 65% (carbon ions), respectively. The corresponding OS rates were 100%, 92%, and 92% (protons) and 99%, 91%, and 83% (carbon ions). No significant prognostic factors for LC or OS could be determined regarding the whole cohort; however, a significantly improved LC could be observed if the tumor was > 3 mm distant from the brainstem in patients presenting in a primary situation.

Conclusion
Outcomes of proton and carbon ion treatment of skull base chordomas seem similar regarding tumor control, survival, and toxicity. Close proximity to the brainstem might be a negative prognostic factor, at least in patients presenting in a primary situation.
Assessment of intrafractional prostate motion and its dosimetric impact in MRI-guided online adaptive radiotherapy with gating
Authors: Xiong Yuqing , Rabe Moritz , Nierer Lukas , Kawula Maria , Corradini Stefanie , Belka Claus , Riboldi Marco , Landry Guillaume , Kurz Christopher 
Published: September 2022

Abstract
Purpose
This study aimed to evaluate the intrafractional prostate motion captured during gated magnetic resonance imaging (MRI)-guided online adaptive radiotherapy for prostate cancer and analyze its impact on the delivered dose as well as the effect of gating.

Methods
Sagittal 2D cine-MRI scans were acquired at 4 Hz during treatment at a ViewRay MRIdian (ViewRay Inc., Oakwood Village, OH, USA) MR linac. Prostate shifts in anterior–posterior (AP) and superior–inferior (SI) directions were extracted separately. Using the static dose cloud approximation, the planned fractional dose was shifted according to the 2D gated motion (residual motion in gating window) to estimate the delivered dose by superimposing and averaging the shifted dose volumes. The dose of a hypothetical non-gated delivery was reconstructed similarly using the non-gated motion. For the clinical target volume (CTV), rectum, and bladder, dose–volume histogram parameters of the planned and reconstructed doses were compared.

Results
In total, 174 fractions (15.7 h of cine-MRI) from 10 patients were evaluated. The average (±1 σ) non-gated prostate motion was 0.6 ± 1.0 mm in the AP and 0.0 ± 0.6 mm in the SI direction with respect to the centroid position of the gating boundary. 95% of the shifts were within [−3.5, 2.7] mm in the AP and [−2.9, 3.2] mm in the SI direction. For the gated treatment and averaged over all fractions, CTV D98% decreased by less than 2% for all patients. The rectum and the bladder D2% increased by less than 3% and 0.5%, respectively. Doses reconstructed for gated and non-gated delivery were similar for most fractions.

Conclusion
A pipeline for extraction of prostate motion during gated MRI-guided radiotherapy based on 2D cine-MRI was implemented. The 2D motion data enabled an approximate estimation of the delivered dose. For the majority of fractions, the benefit of gating was negligible, and clinical dosimetric constraints were met, indicating safety of the currently adopted gated MRI-guided treatment workflow.
Datenstandards für Seltene Erkrankungen
Authors: Robinson Peter N. , Graessner Holm 
Published: September 2022

ZusammenfassungDie Verwendung von einheitlichen Datenformaten (Datenstandards) im Gesundheitswesen dient vier Hauptzwecken: 1) dem Datenaustausch, 2) der Integration von Computersystemen und -instrumenten, 3) der Datenspeicherung und -archivierung und 4) der Unterstützung föderierter Datenbanken. Sie sind besonders wichtig für die Erforschung und die klinische Versorgung Seltener Erkrankungen (SE).In dieser Übersicht stellen wir Standards im Gesundheitswesen vor und präsentieren eine Auswahl von Standards, die im Bereich der seltenen Krankheiten häufig verwendet werden. Die „Human Phenotype Ontology“ (HPO) ist der am häufigsten verwendete Standard zur Annotation phänotypischer Anomalien und zur Unterstützung der phänotypgesteuerten Analyse der diagnostischen Exom- und Genomsequenzierung. Es gibt zahlreiche Standards für Krankheiten, die unterschiedlichen Anforderungen entsprechen. Das „Online Mendelian Inheritance in Man“ (OMIM) und die „Orphanet Rare Disease Ontology“ (ORDO) sind die wichtigsten Standards, die speziell für seltene Krankheiten entwickelt wurden. Die „Mondo Disease Ontology“ (Mondo) ist eine neue Krankheitsontologie, die darauf abzielt, auf umfassende Weise Daten aus aktuellen Nosologien zu integrieren. Neue Standards und Schemata wie die „Medical Action Ontology“ (MAxO) und das „Phenopacket“ der Global Alliance for Genomics and Health (GA4GH) werden gegenwärtig eingeführt, um die Palette der verfügbaren Standards zur Unterstützung der Forschung an seltenen Krankheiten zu erweitern.Um eine optimale Versorgung von Patienten mit SE in verschiedenen Bereichen des Gesundheitswesens zu ermöglichen, müssen die Standards für seltene Krankheiten besser in die elektronischen Ressourcen des Gesundheitswesens integriert werden, z. B. über den Standard „FHIR“ (Fast Healthcare Interoperability Resources).
Hierarchical Means Clustering
Authors: Vichi Maurizio , Cavicchia Carlo , Groenen Patrick J. F. 
Published: September 2022

AbstractIn the cluster analysis literature, there are several partitioning (non-hierarchical) methods for clustering multivariate objects based on model estimation. Distinct to these methods is the use of a system of n nested statistical models and the optimization of a loss function to best-fit a clustering model to observed data. Many hierarchical clustering methods are not model-based where hierarchy is obtained using a divisive or agglomerative greedy procedure. This paper aims to fill this gap by proposing a novel hierarchical cluster analysis methodology called Hierarchical Means Clustering. HMC produces a set of nested partitions with a centroid-based model estimated via least-squares by minimizing the total within-cluster deviance of the n partitions in the hierarchy. Hierarchical Means Clustering produces a hierarchy formed by n-1 nested partitions from 2 to n clusters with minimal total cluster deviance. Six real data examples are featured, and key links to k-means, Ward’s method, Bisecting k-means and model-based hierarchical agglomerative clustering methods are discussed.
Non-pharmacological interventions for vascular health and the role of the endothelium
Authors: Weaver Samuel R. C. , Rendeiro Catarina , Lucas Rebekah A. I. , Cable N. Timothy , Nightingale Tom E. , McGettrick Helen M. , Lucas Samuel J. E. 
Published: September 2022

AbstractThe most common non-pharmacological intervention for both peripheral and cerebral vascular health is regular physical activity (e.g., exercise training), which improves function across a range of exercise intensities and modalities. Numerous non-exercising approaches have also been suggested to improved vascular function, including repeated ischemic preconditioning (IPC); heat therapy such as hot water bathing and sauna; and pneumatic compression. Chronic adaptive responses have been observed across a number of these approaches, yet the precise mechanisms that underlie these effects in humans are not fully understood. Acute increases in blood flow and circulating signalling factors that induce responses in endothelial function are likely to be key moderators driving these adaptations. While the impact on circulating factors and environmental mechanisms for adaptation may vary between approaches, in essence, they all centre around acutely elevating blood flow throughout the circulation and stimulating improved endothelium-dependent vascular function and ultimately vascular health. Here, we review our current understanding of the mechanisms driving endothelial adaptation to repeated exposure to elevated blood flow, and the interplay between this response and changes in circulating factors. In addition, we will consider the limitations in our current knowledge base and how these may be best addressed through the selection of more physiologically relevant experimental models and research. Ultimately, improving our understanding of the unique impact that non-pharmacological interventions have on the vasculature will allow us to develop superior strategies to tackle declining vascular function across the lifespan, prevent avoidable vascular-related disease, and alleviate dependency on drug-based interventions.
Exploring the roles of FGF/MAPK and cVG1/GDF signalling on mesendoderm induction and convergent extension during chick primitive streak formation
Authors: Lee Hyung Chul , Oliveira Nidia M. M. , Stern Claudio D. 
Published: September 2022

Abstract
During primitive streak formation in the chick embryo, cells undergo mesendoderm specification and convergent extension at the same time and in the same cells. Previous work has implicated cVG1 (GDF3) as a key factor for induction of primitive streak identity and positioning the primitive streak, whereas FGF signalling was implicated in regulating cell intercalation via regulation of components of the WNT-planar cell polarity (PCP) pathway. FGF has also been reported to be able to induce a primitive streak (but lacking the most axial derivatives such as notochord/prechordal mesendoderm). These signals emanate from different cell populations in the embryo, so how do they interact to ensure that the same cells undergo both cell intercalation and acquire primitive streak identity? Here we begin to address this question by examining in more detail the ability of the two classes of signals in regulating the two developmental events. Using misexpression of inducers and/or exposure to inhibitors and in situ hybridisation, we study how these two signals regulate expression of Brachyury (TBXT) and PRICKLE1 as markers for the primitive streak and the PCP, respectively. We find that both signals can induce both properties, but while FGF seems to be required for induction of the streak by cVG1, it is not necessary for induction of PRICKLE1. The results are consistent with cVG1 being a common regulator for both primitive streak identity and the initiation of convergent extension that leads to streak elongation.
Metabolic changes during prostate cancer development and progression
Authors: Beier Alicia-Marie K. , Puhr Martin , Stope Matthias B. , Thomas Christian , Erb Holger H. H. 
Published: September 2022

AbstractMetabolic reprogramming has been recognised as a hallmark in solid tumours. Malignant modification of the tumour’s bioenergetics provides energy for tumour growth and progression. Otto Warburg first reported these metabolic and biochemical changes in 1927. In prostate cancer (PCa) epithelial cells, the tumour metabolism also changes during development and progress. These alterations are partly driven by the androgen receptor, the key regulator in PCa development, progress, and survival. In contrast to other epithelial cells of different entities, glycolytic metabolism in prostate cells sustains physiological citrate secretion in the normal prostatic epithelium. In the early stages of PCa, citrate is utilised to power oxidative phosphorylation and fuel lipogenesis, enabling tumour growth and progression. In advanced and incurable castration-resistant PCa, a metabolic shift towards choline, amino acid, and glycolytic metabolism fueling tumour growth and progression has been described. Therefore, even if the metabolic changes are not fully understood, the altered metabolism during tumour progression may provide opportunities for novel therapeutic strategies, especially in advanced PCa stages. This review focuses on the main differences in PCa’s metabolism during tumourigenesis and progression highlighting glutamine’s role in PCa.
Learning to tango with four (or more): the molecular basis of adaptation to polyploid meiosis
Authors: Bomblies Kirsten 
Published: September 2022

AbstractPolyploidy, which arises from genome duplication, has occurred throughout the history of eukaryotes, though it is especially common in plants. The resulting increased size, heterozygosity, and complexity of the genome can be an evolutionary opportunity, facilitating diversification, adaptation and the evolution of functional novelty. On the other hand, when they first arise, polyploids face a number of challenges, one of the biggest being the meiotic pairing, recombination and segregation of the suddenly more than two copies of each chromosome, which can limit their fertility. Both for developing polyploidy as a crop improvement tool (which holds great promise due to the high and lasting multi-stress resilience of polyploids), as well as for our basic understanding of meiosis and plant evolution, we need to know both the specific nature of the challenges polyploids face, as well as how they can be overcome in evolution. In recent years there has been a dramatic uptick in our understanding of the molecular basis of polyploid adaptations to meiotic challenges, and that is the focus of this review.
Skin cancer diagnosis based on deep transfer learning and sparrow search algorithm
Authors: Balaha Hossam Magdy , Hassan Asmaa El-Sayed 
Published: September 2022

AbstractSkin cancer affects the lives of millions of people every year, as it is considered the most popular form of cancer. In the USA alone, approximately three and a half million people are diagnosed with skin cancer annually. The survival rate diminishes steeply as the skin cancer progresses. Despite this, it is an expensive and difficult procedure to discover this cancer type in the early stages. In this study, a threshold-based automatic approach for skin cancer detection, classification, and segmentation utilizing a meta-heuristic optimizer named sparrow search algorithm (SpaSA) is proposed. Five U-Net models (i.e., U-Net, U-Net++, Attention U-Net, V-net, and Swin U-Net) with different configurations are utilized to perform the segmentation process. Besides this, the meta-heuristic SpaSA optimizer is used to perform the optimization of the hyperparameters using eight pre-trained CNN models (i.e., VGG16, VGG19, MobileNet, MobileNetV2, MobileNetV3Large, MobileNetV3Small, NASNetMobile, and NASNetLarge). The dataset is gathered from five public sources in which two types of datasets are generated (i.e., 2-classes and 10-classes). For the segmentation, concerning the “skin cancer segmentation and classification” dataset, the best reported scores by U-Net++ with DenseNet201 as a backbone architecture are 0.104, $$94.16\%$$

94.16
%

, $$91.39\%$$

91.39
%

, $$99.03\%$$

99.03
%

, $$96.08\%$$

96.08
%

, $$96.41\%$$

96.41
%

, $$77.19\%$$

77.19
%

, $$75.47\%$$

75.47
%

in terms of loss, accuracy, F1-score, AUC, IoU, dice, hinge, and squared hinge, respectively, while for the “PH2” dataset, the best reported scores by the Attention U-Net with DenseNet201 as backbone architecture are 0.137, $$94.75\%$$

94.75
%

, $$92.65\%$$

92.65
%

, $$92.56\%$$

92.56
%

, $$92.74\%$$

92.74
%

, $$96.20\%$$

96.20
%

, $$86.30\%$$

86.30
%

, $$92.65\%$$

92.65
%

, $$69.28\%$$

69.28
%

, and $$68.04\%$$

68.04
%

in terms of loss, accuracy, F1-score, precision, sensitivity, specificity, IoU, dice, hinge, and squared hinge, respectively. For the “ISIC 2019 and 2020 Melanoma” dataset, the best reported overall accuracy from the applied CNN experiments is $$98.27\%$$

98.27
%

by the MobileNet pre-trained model. Similarly, for the “Melanoma Classification (HAM10K)” dataset, the best reported overall accuracy from the applied CNN experiments is $$98.83\%$$

98.83
%

by the MobileNet pre-trained model. For the “skin diseases image” dataset, the best reported overall accuracy from the applied CNN experiments is $$85.87\%$$

85.87
%

by the MobileNetV2 pre-trained model. After computing the results, the suggested approach is compared with 13 related studies.
Non-adjustable gravitational valves or adjustable valves in the treatment of hydrocephalus after aneurysmal subarachnoid hemorrhage patients?
Authors: Arts Sebastian , van Lieshout Jasper Hans , van Bilsen Martine , Karadag Cihat , Beez Thomas , van den Abbeele Leonie , Aquarius Rene , Vinke Saman , Bartels Ronald H. M. A. , van Lindert Erik J. , Hänggi Daniel , Boogaarts Hieronymus D. 
Published: September 2022

Abstract

Purpose
Hydrocephalus requiring permanent CSF shunting after aneurysmal subarachnoid hemorrhage (aSAH) is frequent. It is unknown which type of valve is optimal. This study evaluates if the revision rate of gravitational differential pressure valves (G-DPVs, GAV® system (B Braun)) (G-DPV) is comparable to adjustable pressure valves (Codman Medos Hakim) (APV) in the treatment of post-aSAH hydrocephalus.

Methods
The use of a gravitational differential pressure valve is placed in direct comparison with an adjustable pressure valve system. A retrospective chart review is performed to compare the revision rates for the two valve systems.

Results
Within the registry from Radboud University Medical Center, 641 patients with a SAH could be identified from 1 January 2013 until 1 January 2019, whereas at the Heinrich Heine University, 617 patients were identified, totaling 1258 patients who suffered from aSAH. At Radboud University Medical Center, a gravitational differential pressure valve is used, whereas at the Heinrich Heine University, an adjustable pressure valve system is used. One hundred sixty-six (13%) patients required permanent ventricular peritoneal or atrial shunting. Shunt dysfunction occurred in 36 patients: 13 patients of the 53 (25%) of the gravitational shunt cohort, and in 23 of the 113 (20%) patients with an adjustable shunt (p = 0.54). Revision was performed at a mean time of 3.2 months after implantation with the gravitational system and 8.2 months with the adjustable shunt system. Combined rates of over- and underdrainage leading to revision were 7.5% (4/53) for the gravitational and 3.5% (4/113) for the adjustable valve system (p = 0 .27).

Conclusion
The current study does not show a benefit of a gravitational pressure valve (GAV® system) over an adjustable pressure valve (CODMAN ® HAKIM®) in the treatment of post-aSAH hydrocephalus. The overall need for revision is high and warrants further improvements in care.
Early detection of COVID-19 cholangiopathy using cholangioscopy—a case report of two critically ill patients
Authors: Kroepfl Veronika , Treml Benedikt , Freund Martin Cornelius , Profanter Christoph 
Published: September 2022

Summary
Background
The coronavirus disease 2019 (COVID-19) crisis caused by the severe respiratory distress syndrome coronavirus 2 (SARS-CoV-2) rapidly led to a pandemic. While the majority of SARS-CoV-2-infected patients present with fever and respiratory symptoms, gastrointestinal symptoms may also occur. In addition, serious hepatic manifestations like cholangiopathy and liver failure have been described.

Patients and methods
We identified two critically ill patients suffering from SARS-CoV‑2 infection in our intensive care unit (ICU). In both patients, laboratory testing revealed elevated liver chemistries weeks after initial diagnosis with COVID-19.

Results
During repeated endoscopic retrograde cholangiopancreatography (ERCP) with cholangioscopy, a severely destructed biliary mucosa with ischemia and epithelial roughness was seen in both patients. Due to the prolonged course of COVID-19 and chronic liver damage with ongoing sepsis, both patients succumbed to the disease.

Conclusion
In our opinion, a COVID-19 infection can lead to development of cholangiopathy in critically ill patients. Cholangioscopy performed early can confirm the diagnosis of COVID-19-associated cholangioscopy.
Morphometric Characterization of an Ex Vivo Porcine Model of Functional Tricuspid Regurgitation
Authors: Salurso Eleonora , Jaworek Michal , Perico Francesca , Frigelli Matteo , Romagnoni Claudia , Contino Monica , Gelpi Guido , Fiore Gianfranco Beniamino , Vismara Riccardo 
Published: September 2022

AbstractEmerging treatments for tricuspid valve (TV) regurgitation require realistic TV pathological models for preclinical testing. The aim of this work was to investigate structural features of fresh and defrosted porcine right-heart samples as models of mild and severe functional tricuspid regurgitation (FTR) condition in ex-vivo pulsatile flow platform. Ten fresh hearts were tested ex-vivo under steady and pulsatile flow in typical right-heart loading conditions. Hemodynamics and 3D echocardiographic imaging of TV and right ventricle (RV) were acquired. Hearts were then kept frozen for 14 days, defrosted, and tested again with the same protocol. Morphometric parameters of TV and RV were derived from 3D reconstructions based on echo data. Fresh samples showed a slightly dilated TV morphology, with coaptation gaps among the leaflets. Sample freezing induced worsening of TV insufficiency, with significant (p < 0.05) increases in annulus size (annulus area and perimeter 7.7–3.1% respectively) and dilation of RV (9.5%), which led to an increase in tenting volume (123.7%). These morphologic alterations reflected into a significant increment of regurgitation fraction (27%). Together, such results suggest that fresh porcine heart samples may be a reliable ex-vivo model of mild FTR condition, which can be enhanced through freezing/thawing treatment to model a severe pathological condition.