bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semantic Annotation of Predictive Modelling Experiments
Authors: Tolovski Ilin , Džeroski Sašo , Panov Panče 
Published: October 2020

AbstractIn this paper, we address the task of representation, semantic annotation, storage, and querying of predictive modelling experiments. We introduce OntoExp, an OntoDM module which gives a more granular representation of a predictive modeling experiment and enables annotation of the experiment’s provenance, algorithm implementations, parameter settings and output metrics. This module is incorporated in SemanticHub, an online system that allows execution, annotation, storage and querying of predictive modeling experiments. The system offers two different user scenarios. The users can either define their own experiment and execute it, or they can browse the repository of completed experimental workflows across different predictive modelling tasks. Here, we showcase the capabilities of the system with executing multi-target regression experiment on a water quality prediction dataset using the Clus software. The system and created repositories are evaluated based on the FAIR data stewardship guidelines. The evaluation shows that OntoExp and SemanticHub provide the infrastructure needed for semantic annotation, execution, storage, and querying of the experiments.
Cancer research using organoid technology
Authors: Kretzschmar Kai 
Published: October 2020

AbstractOrganoid technology has rapidly transformed basic biomedical research and contributed to significant discoveries in the last decade. With the application of protocols to generate organoids from cancer tissue, organoid technology has opened up new opportunities for cancer research and therapy. Using organoid cultures derived from healthy tissues, different aspects of tumour initiation and progression are widely studied including the role of pathogens or specific cancer genes. Cancer organoid cultures, on the other hand, are applied to generate biobanks, perform drug screens, and study mutational signatures. With the incorporation of cellular components of the tumour microenvironment such as immune cells into the organoid cultures, the technology is now also exploited in the rapidly advancing field of immuno-oncology. In this review, I discuss how organoid technology is currently being utilised in cancer research and what obstacles are still to be overcome for its broader use in anti-cancer therapy.
Schulden, Kredite und unbezahlte Rechnungen unter Nutzer*Innen teilstationärer und stationärer psychiatrischer Behandlung in Berlin
Authors: Schreiter Stefanie , Heidrich Sascha , Heinz Andreas , Rössler Wulf , Krausz Reinhard Michael , Schouler-Ocak Meryam , Bermpohl Felix , Gutwinski Stefan 
Published: October 2020

Zusammenfassung
Hintergrund
Bisherige Studien der Allgemeinbevölkerung weisen auf eine Assoziation zwischen psychischen Erkrankungen und verschiedenen Formen finanzieller Schwierigkeiten wie Verschuldung hin.

Ziel der Arbeit
Untersuchung der finanziellen Belastungen und assoziierter Faktoren bei Patient*Innen in (teil-)stationärer psychiatrischer Behandlung.

Material und Methoden
Insgesamt 488 Teilnehmer*Innen einer querschnittlichen Patientenbefragung mittels eines strukturierten Interviews zu soziodemografischen sowie klinischen Variablen in (teil-)stationärer psychiatrischer Behandlung in der psychiatrischen Universitätsklinik der Charité im St. Hedwig, zuständig für einen spezifischen Versorgungsbereich in Berlin, gaben Auskunft zu finanziellen Belastungen.

Ergebnisse
Insgesamt 269 (55,1 %) Teilnehmer*Innen wiesen Schulden, Kredite oder offene Rechnungen auf. Unter den Teilnehmer*Innen, die Auskunft zur Kredit- oder Schuldenhöhe machten (n = 215), wies der größte Teil (47,0 %) Schulden oder Kredite in der Höhe zwischen 1000 und 9999 € auf, gefolgt von 36,3 % mit Schulden/Krediten zwischen 10.000 und 99.999 €. In den Regressionsmodellen hinsichtlich des Vorliegens von Schulden erwiesen sich ein jüngeres Alter und das Vorliegen einer Substanzabhängigkeit als signifikant assoziierte Faktoren. 22,3 % der Befragten wiesen Schulden in Höhe >10.000 € auf und lebten von Sozialleistung, sodass eine Überschuldung angenommen werden könnte.

Diskussion
Finanzielle Belastungen und bestehende Schulden sollten im psychiatrischen Bereich stärker in der Praxis erfragt und beachtet werden. Geeignete Unterstützungsformen sollten entwickelt und evaluiert werden.
Global impact of COVID-19 on non-communicable disease management: descriptive analysis of access to FRAX fracture risk online tool for prevention of osteoporotic fractures
Authors: McCloskey E. V. , Harvey N. C. , Johansson H. , Lorentzon M. , Vandenput L. , Liu E. , Kanis J. A. 
Published: October 2020

Abstract
Summary
The COVID-19 pandemic, and its management, is markedly impacting the management of osteoporosis as judged by access to online FRAX fracture risk assessments. Globally, access was 58% lower in April than in February 2020. Strategies to improve osteoporosis care, with greater use of fracture risk assessments, offer a partial solution.

Introduction
The COVID-19 pandemic is having a significant detrimental impact on the management of chronic diseases including osteoporosis. We have quantified the global impact by examining changes in the usage of online FRAX fracture risk assessments before and after the declaration of the pandemic (11 March 2020).

Methods
The study comprised a retrospective analysis using GoogleAnalytics data on daily sessions on the FRAX® website (www.sheffield.ac.uk/FRAX) from November 2019 to April 2020 (main analysis period February–April 2020), and the geographical source of that activity.

Results
Over February–April 2020, the FRAX website recorded 460,495 sessions from 184 countries, with 210,656 sessions in February alone. In March and April, the number of sessions fell by 23.1% and 58.3% respectively, a pattern not observed over the same period in 2019. There were smaller reductions in Asia than elsewhere, partly related to earlier and less-marked nadirs in some countries (China, Taiwan, Hong Kong, South Korea and Vietnam). In Europe, the majority of countries (24/31, 77.4%) reduced usage by at least 50% in April. Seven countries showed smaller reductions (range − 2.85 to − 44.1%) including Poland, Slovakia, Czech Republic, Germany, Norway, Sweden and Finland. There was no significant relationship between the reduction in FRAX usage and measures of disease burden such as COVID-attributed deaths per million of the population.

Conclusion
This study documents a marked global impact of the COVID-19 pandemic on the management of osteoporosis as reflected by FRAX online fracture risk assessments. The analysis suggests that impact may relate to the societal and healthcare measures taken to ameliorate the pandemic.
Weak Solutions to the Muskat Problem with Surface Tension Via Optimal Transport
Authors: Jacobs Matt , Kim Inwon , Mészáros Alpár R. 
Published: October 2020

AbstractInspired by recent works on the threshold dynamics scheme for multi-phase mean curvature flow (by Esedoḡlu–Otto and Laux–Otto), we introduce a novel framework to approximate solutions of the Muskat problem with surface tension. Our approach is based on interpreting the Muskat problem as a gradient flow in a product Wasserstein space. This perspective allows us to construct weak solutions via a minimizing movements scheme. Rather than working directly with the singular surface tension force, we instead relax the perimeter functional with the heat content energy approximation of Esedoḡlu–Otto. The heat content energy allows us to show the convergence of the associated minimizing movement scheme in the Wasserstein space, and makes the scheme far more tractable for numerical simulations. Under a typical energy convergence assumption, we show that our scheme converges to weak solutions of the Muskat problem with surface tension. We then conclude the paper with a discussion on some numerical experiments and on equilibrium configurations.
Purification of a heterodimeric Reelin construct to investigate binding stoichiometry
Authors: Turk Liam S. , Mitchell Daniel , Comoletti Davide 
Published: October 2020

AbstractReelin is a secreted glycoprotein that is integral in neocortex development and synaptic function. Reelin exists as a homodimer with two chains linked by a disulfide bond at cysteine 2101, a feature that is vital to the protein’s function. This is highlighted by the fact that only dimeric Reelin can elicit efficient, canonical signaling, even though a mutated (C2101A) monomeric construct of Reelin retains the capacity to bind to its receptors. Receptor clustering has been shown to be important in the signaling pathway, however direct evidence regarding the stoichiometry of Reelin-receptor binding interaction is lacking. Here we describe the construction and purification of a heterodimeric Reelin construct to investigate the stoichiometry of Reelin-receptor binding and how it affects Reelin pathway signaling. We have devised different strategies and have finalized a protocol to produce a heterodimer of Reelin’s central fragment using differential tagging and tandem affinity chromatography, such that chain A is wild type in amino acid sequence whereas chain B includes a receptor binding site mutation (K2467A). We also validate that the heterodimer is capable of binding to the extracellular domain of one of Reelin’s known receptors, calculating the KD of the interaction. This heterodimeric construct will enable us to understand in greater detail the mechanism by which Reelin interacts with its known receptors and initiates pathway signaling.
Helicobacter pylori treatment in the post-antibiotics era—searching for new drug targets
Authors: Roszczenko-Jasińska Paula , Wojtyś Marta Ilona , Jagusztyn-Krynicka Elżbieta K. 
Published: October 2020

Abstract
Helicobacter pylori, a member of Epsilonproteobacteria, is a Gram-negative microaerophilic bacterium that colonizes gastric mucosa of about 50% of the human population. Although most infections caused by H. pylori are asymptomatic, the microorganism is strongly associated with serious diseases of the upper gastrointestinal tract such as chronic gastritis, peptic ulcer, duodenal ulcer, and gastric cancer, and it is classified as a group I carcinogen. The prevalence of H. pylori infections varies worldwide. The H. pylori genotype, host gene polymorphisms, and environmental factors determine the type of induced disease. Currently, the most common therapy to treat H. pylori is the first line clarithromycin–based triple therapy or a quadruple therapy replacing clarithromycin with new antibiotics. Despite the enormous recent effort to introduce new therapeutic regimens to combat this pathogen, treatment for H. pylori still fails in more than 20% of patients, mainly due to the increased prevalence of antibiotic resistant strains. In this review we present recent progress aimed at designing new anti-H. pylori strategies to combat this pathogen. Some novel therapeutic regimens will potentially be used as an extra constituent of antibiotic therapy, and others may replace current antibiotic treatments.

Key points
• Attempts to improve eradication rate of H. pylori infection.
• Searching for new drug targets in anti-Helicobacter therapies.
Urine NGAL and KIM-1: tubular injury markers in acute lymphoblastic leukemia survivors
Authors: Latoch Eryk , Konończuk Katarzyna , Taranta-Janusz Katarzyna , Muszyńska-Rosłan Katarzyna , Szymczak Edyta , Wasilewska Anna , Krawczuk-Rybak Maryna 
Published: October 2020

Abstract
Introduction
Nephrotoxicity is a potential adverse effect of anticancer treatment in childhood. Cytostatics, abdominal radiotherapy, total body irradiation (TBI) and some agents used in supportive care may induce acute kidney injury (AKI) or lead to chronic kidney disease (CKD). The aim of this study was to test the hypothesis whether urinary kidney injury molecule-1 (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL) are increased in acute lymphoblastic leukemia (ALL) survivors.

Method
The study cohort consisted of 86 patients (42 females) previously treated for ALL. The median time after cessation of treatment was 6.55 (IQR: 1.96–9.93) years and median age at the time of study: 12 (IQR: 6.76–16.00). The control group included 53 healthy peers. Immunoenzymatic ELISA commercial kits were used to measure urine KIM-1 and NGAL levels.

Results
The median levels of urine uNGAL (p < 0.05), uNGAL/creatinine (cr.) ratio (p < 0.0001) and uKIM-1/creatinine ratio (p < 0.0001) were significantly higher in ALL survivors in comparison with healthy controls. Female patients had significantly higher levels of NGAL and NGAL/cr. than males (mean 8.42 ± 7.1 vs. 4.59 ± 4.5 ng/mL and 86.57 ± 77 vs. 37.7 ± 37 ng/mg, respectively; p < 0.01). Of all the study participants, 11 (13%) presented eGFR below 90 mL/min/1.73 m2. The NGAL/cr. ratio seemed to be the best predictor of decreased eGFR (AUC = 0.65). The cumulative dose of methotrexate and cyclophosphamide did not predict the values of the urine NGAL, NGAL/cr., KIM-1/cr. and eGFR.
Five years after the end of treatment, the patients had higher levels of uKIM-1 (1.02 ± 0.8 vs. 0.62 ± 0.6 ng/mL, p < 0.01), uNGAL (7.9 ± 6.7 vs. 4.6 ± 5 ng/mL, p < 0.01) and lower eGFR (114 ± 29 vs. 134 ± 35 mL/min/1.73 m2, p < 0.01) in comparison with ALL survivors with the observation period of less than 5 years.

Conclusion
We demonstrated that ALL survivors have higher levels of urine NGAL, NGAL/cr. and uKIM-1/cr. ratio as compared to the control group. Further long-term follow-up studies are necessary to assess the significance of the NGAL and KIM-1 and their relationship to kidney damage after anticancer treatment in childhood.
Opportunistic osteoporosis screening: contrast-enhanced dual-layer spectral CT provides accurate measurements of vertebral bone mineral density
Authors: Roski Ferdinand , Hammel Johannes , Mei Kai , Haller Bernhard , Baum Thomas , Kirschke Jan S. , Pfeiffer Daniela , Woertler Klaus , Pfeiffer Franz , Noël Peter B. , Gersing Alexandra S. , Schwaiger Benedikt J. 
Published: October 2020

Abstract
Objectives
Osteoporosis remains under-diagnosed, which may be improved by opportunistic bone mineral density (BMD) measurements on CT. However, correcting for the influence of intravenous iodine-based contrast agent is challenging. The purpose of this study was to assess the diagnostic accuracy of iodine-corrected vertebral BMD measurements derived from non-dedicated contrast-enhanced phantomless dual-layer spectral CT (DLCT) examinations.

Methods
Vertebral volumetric DLCT-BMD was measured in native, arterial, and portal-venous scans of 132 patients (63 ± 16 years; 32% women) using virtual monoenergetic images (50 and 200 keV). For comparison, conventional BMD was determined using an asynchronous QCT calibration. Additionally, iodine densities were measured in the abdominal aorta (AA), inferior vena cava, and vena portae (VP) on each CT phase to adjust for iodine-related measurement errors in multivariable linear regressions and a generalized estimated equation, and conversion equations were calculated.

Results
BMD values derived from contrast-enhanced phases using conversion equations adjusted for individual vessel iodine concentrations of VP and/or AA showed a high agreement with those from non-enhanced scans in Bland-Altman plots. Mean absolute errors (MAE) of DLCT-BMD were 3.57 mg/ml for the arterial (R2 = 0.989) and 3.69 mg/ml for the portal-venous phase (R2 = 0.987) (conventional BMD: 4.70 [R2 = 0.983] and 5.15 mg/ml [R2 = 0.981]). In the phase-independent analysis, MAE was 4.49 mg/ml for DLCT (R2 = 0.989) (conventional BMD: 4.82 mg/ml [R2 = 0.981]).

Conclusions
Converted BMD derived from contrast-enhanced DLCT examinations and adjusted for individual vessel iodine concentrations showed a high agreement with non-enhanced DLCT-BMD, suggesting that opportunistic BMD measurements are feasible even in non-dedicated contrast-enhanced DLCT examinations.

Key Points
• Accurate BMD values can be converted from contrast-enhanced DLCT scans, independent from the used scan phase.
• DLCT-BMD measurements from contrast-enhanced scans should be adjusted with iodine concentrations of portal vein and/or abdominal aorta, which significantly improves the goodness-of-fit of conversion models.
Targeting myocardial ischaemic injury in the absence of reperfusion
Authors: Basalay M. V. , Yellon D. M. , Davidson S. M. 
Published: October 2020

AbstractSudden myocardial ischaemia causes an acute coronary syndrome. In the case of ST-elevation myocardial infarction (STEMI), this is usually caused by the acute rupture of atherosclerotic plaque and obstruction of a coronary artery. Timely restoration of blood flow can reduce infarct size, but ischaemic regions of myocardium remain in up to two-thirds of patients due to microvascular obstruction (MVO). Experimentally, cardioprotective strategies can limit infarct size, but these are primarily intended to target reperfusion injury. Here, we address the question of whether it is possible to specifically prevent ischaemic injury, for example in models of chronic coronary artery occlusion. Two main types of intervention are identified: those that preserve ATP levels by reducing myocardial oxygen consumption, (e.g. hypothermia; cardiac unloading; a reduction in heart rate or contractility; or ischaemic preconditioning), and those that increase myocardial oxygen/blood supply (e.g. collateral vessel dilation). An important consideration in these studies is the method used to assess infarct size, which is not straightforward in the absence of reperfusion. After several hours, most of the ischaemic area is likely to become infarcted, unless it is supplied by pre-formed collateral vessels. Therefore, therapies that stimulate the formation of new collaterals can potentially limit injury during subsequent exposure to ischaemia. After a prolonged period of ischaemia, the heart undergoes a remodelling process. Interventions, such as those targeting inflammation, may prevent adverse remodelling. Finally, harnessing of the endogenous process of myocardial regeneration has the potential to restore cardiomyocytes lost during infarction.
European Laryngological Society position paper on laryngeal dysplasia Part II: diagnosis, treatment, and follow-up
Authors: Eckel Hans Edmund , Simo Ricard , Quer Miquel , Odell Edward , Paleri Vinidh , Klussmann Jens Peter , Remacle Marc , Sjögren Elisabeth , Piazza Cesare 
Published: October 2020

Abstract
Purpose of review
To give an overview of the current knowledge regarding the diagnosis, treatment, and follow-up of laryngeal dysplasia (LD) and to highlight the contributions of recent literature.

Summary
The diagnosis of LD largely relies on endoscopic procedures and on histopathology. Diagnostic efficiency of endoscopy may be improved using videolaryngostroboscopy (VLS) and bioendoscopic tools such as Narrow Band Imaging (NBI) or Storz Professional Image Enhancement System (SPIES). Current histological classifications are not powerful enough to clearly predict the risk to carcinoma evolution and technical issues such as sampling error, variation in epithelial thickness and inflammation hamper pathological examination. Almost all dysplasia grading systems are effective in different ways. The 2017 World Health Organization (WHO) system should prove to be an improvement as it is slightly more reproducible and easier for the non-specialist pathologist to apply. To optimize treatment decisions, surgeons should know how their pathologist grades samples and preferably audit their transformation rates locally. Whether carcinoma in situ should be used as part of such classification remains contentious and pathologists should agree with their clinicians whether they find this additional grade useful in treatment decisions. Recently, different studies have defined the possible utility of different biomarkers in risk classification. The main treatment modality for LD is represented by transoral laser microsurgery. Radiotherapy may be indicated in specific circumstances such as multiple recurrence or wide-field lesions. Medical treatment currently does not have a significant role in the management of LD. Follow-up for patients treated with LD is a fundamental part of their care and investigations may be supported by the same techniques used during diagnosis (VLS and NBI/SPIES).
Intraoperative endoluminal pyloromyotomy as a novel approach to reduce delayed gastric emptying after pylorus-preserving pancreaticoduodenectomy—a retrospective study
Authors: Schrempf Matthias C. , Pinto David R. M. , Gutschon Johanna , Schmid Christoph , Hoffmann Michael , Geissler Bernd , Wolf Sebastian , Sommer Florian , Anthuber Matthias 
Published: October 2020

Abstract
Background
Delayed gastric emptying (DGE) is one of the most common complications after pylorus-preserving partial pancreaticoduodenectomy (ppPD). The aim of this retrospective study was to assess whether an intraoperative pyloromyotomy during ppPD prior to the creation of duodenojejunostomy reduces DGE.

Methods
Patients who underwent pylorus-preserving pancreaticoduodenectomy between January 2015 and December 2017 were divided into two groups on the basis of whether an intraoperative pyloromyotomy was performed (pyloromyotomy (PM) group) or not (no pyloromyotomy (NP) group). The primary endpoint was DGE according to the ISGPS definition. The confirmatory analysis of the primary endpoint was performed with multivariate analysis.

Results
One hundred and ten patients were included in the statistical analysis. Pyloromyotomy was performed in 44 of 110 (40%) cases. DGE of any grade was present in 62 patients (56.4%). The DGE rate was lower in the PM group (40.9%) compared with the NP group (66.7%), and pyloromyotomy was associated with a reduced risk for DGE in univariate (OR 0.35, 95% CI 0.16–0.76; P = 0.008) and multivariate analyses (OR 0.32, 95% CI 0.13–0.77; P = 0.011). The presence of an intra-abdominal complication was an independent risk factor for DGE in the multivariate analysis (OR 5.54, 95% CI 2.00–15.36; P = 0.001).

Conclusion
Intraoperative endoluminal pyloromyotomy during ppPD was associated with a reduced risk for DGE in this retrospective study. Pyloromyotomy should be considered a simple technique that can potentially reduce DGE rates after ppPD.