bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circulating tumor DNA in Hodgkin lymphoma
Authors: Maco Maria , Kupcova Kristyna , Herman Vaclav , Ondeckova Iva , Kozak Tomas , Mocikova Heidi , Havranek Ondrej ,   On behalf of the Czech Hodgkin Lymphoma Study Group
Published: September 2022

Abstract
Somatic mutations of genes involved in NF-κB, PI3K/AKT, NOTCH, and JAK/STAT signaling pathways play an important role in the pathogenesis of Hodgkin lymphoma (HL). HL tumor cells form only about 5% of the tumor mass; however, it was shown that HL tumor-derived DNA could be detected in the bloodstream. This circulating tumor DNA (ctDNA) reflects the genetic profile of HL tumor cells and can be used for qualitative and quantitative analysis of tumor-specific somatic DNA mutations within the concept of liquid biopsy. Overall, the most frequently mutated gene in HL is STAT6; however, the exact spectrum of mutations differs between individual HL histological subtypes. Importantly, reduction of ctDNA plasma levels after initial treatment is highly correlated with prognosis. Therefore, ctDNA shows great promise as a novel tool for non-invasive tumor genome analysis for biomarker driven therapy as well as for superior minimal residual disease monitoring and treatment resistance detection. Here, we summarize the recent advancements of ctDNA analysis in HL with focus on ctDNA detection methodologies, genetic profiling of HL and its clonal evolution, and the emerging prognostic value of ctDNA.
Heterogeneities among credit risk parameter distributions: the modality defines the best estimation method
Authors: Gürtler Marc , Zöllner Marvin 
Published: September 2022

AbstractComparative studies investigating the estimation accuracy of statistical methods often arrive at different conclusions. Therefore, it remains unclear which method is best suited for a particular estimation task. While this problem exists in many areas of predictive analytics, it has particular relevance in the banking sector owing to regulatory requirements regarding transparency and quality of estimation methods. For the estimation of the relevant credit risk parameter loss given default (LGD), we find that the different results can be attributed to the modality type of the respective LGD distribution. Specifically, we use cluster analysis to identify heterogeneities among the LGD distributions of loan portfolios of 16 European countries with 32,851 defaulted loans. The analysis leads to three clusters, whose distributions essentially differ in their modality type. For each modality type, we empirically determine the accuracy of 20 estimation methods, including traditional regression and advanced machine learning. We show that the specific modality type is crucial for the best method. The results are not limited to the banking sector, because the present distribution type-dependent recommendation for method selection, which is based on cluster analysis, can also be applied to parameter estimation problems in all areas of predictive analytics.
Visual ensemble selection of deep convolutional neural networks for 3D segmentation of breast tumors on dynamic contrast enhanced MRI
Authors: Rahimpour Masoomeh , Saint Martin Marie-Judith , Frouin Frédérique , Akl Pia , Orlhac Fanny , Koole Michel , Malhaire Caroline 
Published: September 2022

Abstract
Objectives
To develop a visual ensemble selection of deep convolutional neural networks (CNN) for 3D segmentation of breast tumors using T1-weighted dynamic contrast-enhanced (T1-DCE) MRI.

Methods
Multi-center 3D T1-DCE MRI (n = 141) were acquired for a cohort of patients diagnosed with locally advanced or aggressive breast cancer. Tumor lesions of 111 scans were equally divided between two radiologists and segmented for training. The additional 30 scans were segmented independently by both radiologists for testing. Three 3D U-Net models were trained using either post-contrast images or a combination of post-contrast and subtraction images fused at either the image or the feature level. Segmentation accuracy was evaluated quantitatively using the Dice similarity coefficient (DSC) and the Hausdorff distance (HD95) and scored qualitatively by a radiologist as excellent, useful, helpful, or unacceptable. Based on this score, a visual ensemble approach selecting the best segmentation among these three models was proposed.

Results
The mean and standard deviation of DSC and HD95 between the two radiologists were equal to 77.8 ± 10.0% and 5.2 ± 5.9 mm. Using the visual ensemble selection, a DSC and HD95 equal to 78.1 ± 16.2% and 14.1 ± 40.8 mm was reached. The qualitative assessment was excellent (resp. excellent or useful) in 50% (resp. 77%).

Conclusion
Using subtraction images in addition to post-contrast images provided complementary information for 3D segmentation of breast lesions by CNN. A visual ensemble selection allowing the radiologist to select the most optimal segmentation obtained by the three 3D U-Net models achieved comparable results to inter-radiologist agreement, yielding 77% segmented volumes considered excellent or useful.

Key Points
• Deep convolutional neural networks were developed using T1-weighted post-contrast and subtraction MRI to perform automated 3D segmentation of breast tumors.
• A visual ensemble selection allowing the radiologist to choose the best segmentation among the three 3D U-Net models outperformed each of the three models.
• The visual ensemble selection provided clinically useful segmentations in 77% of cases, potentially allowing for a valuable reduction of the manual 3D segmentation workload for the radiologist and greatly facilitating quantitative studies on non-invasive biomarker in breast MRI.
Influence of preoperative weight loss on gastric wall thickness—analysis of laparoscopic sleeve gastrectomy histological material
Authors: Barski Krzysztof , Binda Artur , Jaworski Paweł , Gonciarska Agnieszka , Kudlicka Emilia , Żurkowska Joanna , Wawiernia Karolina , Tałałaj Marek , Wąsowski Michał , Tarnowski Wiesław 
Published: September 2022

Abstract
Purpose
The variables possibly enabling the prediction of gastric wall thickness during laparoscopic sleeve gastrectomy remain undetermined. The aim of the study was to identify preoperative factors affecting gastric wall thickness in patients undergoing laparoscopic sleeve gastrectomy.

Methods
The measurements of the double-wall thickness of gastric specimen excised during sleeve gastrectomy were taken at three locations after 15 s of compression with an applied pressure of 8 g/mm2. Statistical calculations were used to determine the influence of preoperative weight loss and other perioperative parameters on gastric wall thickness.

Results
The study involved one hundred patients (78 female; 22 male). The thickest tissue was observed at the antrum with the mean value 2.55 mm (range 1.77–4.0 mm), followed by the midbody, mean 2.13 mm (range 1.34–3.20 mm), and the fundus, mean 1.69 mm (range 0.99–2.69 mm). Positive relationships were found between gastric wall thickness and both preoperative weight loss and age in all three measured locations; p < 0.05. In a linear regression model, age and preoperative weight loss were found to be statistically significant and positive predictors of higher gastric wall thickness only at the antrum. Male patients were observed to have thicker gastric wall at all three locations as compared to female patients.

Conclusion
Preoperative weight loss should be considered an important factor influencing gastric wall thickness. Age and gender can also be helpful in predicting the varying tissue thickness. Anatomical region is a key factor determining thickness of the stomach walls.
Does the composition of urinary extracellular vesicles reflect the abundance of renal Na+/phosphate transporters?
Authors: Radvanyi Zsuzsi , Daryadel Arezoo , Pastor-Arroyo Eva Maria , Hernando Nati , Wagner Carsten Alexander 
Published: September 2022

AbstractStudies addressing homeostasis of inorganic phosphate (Pi) are mostly restricted to murine models. Data provided by genetically modified mice suggest that renal Pi reabsorption is primarily mediated by the Na+/Pi cotransporter NaPi-IIa/Slc34a1, whereas the contribution of NaPi-IIc/Slc34a3 in adult animals seems negligible. However, mutations in both cotransporters associate with hypophosphatemic syndromes in humans, suggesting major inter-species heterogeneity. Urinary extracellular vesicles (UEV) have been proposed as an alternative source to analyse the intrinsic expression of renal proteins in vivo. Here, we analyse in rats whether the protein abundance of renal Pi transporters in UEV correlates with their renal content. For that, we compared the abundance of NaPi-IIa and NaPi-IIc in paired samples from kidneys and UEV from rats fed acutely and chronically on diets with low or high Pi. In renal brush border membranes (BBM) NaPi-IIa was detected as two fragments corresponding to the full-length protein and to a proteolytic product, whereas NaPi-IIc migrated as a single full-length band. The expression of NaPi-IIa (both fragments) in BBM adapted to acute as well to chronic changes of dietary Pi, whereas adaptation of NaPi-IIc was only detected in response to chronic administration. Both transporters were detected in UEV as well. UEV reflected the renal adaptation of the NaPi-IIa proteolytic fragment (but not the full-length protein) upon chronic but not acute dietary changes, while also reproducing the chronic regulation of NaPi-IIc. Thus, the composition of UEV reflects only partially changes in the expression of NaPi-IIa and NaPi-IIc at the BBM triggered by dietary Pi.
Identification of a new prognostic score for patients with high-grade metastatic GEP-NEN treated with palliative chemotherapy
Authors: Rosery Vivian , Mika Stephan , Schmid Kurt Werner , Reis Henning , Stuschke Martin , Treckmann Jürgen , Markus Peter , Schumacher Brigitte , Albers David , Mende Bastian , Lahner Harald , Wiesweg Marcel , Schuler Martin , Siveke Jens T. , Kasper Stefan 
Published: September 2022

Abstract
Purpose
High-grade gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN G3) are rare and heterogeneous malignancies with poor prognosis. Aim of this study was to develop prognosticators identifying those patients that derive the most benefit from currently available systemic therapies.

Methods
This retrospective analysis included 78 patients with metastatic GEP-NEN G3. For patients with imaging data available (n = 52), the overall response rate (ORR) and disease control rate (DCR) were evaluated according to the Response Evaluation Criteria in Solid Tumors 1.1 (RECIST 1.1). A Cox proportional hazard model was used to analyze the prognostic value of selected clinical and blood-based biomarkers. The impact of palliative chemotherapy regimens on time-to-treatment-failure (TTF) and overall survival (OS) was assessed.

Results
Median OS of the study cohort was 9.0 months (95% CI 7.0–11.1). The majority of patients received first-line treatment with platinum plus etoposide (83.3%). The ORR and DCR of the RECIST-evaluable subgroup were 34.6% and 76.9%. Median TTF upon first-line treatment was 4.9 months (95% CI 3.4–6.4). Multivariate analysis identified the Eastern Cooperative Oncology Group performance status (ECOG PS), lactate dehydrogenase (LDH) and absolute lymphocyte count as independent prognostic factors. A prognostic score based on these parameters discriminated patients with favorable and unfavorable outcomes.

Conclusion
Outcomes of patients with GEP-NEN G3 are still limited. A new prognostic score identifying those patients benefitting from current platinum/etoposide-based chemotherapy protocols may help as stratification factor in future trial design.
Cost-effectiveness analysis of NEPA, a fixed-dose combination of netupitant and palonosetron, for the prevention of highly emetogenic chemotherapy-induced nausea and vomiting: an international perspective
Authors: Nilsson Jonas , Piovesana Vittoria , Turini Marco , Lezzi Claudio , Eriksson Jennifer , Aapro Matti 
Published: September 2022

Abstract
Purpose
The aim of this study was to assess the cost-effectiveness of NEPA, a fixed-dose combination of oral netupitant (300 mg) and palonosetron (0.5 mg), compared to available treatments in Spain after aprepitant generic introduction in the market, and to discuss results in previously performed analyses in different wordwide settings.

Methods
A Markov model including three health states, complete protection, complete response at best and incomplete response, was used to evaluate the cost-effectiveness of NEPA versus common treatment options in Spain during 5 days after chemotherapy. Incremental costs including treatment costs and treatment failure management cost as well as incremental effects including quality adjusted life days (QALDs) and emesis-free days were compared between NEPA and the comparator arms. The primary outcomes were cost per avoided emetic event and cost per QALDs gained.

Results
NEPA was dominant (more effective and less costly) against aprepitant combined with palonosetron, and fosaprepitant combined with granisetron, while, compared to generic aprepitant plus ondansetron, NEPA showed an incremental cost per avoided emetic event of €33 and cost per QALD gained of €125.

Conclusion
By most evaluations, NEPA is a dominant or cost-effective treatment alternative to current antiemetic standards of care in Spain during the first 5 days of chemotherapy treatment in cancer patients, despite the introduction of generics. These results are in line with previously reported analyses throughout different international settings.
A comparative study of receptor interactions between SARS-CoV and SARS-CoV-2 from molecular modeling
Authors: Lai Hien T. T. , Nguyen Ly H. , Phan Anh D. , Kranjc Agata , Nguyen Toan T. , Nguyen-Manh Duc 
Published: September 2022

AbstractThe pandemic of COVID-19 severe acute respiratory syndrome, which was fatal for millions of people worldwide, triggered the race to understand in detail the molecular mechanisms of this disease. In this work, the differences of interactions between the SARS-CoV/SARS-CoV-2 Receptor binding domain (RBD) and the human Angiotensin Converting Enzyme 2 (ACE2) receptor were studied usingin silicotools. Our results show that SARS-CoV-2 RBD is more stable and forms more interactions with ACE2 than SARS-CoV. At its interface, three stable binding patterns are observed and named red-K31, green-K353 and blue-M82 according to the central ACE2 binding residue. In SARS-CoV instead, only the first two binding patches are persistently formed during the MD simulation. Our MM/GBSA calculations indicate the binding free energy difference of about 2.5 kcal/molbetween SARS-CoV-2 and SARS-CoV which is compatible with the experiments. The binding free energy decomposition points out that SARS-CoV-2 RBD–ACE2 interactions of the red-K31 ($$-23.5~\pm ~0.2~kcal/mol$$-23.5±0.2kcal/mol) and blue-M82 ($$-9.1~\pm ~0.1~kcal/mol$$-9.1±0.1kcal/mol) patterns contribute more to the binding affinity than in SARS-CoV ($$-1.8~\pm ~0.02~kcal/mol$$-1.8±0.02kcal/molfor red-K31), while the contribution of the green-K353 pattern is very similar in the two strains ($$-17.8~\pm ~0.2~kcal/mol$$-17.8±0.2kcal/moland$$-22.7~\pm ~0.1~kcal/mol$$-22.7±0.1kcal/molfor SARS-CoV-2 and SARS-CoV, respectively). Five groups of mutations draw our attention at the RBD–ACE2 binding interface, among them, the mutation –PPA469-471/GVEG482-485 has the most important and favorable impact on SARS-CoV-2 binding to the ACE2 receptor. These results, highlighting the molecular differences in the binding between the two viruses, contribute to the common knowledge about the new corona virus and to the development of appropriate antiviral treatments, addressing the necessity of ongoing pandemics.
Combined retention of large living and dead trees can improve provision of tree-related microhabitats in Central European montane forests
Authors: Spînu Andreea Petronela , Asbeck Thomas , Bauhus Jürgen 
Published: September 2022

AbstractRetention of habitat trees is a common biodiversity conservation practice in continuous cover forests of temperate Europe. Commonly, living habitat trees are selected on the basis of their tree-related microhabitats (TreMs) such as cavities or crown deadwood. Owing to the increasing frequency and intensity of climate change-related disturbances, habitat trees in particular are expected to experience increased mortality rates. This may impact the long-term provisioning of TreMs. Here, we compared the TreM occurrence on living and dead trees to investigate whether dead trees support more and other TreMs than living trees. We also hypothesized that a combination of living and dead trees results in the most diverse stand-level TreM composition. We surveyed the TreM composition of living and dead habitat trees in 133 one-hectare plots in the Black Forest region managed according to a continuous cover approach. We fitted generalized linear mixed models to identify the main predictors of TreM occurrence to predict their abundance and richness. Tree identity (as a combination of species and vitality status) and diameter were the main drivers of TreM abundance and richness, which were highest on dead Abies alba. Even though dead A. alba and Picea abies supported TreM numbers similar to those provided by large living trees, their TreM composition was significantly different. This suggests that dead trees cannot substitute the habitat functions of living habitat trees, but they can complement them to increase the overall stand-level TreM diversity, in particular through decayed, large snags.
Comparing Reading Comprehension of Narrative and Expository Texts Based on the Direct and Inferential Mediation Model
Authors: Härtig Hendrik , Bernholt Sascha , Fraser Nicole , Cromley Jennifer G. , Retelsdorf Jan 
Published: September 2022

AbstractReading comprehension is an essential skill for learning in general and in science classes. Problems with reading comprehension might hinder students’ participation in learning science. Text in science includes specific language features that distinguishes it from narrative text, so should reading instruction be part of teaching science? The direct and inferential mediation (DIME) model of reading comprehension subsumes factors that influence reading comprehension. It was tested separately regarding narrative text as well as expository text in English; however, both have not been tested by directly comparing them to each other. In this study, we investigated to what degree general reading comprehension of narrative text is directly comparable to topic-specific reading comprehension of science text. Hence, first the applicability of the DIME model of reading comprehension in another language (i.e. German) was tested. Second, a general reading comprehension model was directly compared to a topic-specific model for reading comprehension of science text. Participants across the two studies were 704 German Grade 8 students who completed measures of comprehension and the DIME predictor variables. Results of two path analyses indicate the general applicability of the model for another language and additionally for both genres. However, some differences are highlighted that may be of importance in future science-specific studies as well as for teaching science.
Strengthening mechanisms and wear behavior of electrodeposited Ni–SiC nanocomposite coatings
Authors: Pinate S. , Ghassemali E. , Zanella C. 
Published: September 2022

AbstractThe present paper describes the study of the synergism between the matrix microstructure and reinforcement phase in electrodeposited nanocomposite coatings. Adding hard nanoparticles into the metallic matrix leads to hardening of the coating. The effects of particle load, size and dispersion on hardening as well as their influence on metal microstructure refinement were studied. The relative contributions of strengthening factors in Ni/nano-SiC composites, namely, Hall–Petch strengthening, Orowan strengthening, enhanced dislocation density and particles incorporation, were evaluated. The production of various coatings under different stirring conditions and powders resulted in dissimilarities in the incorporation of particles. The Hall–Petch relationship for pure nickel was determined using samples produced under different current densities. Additionally, the grain refinement resulting from the particle codeposition and agitation mode were identified as influential factors in grain-size strengthening. Dislocation density strengthening was significant in electrodeposits produced using ultrasonic agitation, while it was negligible in layers produced under other conditions. Particles codeposition affected the magnitude of Orowan strengthening, resulting in cases where strengthening was negligible despite the presence of particles. The sum of contributions and the modified Clyne methods were used to calculate the hardness of the composites based on the contribution of each strengthening factor, and the calculation results were in good agreement with experimental data. The wear behavior of the composites was analyzed by pin-on-disk measurements, and the results correlated with the strengthening mechanisms. Particle size, dispersion and content increased the strengthening effects as well as the hardness and wear resistance of the coatings.
Graphical abstract
Elasmobranchs from Indonesian Waters: Feeding Ecology and Trypanorhynch Cestode Fauna Composition to Support Efforts in Shark and Ray Conservation
Authors: Kleinertz S. , Yulianto I. , Kurschat C. , Koepper S. , Simeon B. M. , Klimpel S. , Theisen S. , Unger P. , Retnoningtyas H. , Neitemeier-Duventester X. , Barton D. P. , Damriyasa I. M. , Palm H. W. 
Published: September 2022

Abstract
Purpose
The stomachs and spiral valves of sharks and rays were examined for their trypanorhynch (Cestoda) parasite fauna and dietary items to infer feeding ecology. In Indonesia, sharks and rays have been experiencing increasing awareness and conservation in the recent years due to high fisheries activities and to avoid future species extinction.

Methods
The samples were collected in 2009 from two different sampling sites at the southern coasts of Java and Bali in Indonesia. The parasite fauna was studied for 41 elasmobranch fishes. Amongst these, three shark species, Carcharhinus sorrah, Carcharhinus sp. I and Squalus megalops and seven ray species, Brevitrygon heterura, B. cf. heterura, Gymnura zonura, Maculabatis gerrardi, Mobula kuhlii, Neotrygon cauruleopuncatata and Rhinobatos penggali were studied. Four additional specimens, belonging to the shark species Carcharhinus sp. II and Mustelus cf. manazo and the ray species Maculabatis gerrardi were studied from the waters of South Bali.

Results
Analyses of the feeding ecology of the ray M. gerrardi revealed distinct differences between both sampling sites, indicating the presence of ecological differences between the geographically independent regions. A total of 11 different trypanorhynch species/taxa belonging to the five families Eutetrarhynchidae (5), Gilquiniidae (1), Lacistorhynchidae (1), Pterobothriidae (1) and Tentaculariidae (3) were found. Ten trypanorhynch species from Penyu Bay and four species from South Bali could be identified. Two taxa that might represent new species were collected: Dollfusiella sp. from Brevitrygon heterura and Prochristianella sp. from Maculabatis gerrardi.

Conclusions
The present paper gives insights in using the trypanorhynch cestode community in combination with feeding ecology analyses to support conservation of elasmobranchs in Indonesian waters.
Existence of solutions of discrete fractional problem coupled to mixed fractional boundary conditions
Authors: Bourguiba Rim , Cabada Alberto , Kalthoum Wanassi Om 
Published: September 2022

AbstractIn this paper, we introduce a two-point nonlinear boundary value problem for a finite fractional difference equation. An associated Green’s function is constructed as a series of functions and some of its properties are obtained. Some existence results are deduced from fixed point theory and lower and upper solutions.