bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellular levels and molecular dynamics simulations of estragole DNA adducts point at inefficient repair resulting from limited distortion of the double-stranded DNA helix
Authors: Yang Shuo , Diem Matthias , Liu Jakob D. H. , Wesseling Sebastiaan , Vervoort Jacques , Oostenbrink Chris , Rietjens Ivonne M. C. M. 
Published: March 2020

AbstractEstragole, naturally occurring in a variety of herbs and spices, can form DNA adducts after bioactivation. Estragole DNA adduct formation and repair was studied in in vitro liver cell models, and a molecular dynamics simulation was used to investigate the conformation dependent (in)efficiency of N2-(trans-isoestragol-3′-yl)-2′-deoxyguanosine (E-3′-N2-dG) DNA adduct repair. HepG2, HepaRG cells, primary rat hepatocytes and CHO cells (including CHO wild-type and three NER-deficient mutants) were exposed to 50 μM estragole or 1′-hydroxyestragole and DNA adduct formation was quantified by LC–MS immediately following exposure and after a period of repair. Results obtained from CHO cell lines indicated that NER plays a role in repair of E-3′-N2-dG adducts, however, with limited efficiency since in the CHO wt cells 80% DNA adducts remained upon 24 h repair. Inefficiency of DNA repair was also found in HepaRG cells and primary rat hepatocytes. Changes in DNA structure resulting from E-3′-N2-dG adduct formation were investigated by molecular dynamics simulations. Results from molecular dynamics simulations revealed that conformational changes in double-stranded DNA by E-3′-N2-dG adduct formation are small, providing a possible explanation for the restrained repair, which may require larger distortions in the DNA structure. NER-mediated enzymatic repair of E-3′-N2-dG DNA adducts upon exposure to estragole will be limited, providing opportunities for accumulation of damage upon repeated daily exposure. The inability of this enzymatic repair is likely due to a limited distortion of the DNA double-stranded helix resulting in inefficient activation of nucleotide excision repair.
Predictors and Survival of Patients with Osteosarcoma After Limb Salvage versus Amputation: A Population‐Based Analysis with Propensity Score Matching
Authors: Qi Lin , Ren Xiaolei , Liu Zhongyue , Li Shuangqing , Zhang Wenchao , Chen Ruiqi , Chen Congzhou , Tu Chao , Li Zhihong 
Published: March 2020

AbstractBackgroundConflicting findings have been reported concerning the survival of patients treated with limb salvage and amputation for osteosarcoma. This study aimed to identify predictors associated with surgery types and survival difference.MethodsPatients with osteosarcoma were selected from the Surveillance Epidemiology and End Results database (1975–2016). Multivariable logistic regression analysis was conducted, and a nomogram was further established. Propensity score matching (PSM)‐adjusted Kaplan–Meier curves, log‐rank tests, Cox proportional hazards regression analysis were performed to compare overall survival (OS) and cancer‐specific survival (CSS).ResultsAmong 3363 patients with osteosarcoma, 2447 and 916 underwent limb salvage and amputation. Predictors associated with amputation in the nomogram included age, gender, primary tumor site, tumor grade, tumor stage, tumor size and radiotherapy. Totally 900 pairs of patients treated with limb salvage and amputation were matched after PSM. Limb salvage was significantly associated with improved OS (HR, 0.773; 95% CI, 0.670–0.892; p < 0.001) and CSS (HR, 0.795; 95% CI, 0.681–0.927; p = 0.003) in PSM‐adjusted cohort after adjusting for related variables. The significant treatment effect of limb salvage was consistent within most subgroups. Among patients treated with surgery for osteosarcoma, age between 41 and 60, age ≥ 61, pelvis as the primary site, high tumor grade (III/IV), regional and distant tumor stage, tumor size ≥ 92 mm and radiotherapy were independent prognostic factors in PSM cohort.ConclusionsLimb salvage exhibits significant benefit on OS and CSS compared with amputation for osteosarcoma. Predicators and survival differences should be given full consideration for the treatment of osteosarcoma.
Impact of tumour size measurement inter-operator variability on model-based drug effect evaluation
Authors: Lombard Aurélie , Mistry Hitesh , Chapman Sonya C. , Gueoguieva Ivelina , Aarons Leon , Ogungbenro Kayode 
Published: March 2020

Abstract
Purpose
During oncology clinical trials, tumour size (TS) measurements are commonly used to monitor disease progression and to assess drug efficacy. We explored inter-operator variability within a subset of a phase III clinical trial conducted from August 1995 to February 1997 and its impact on drug effect evaluation using a tumour growth inhibition model.

Methods
One hundred twenty lesions were measured twice at each time point; once at the hospital and once at the centralised centre. A visual analysis was performed to identify trends within the profiles over time. Linear regression and relative error ratios were used to explore the inter-operator variability of raw TS measurements and model-based estimates.

Results
While correlation between patient-level estimates of drug effect was poor (r2 = 0.28), variability between the study-level estimates was much less affected (9%).

Conclusions
The global evaluation of drug effect using modelling approaches might not be affected by inter-operator variability. However, the exploration of covariates for drug effect and the characterisation of an exposure–tumour shrinkage relationship seems limited by the high measurement variability that translates to a poor correlation of individual drug effect estimates. This might be addressed by the use of more precise computer-aided measurement methods.
Implications of asymptomatic infection for the natural history of selected parasitic tropical diseases
Authors: Alvar Jorge , Alves Fabiana , Bucheton Bruno , Burrows Louise , Büscher Philippe , Carrillo Eugenia , Felger Ingrid , Hübner Marc P. , Moreno Javier , Pinazo Maria-Jesus , Ribeiro Isabela , Sosa-Estani Sergio , Specht Sabine , Tarral Antoine , Wourgaft Nathalie Strub , Bilbe Graeme 
Published: March 2020

AbstractProgress has been made in the control or elimination of tropical diseases, with a significant reduction of incidence. However, there is a risk of re-emergence if the factors fueling transmission are not dealt with. Although it is essential to understand these underlying factors for each disease, asymptomatic carriers are a common element that may promote resurgence; their impact in terms of proportion in the population and role in transmission needs to be determined. In this paper, we review the current evidence on whether or not to treat asymptomatic carriers given the relevance of their role in the transmission of a specific disease, the efficacy and toxicity of existing drugs, the Public Health interest, and the benefit at an individual level, for example, in Chagas disease, to prevent irreversible organ damage. In the absence of other control tools such as vaccines, there is a need for safer drugs with good risk/benefit profiles in order to change the paradigm so that it addresses the complete infectious process beyond manifest disease to include treatment of non-symptomatic infected persons.
Pseudomonas atagosis sp. nov., and Pseudomonas akappagea sp. nov., New Soil Bacteria Isolated from Samples on the Volcanic Island Izu Oshima, Tokyo
Authors: Morimoto Yuh , Uwabe Kazuki , Tohya Mari , Hiramatsu Keiichi , Kirikae Teruo , Baba Tadashi 
Published: March 2020

AbstractDuring the exploration of microbial natural resources, two strains of Pseudomonas, PS14T and PS24T, were isolated from samples taken from Izu Oshima, a volcanic island located 120 km southwest of central Tokyo. Phylogenetic analysis based on 16S rRNA gene sequences showed that PS14T was most similar to Pseudomonas baetica a390T (99.6%) and Pseudomonas helmanticensis OHA11T (99.5%), and that PS24T was most similar to Pseudomonas qingdaonensis JJ3T (98.8%) and Pseudomonas lutea OK2T (98.7%). The major fatty acids of these two strains were C16:0 and C17:0 cyclo, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), and summed feature 8 (C18:1 ω7c and/or 18:1 ω6c). The phylogenetic analyses, DNA-DNA hybridization results and phenotypic traits indicated that PS14T and PS24T constitute two novel species, Pseudomonas atagosis sp. nov. (type strain PS14T = CECT 9940T, = LMG 31496T) and Pseudomonas akappagea sp. nov. (type strain PS24T = CECT 9941T, = LMG 31497T), respectively. The sequence data of the draft genomes of PS14T and PS24T were deposited in the GenBank database under accession numbers VXCA00000000 and VXCP00000000, respectively, and the sequence data of their 16S rRNA genes were deposited in the GenBank database under accession numbers MN396717 and MN382268, respectively.
Applicability of pulsed 2cLIF-EET for micro-droplet internal thermometry under evaporation conditions
Authors: Palmer Johannes , Schumacher Leif , Reddemann Manuel A. , Kirsch Valeri , Kneer Reinhold 
Published: March 2020

Abstract
The relatively new thermometry technique “pulsed 2cLIF with MDR-enhanced energy transfer” is tested for the first time on micro-droplet streams in a heated air flow. The method allows simultaneous measurements of the droplet internal temperature-field, droplet size and droplet velocity. Plausibility of the measurement results is evaluated by comparing results of various experimental conditions among each other and by comparison with analytic modeling. Overall, measurement results are plausible. However, measured temperature-fields are biased by the integral fluorescence signal and initial conditions of the models are limited by the Rayleigh jet breakup that creates the droplet stream.

Graphic abstract
Downregulation of SFRP1 is a protumorigenic event in hepatoblastoma and correlates with beta-catenin mutations
Authors: Regel Ivonne , Eichenmüller Melanie , Mahajan Ujjwal Mukund , Hagl Beate , Benitz Simone , Häberle Beate , Vokuhl Christian , von Schweinitz Dietrich , Kappler Roland 
Published: March 2020

Abstract
Background
Hepatoblastoma (HB) and pediatric hepatocellular carcinoma (HCC) are the most common malignant liver tumors in childhood. Both tumor types exhibit genetic and epigenetic alterations in the WNT/β-catenin signaling pathway, which is a key regulator of liver progenitor cells in embryonic development. The tumors demonstrate a high rate of β-catenin mutations and gene expression changes of several WNT antagonists. However, the role of the WNT inhibitory factor secreted frizzled-related protein 1 (SFRP1) has not been addressed in pediatric liver cancer so far.

Results
In our study, we investigated the gene expression level, DNA methylation status and functional relevance of SFRP1 in HB cell lines and in pediatric liver tumor patient samples. SFRP1 was downregulated due to DNA promoter methylation in all tested HB cell lines. Overexpression of SFRP1 in HB cell lines diminished tumor cell proliferation, colony formation and migration potential. In addition, the SFRP1-expressing HB cell lines showed reduced WNT/β-catenin signaling pathway activity and decreased expression of WNT target genes. To evaluate the utility of SFRP1 as a biomarker in pediatric liver cancer, we determined the gene expression level and DNA methylation status of SFRP1 in 45 pediatric liver tumor patient samples. The correlation analysis of different clinical parameters and tumor characteristics revealed a significant correlation of reduced SFRP1 expression with the presence of mutant β-catenin. The methylation status of SFRP1 was furthermore associated to a pediatric liver tumor type with HCC-like characteristics, TERT mutations and an older age at diagnosis.

Conclusion
Altogether, our data demonstrate that the epigenetic suppression of the WNT/β-catenin antagonist SFRP1 has an important impact on the malignant behavior of HB cells. Although SFRP1 methylation is a common event in HCC-like pediatric liver tumors, its potential as a prognostic or diagnostic biomarker needs to be further investigated.
Inhibition of oxygen-sensing prolyl hydroxylases increases lipid accumulation in human primary tubular epithelial cells without inducing ER stress
Authors: Schley Gunnar , Grampp Steffen , Goppelt-Struebe Margarete 
Published: March 2020

AbstractThe role of the hypoxia-inducible transcription factor (HIF) pathway in renal lipid metabolism is largely unknown. As HIF stabilizing prolyl hydroxylase (PHD) inhibitors are currently investigated in clinical trials for the treatment of renal anemia, we studied the effects of genetic deletion and pharmacological inhibition of PHDs on renal lipid metabolism in transgenic mice and human primary tubular epithelial cells (hPTEC). Tubular cell-specific deletion of HIF prolyl hydroxylase 2 (Phd2) increased the size of Oil Red-stained lipid droplets in mice. In hPTEC, the PHD inhibitors (PHDi) DMOG and ICA augmented lipid accumulation, which was visualized by Oil Red staining and assessed by microscopy and an infrared imaging system. PHDi-induced lipid accumulation required the exogenous availability of fatty acids and was observed in both proximal and distal hPTEC. PHDi treatment was not associated with structural features of cytotoxicity in contrast to treatment with the immunosuppressant cyclosporine A (CsA). PHDi and CsA differentially upregulated the expression of the lipid droplet-associated genes PLIN2, PLIN4 and HILPDA. Both PHDi and CsA activated AMP-activated protein kinase (AMPK) indicating the initiation of a metabolic stress response. However, only CsA triggered endoplasmic reticulum (ER) stress as determined by the increased mRNA expression of multiple ER stress markers but CsA-induced ER stress was not linked to lipid accumulation. Our data raise the possibility that PHD inhibition may protect tubular cells from toxic free fatty acids by trapping them as triacylglycerides in lipid droplets. This mechanism might contribute to the renoprotective effects of PHDi in experimental kidney diseases.
On some properties of the number of permutations being products of pairwise disjoint d-cycles
Authors: Miska Piotr , Ulas Maciej 
Published: March 2020

AbstractLet $$d\ge 2$$d≥2 be an integer. In this paper we study arithmetic properties of the sequence $$(H_d(n))_{n\in \mathbb {N}}$$(Hd(n))n∈N, where $$H_{d}(n)$$Hd(n) is the number of permutations in $$S_{n}$$Sn being products of pairwise disjoint cycles of a fixed length d. In particular we deal with periodicity modulo a given positive integer, behaviour of the p-adic valuations and various divisibility properties. Moreover, we introduce some related families of polynomials and study their properties. Among many results we obtain qualitative description of the p-adic valuation of the number $$H_{d}(n)$$Hd(n) extending in this way earlier results of Ochiai and Ishihara, Ochiai, Takegehara and Yoshida.
Growth-Promoting Treatment Screening for Corticospinal Neurons in Mouse and Man
Authors: Hanuscheck Nicholas , Schnatz Andrea , Thalman Carine , Lerch Steffen , Gärtner Yvonne , Domingues Micaela , Bitar Lynn , Nitsch Robert , Zipp Frauke , Vogelaar Christina F. 
Published: March 2020

AbstractNeurons of the central nervous system (CNS) that project long axons into the spinal cord have a poor axon regenerative capacity compared to neurons of the peripheral nervous system. The corticospinal tract (CST) is particularly notorious for its poor regeneration. Because of this, traumatic spinal cord injury (SCI) is a devastating condition that remains as yet uncured. Based on our recent observations that direct neuronal interleukin-4 (IL-4) signaling leads to repair of axonal swellings and beneficial effects in neuroinflammation, we hypothesized that IL-4 acts directly on the CST. Here, we developed a tissue culture model for CST regeneration and found that IL-4 promoted new growth cone formation after axon transection. Most importantly, IL-4 directly increased the regenerative capacity of both murine and human CST axons, which corroborates its regenerative effects in CNS damage. Overall, these findings serve as proof-of-concept that our CST regeneration model is suitable for fast screening of new treatments for SCI.
Attitudes towards climate change migrants
Authors: Helbling Marc 
Published: March 2020

AbstractWhile climate change has become a salient political and social issue in Western societies, we know relatively little about how these societies will react to one of the potentially important consequences of climate change: increasing migration flows. By means of a representative online survey in Germany, this paper therefore investigates for the very first time to what extent citizens in industrialized societies are willing to accept climate change migrants, especially in comparison with other groups of migrants and refugees, and the circumstances and principles under which they would accept them. The findings show that climate change migrants receive high support levels comparable with those enjoyed by political refugees (migrants who need special protection) and that contrast with attitudes towards economic migrants (who are often not seen as in need of special protection). We also see that people are more likely to accept justifications for taking climate change migrants when they realize that the expected number of migrants is relatively low. While arguments about morality, corrective justice, and a country’s capacity lead to similar acceptance rates in general, the latter argument plays a more important role for highly educated people and non-environmentalists than the former two. The findings of this study allow us to better prepare for potential conflicts that might emerge with increasing migration flows caused by climate change.
Arthropod traits and assemblages differ between core patches, transient stepping-stones and landscape corridors
Authors: Pedley Scott M. , Dolman Paul M. 
Published: March 2020

AbstractContextRestoring landscape connectivity can mitigate fragmentation and improve population resilience, but functional equivalence of contrasting elements is poorly understood. Evaluating biodiversity outcomes requires examining assemblage-responses across contrasting taxa.ObjectivesWe compared arthropod species and trait composition between contrasting open-habitat network elements: core patches, corridors (allowing individual dispersal and population percolation), and transient stepping-stones (potentially enhancing meta-population dynamics).MethodsCarabids and spiders were sampled from core patches of grass-heath habitat (n = 24 locations across eight sites), corridors (trackways, n = 15) and recently-replanted clear-fells (transient patches, n = 19) set in a forest matrix impermeable to open-habitat arthropods. Species and trait (habitat association, diet, body size, dispersal ability) composition were compared by ordination and fourth corner analyses.ResultsEach network element supported distinct arthropod assemblages with differing functional trait composition. Core patches were dominated by specialist dry-open habitat species while generalist and woodland species contributed to assemblages in connectivity elements. Nevertheless, transient patches (and to a lesser degree, corridors) supported dry-open species characteristic of the focal grass-heath sites. Trait associations differed markedly among the three elements. Dispersal mechanisms and their correlates differed between taxa, but dry-open species in transient patches were characterised by traits favouring dispersal (large running hunter spiders and large, winged, herbivorous carabids), in contrast to wingless carabids in corridors.ConclusionsCore patches, dispersal corridors and transient stepping-stones are not functionally interchangeable within this system. Semi-natural core patches supported a filtered subset of the regional fauna. Evidence for enhanced connectivity through percolation (corridors) or meta-population dynamics (stepping stones) differed between the two taxa.
Disruptive papers published in Scientometrics: meaningful results by using an improved variant of the disruption index originally proposed by Wu, Wang, and Evans (2019)
Authors: Bornmann Lutz , Devarakonda Sitaram , Tekles Alexander , Chacko George 
Published: March 2020

AbstractWu et al. (Nature 566:378–382, 2019) introduced a new indicator measuring disruption ($${DI}_{1}$$DI1). Bornmann et al. (Do disruption index indicators measure what they propose to measure? The comparison of several indicator variants with assessments by peers, 2019. https://arxiv.org/abs/1911.08775) compared variants of the disruption index and pointed to $${DI}_{5}$$DI5 as an interesting variant. The calculation of a field-specific version of $${DI}_{5}$$DI5 (focusing on disruptiveness within the same field) for Scientometrics papers in the current study reveals that the variant is possibly able to identify landmark papers in scientometrics. This result is in contrast to the Scientometrics analysis previously published by Bornmann and Tekles (Scientometrics 120(1):331–336, 2019) based on the original disruption index ($${DI}_{1}$$DI1).
Evaluating semantometrics from computer science publications
Authors: Kreutz Christin Katharina , Sahitaj Premtim , Schenkel Ralf 
Published: March 2020

AbstractIdentification of important works and assessment of importance of publications in vast scientific corpora are challenging yet common tasks subjected by many research projects. While the influence of citations in finding seminal papers has been analysed thoroughly, citation-based approaches come with several problems. Their impracticality when confronted with new publications which did not yet receive any citations, area-dependent citation practices and different reasons for citing are only a few drawbacks of them. Methods relying on more than citations, for example semantic features such as words or topics contained in publications of citation networks, are regarded with less vigour while providing promising preliminary results. In this work we tackle the issue of classifying publications with their respective referenced and citing papers as either seminal, survey or uninfluential by utilising semantometrics. We use distance measures over words, semantics, topics and publication years of papers in their citation network to engineer features on which we predict the class of a publication. We present the SUSdblp dataset consisting of 1980 labelled entries to provide a means of evaluating this approach. A classification accuracy of up to .9247 was achieved when combining multiple types of features using semantometrics. This is +.1232 compared to the current state of the art (SOTA) which uses binary classification to identify papers from classes seminal and survey. The utilisation of one-vector representations for the ternary classification task resulted in an accuracy of .949 which is +.1475 compared to the binary SOTA. Classification based on information available at publication time derived with semantometrics resulted in an accuracy of .8152 while an accuracy of .9323 could be achieved when using one-vector representations.